Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel immune-related gene signature correlated with serum IL33 expression in acute myeloid leukemia prognosis.

PURPOSE To identify and validate the immune-related gene signature in patients with acute myeloid leukemia (AML). METHODS Differentially expressed genes (DEGs) profiles and survival data were obtained from The Cancer Genome Atlas (TCGA), following screened immune-associated genes from the InnateDB database. Subsequently, the weighted gene co-expression network analysis (WGCNA) was used to detect functional modules, and survival analysis was performed. The least absolute shrinkage and selection operator (LASSO) regression model combined with a partial likelihood-based Cox proportional hazard regression model was applied to select prognostic genes, and the ESTIMATE algorithm was used to construct an immune score-based risk assessment model. Finally, two independent datasets from the Gene Expression Omnibus (GEO) and our clinical data were used for external validation. Moreover, a subpopulation of the immune microenvironment cells was analyzed by the CIBERSORT algorithm, and its related serum indicator was identified by the enzyme-linked immunosorbent assay (ELISA) in clinical samples. RESULTS Finally, CTSD, GNB2, CDK6, and WAS were identified as the immune-related gene signature, and the risk stratification model was validated in both the GSE12417 database and our clinical cohort. Furthermore, the fraction of activated mast cells was identified. CIBERSORT algorithm showed that these cells have a positive association with prognosis. In addition, mast cell stimulator IL-33 was markedly decreased in AML patients with poor prognoses. CONCLUSION A novel immune-related gene signature (CTSD, GNB2, CDK6 and WAS) and its associated plasma indicator (mast cells activator, IL-33) were found to have prognostic value in AML patients.
Conditional Γ-minimax prediction with a precautionary loss function in a marked point process model

ABSTRACT A robust Bayesian approach is used to construct optimal predictors of the total size of future marks of a marked point process in the presence of uncertainty regarding the prior distribution. A stochastic marked point process model based on a doubly stochastic Poisson process is considered. The underlying marked point process is assumed to be a two-dimensional non-homogeneous Poisson process with intensity measure , where P is fixed, whereas Θ is treated as a random measure. The prior distribution of Θ is described by an unknown process from a family Γ of gamma processes. Conditional Γ-minimax predictors are constructed under different types of uncertainty about the prior. A precautionary loss function is considered to prevent underestimation. Some properties of the derived predictors are investigated in a simulation study.
Development and experiments of lateral shearing interferometer for parabolic surface measurement

Large aperture parabolic mirrors are widely used in high technology areas, such as astronomical optics, space optics et.al. In order to obtain better optical performance, the lateral shearing interferometer was developed for characterizing the surface figure of parabolic mirror. Firstly, based on penta-prism and shearing optical flat, lateral shearing interferometry device was installed; secondly, the shearing phase was calculated by four-step phase shifting algorithm, the transform from shearing phase to primary phase was reconstructed through the selection of discrete sampling points and wave-front fitting, and the shearing interferometry software was programed. Lastly, through a concave parabolic mirror inspection, the precision of the shearing interferometer and the anti-vibration characteristic were verified.
The Impact of Helping Children with Distance Learning During COVID-19 on U.S. Parents’ Alcohol Consumption

We examined the impact of distance learning-related parental stress due to COVID-19 on parental alcohol consumption using an online survey in May 2020 with a convenience sample of U.S. adults. This article focuses on the 361 parents who had children under the age of 18 living with them. Seventy-eight percent had children who were engaged in distance learning; 59% reported being stressed because they were not sure how to help their children with distance learning. Stressed parents reported consuming significantly more alcohol and binge drinking more often than parents who were not stressed by distance learning. We hope that public health professionals can use our findings to better target alcohol prevention programs aimed at parents to reduce parental stress, and hopefully, parental alcohol consumption.
Poliovirus outbreak in New York State, August 2022: qualitative assessment of immediate public health responses and priorities for improving vaccine coverage

Abstract In 2022, a case of paralysis was reported in an unvaccinated adult in Rockland County (RC), New York. Genetically linked detections of vaccine-derived poliovirus type 2 (VDPV2) were reported in multiple New York counties, England, Israel, and Canada. The aims of this qualitative study were to: i) review immediate public health responses in New York to assess the challenges in addressing gaps in vaccination coverage; ii) inform a longer-term strategy to improving vaccination coverage in under-vaccinated communities, and iii) collect data to support comparative evaluations of transnational poliovirus outbreaks. Twenty-three semi-structured interviews were conducted with public health professionals, healthcare professionals, and community partners. Results indicate that i) addressing suboptimal vaccination coverage in RC remains a significant challenge after recent disease outbreaks; ii) the poliovirus outbreak was not unexpected and effort should be invested to engage mothers, the key decision-makers on childhood vaccination; iii) healthcare providers (especially paediatricians) received technical support during the outbreak, and may require resources and guidance to effectively contribute to longer-term vaccine engagement strategies; vi) data systems strengthening is required to help track under-vaccinated children. Public health departments should prioritize long-term investments in appropriate communication strategies, countering misinformation, and promoting the importance of the routine immunization schedule.
Bursting Dynamics Based on the Persistent Na+ and Na+/K+ Pump Currents: A Dynamic Clamp Approach

Abstract Life-supporting rhythmic motor functions like heart-beating in invertebrates and breathing in vertebrates require an indefatigable generation of a robust rhythm by specialized oscillatory circuits, central pattern generators (CPGs). These CPGs should be sufficiently flexible to adjust to environmental changes and behavioral goals. Continuous self-sustained operation of bursting neurons requires intracellular Na+ concentration to remain in a functional range and to have checks and balances of the Na+ fluxes met on a cycle-to-cycle basis during bursting. We hypothesize that at a high excitability state, the interaction of the Na+/K+ pump current, Ipump, and persistent Na+ current, INaP, produces a mechanism supporting functional bursting. INaP is a low voltage-activated inward current that initiates and supports the bursting phase. This current does not inactivate and is a significant source of Na+ influx. Ipump is an outward current activated by [Na+]i and is the major source of Na+ efflux. Both currents are active and counteract each other between and during bursts. We apply a combination of electrophysiology, computational modeling, and dynamic clamp to investigate the role of Ipump and INaP in the leech heartbeat CPG interneurons (HN neurons). Applying dynamic clamp to introduce additional Ipump and INaP into the dynamics of living synaptically isolated HN neurons in real time, we show that their joint increase produces transition into a new bursting regime characterized by higher spike frequency and larger amplitude of the membrane potential oscillations. Further increase of Ipump speeds up this rhythm by shortening burst duration (BD) and interburst interval (IBI).
16S rRNA Gene PCR/Sequencing of Heart Valves for Diagnosis of Infective Endocarditis in Routine Clinical Practice

Sequencing is increasingly used for infective endocarditis (IE) diagnosis. Here, the performance of 16S rRNA gene PCR/sequencing of heart valves utilized in routine clinical practice was compared with conventional IE diagnostics. ABSTRACT Sequencing is increasingly used for infective endocarditis (IE) diagnosis. Here, the performance of 16S rRNA gene PCR/sequencing of heart valves utilized in routine clinical practice was compared with conventional IE diagnostics. Subjects whose heart valves were sent to the clinical microbiology laboratory for 16S rRNA gene PCR/sequencing from August 2020 through February 2022 were studied. A PCR assay targeting V1 to V3 regions of the 16S rRNA gene was performed, followed by Sanger and/or next-generation sequencing (NGS) (using an Illumina MiSeq), or reported as negative, depending on an algorithm that included the PCR cycle threshold value. Fifty-four subjects, including 40 with IE, three with cured IE, and 11 with noninfective valvular disease, were studied. Thirty-one positive results, 11 from NGS and 20 from Sanger sequencing, were generated from analysis of 16S rRNA gene sequence(s). Positivity rates of blood cultures and 16S rRNA gene PCR/sequencing of valves were 55% and 75%, respectively (P = 0.06). In those with prior antibiotic exposure, positivity rates of blood cultures and 16S rRNA gene PCR/sequencing of valves were 11% and 76%, respectively (P < 0.001). Overall, 61% of blood culture-negative IE subjects had positive valve 16S rRNA gene PCR/sequencing results. 16S rRNA gene-based PCR/sequencing of heart valves is a useful diagnostic tool for pathogen identification in patients with blood culture-negative IE undergoing valve surgery in routine clinical practice.
Using Artificial Intelligence to Predict Cirrhosis From Computed Tomography Scans

INTRODUCTION: Undiagnosed cirrhosis remains a significant problem. In this study, we developed and tested an automated liver segmentation tool to predict the presence of cirrhosis in a population of patients with paired liver biopsy and computed tomography (CT) scans. METHODS: We used a cohort of 1,590 CT scans within the Morphomics database to train an automated liver segmentation model using 3D-U-Net and Google's DeeplLabv3+. Imaging features were then automatically calculated from an external test cohort of patients with chronic liver disease who had a paired liver biopsy and CT within 6 months of each other in January 2004–2012. Using gradient boosting decision trees, we developed multivariate models to predict the presence of histologic cirrhosis and evaluated with 5-fold cross-validated c-statistic. RESULTS: Our cohort had 351 patients; 96 patients had cirrhosis. Of the total cohort, 72 were postliver transplant. Both fibrosis (FIB)-4 and liver morphomics alone performed equally well with area under the receiving operating characteristics of 0.76 (95% confidence interval 0.70–0.81) and 0.71 (95% confidence interval 0.65–0.76), respectively (P = 0.2). However, the combination of liver morphomics with laboratory values or liver morphomics with laboratory and demographic data resulted in significant improved performance with area under the receiving operating characteristics of 0.84 (0.80–0.89) and 0.85 (0.81–0.90), respectively, compared with FIB-4 alone (P < 0.001). In a subgroup analysis, we also examined performance in patients without liver transplantation and saw similar augmentation of FIB-4. DISCUSSION: This proof-of-principle study demonstrates that automatically extracted features within CT scans can be combined with classic electronic medical record data to improve the prediction of cirrhosis in patients with liver disease. This tool may be used in both pretransplant and posttransplant patients and has the potential to improve our ability to detect undiagnosed cirrhosis.
Clinical and Molecular Features of Long-term Response to Immune Checkpoint Inhibitors in Patients with Advanced Non–Small Cell Lung Cancer

Abstract Purpose: We sought to identify features of patients with advanced non–small cell lung cancer (NSCLC) who achieve long-term response (LTR) to immune checkpoint inhibitors (ICI), and how these might differ from features predictive of short-term response (STR). Experimental Design: We performed a multicenter retrospective analysis of patients with advanced NSCLC treated with ICIs between 2011 and 2022. LTR and STR were defined as response ≥ 24 months and response < 12 months, respectively. Tumor programmed death ligand 1 (PD-L1) expression, tumor mutational burden (TMB), next-generation sequencing (NGS), and whole-exome sequencing (WES) data were analyzed to identify characteristics enriched in patients achieving LTR compared with STR and non-LTR. Results: Among 3,118 patients, 8% achieved LTR and 7% achieved STR, with 5-year overall survival (OS) of 81% and 18% among LTR and STR patients, respectively. High TMB (≥50th percentile) enriched for LTR compared with STR (P = 0.001) and non-LTR (P < 0.001). Whereas PD-L1 ≥ 50% enriched for LTR compared with non-LTR (P < 0.001), PD-L1 ≥ 50% did not enrich for LTR compared with STR (P = 0.181). Nonsquamous histology (P = 0.040) and increasing depth of response [median best overall response (BOR) −65% vs. −46%, P < 0.001] also associated with LTR compared with STR; no individual genomic alterations were uniquely enriched among LTR patients. Conclusions: Among patients with advanced NSCLC treated with ICIs, distinct features including high TMB, nonsquamous histology, and depth of radiographic improvement distinguish patients poised to achieve LTR compared with initial response followed by progression, whereas high PD-L1 does not.
Phylogeography of the red alga Gracilariopsis tenuifrons (Gracilariales) along the Brazilian coast

Changes in the sea level during the Holocene are regarded as one of the most prevalent drivers of the diversity and distribution of macroalgae in Brazil, influenced by the emergence of the Vitória‐Trindade seamount chain (VTC). Gracilariopsis tenuifrons has a wide geographic distribution along the Brazilian coast, from Maranhão state (2°48′64.3" S) to Santa Catarina state (27.5°73′83" S). The knowledge of historical processes affecting diversity may allow the development of conservation strategies in environments against anthropogenic influence. Therefore, knowledge about phylogeography and populational genetic diversity in G. tenuifrons is necessary. Six populations were sampled along the northeastern tropical (Maranhão—MA, Rio Grande do Norte—RN, Alagoas—AL, and Bahia—BA States) and southeastern subtropical (São Paulo “Ubatuba”—SP1 and São Paulo “Itanhaém”—SP2 States) regions along the Brazilian coast. The genetic diversity and structure of G. tenuifrons were inferred using mitochondrial (COI‐5P and cox2‐3 concatenated) DNA markers. Gracilariopsis tenuifrons populations showed an evident separation between the northeast (from 2°48′64.3" S to 14°18′23" S; 17 haplotypes) and the southeast (from 23°50′14.9" S to 24°20′04.7" S; 10 haplotypes) regions by two mutational steps between them. The main biogeographical barrier to gene flow is located nearby the VTC. The southeast region (São Paulo State) is separated by two subphylogroups (SP1, three haplotypes and SP2, six haplotypes), and Santos Bay (estuary) has been considered a biogeographical barrier between them. The presence of genetic structure and putative barriers to gene flow are in concordance with previous studies reporting biogeographic breaks in the southwest Atlantic Ocean, including the genetic isolation between northeast and southeast regions for red and brown algae in the vicinity of the VTC.
Short Communications / Kurze Mitteilungen An Improved Transitive Closure Algorithm

Zusammenfassung An Improved Transitive Closure Algorithm. Several efficient transitive closure algorithms operate on the strongly connected components of a digraph, some of them using Tarjan's algorithm ( 17). Exploiting facts from graph theory and the special properties of Tarjan's algorithm we develop a new, improved algorithm. The transitive reduction of a digraph defined in (1) may be obtained as a byproduct.
Solution of one-dimensional fractional order partial integro-differential equations using variational iteration method

In this paper, we will employ the variational iteration method to find the approximate solution of one-dimensional fractional order partial integro-differential equations. Sometimes, the variational iteration method VIM is a highly efficient technique used to approximate analytical solution of fractional differential equations, applicability of VIM to the one-dimensional fractional order partial integro-differential equations has not been studied in details previously in the literatures. Details of this method are presented also in this paper.
Chemical Reaction Paths in Classical Potentials

Chemical reaction dynamics are usually tackled within the framework of Quantum Mechanics which can be computationally demanding. Here we suggest to use the energy-dependent Hamilton-Jacobi description with a classical reactive force eld to obtain the most probable path. This may enable to calculate the reaction rate. Reaction rates are an important characteristic of molecular processes and determine their speed. The chemical reaction rate is usually governed by the free energy barriers encountered during the reaction. The reaction dynamics can be analyzed by QM calculations [1] which can be computationally demanding. When the reaction time is shorter than the time period simulated by the classical molecular simulation, one can observe its dynamics by performing classical simulations with reactive force elds [2]. However, when the reaction is slower than the simulation time, the reaction typically does not occur during the simulation and therefore its dynamics cannot be determined by performing a standard simulation. It has been suggested in a study on protein folding to switch from the timedependent Newtonian description to the energy-dependent Hamilton-Jacobi (HJ) description in order to obtain the most probable path in protein folding, given the initial and nal con gurations. The HJ formulation considers intervals of xed displacements rather than xed time length and thus avoids the long times needed to cross high energy barriers [3, 4]. Here we suggest to use this technique to propagate the system from the reactants to the products of a chemical reaction (assuming the reaction occurs) using reactive force elds such as ReaxFF [2, 5]. The path obtained has a dominant contribution in the calculation of the path integral p (x1, t1|x2, t2) (see Ref. [4]). If the reaction is known as a function of time it may be used to approximate the probability of the reaction p (x1, t1|x2, t2) = e−(U(xf )−U(xi))/2kBT xf ˆ xi Dx (τ) e−Seff [x]/2D
Texture Image Compression using Tree Structured Wavelet Transform

Pyramid structured wavelet transform is best suited for natural images as most of the energy is contained in the low frequency band. But, in the case of texture images, dominant frequencies are located in the middle frequency bands, which make traditional wavelet transform ill suited. Adaptive tree structured wavelet packet coders [1] are more popular because of their ability to reproduce the texture image with good quality. In this paper, a new tree structured wavelet transform (TWT) is proposed for texture image compression. A technique has been developed, which gives best basis selection with computational efficiency. The performance of the proposed method is compared with the standard wavelet set partitioning in hierarchical trees coder, (SPIHT) [2].
Bayesian estimation of the scale parameter and survival function of weighted weibull distribution under different loss functions using r software

In this paper, we propose to obtain the Bayesian estimators of the scale parameter of a three parameter weighted weibull distribution, based on non-informative and informative priors using Entropy loss function and Quadratic loss function. The risk functions of these estimators have been studied. A real life example has been used to compare the performance of the estimates under different loss functions. Keywords: Weighted Weibull distribution, Jeffery’s prior and Gamma prior, loss functions.
Neighboring extremal optimal control for mechanical systems on Riemannian manifolds

In this paper, we extend neighboring extremal optimal control, which is well established for optimal control problems defined on a Euclidean space (see, e.g., [8]) to the setting of Riemannian manifolds. We further specialize the results to the case of Lie groups. An example along with simulation results is presented.
Detección y expresión de SapS, una fosfatasa ácida no específica de clase C con actividad de fosfatasa O-fosfotirosina, en aislamientos de Staphylococcus aureus de pacientes con osteomielitis crónica

Resumen Introducción. Se desconoce la identidad de los factores de virulencia de Staphylococcus aureus implicados en la osteomielitis crónica. Sin embargo, SapS, una fosfatasa ácida no específica de clase C, es un factor de virulencia reconocido y ya fue identificada en la cepa 154 de S. aureus, pero en extractos proteicos de vegetales podridos. Objetivo. Detectar el gen SapS y caracterizar la actividad de la fosfatasa SapS en cepas de S. aureus aisladas de pacientes con osteomielitis crónica y en las reportadas en una base de datos de análisis in silico de genomas bacterianos completos. Materiales y métodos. Se aisló y secuenció el gen SapS en los 12 aislamientos clínicos de S. aureus y en dos cepas de referencia; estas secuencias se analizaron junto con las secuencias de las cepas reportadas en la base de datos de genomas bacterianos: 49 cepas de S. aureus y 11 cepas de estafilococos negativos para coagulasa. Se evalúo la actividad de la fosfatasa SapS, presente en los extractos de los sobrenadantes de los cultivos de las cepas clínicas, mediante la hidrólisis de fosfato p-nitrofenil, O-fosfo-L- tirosina, O-fosfo-L serina y O-fosfo-L treonina junto con varios inhibidores de fosfatasas. Resultados. Se detectó el gen SapS en el genoma de las cepas clínicas y en las 49 cepas de S. aureus analizadas in silico, pero no en las 11 cepas de estafilococos negativos para coagulasa. La secuenciación de SapS reveló un péptido señal presente en el extremo N-terminal de proteínas extracelulares y los dominios bipartitos de aspartato (DDDD) en su sitio catalítico. SapS hidroliza selectivamente el fosfato p-nitrofenil y la O-fosfo-L-tirosina, pero es sensible a vanadato y molibdato. Conclusión. Se encontró SapS en el genoma de S. aureus de las cepas clínicas y de las cepas de simulación computacional. La SapS con actividad específica para la hidrólisis de la O-fosfo-L-tirosina comparte similitudes bioquímicas con las fosfatasas-tirosina bacterianas, por lo que puede formar parte de la red de factores de virulencia de la osteomielitis crónica.