Miracle-dz/UniFAR-FTUs huggingface dataset:
Associations of Household Income with Health-Related Quality of Life Following a Colorectal Cancer Diagnosis Varies With Neighborhood Socioeconomic Status

Background: Existing evidence indicates household income as a predictor of health-related quality of life (HRQoL) following a colorectal cancer diagnosis. This association likely varies with neighborhood socioeconomic status (nSES), but evidence is limited. Methods: We included data from 1,355 colorectal cancer survivors participating in the population-based Puget Sound Colorectal Cancer Cohort (PSCCC). Survivors reported current annual household income; we measured HRQoL via the Functional Assessment of Cancer Therapy - Colorectal (FACT-C) tool. Using neighborhood data summarized within a 1-km radial buffer of Census block group centroids, we constructed a multidimensional nSES index measure. We employed survivors' geocoded residential addresses to append nSES score for Census block group of residence. With linear generalized estimating equations clustered on survivor location, we evaluated associations of household income with differences in FACT-C mean score, overall and stratified by nSES. We used separate models to explore relationships for wellbeing subscales. Results: We found lower household income to be associated with clinically meaningful differences in overall FACT-C scores [<$30K: −13.6; 95% confidence interval (CI): −16.8 to −10.4] and subscale wellbeing after a recent colorectal cancer diagnosis. Relationships were slightly greater in magnitude for survivors living in lower SES neighborhoods. Conclusions: Our findings suggest that recently diagnosed lower income colorectal cancer survivors are likely to report lower HRQoL, and modestly more so in lower SES neighborhoods. Impact: The findings from this work will aid future investigators' ability to further consider the contexts in which the income of survivors can be leveraged as a means of improving HRQoL
The Dynamic Interaction between Extracellular Matrix Remodeling and Breast Tumor Progression

Desmoplastic tumors correspond to a unique tissue structure characterized by the abnormal deposition of extracellular matrix. Breast tumors are a typical example of this type of lesion, a property that allows its palpation and early detection. Fibrillar type I collagen is a major component of tumor desmoplasia and its accumulation is causally linked to tumor cell survival and metastasis. For many years, the desmoplastic phenomenon was considered to be a reaction and response of the host tissue against tumor cells and, accordingly, designated as “desmoplastic reaction”. This notion has been challenged in the last decades when desmoplastic tissue was detected in breast tissue in the absence of tumor. This finding suggests that desmoplasia is a preexisting condition that stimulates the development of a malignant phenotype. With this perspective, in the present review, we analyze the role of extracellular matrix remodeling in the development of the desmoplastic response. Importantly, during the discussion, we also analyze the impact of obesity and cell metabolism as critical drivers of tissue remodeling during the development of desmoplasia. New knowledge derived from the dynamic remodeling of the extracellular matrix may lead to novel targets of interest for early diagnosis or therapy in the context of breast tumors.
Identification of Internal Defects in Potato Using Spectroscopy and Computational Intelligence Based on Majority Voting Techniques

Potatoes are one of the most demanded products due to their richness in nutrients. However, the lack of attention to external and, especially, internal defects greatly reduces its marketability and makes it prone to a variety of diseases. The present study aims to identify healthy-looking potatoes but with internal defects. A visible (Vis), near-infrared (NIR), and short-wavelength infrared (SWIR) spectrometer was used to capture spectral data from the samples. Using a hybrid of artificial neural networks (ANN) and the cultural algorithm (CA), the wavelengths of 861, 883, and 998 nm in Vis/NIR region, and 1539, 1858, and 1896 nm in the SWIR region were selected as optimal. Then, the samples were classified into either healthy or defective class using an ensemble method consisting of four classifiers, namely hybrid ANN and imperialist competitive algorithm (ANN-ICA), hybrid ANN and harmony search algorithm (ANN-HS), linear discriminant analysis (LDA), and k-nearest neighbors (KNN), combined with the majority voting (MV) rule. The performance of the classifier was assessed using only the selected wavelengths and using all the spectral data. The total correct classification rates using all the spectral data were 96.3% and 86.1% in SWIR and Vis/NIR ranges, respectively, and using the optimal wavelengths 94.1% and 83.4% in SWIR and Vis/NIR, respectively. The statistical tests revealed that there are no significant differences between these datasets. Interestingly, the best results were obtained using only LDA, achieving 97.7% accuracy for the selected wavelengths in the SWIR spectral range.
Possible reasons for the regrettable results of patency of an inside stent in endoscopic transpapillary biliary stenting

Endoscopic biliary decompression is a minimally invasive procedure for cholestasis since the first endoscopic retrograde cholangiopancreatography‐guided biliary stenting performed by Soehendra and Reynders‐Frederix. Among the endoscopic biliary decompression, endoscopic transpapillary biliary stenting (EBS), is a mainstream choice and presently has two methods of placement: stenting above the sphincter of Oddi (SO) (suprapapillary) and stenting across the SO (transpapillary). Stent patency is the most important concern for patients, endoscopists and physicians because it can affect both the life prognosis and treatment schedule of patients. Biliary stent occlusion can occur because of several factors. Among them, direct food impaction, biofilm formation, and sludge formation play important roles and are presumed to be theoretically overcome by EBS above the SO. Thus, EBS above the SO is expected to result in a longer patency than EBS across the SO. In the literature, there have been six comparative studies on EBS for distal biliary obstruction in which the stent was placed above or across the SO, including two randomized controlled trials (RCTs) with negative results of stenting above the SO. With respect to EBS for hilar biliary obstruction, there have been no RCTs, whereas four retrospective comparative studies with negative results and four retrospective comparative studies showing positive results of stenting above the SO have been reported. In this review, we focused on EBS above and across the SO, and summarized the positive and negative results of the two types of stenting to promote effective clinical practice and to provide a basis for future studies.
Detecting Topic and Sentiment Trends in Physician Rating Websites: Analysis of Online Reviews Using 3-Wave Datasets

(1) Background: Physician rating websites (PRWs) are a rich resource of information where individuals learn other people response to various health problems. The current study aims to investigate and analyze the people top concerns and sentiment dynamics expressed in physician online reviews (PORs). (2) Methods: Text data were collected from four U.S.-based PRWs during the three time periods of 2018, 2019 and 2020. Based on the dynamic topic modeling, hot topics related to different aspects of healthcare were identified. Following the hybrid approach of aspect-based sentiment analysis, the social network of prevailing topics was also analyzed whether people expressed positive, neutral or negative sentiments in PORs. (3) Results: The study identified 30 dominant topics across three different stages which lead toward four key findings. First, topics discussed in Stage III were quite different from the earlier two stages due to the COVID-19 outbreak. Second, based on the keyword co-occurrence analysis, the most prevalent keywords in all three stages were related to the treatment, questions asked by patients, communication problem, patients’ feelings toward the hospital environment, disease symptoms, time spend with patients and different issues related to the COVID-19 (i.e., pneumonia, death, spread and cases). Third, topics related to the provider service quality, hospital servicescape and treatment cost were the most dominant topics in Stages I and II, while the quality of online information regarding COVID-19 and government countermeasures were the most dominant topics in Stage III. Fourth, when zooming into the topic-based sentiments analysis, hot topics in Stage I were mostly positive (joy be the dominant emotion), then negative (disgust be the dominant emotion) in Stage II. Furthermore, sentiments in the initial period of Stage III (COVID-19) were negative (anger be the dominant emotion), then transformed into positive (trust be the dominant emotion) later. The findings also revealed that the proposed method outperformed the conventional machine learning models in analyzing topic and sentiment dynamics expressed in PRWs. (4) Conclusions: Methodologically, this research demonstrates the ability and importance of computational techniques for analyzing large corpora of text and complementing conventional social science approaches.
Enhancing Nature Connection and Positive Affect in Children through Mindful Engagement with Natural Environments

Nature connection, which describes a positive relationship between humans and the rest of nature, has been recognised as a worthwhile goal of all education. Given its association with wellbeing, as well as the fact that it can predict ecological behaviours in children, there have been several calls for it to become central to environmental education, and an important tool in tackling climate change. Previous research has reported the success of short-term interventions in increasing nature connection in children, but to date no empirical studies have looked at how mindful engagement with nature can promote both nature connection and positive affect. This study took place in a nature reserve in Wales and included n = 74 children, aged 9–10, who took part in three mindful activities. Pre- and post- measures included nature connection and positive/negative affect. Analysis showed a significant small to medium effect of the activity on nature connection. Moreover, positive affect significantly increased post-activity, while negative affect showed a small decrease.
Uncertainty Guided Multi-Scale Attention Network for Raindrop Removal From a Single Image

Raindrops adhered to a glass window or camera lens appear in various blurring degrees and resolutions due to the difference in the degrees of raindrops aggregation. The removal of raindrops from a rainy image remains a challenging task because of the density and diversity of raindrops. The abundant location and blur level information are strong prior guide to the task of raindrop removal. However, existing methods use a binary mask to locate and estimate the raindrop with the value 1 (adhesion of raindrops) and 0 (no adhesion), which ignores the diversity of raindrops. Meanwhile, it is noticed that different scale versions of a rainy image have similar raindrop patterns, which makes it possible to employ such complementary information to represent raindrops. In this work, we first propose a soft mask with the value in [−1,1] indicating the blurring level of the raindrops on the background, and explore the positive effect of the blur degree attribute of raindrops on the task of raindrop removal. Secondly, we explore the multi-scale fusion representation for raindrops based on the deep features of the input multi-scale images. The framework is termed uncertainty guided multi-scale attention network (UMAN). Specifically, we construct a multi-scale pyramid structure and introduce an iterative mechanism to extract blur-level information about raindrops to guide the removal of raindrops at different scales. We further introduce the attention mechanism to fuse the input image with the blur-level information, which will highlight raindrop information and reduce the effects of redundant noise. Our proposed method is extensively evaluated on several benchmark datasets and obtains convincing results.
Trimerization of the N-Terminal Tail of Zika Virus NS4A Protein: A Potential In Vitro Antiviral Screening Assay

The nonstructural (NS) protein NS4A in flaviviruses is a membrane protein that is critical for virulence, and, among other roles, it participates in membrane morphogenesis. In dengue virus (DENV), the NS4A hydrophilic N–terminal tail, together with the first transmembrane domain, is involved in both homo-oligomerization and hetero–oligomerization with NS4B. In both DENV and Zika virus (ZIKV), this N-terminal tail (residues 1–48) forms a random coil in solution but becomes mostly α-helical upon interaction with detergents or lipid membranes. Herein, we show that a peptide from ZIKV NS4A that spans residues 4–58, which includes most of the N–terminal tail and a third of its first transmembrane domain, forms homotrimers in the absence of detergents or liposomes. After interaction with the latter, α–helical content increases, consistent with binding. The oligomeric size of NS4A is not known, as it has only been reported in SDS gels. Therefore, we propose that full-length NS4A forms homotrimers mediated by this region, and that disruption of the oligomerization of peptide ZIKV NS4A 4–58 in solution can potentially constitute the basis for an in vitro assay to discover antivirals.
The Peroxiredoxin Asp f3 Acts as Redox Sensor in Aspergillus fumigatus

The human pathogenic fungus Aspergillus fumigatus is readily eradicated by the innate immunity of immunocompetent human hosts, but can cause severe infections, such as invasive aspergillosis (IA), in immunocompromised individuals. During infection, the fungal redox homeostasis can be challenged by reactive oxygen species (ROS), either derived from the oxidative burst of innate immune cells or the action of antifungal drugs. The peroxiredoxin Asp f3 was found to be essential to cause IA in mice, but how Asp f3 integrates with fungal redox homeostasis remains unknown. Here, we show that in vivo, Asp f3 acts as a sensor for ROS. While global transcription in fungal hyphae under minimal growth conditions was fully independent of Asp f3, a robust induction of the oxidative stress response required the presence of the peroxiredoxin. Hyphae devoid of Asp f3 failed to activate several redox active genes, like members of the gliotoxin biosynthesis gene cluster and integral members of the Afyap1 regulon, the central activator of the ROS defense machinery in fungi. Upon deletion of the asp f3 gene Afyap1 displayed significantly reduced nuclear localization during ROS exposure, indicating that Asp f3 can act as an intracellular redox sensor for several target proteins.
Back to the Basics: Two Approaches for the Identification and Extraction of Lipid Droplets from Malassezia pachydermatis CBS1879 and Malassezia globosa CBS7966

Malassezia spp. are lipid‐dependent yeasts that have been related to skin mycobiota and dermatological and systemic diseases. Study of lipid droplets (LDs) is relevant to elucidate the unknown role of these organelles in Malassezia and to gain a broader overview of lipid metabolism in Malassezia. Here, we standardized two protocols for the analysis of LDs in M. pachydermatis and M. globosa. The first describes co‐staining for confocal laser‐scanning fluorescence microscopy, and the second details extraction and purification of LDs. The double stain is achieved with three different neutral lipid fluorophores, namely Nile Red, BODIPY™ 493/503, and HCS LipidTOX™ Deep Red Neutral, in combination with Calcofluor White. For LD extraction, cell wall rupture is conducted using Trichoderma harzianum enzymes and cycles of vortexing with zirconium beads. LD purification is performed in a three‐step ultracentrifugation process. These standardizations will contribute to the study of the dynamics, morphology, and composition of LDs in Malassezia. © 2021 Wiley Periodicals LLC.
Effects of Heat Stress on Gut-Microbial Metabolites, Gastrointestinal Peptides, Glycolipid Metabolism, and Performance of Broilers

Simple Summary In the summer, heat stress is a main factor that causes poor performance in broilers. Broilers are more susceptible to high temperature environments than mammals due to their lack of sweat glands and being covered in feathers. Heat stress can alter the regulation of glycolipid metabolism, which is manifested by unstable levels of blood glucose, insulin, total cholesterol, and triglyceride. Heat stress also affects the structure of gut microbes and gastrointestinal peptides. However, the relationship among microbiota, gastrointestinal peptides, glycolipid metabolism, and production performance under heat stress is still unclear. Moreover, exploring these mechanisms can help in the development of strategies that alleviate the negative effects of performance by heat stress. Our results suggest that the poor production performance of broilers under heat stress may be related to short chain fatty acids fermented by intestinal microbiota involved in regulating metabolic disorders. Abstract This paper investigated the effects of heat stress on gut-microbial metabolites, gastrointestinal peptides, glycolipid metabolism, and performance of broilers. Thus, 132 male Arbor Acres broilers, 28-days-old, were randomly distributed to undergo two treatments: thermoneutral control (TC, 21 °C) and high temperature (HT, 31 °C). The results showed that the average daily gain (ADG), average daily feed intake (ADFI), and gastric inhibitory polypeptide (GIP) concentration in the jejunum significantly decreased the core temperature, feed conversion ratio (FCR), and ghrelin of the hypothalamus, and cholecystokinin (CCK) in jejunum, and serum significantly increased in the HT group (p < 0.05). Exploration of the structure of cecal microbes was accomplished by sequencing 16S rRNA genes. The sequencing results showed that the proportion of Christensenellaceae and Lachnospiraceae decreased significantly whereas the proportion of Peptococcaceae increased at the family level (p < 0.05). Ruminococcus and Clostridium abundances significantly increased at the genus level. Furthermore, the content of acetate in the HT group significantly increased. Biochemical parameters showed that the blood glucose concentration of the HT group significantly decreased, and the TG (serum triglycerides), TC (total cholesterol), insulin concentration, and the insulin resistance index significantly increased. Nonesterified fatty acid (NEFA) in the HT group decreased significantly. In conclusion, the results of this paper suggest that the poor production performance of broilers under heat stress may be related to short-chain fatty acids (SCFAs) fermented by intestinal microbiota involved in regulating metabolic disorders.
SIK2 orchestrates actin-dependent host response upon Salmonella infection

Significance Through conducting quantitative proteomics upon Salmonella infection, we identified a SIK2 signaling network, implementing the kinase into a so far concealed biological function. Our data exposed SIK2 as a central orchestrator of an actin regulatory network, coordinating the stability of Salmonella-containing vacuole (SCV) and cellular actin assembly, in order to limit the acute phase of the infection. Most strikingly, SIK2 is not exclusively acting locally on actin assembly associated with the SCV but impacts the actin cytoskeleton architecture in its entirety upon Salmonella infection. Our work provides a mechanistic framework for how the actin cytoskeleton is regulated and how it helps to control an acute Salmonella infection. Salmonella is an intracellular pathogen of a substantial global health concern. In order to identify key players involved in Salmonella infection, we performed a global host phosphoproteome analysis subsequent to bacterial infection. Thereby, we identified the kinase SIK2 as a central component of the host defense machinery upon Salmonella infection. SIK2 depletion favors the escape of bacteria from the Salmonella-containing vacuole (SCV) and impairs Xenophagy, resulting in a hyperproliferative phenotype. Mechanistically, SIK2 associates with actin filaments under basal conditions; however, during bacterial infection, SIK2 is recruited to the SCV together with the elements of the actin polymerization machinery (Arp2/3 complex and Formins). Notably, SIK2 depletion results in a severe pathological cellular actin nucleation and polymerization defect upon Salmonella infection. We propose that SIK2 controls the formation of a protective SCV actin shield shortly after invasion and orchestrates the actin cytoskeleton architecture in its entirety to control an acute Salmonella infection after bacterial invasion.
Recent Advances in the Plasma-Assisted Synthesis of Zinc Oxide Nanoparticles

An overview of recent work on the low-temperature plasma-assisted synthesis of zinc oxide (ZnO) nanoparticles is presented and interpreted in terms of gas-phase and surface reactions with illustrated examples. The thermodynamical nonequilibrium conditions allow the formation of chemically reactive species with a potential energy of several eV, which readily interact with the Zn precursors and initiate reactions leading to the formation of nanoparticles or nanowires. The high-quality nanowires were synthesized from Zn powders only upon interaction with moderately ionized plasma in a narrow range of plasma parameters. This technique is promising for the synthesis of large quantities of nanowires with aspect ratios well above 10, but the exact range of parameters remains to be determined. Apart from the ex situ techniques, the ZnO nanoparticles can be synthesized by depositing a film of precursors (often Zn salts or Zn-containing organometallic compounds) and exposing them to oxygen plasma. This technique is useful for the synthesis of well-adherent ZnO nanoparticles on heat-sensitive objects but requires further scientific validation as it often leads to the formation of a semicontinuous ZnO film rather than nanoparticles. Both low-pressure and atmospheric plasmas are useful in converting the precursor film into ZnO nanoparticles despite completely different mechanisms.
Utility of Routine Laboratory Biomarkers to Detect COVID-19: A Systematic Review and Meta-Analysis

No routine laboratory biomarkers perform well enough in diagnosing COVID-19 in isolation for them to be used as a standalone diagnostic test or to help clinicians prioritize patients for treatment. Instead, other diagnostic tests are needed. The aim of this work was to statistically summarise routine laboratory biomarker measurements in COVID-19-positive and -negative patients to inform future work. A systematic literature review and meta-analysis were performed. The search included names of commonly used, routine laboratory tests in the UK NHS, and focused on research papers reporting laboratory results of patients diagnosed with COVID-19. A random effects meta-analysis of the standardized mean difference between COVID-19-positive and -negative groups was conducted for each biomarker. When comparing reported laboratory biomarker results, we identified decreased white blood cell, neutrophil, lymphocyte, eosinophil, and platelet counts; while lactate dehydrogenase, aspartate aminotransferase, and alanine aminotransferase were elevated in COVID-19-positive compared to COVID-19-negative patients. Differences were identified across a number of routine laboratory biomarkers between COVID-19-positive and -negative patients. Further research is required to identify whether routine laboratory biomarkers can be used in the development of a clinical scoring system to aid with triage of patients.