Miracle-dz/UniFAR-FTUs huggingface dataset:
Disentangling the causes of mumps reemergence in the United States

Significance Mumps is a vaccine-preventable childhood infection that has undergone a resurgence in many developed countries boasting high immunization coverage. The recent reemergence of this viral infection, once considered a candidate for eradication, has raised suspicions regarding the effectiveness of current vaccines. There are also outstanding questions about why the mumps vaccine has failed to generate population-level immunity. The mechanism underlying vaccine failure has substantive impacts on the development of new vaccines. Here, we confronted multiple epidemiological models of vaccine failure with data from the past three decades in the United States to identify the causative mechanism for mumps emergence. We found waning of vaccine-derived immunity to be the most likely reason for mumps reemergence in the early 21st century US.
Anytime Minibatch with Stale Gradients : (Invited Paper)

Large-scale machine learning problems are often solved using distributed optimization techniques by dividing tasks across multiple compute nodes. Due to variability in compute time amongst nodes, distributed systems suffer from slow nodes known as stragglers that can have a big impact on convergence speed. Recently, Anytime Minibatch (AMB) technique has been proposed to speed up convergence by exploiting work done by stragglers rather than avoiding them. In AMB, workers are given a fixed time to calculate gradients, followed by a fixed communication time to average gradients. We observe that nodes stay idle during communication time. In our work, we allow workers to compute gradients during communication time resulting in what is known as stale gradients due to gradients calculated on out-of-date parameters. Our simulation results show that such approach achieves up to 60% faster convergence in wall time.
Exploration of bioactive molecules from Tinospora cordifolia and Actinidia deliciosa as an immunity modulator via molecular docking and molecular dynamics simulation study

Abstract Tinospora cordifolia and Actinidia deliciosa are the widely used plant in Ayurvedic systems of medicine. Both plants are well known for their immunomodulatory activity. In the current study, in silico exploration was performed using advanced computational techniques such as molecular docking and molecular dynamics simulation approach. Bioactive molecules from the Tinospora cordifolia and Actinidia deliciosa were docked against the Human IL-2. Out of all the docked bioactive molecules, Pygenic acid-B (PubChem CID:146157192) showed the highest negative binding affinity. GRAPHICAL ABSTRACT
Topological structure and global features enhanced graph reasoning model for non-small cell lung cancer segmentation from CT

Objective. Accurate and automated segmentation of lung tumors from computed tomography (CT) images is critical yet challenging. Lung tumors are of various sizes and locations and have indistinct boundaries adjacent to other normal tissues. Approach. We propose a new segmentation model that can integrate the topological structure and global features of image region nodes to address the challenges. Firstly, we construct a weighted graph with image region nodes. The graph topology reflects the complex spatial relationships among these nodes, and each node has its specific attributes. Secondly, we propose a node-wise topological feature learning module based on a new graph convolutional autoencoder (GCA). Meanwhile, a node information supplementation (GNIS) module is established by integrating specific features of each node extracted by a convolutional neural network (CNN) into each encoding layer of GCA. Afterwards, we construct a global feature extraction model based on multi-layer perceptron (MLP) to encode the features learnt from all the image region nodes which are crucial complementary information for tumor segmentation. Main results. Ablation study results over the public lung tumor segmentation dataset demonstrate the contributions of our major technical innovations. Compared with other segmentation methods, our new model improves the segmentation performance and has generalization ability on different 3D image segmentation backbones. Our model achieved Dice of 0.7827, IoU of 0.6981, and HD of 32.1743 mm on the public dataset 2018 Medical Segmentation Decathlon challenge, and Dice of 0.7004, IoU of 0.5704 and HD of 64.4661 mm on lung tumor dataset from Shandong Cancer Hospital. Significance. The novel model improves automated lung tumor segmentation performance especially the challenging and complex cases using topological structure and global features of image region nodes. It is of great potential to apply the model to other CT segmentation tasks.
Control of Cell Size by c-di-GMP Requires a Two-Component Signaling System in the Cyanobacterium Anabaena sp. Strain PCC 7120

Cyanobacteria are considered the first organisms to produce oxygen on Earth, and their activities shaped the evolution of our ecosystems. Cell size is an important trait fixed early in evolution, with the diversification of micro- and macrocyanobacterial species during the Great Oxidation Event. ABSTRACT Each bacterial species possesses a specific cell size and morphology, which constitute important and recognizable physical traits. How bacteria maintain their particular cell size and morphology remains an essential question in microbiology. Cyanobacteria are oxygen-evolving photosynthetic prokaryotes. Although monophyletic, these organisms are highly diverse in their cell morphology and cell size. How these physical traits of cyanobacteria are controlled is poorly understood. Here, we report the identification of a two-component signaling system, composed of a histidine kinase CdgK and a response regulator CdgS, involved in cell size regulation in the filamentous, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120. Inactivation of cdgK or cdgS led to reduction of cell length and width with little effect on cell growth capacity. CdgS has a GGDEF domain responsible for the synthesis of the second messenger c-di-GMP. Based on genetic and biochemical studies, we proposed a signaling pathway initiated by CdgK, leading to the phosphorylation of CdgS, and thereby an enhanced enzymatic activity for c-di-GMP synthesis of the latter. The GGDEF domain of CdgS was essential in cell size control, and the reduction of cell size observed in various mutants could be rescued by the expression of a c-di-GMP synthetase from E. coli. These results provided evidence that a minimal threshold of c-di-GMP level was required for maintaining cell size in Anabaena. IMPORTANCE Cyanobacteria are considered the first organisms to produce oxygen on Earth, and their activities shaped the evolution of our ecosystems. Cell size is an important trait fixed early in evolution, with the diversification of micro- and macrocyanobacterial species during the Great Oxidation Event. However, the genetic basis underlying cell size control in cyanobacteria was not understood. Our studies demonstrated that the CdgK-CdgS signaling pathway participates in the control of cell size, and their absence did not affect cell growth. CdgK has multiple domains susceptible to signal input, which are necessary for cell size regulation. This observation suggests that cell size in Anabaena could respond to environmental signals. These studies paved the way for genetic dissection of cell size regulation in cyanobacteria.
Galaxy Formation: What the Future May Hold

It is certainly foolhardy to attempt to predict the future in a domain of astrophysics that is advancing as rapidly as that of galaxy formation. Nevertheless, I will try to do so. I begin with some historical reÑections. Galaxy formation was pioneered in classic papers by de Sitter, and Lema•ü tre, McVittie, who studied linear and nonlinear perturbations in a dust-Ðlled universe, and by Lifschitz Friedmann-Lema•ü tre and Bardeen, who provided the Ðrst complete treatments of linear perturbation evolution. What has long been clear is that the problem of gravitational instability in the expanding universe reduces to an initial-value problem. What are the amplitude and spectrum of the primordial energy density Ñuctuations required to seed structure formation? There have been three modern developments that have revolutionized studies of large-scale structure formation. The initial-value problem has been solved empirically, via discovery of the Ñuctuations in the cosmic microwave background, which strongly constrain the nature of the primordial seed density Ñuctuations. InÑationary cosmology has provided the theoretical framework which accounts for the origin and spectrum of primordial Ñuctuations as a consequence of the inevitable ampliÐcation of quantum Ñuctuations. The amplitude is not predicted, but its empirical determination constrains the inÑaton potential. N-body simulations have modeled the nonlinear evolution of the Ñuctuations with sufficient precision so as to be able to confront and account for a wide variety of observations of galaxy clustering. The large-scale structure of the universe is now well understood. One can understand its origin via inÐnitesimal relic Ñuctuations from inÑation and its evolution via gravitational instability in the matter-dominated era of the universe. The clustering of galaxies, the properties of galaxy clusters, and even the spatial and velocity distribution both of galaxies and of di†use intergalactic gas are well modeled by simulations. The statistical properties of these distributions are understood. The basic framework for our successful theory of largescale structure is provided by the cold dark matter hypothe-
Study of photosensitizer diffusion in a photopolymer material for holographic applications

Photopolymer materials exhibit good characteristics when used as holographic recording media. Extensive studies have been carried out on the behavior of the various chemical components in such materials, with photosensitizers in particular receiving much attention. In all previous analysis of photopolymer kinetics, the effects of photosensitiser diffusion have been neglected. For rapid sequential holographic recordings in photopolymers, for example, in an application such as holographic data storage, dye diffusion effects may become more pronounced. Therefore, we examine the dye diffusion effects of erythrosine B in an acrylamide/polyvinyl alcohol material. This is achieved using simple experimental techniques and a proposed theoretical model.
Who's talking to who: microbiome-enteric nervous system interactions in early life.

The enteric nervous system (ENS) is the intrinsic nervous system of the intestine and regulates important gut functions, including motility, nutrient uptake, and immune response. The development of the ENS begins during early organogenesis and continues to develop once feeding begins, with ongoing plasticity in adulthood. There has been increasing recognition that the intestinal microbiota and ENS interact during critical periods, with implications for normal development and potentially disease pathogenesis. In this review, we will focus on insights from mouse and zebrafish model systems to compare and contrast how each model can serve in elucidating the bidirectional communication between the ENS and the microbiome. At the end of this review, we further outline implications for human disease and highlight research innovations that can lead the field forward.
Infrared photometry of the nuclei of early-type radio galaxies.

On presente la photometrie J, H, K, L' a deux ouvertures et la photometrie a 10 μm (N) a une ouverture du noyau de 44 galaxies elliptiques et SO proches. Il n'y a pas de correlation entre les flux radio et les exces a 10 μm comme pour les galaxies de Seyfert
Respiratory complications during recovery from gastrointestinal endoscopies performed by gastroenterologists under moderate sedation

Background/Aims Data on the incidence of adverse respiratory events during recovery from gastrointestinal endoscopy are limited. The aim of this study was to investigate the incidence of these complications. Methods In this retrospective cohort study, data were obtained from the electronic records of 657 consecutive patients, who underwent gastroenterological procedures under sedation. Results Pulse oximetry oxygen saturation (SpO2) <90% for <60 seconds occurred in 82 patients (12.5%), and in 11 patients (1.7%), SpO2 of <90% for >60 seconds occurred in 79 patients (12.0%) and in 14 patients (2.1%), and SpO2 <75% occurred in four patients (0.6%) and in no patients during the procedure and recovery period, respectively. No major complications were noted. The occurrence of desaturation during recovery was correlated with desaturation during the procedure (p<0.001). Higher American Society of Anesthesiologists score (odds ratio [OR], 1.867; 95% confidence interval [CI], 1.008–3.458), ischemic heart disease (OR, 1.815; 95% CI, 0.649–5.080), hypertension (OR, 1.289; 95% CI, 0.472–3.516), and diabetes mellitus (OR, 2.406; 95% CI, 0.950–6.095) increased the occurrence of desaturation during recovery. Conclusions We found no major complications during recovery after balanced propofol-based sedation administered by a gastroenterologist-nurse team. Patients with the identified risk predictors must be monitored carefully.
Newcomb's Paradox Revisited

This paper attempts to provide a solution to the Newcomb Problem, which was first presented in Nozick [1969]. The author suggested there a solution of his own, with which he admitted to being dissatisfied, and invited further comments that might 'enable [Nozick] to stop returning periodically to [the paradox]' (op. cit. p. 143). We found the paradox every bit as intriguing as Nozick did, and hope that our solution can restore his peace of mind. Suppose you are playing a game with a Being whom you believe to possess extraordinary predictive powers. The game proceeds as follows: Before you are two boxes. In one you can plainly see $I,ooo. The other is covered, so you cannot see what it contains. But you know that the Being has put into it either a million dollars or nothing, depending on what he had predicted that you will do come your turn to play. You have a choice between two actions: taking what is in both boxes, or taking what is in the covered box only. You know, however, that the Being played his move as follows: if he predicted that you will take both boxes, he has left the covered box empty; if he predicted that you will take the covered box only, he has put a million dollars in it. You are not allowed to use a chance device to determine your choice. You have enormous confidence in the Being's ability to predict your actions, and you know that he has correctly predicted
Proline and glucose metabolic reprogramming supports vascular endothelial and medial biomass in pulmonary arterial hypertension

In pulmonary arterial hypertension (PAH), inflammation promotes a fibroproliferative pulmonary vasculopathy. Reductionist studies emphasizing single biochemical reactions suggest a shift toward glycolytic metabolism in PAH; however, key questions remain regarding the metabolic profile of specific cell types within PAH vascular lesions in vivo. We used RNA-Seq to profile the transcriptome of pulmonary artery endothelial cells (PAECs) freshly isolated from an inflammatory vascular injury model of PAH ex vivo, and these data were integrated with information from human gene ontology pathways. Network medicine was then used to map all aa and glucose pathways to the consolidated human interactome, which includes data on 233,957 physical protein-protein interactions. Glucose and proline pathways were significantly close to the human PAH disease module, suggesting that these pathways are functionally relevant to PAH pathobiology. To test this observation in vivo, we used multi-isotope imaging mass spectrometry to map and quantify utilization of glucose and proline in the PAH pulmonary vasculature at subcellular resolution. Our findings suggest that elevated glucose and proline avidity underlie increased biomass in PAECs and the media of fibrosed PAH pulmonary arterioles. Overall, these data show that anabolic utilization of glucose and proline are fundamental to the vascular pathology of PAH.
High-Dose Once-Daily Thoracic Radiotherapy in Limited-Stage Small-Cell Lung Cancer: CALGB 30610 (Alliance)/RTOG 0538

PURPOSE Although level 1 evidence supports 45-Gy twice-daily radiotherapy as standard for limited-stage small-cell lung cancer, most patients receive higher-dose once-daily regimens in clinical practice. Whether increasing radiotherapy dose improves outcomes remains to be prospectively demonstrated. METHODS This phase III trial, CALGB 30610/RTOG 0538 (ClinicalTrials.gov identifier: NCT00632853), was conducted in two stages. In the first stage, patients with limited-stage disease were randomly assigned to receive 45-Gy twice-daily, 70-Gy once-daily, or 61.2-Gy concomitant-boost radiotherapy, starting with either the first or second (of four total) chemotherapy cycles. In the second stage, allocation to the 61.2-Gy arm was discontinued following planned interim toxicity analysis, and the study continued with two remaining arms. The primary end point was overall survival (OS) in the intention-to-treat population. RESULTS Trial accrual opened on March 15, 2008, and closed on December 1, 2019. All patients randomly assigned to 45-Gy twice-daily (n = 313) or 70-Gy once-daily radiotherapy (n = 325) are included in this analysis. After a median follow-up of 4.7 years, OS was not improved on the once-daily arm (hazard ratio for death, 0.94; 95% CI, 0.76 to 1.17; P = .594). Median survival is 28.5 months for twice-daily treatment, and 30.1 months for once-daily treatment, with 5-year OS of 29% and 32%, respectively. Treatment was tolerable, and the frequency of severe adverse events, including esophageal and pulmonary toxicity, was similar on both arms. CONCLUSION Although 45-Gy twice-daily radiotherapy remains the standard of care, this study provides the most robust information available to help guide the choice of thoracic radiotherapy regimen for patients with limited-stage small-cell lung cancer.
Fasting Plasma Glucose Increase and Neutrophil-to-Lymphocyte Ratio as Risk Predictors of Clinical Outcome of COVID-19 Pneumonia in Type 2 Diabetes Mellitus

Abstract Aim of the study To evaluate fasting plasma glucose (FPG) increase and neutrophil-to-lymphocyte ratio (NLR) as risk predictors of severe clinical outcome of COVID-19 pneumonia in type 2 diabetes mellitus (T2DM) hospitalised patients. Patients and methods Type 2 diabetes mellitus (T2DM) patients hospitalised between March 2020 and February 2021 were studied retrospectively. The NLR ratio at admission and FPG increase (day 7, day with maximal FPG) were evaluated in association with the clinical progression of SARS-CoV-2 infection. Results Three hundred patients (165 men, 135 women) were included in the study. The mean age was 67.17±8.65 years. Severe COVID-19 pneumonia was diagnosed in 170 patients (56.7%). Fifty-four patients (18%) were intubated and 49 (16.3%) died. Greater increase in FPG (79.5 vs. 44.5 mg/dL for day 1–7, p<0.001; and 113.5 vs. 75 mg/dL for day 1-day with maximum glucose value, p<0.001) and higher NLR at admission (10.65 vs. 6.85) were seen in patients with need of high-flow oxygen compared to those without need, and they were associated with a higher probability of intubation and death. Conclusion FPG increase and NLR could be significant risk predictors of severe COVID-19 pneumonia in T2DM hospitalised patients.
A Novel Fusion Method for Multi-Focus Images

A simple but efficient algorithm for multi-focus image fusion is proposed in this paper, which is realized based on Laplacian pyramid decomposition. Firstly, the Laplacian pyramids for each source images are decomposed separately, and then each level of new Laplacian pyramid is fused by adopting a simple fusion rule. Finally, the end fused image is obtained by inverse Laplacian pyramid transform. The experiment showed that this method is effective and can get a fine fusion result for multi-focus images.
Caractères à valeurs dans le centre de Bernstein

Abstract Let G be a reductive p-adic group, we are interested in finitely generated projective smooth G-modules. Let P be such a module, consider it as a З-module, where З is the Bernstein center of the category of smooth G-modules. Then we can form P ⊗З. χℂ for every complex-valued character of З: it is a finite length smooth representation of G. We describe its image in the Grothendieck group of finite length smooth G-modules. To do this, we define under suitable assumptions a З-valued character on the З-admissible (but not admissible! ) representation P. The case of indGK(1) where K is a special compact open subgroup of G is an interesting example. Some of his properties are discussed and extended to other representations of K using Bushnell and Kutzko's theory of types, when G = GL(n).
A discrete-choice experiment study of physicians’ prioritization of attributes of medical treatments for endometriosis-associated pain

ABSTRACT Background Physicians’ preferences for attributes of medical treatments for endometriosis-associated pain have not previously been quantified. Methods US obstetrician-gynecologists completed an online discrete-choice experiment survey. In a series of questions, physicians chose a medical treatment for a hypothetical patient with endometriosis experiencing severe, persistent dysmenorrhea, nonmenstrual pelvic pain, and/or dyspareunia. Each question presented two hypothetical medical treatments for endometriosis-associated pain, defined by seven attributes with varying levels. Preferences weights and conditional relative importance (CRI) were calculated using a random-parameters logit model. Results Respondents (N = 250) had an average age of 53 years; 36% were female. The most important attribute, conditional on the attributes and levels evaluated, was risk of moderate-to-severe hot flashes (CRI, 3.34). In descending order of importance, the CRIs of the other attributes were 2.13 for improvement in nonmenstrual pelvic pain, 2.04 for improvement in dyspareunia, 1.88 for improvement in dysmenorrhea, 1.16 for risk of pregnancy-related complications if pregnancy occurs during treatment, 0.62 for increased risk of bone fracture later in life, and 0.48 for mode of administration. Conclusions In addition to valuing pain reduction, respondents prioritized avoiding moderate-to-severe hot flashes, followed by less common and less immediate risks of pregnancy-related complications and bone fracture.
Analytical thermal lens instrumentation

This review describes recent instrumentation developments of the thermal lens techniques. It will begin with a brief discussion of the theory of the techniques. Its main focus is, however, on the detail description of various instruments. Specifically, the discussion will begin with the description of single beam instruments which were initially developed following by dual beam instruments. Elaboration will be focused on some of the most sophisticated instruments which were developed recently. These include differential thermal lens instruments, multiwavelength and spectral tunable instruments, circular dichroism spectropolarimeters, rotoreflecting instruments, and miniaturized thermal lens instruments. Selection of lasers, focusing, modulation, sample position, sample cells, data acquisition, noise reduction, and applications of acousto‐optic tunable filters will also be discussed. The future of the techniques in terms of instrumentation will be finally forecasted.