Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of 5-Gene Signature Improves Lung Adenocarcinoma Prognostic Stratification Based on Differential Expression Invasion Genes of Molecular Subtypes

Background The acquisition of invasive tumor cell behavior is considered to be the cornerstone of the metastasis cascade. Thus, genetic markers associated with invasiveness can be stratified according to patient prognosis. In this study, we aimed to identify an invasive genetic trait and study its biological relevance in lung adenocarcinoma. Methods 250 TCGA patients with lung adenocarcinoma were used as the training set, and the remaining 250 TCGA patients, 500 ALL TCGA patients, 226 patients with GSE31210, 83 patients with GSE30219, and 127 patients with GSE50081 were used as the verification data sets. Subtype classification of all TCGA lung adenocarcinoma samples was based on invasion-associated genes using the R package ConsensusClusterPlus. Kaplan-Meier curves, LASSO (least absolute contraction and selection operator) method, and univariate and multivariate Cox analysis were used to develop a molecular model for predicting survival. Results As a consequence, two molecular subtypes for LUAD were first identified from all TCGA all data sets which were significant on survival time. C1 subtype with poor prognosis has higher clinical characteristics of malignancy, higher mutation frequency of KRAS and TP53, and a lower expression of immune regulatory molecules. 2463 differentially expressed invasion genes between C1 and C2 subtypes were obtained, including 580 upregulation genes and 1883 downregulation genes. Functional enrichment analysis found that upregulated genes were associated with the development of tumor pathways, while downregulated genes were more associated with immunity. Furthermore, 5-invasion gene signature was constructed based on 2463 genes, which was validated in four data sets. This signature divided patients into high-risk and low-risk groups, and the LUDA survival rate of the high-risk group is significantly lower than that of the low-risk group. Multivariate Cox analysis revealed that this gene signature was an independent prognostic factor for LUDA. Compared with other existing models, our model has a higher AUC. Conclusion In this study, two subtypes were identified. In addition, we developed a 5-gene signature prognostic risk model, which has a good AUC in the training set and independent validation set and is a model with independent clinical characteristics. Therefore, we recommend using this classifier as a molecular diagnostic test to assess the prognostic risk of patients with LUDA.
Survey on the Use of Calcium Carbide as Ripening Agent in Ilorin Metropolis

DOI: http://dx.doi. org/10.24018/ejfood.2020. 2.6. 178 Vol 2 | Issue 6 | December 2020 1 Abstract — This research work examined the use of calcium carbide as ripening agent for banana and plantain in major markets within Ilorin metropolis. Open ended/structured questionnaires were administered to banana/plantain handlers in six different markets, afterward samples of ripe banana and plantain were also collected from different points in each market at the same time for physicochemical and mineral analyses. Results showed that a total of 85 respondents returned their questionnaires from all the markets; of which majority were female (99 percent), 89 percent of them were married, only 35 percent had formal education, 94 percent of them do store their plantain/banana, 83 percent were aware of the use of calcium carbide in ripening of plantain/banana but only 1 percent admitted using it. Comparing with the control samples, the physicochemical and mineral analyses showed that there were reduced moisture and vitamin C contents with increased values of arsenic and phosphorus being recovered from banana and plantain samples. Many authors had associated induced ripening with the use of ripening agent such as calcium carbide with reduced moisture and vitamin C contents with elevated values of arsenic and phosphorus in ripe fruits which had many health risks. Samples of banana and plantain collected from Ilorin markets were probably forced ripen with artificial ripening agents. The needs for constant education of the public especially fruits handlers on the health implications of the use of calcium carbide as ripening agent cannot be overemphasized.
Rapid and Sensitive High Performance Liquid Chromatography Method for The Determination of Amphotericin B in Rat Plasma

A simple and sensitive reverse phase high-performance liquid chromatographic (RP-HPLC) method for the determination of amphotericin B (AMB) in rat plasma has been developed. An aliquot quantity of 225 µL plasma sample was taken and 25 µL internal standard (IS) was added to it and mixed well. 250 µL methanol was added to it and sonicated for 10 minutes followed by 20 minutes centrifugation at 5000 rpm. The supernatant layer was separated and filtered through sample filtration unit (membrane filter, 0. 45 µm) and injected into the HPLC system consisting of Hypersil ODS, C18 (250×4.6 mm, 5 µm particle size) column, using 10 mmol phosphate buffer : acetonitrile = 65:35 (v/v) as mobile phase and detected at 407 nm. Lower limit of detection (LOD) was 3 ng/ mL and lower limit of quantitation (LOQ) was 10 ng/mL. Maximum between-run precision was 1.973%. Mean extraction recovery was found to be 91.764% to 96.457%. Stability study showed that after three freeze-thaw cycles the loss of three quality control samples were less than 15%. The processed samples were stable for at least 8 h. The method is simple, sensitive and rapid and applicable for pharmacokinetic study of amphotericin B formulation in rat model.
Utilization of organic phosphorus sources by oilseed rape, sunflower, and soybean

We evaluated the ability of Brassica napus L. (oilseed rape), Helianthus annus L. (sunflower), and Glycine max L. (soybean) plants grown inoculated with or without bacteria to utilize organic P sources. Plants were supplied with inorganic (dibasic sodium phosphate) and organic P sources (phytate and glucose phosphate) at three concentrations and grown for 40 d under sterile conditions. Three inoculation treatments were compared: control (non-inoculated plants), inoculation with Bacillus amyloliquefaciens BNM340, and inoculation with Pseudomonas fluorescens BNM296 (two bacteria with proven phytase activity). Oilseed rape, sunflower and soybean could utilize organic P sources. For example, when phytate (0.5 mM) P was used as the external P source, the increase factors over the no-P treatments were 4.5, 1.4, and 1.4 for oilseed rape, sunflower, and soybean P uptake, respectively. When glucose 1-phosphate disodium salt (G1P, 0.5 mM) was the P source, the increase factors were 8.8, 1.7, and 1.9 respectively. Positive responses to the organic P sources were found for the biomass accumulation of oilseed rape and soybean but not for sunflower. The inoculation with bacteria did not exert a promoting effect on P uptake. We demonstrate that the three species can effectively use organic P sources. The existence of crop plants that are more efficient in the utilization of different soil P sources would be particularly beneficial to improve P recycling and use of P fertilizers in agriculture.
Socio-economic characteristics and willingness of consumers to pay for the safety of fura de nunu in Ilorin, Nigeria

This study investigated the socio-economic characteristics, safety perception and willingness of consumers to pay premium (WTP) for the safety of fura (a semi-solid cereal-based dumpling) and nunu (West African yoghurt) in Ilorin metropolis, Nigeria. Primary data, generated through the use of structured questionnaires, and purpose interviews were used for the study. Data were analysed using descriptive statistics, logit regression analysis and Pearson correlation. The majority of the consumers were low income earners with low level of education. The consumers were willing to pay extra for safety intervention because of the need to safeguard their health. Income was the only variable that had significant (P≤0.01) influence on WTP. Level of education (P≤0.05), income (P≤0.01) and safety perception (P≤0.05) had a positive relationship with WTP. The consumers’ willingness to pay premium provides a good baseline for safety intervention throughout the chain of this nutritious product. It is hoped that the safet.
PSD-95 in CA1 Area Regulates Spatial Choice Depending on Age

Cognitive processes that require spatial information rely on synaptic plasticity in the dorsal CA1 area (dCA1) of the hippocampus. Since the function of the hippocampus is impaired in aged individuals, it remains unknown how aged animals make spatial choices. Here, we used IntelliCage to study behavioral processes that support spatial choices of aged female mice living in a group. Cognitive processes that require spatial information rely on synaptic plasticity in the dorsal CA1 area (dCA1) of the hippocampus. Since the function of the hippocampus is impaired in aged individuals, it remains unknown how aged animals make spatial choices. Here, we used IntelliCage to study behavioral processes that support spatial choices of aged female mice living in a group. As a proxy of training-induced synaptic plasticity, we analyzed the morphology of dendritic spines and the expression of a synaptic scaffold protein, PSD-95. We observed that spatial choice training in young adult mice induced correlated shrinkage of dendritic spines and downregulation of PSD-95 in dCA1. Moreover, long-term depletion of PSD-95 by shRNA in dCA1 limited correct choices to a reward corner, while reward preference was intact. In contrast, old mice used behavioral strategies characterized by an increased tendency for perseverative visits and social interactions. This strategy resulted in a robust preference for the reward corner during the spatial choice task. Moreover, training decreased the correlation between PSD-95 expression and the size of dendritic spines. Furthermore, PSD-95 depletion did not impair place choice or reward preference in old mice. Thus, our data indicate that while young mice require PSD-95-dependent synaptic plasticity in dCA1 to make correct spatial choices, old animals observe cage mates and stick to a preferred corner to seek the reward. This strategy is resistant to the depletion of PSD-95 in the CA1 area. Overall, our study demonstrates that aged mice combine alternative behavioral and molecular strategies to approach and consume rewards in a complex environment. SIGNIFICANCE STATEMENT It remains poorly understood how aging affects behavioral and molecular processes that support cognitive functions. It is, however, essential to understand these processes to develop therapeutic interventions that support successful cognitive aging. Our data indicate that while young mice require PSD-95-dependent synaptic plasticity in dCA1 to make correct spatial choices (i.e., choices that require spatial information), old animals observe cage mates and stick to a preferred corner to seek the reward. This strategy is resistant to the depletion of PSD-95 in the CA1 area. Overall, our study demonstrates that aged mice combine alternative behavioral and molecular strategies to approach and consume rewards in a complex environment. Second, the contribution of PSD-95-dependent synaptic functions in spatial choice changes with age.
Energetics of heterometal substitution in ε-Keggin [MO4Al12(OH)24(OH2)12]6/7/8+ ions

Abstract Aluminum hydroxide ions in the e-Keggin structure provide geochemical models for how structure affects reactivity, and consequently, how aqueous ions evolve to bulk precipitates. Here we report a systematic comparison of heterometal substitution into the MAl12 e-Keggin structure, where M = GaIII, AlIII, or GeIV. We use direct solution calorimetric techniques to compare the energetics of these substituted structures and complement these measurements with density functional theory (DFT) calculations to further examine this structure as a host to alternative heterometals. The measured enthalpy of solution (DHsoln) at 28 °C in 5 N HCl for the selenate salts of GaAl12 7+ and AlAl127+, was measured as -869.71 ± 5.18 and -958.04 ± 2.79 kJ/mol, respectively. The enthalpies of formation from the elements, DH°f,el, for the selenate salts of GaAl127+ and AlAl127+, are -23 075.02 ± 61.68 and -23 334.18 ± 60.38 kJ/mol, respectively, supplanting previous values. We compare structural relationships to both experimental and calculated energies to identify the driving forces that control these substitutions and stability, and establish that tetrahedral M-O bond lengths are closely related to the strain and stability of the structure. We show that substitution depends on the size and valence of the heterometal through energetics, and we extend our thermodynamic and structural relationships to other not yet synthesized MAl12 clusters (M = SiIV, FeIII, BeII, MgII, or ZnII).
Bulk volume susceptibility difference between deoxyhemoglobin and oxyhemoglobin for HbA and HbS: A comparative study

Sickle cell anemia is a blood disorder that alters the morphology and the oxygen affinity of the red blood cells. Cerebral oxygen extraction fraction measurements using quantitative BOLD contrast have been used for assessing inadequate oxygen delivery and the subsequent risk of ischemic stroke in sickle cell anemia. The BOLD signal in MRI studies relies on Δχdo , the bulk volume susceptibility difference between fully oxygenated and fully deoxygenated blood. Several studies have measured Δχdo for normal hemoglobin A (HbA). However, it is not known whether the value is different for sickle hemoglobin. In this study, Δχdo was measured for both HbA and sickle hemoglobin.
Postcondensation and Oxidation Processes in Molten Polyamide 6

Polyamide samples were heated under vacuum or mixed in a Brabender plastograph. UV absorbance, chain end concentration, and molecular weight were studied. Postcondensation was observed for polyamide heated under vacuum. For polyamide samples mixed in the plastograph, atmosphere, shear rate, and temperature changed. Melt viscosity and intrinsic viscosity are in good correlation in a log-log plot. Oxidation effect on molecular weight and amine chain end concentration could be well related to UV absorbance. The oxygen diffusion into the molten polyamide is a critical parameter. The oxygen concentration in the polyamide mixed under air is ca. 20 times higher than when mixed under nitrogen. The introduction of preoxidized material in the molten polyamide or mixing in the presence of oxygen have similar effects. Postcondensation and oxidation strongly influence the melt behavior of polyamides.
“Just tell me in a simple way”: A qualitative study on opportunities to improve the transition from acute hospital care to home from the perspectives of patients with traumatic brain injury, families, and providers

Objective: The purpose of this study was to identify areas to improve the transition from acute hospital care to home for patients with traumatic brain injury and their families. Design: Qualitative, descriptive. Setting: Level I trauma centered located in the Southeastern United States. Subjects: A total of 36 participants (12 patients with traumatic brain injury, 8 family caregivers, 16 providers). Main Measures: We conducted 55 semi-structured interviews with participants and used conventional content analysis to analyze the data. Results: Findings showed patients, families, and providers recommend three areas for improvement in the transition home from acute hospital care, described in three themes. Theme 1 was “improving patient and family education,” with the following sub-themes: (a) TBI-related information and (b) discharge preparation. Theme 2 was “additional provider guidance,” with the following sub-themes: (a) communication about patient’s recovery timeline and (b) recovery roadmap development. Theme 3 was “increasing systems-level support,” with the following sub-themes: (a) scheduling follow-up appointments, (b) using a patient navigator, (c) creating a provider follow-up structure, (d) linking pre-discharge care with post-discharge resources, and (e) addressing social issues. Conclusions: These findings delineate multiple areas where patients and families need additional support and education during the transition from acute hospital care to home in ways that are currently not being addressed. Findings may be used to improve education and support from providers and health systems given to patients with traumatic brain injury and families and to inform development and testing of transitional care interventions from acute hospital care to home.
The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome

The COVID-19 pandemic has the potential to affect the human microbiome in infected and uninfected individuals, having a substantial impact on human health over the long term. This pandemic intersects with a decades-long decline in microbial diversity and ancestral microbes due to hygiene, antibiotics, and urban living (the hygiene hypothesis). High-risk groups succumbing to COVID-19 include those with preexisting conditions, such as diabetes and obesity, which are also associated with microbiome abnormalities. Current pandemic control measures and practices will have broad, uneven, and potentially long-term effects for the human microbiome across the planet, given the implementation of physical separation, extensive hygiene, travel barriers, and other measures that influence overall microbial loss and inability for reinoculation. Although much remains uncertain or unknown about the virus and its consequences, implementing pandemic control practices could significantly affect the microbiome. In this Perspective, we explore many facets of COVID-19−induced societal changes and their possible effects on the microbiome, and discuss current and future challenges regarding the interplay between this pandemic and the microbiome. Recent recognition of the microbiome’s influence on human health makes it critical to consider both how the microbiome, shaped by biosocial processes, affects susceptibility to the coronavirus and, conversely, how COVID-19 disease and prevention measures may affect the microbiome. This knowledge may prove key in prevention and treatment, and long-term biological and social outcomes of this pandemic.
A targeted rheological bioink development guideline and its systematic correlation with printing behavior

Bioprinting for tissue or disease models is a promising but complex process involving biofabrication, cell culture and a carrier material known as bioink. The native extracellular matrix (ECM), which forms the scaffold for cells in vivo, consists of several components including collagen as a gelling agent to confer mechanical stiffness and provide a substrate for cell attachment. Bioprinting therefore needs an artificial ECM that fulfills the same functions as its natural counterpart during and after the printing process. The combination of bioink materials determines the immune response of the host, cell compatibility and adhesion. Here we evaluate multi-material blending with four pre-selected components using a design of experiments approach. Our exemplary designed hydrogel is highly reproducible for the development of artificial ECM and can be expanded to incorporate additional requirements. The bioink displays shear-thinning behavior and a high zero-shear viscosity, which is essential for the printing process. We assessed the printing behavior of our bioink over a wide range of the key process parameters for extrusion-based bioprinting (temperature, pressure, feed rate, and nozzle geometry). Several processing temperatures were linked by rheological measurements directly to the 3D printing process. The printing results were evaluated using a self-developed categoric strand screening process, varying the feed rate and pressure with a fixed nozzle. Accordingly, nozzles differing in size and shape were evaluated and the interactions between printing pressure and feed rate were characterized separately by applying a modified O-R-O test. We tested the short-term cultivation stability of our bioink to mimic the hypothermic and hyperthermic conditions of the human body. As result we present an expandable concept for bioink development and a highly reproducible and well-characterized procedure for printing with the newly developed hydrogel. We provide detailed insights into the relationship between printing parameters, rheological parameters and short-term cultivation stability.
Training deep-learning segmentation models from severely limited data.

PURPOSE To enable generation of high-quality deep learning segmentation models from severely limited contoured cases (e.g. ~10 cases). METHODS Thirty head-and-neck CT scans with well-defined contours were deformably registered to 200 CT scans of the same anatomic site without contours. Acquired deformation vector fields were used to train a principal component analysis (PCA) model for each of the 30 contoured CT scans by capturing the mean deformation and most prominent variations. Each PCA model can produce an infinite number of synthetic CT scans and corresponding contours by applying random deformations. We used 300, 600, 1000, and 2000 synthetic CT scans and contours generated from one PCA model to train V-Net, a 3D convolutional neural network architecture, to segment parotid and submandibular glands. We repeated the training using same numbers of training cases generated from 7, 10, 20, and 30 PCA models, with the data distributed evenly between each PCA model. Performance of the segmentation models was evaluated with Dice similarity coefficients between auto-generated contours and physician-drawn contours on 162 test CT scans for parotid glands and another 21 test CT scans for submandibular glands. RESULTS Dice values varied with the number of synthetic CT scans and the number of PCA models used to train the network. By using 2000 synthetic CT scans generated from 10 PCA models, we achieved Dice values of 82.8%±6.8% for right parotid, 82.0%±6.9% for left parotid, and 74.2%±6.8% for submandibular glands. These results are comparable with those obtained from state-of-the-art auto-contouring approaches, including a deep-learning network trained from more than 1000 contoured patients and a multi-atlas algorithm from 12 well-contoured atlases. Improvement was marginal when >10 PCA models or >2000 synthetic CT scans were used. CONCLUSIONS We demonstrated an effective data augmentation approach to train high-quality deep learning segmentation models from a limited number of well-contoured patient cases.