Miracle-dz/UniFAR-FTUs huggingface dataset:
Calculation of improved enthalpy and entropy of vaporization by a modified partition function in quantum cluster equilibrium theory.

In this work, we present an altered partition function that leads to an improved calculation of the enthalpy and entropy of vaporization in the framework of quantum cluster equilibrium theory. The changes are based on a previously suggested modification [S. Grimme, Chem. Eur. J. 18, 9955-9964 (2012)] of the molecular entropy calculation in the gas phase. Here, the low energy vibrational frequencies in the vibrational partition function are treated as hindered rotations instead of vibrations. The new scheme is tested on a set of nine organic solvents for the calculation of the enthalpy and entropy of vaporization. The enthalpies and entropies of vaporization show improvements from 6.5 error to 3.3 kJ mol-1 deviation to experiment and from 28.4 error to 13.5 J mol-1 K-1 deviation to experiment, respectively. The effect of the corrected partition function is visible in the different populations of clusters, which become physically more meaningful in that larger clusters are higher populated in the liquid phase and the gas phase is mainly populated by the monomers. Furthermore, the corrected partition function also overcomes technical difficulties and leads to an increased stability of the calculations in regard to the size of the cluster set.
Updates in Diabetic Wound Healing, Inflammation, and Scarring

Abstract Diabetic patients can sustain wounds either as a sequelae of their disease process or postoperatively. Wound healing is a complex process that proceeds through phases of inflammation, proliferation, and remodeling. Diabetes results in several pathological changes that impair almost all of these healing processes. Diabetic wounds are often characterized by excessive inflammation and reduced angiogenesis. Due to these changes, diabetic patients are at a higher risk for postoperative wound healing complications. There is significant evidence in the literature that diabetic patients are at a higher risk for increased wound infections, wound dehiscence, and pathological scarring. Factors such as nutritional status and glycemic control also significantly influence diabetic wound outcomes. There are a variety of treatments available for addressing diabetic wounds.
Curcumin, a potential initiator of apoptosis via direct interactions with Bcl‐xL and Bid

Apoptosis is a naturally occurring process during the growth and development of multicellular organisms and is increasingly active during times of cellular stress such as in response to intracellular DNA damage when removal of the host cell is paramount to prevent cancer. Unfortunately, once formed, cancer cells become impervious to apoptosis, creating a desperate need to identify an approach to induce apoptosis in these cells. An attractive option is to focus efforts on developing and locating compounds which activate apoptosis using natural compounds. Curcumin is a natural component in turmeric and is well‐known for its pharmacological effects in preventing and combating many ailments and has been shown to decrease the rapid proliferation of a wide variety of tumor cells. However, to date, the apoptotic intermediates and interactions through which curcumin exerts its cytotoxic effects are unknown. Motivated by reports linking the intracellular modulation of the concentrations of Bid and Bcl‐xL, following curcumin administration to cancer cells, we set out to probe for potential intermolecular interactions of these proteins with curcumin. Using several biophysical techniques, most notably, fluorescence, circular dichroism and nuclear magnetic resonance spectroscopy, we reveal binding interactions of curcumin with both Bcl‐xLΔC and full‐length Bid (Bid‐FL) and prove that this binding is hydrophobically driven and localized to well‐known functional regions of each protein. Specifically, our NMR studies show that while Bid‐FL interacts with curcumin through its hydrophobic and pore forming helices (α6‐α7), Bcl‐xLΔC interacts with curcumin via its BH3 binding pocket (α2‐α3‐α4‐α5), a critical region for mediating apoptosis.
Cognition‐Enhanced Machine Learning for Better Predictions with Limited Data

Abstract The fields of machine learning (ML) and cognitive science have developed complementary approaches to computationally modeling human behavior. ML's primary concern is maximizing prediction accuracy; cognitive science's primary concern is explaining the underlying mechanisms. Cross‐talk between these disciplines is limited, likely because the tasks and goals usually differ. The domain of e‐learning and knowledge acquisition constitutes a fruitful intersection for the two fields’ methodologies to be integrated because accurately tracking learning and forgetting over time and predicting future performance based on learning histories are central to developing effective, personalized learning tools. Here, we show how a state‐of‐the‐art ML model can be enhanced by incorporating insights from a cognitive model of human memory. This was done by exploiting the predictive performance equation's (PPE) narrow but highly specialized domain knowledge with regard to the temporal dynamics of learning and forgetting. Specifically, the PPE was used to engineer timing‐related input features for a gradient‐boosted decision trees (GBDT) model. The resulting PPE‐enhanced GBDT outperformed the default GBDT, especially under conditions in which limited data were available for training. Results suggest that integrating cognitive and ML models could be particularly productive if the available data are too high‐dimensional to be explained by a cognitive model but not sufficiently large to effectively train a modern ML algorithm. Here, the cognitive model's insights pertaining to only one aspect of the data were enough to jump‐start the ML model's ability to make predictions—a finding that holds promise for future explorations.
Neuroinflammatory Signaling in the Pathogenesis of Alzheimer’s Disease

Alzheimer’s disease (AD) is a chronic neurodegenerative disease characterized by the formation of intracellular neurofibrillary tangles (NFTs) and extracellular amyloid plaques. Growing evidence has suggested that AD pathogenesis is not only limited to the neuronal compartment but also strongly interacts with immunological processes in the brain. On the other hand, aggregated and misfolded proteins can bind with pattern recognition receptors located on astroglia and microglia and can, in turn, induce an innate immune response, characterized by the release of inflammatory mediators, ultimately playing a role in both the severity and the progression of the disease. It has been reported by genome-wide analysis that several genes which elevate the risk for sporadic AD encode for factors controlling the inflammatory response and glial clearance of misfolded proteins. Obesity and systemic inflammation are examples of external factors which may interfere with the immunological mechanisms of the brain and can induce disease progression. In this review, we discussed the mechanisms and essential role of inflammatory signaling pathways in AD pathogenesis. Indeed, interfering with immune processes and modulation of risk factors may lead to future therapeutic or preventive AD approaches.
Fifteen compelling open questions in plant cell biology

Abstract As scientists, we are at least as excited about the open questions—the things we do not know—as the discoveries. Here, we asked 15 experts to describe the most compelling open questions in plant cell biology. These are their questions: How are organelle identity, domains, and boundaries maintained under the continuous flux of vesicle trafficking and membrane remodeling? Is the plant cortical microtubule cytoskeleton a mechanosensory apparatus? How are the cellular pathways of cell wall synthesis, assembly, modification, and integrity sensing linked in plants? Why do plasmodesmata open and close? Is there retrograde signaling from vacuoles to the nucleus? How do root cells accommodate fungal endosymbionts? What is the role of cell edges in plant morphogenesis? How is the cell division site determined? What are the emergent effects of polyploidy on the biology of the cell, and how are any such “rules” conditioned by cell type? Can mechanical forces trigger new cell fates in plants? How does a single differentiated somatic cell reprogram and gain pluripotency? How does polarity develop de-novo in isolated plant cells? What is the spectrum of cellular functions for membraneless organelles and intrinsically disordered proteins? How do plants deal with internal noise? How does order emerge in cells and propagate to organs and organisms from complex dynamical processes? We hope you find the discussions of these questions thought provoking and inspiring.
Biogas production and its application in compressed gas

ABSTRACT Nowadays, the world is facing critical problem of energy deficit, global warming, and deterioration of the environment. Under the current scenario, the biogas energy source is the most challenging one to cope up with the scarcity of energy. Biogas is a renewable energy source which can be obtained by fermentation of organic matter also known as biomass. The biomass includes livestock waste (cow dung, manure, and uneaten food), food waste, and residues from meat, fish and dairy processing. The present study is to explore the potential of biogas production from cow dung and its usage through compressed form in a cylinder. This stored biogas can be put in use to the extent where it is required and it also reduces transportation costs, which is a major hurdle in the biogas usage. This paper summarizes an idea that can be carried out for effective biogas production, scrubbing, compression, and bottling process.
Retinal Optical Coherence Tomography in Neuromyelitis Optica

To determine optic nerve and retinal damage in aquaporin-4 antibody (AQP4-IgG)-seropositive neuromyelitis optica spectrum disorders (NMOSD) in a large international cohort after previous studies have been limited by small and heterogeneous cohorts.The cross-sectional Collaborative Retrospective Study on retinal optical coherence tomography (OCT) in neuromyelitis optica collected retrospective data from 22 centers. Of 653 screened participants, we included 283 AQP4-IgG–seropositive patients with NMOSD and 72 healthy controls (HCs). Participants underwent OCT with central reading including quality control and intraretinal segmentation. The primary outcome was thickness of combined ganglion cell and inner plexiform (GCIP) layer; secondary outcomes were thickness of peripapillary retinal nerve fiber layer (pRNFL) and visual acuity (VA). Eyes with ON (NMOSD-ON, N = 260) or without ON (NMOSD-NON, N = 241) were assessed compared with HCs (N = 136). In NMOSD-ON, GCIP layer (57.4 ± 12.2 μm) was reduced compared with HC (GCIP layer: 81.4 ± 5.7 μm, p < 0.001). GCIP layer loss (−22.7 μm) after the first ON was higher than after the next (−3.5 μm) and subsequent episodes. pRNFL observations were similar. NMOSD-NON exhibited reduced GCIP layer but not pRNFL compared with HC. VA was greatly reduced in NMOSD-ON compared with HC eyes, but did not differ between NMOSD-NON and HC.Our results emphasize that attack prevention is key to avoid severe neuroaxonal damage and vision loss caused by ON in NMOSD. Therapies ameliorating attack-related damage, especially during a first attack, are an unmet clinical need. Mild signs of neuroaxonal changes without apparent vision loss in ON-unaffected eyes might be solely due to contralateral ON attacks and do not suggest clinically relevant progression but need further investigation.
Prognostic value of CT-derived myocardial blood flow, CT fractional flow reserve and high-risk plaque features for predicting major adverse cardiac events.

Background Myocardial blood flow (MBF), CT fractional flow reserve (CT-FFR) and high-risk plaque (HRP) features have been revealed to be associated with patients' prognosis. However, direct intra-individual comparison of these CT-derived parameters has not been explored yet. The aim of this study was to investigate the prognostic value of CT-derived MBF, CT-FFR and HRP features for predicting major adverse cardiac events (MACEs). Methods Consecutive patients with chest pain and intermediate-to-high pre-test probability of coronary artery disease (CAD) were prospectively enrolled. All patients were referred for dynamic CT myocardial perfusion imaging (CT-MPI) + coronary CT angiography (CCTA) and followed up for at least 1 year. MBFischemic (mean MBF of all ischemic segments), MBFratio (MBF of ischemic segments/MBF of reference segments), CT-FFR and HRP features were measured and multivariate analysis was used to evaluate the predictive value of all above parameters for MACEs. Results One hundred and forty-two patients were included into final analysis. MBFischemic and MBFratio was significantly lower in patients with MACE compared to patients without MACE (87 vs. 153 mL/100 mL/min and 0.64 vs. 0.95, both P<0.001). Similarly, CT-FFR was also markedly lower in patients with MACE (0.58 vs. 0.88, P<0.001) whereas coronary artery calcium score (CACS) was significantly higher (1,038.9 vs. 34.2, P<0.001). According to ROC curve analysis, MBFischemic, MBFratio and CACS had largest area under curve (AUC =0.872, 0.855 and 0.813 respectively, all P<0.001) for identifying patients with MACE. After adjusted by multivariate analysis, MBFischemic (hazard ratio =23.382, P=0.003) and CACS (hazard ratio =3.759, P=0.029) were revealed to be the independent predictors for MACE where CT-FFR and HRP features failed to have prognostic value. Conclusions MBFischemic derived from dynamic CT-MPI was the strongest predictor for MACE, followed by CACS. MBFischemic outperformed HRP features and CT-FFR for prediction of unfavorable clinical outcome.
Genome Sequences of Community Carriage Strains of Staphylococcus aureus from Yuma, Arizona

Staphylococcus aureus exists as a pathogen and commensal. Individuals with asymptomatic carriage serve as a reservoir for transmission and are at increased risk of infecting themselves. In order to characterize the genomic diversity of S. aureus circulating in the community, we sequenced 166 genomes collected from individuals in Yuma, AZ. ABSTRACT Staphylococcus aureus exists as a pathogen and commensal. Individuals with asymptomatic carriage serve as a reservoir for transmission and are at increased risk of infecting themselves. In order to characterize the genomic diversity of S. aureus circulating in the community, we sequenced 166 genomes collected from individuals in Yuma, AZ.
Genome‐ and transcriptome‐wide association studies reveal the genetic basis and the breeding history of seed glucosinolate content in Brassica napus

Summary A high content of seed glucosinolates and their degradation products imposes anti‐nutritional effects on livestock; therefore, persistent efforts are made to reduce the seed GSL content to increase the commercial value of rapeseed meal. Here, we dissected the genetic structure of SGC by genome‐wide association studies (GWAS) combined with transcriptome‐wide association studies (TWAS). Fifteen reliable quantitative trait loci (QTLs) were identified to be associated with the reduced SGC in modern B. napus cultivars by GWAS. Analysis of the selection strength and haplotypes at these QTLs revealed that low SGC was predominantly generated by the co‐selection of qGSL.A02. 2, qGSL.C02. 1, qGSL.A09. 2, and qGSL.C09. 1. Integration of the results from TWAS, comprehensive bioinformatics, and POCKET algorithm analyses indicated that BnaC02.GTR2 (BnaC02g42260D) is a candidate gene underlying qGSL.C02. 1. Using CRISPR/Cas9‐derived Bna.gtr2s knockout mutants, we experimentally verified that both BnaC02.GTR2 and its three paralogs positively regulate seed GSL accumulation but negatively regulated vegetative tissue GSL contents. In addition, we observed smaller seeds with higher seed oil content in these Bna.gtr2 mutants. Furthermore, both RNA‐seq and correlation analyses suggested that Bna.GTR2s might play a comprehensive role in seed development, such as amino acid accumulation, GSL synthesis, sugar assimilation, and oil accumulation. This study unravels the breeding selection history of low‐SGC improvement and provides new insights into the molecular function of Bna.GTR2s in both seed GSL accumulation and seed development in B. napus.
ARHGAP4-SEPT2-SEPT9 complex enables both up- and down-modulation of integrin-mediated focal adhesions, cell migration, and invasion

The Rho family of GTPases are inactivated in a cell context–dependent manner by Rho-GTPase-activating proteins (Rho-GAPs), but their signaling mechanisms are poorly understood. Here we demonstrate that ARHGAP4, one of the Rho-GAPs, forms a complex with SEPT2 and SEPT9 via its Rho-GAP domain and SH3 domain to enable both up- and down-modulation of integrin-mediated focal adhesions (FAs). We show that silencing ARHGAP4 and overexpressing its two mutually independent upstream regulators, SEPT2 and SEPT9, all induce reorganization of FAs to newly express Integrin Beta 1 and also enhance both cell migration and invasion. Interestingly, even if these cell migration/invasion–associated phenotypic changes are induced upon perturbations to the complex, it does not necessarily cause enhanced clustering of FAs. Instead, its extent depends on whether the microenvironment contains ligands suitable for the up-regulated Integrin Beta 1. These results provide novel insights into cell migration, invasion, and microenvironment-dependent phenotypic changes regulated by the newly identified complex.
D4F alleviates the C/EBP homologous protein-mediated apoptosis in glycated high-density lipoprotein-treated macrophages by facilitating autophagy

The present study aimed to investigate the role of D4F, an apolipoprotein A-I mimetic peptide, in macrophage apoptosis induced by the glycated high-density lipoprotein (gly-HDL)-induced endoplasmic reticulum (ER) stress C/EBP homologous protein (CHOP) pathway, and unravel the regulatory role of autophagy in this process. Our results revealed that except for suppressing the accumulation of lipids within RAW264.7 macrophages caused by gly-HDL, D4F inhibited gly-HDL-induced decrease in the cell viability and increase in lactate dehydrogenase leakage and cell apoptosis, which were similar to 4-phenylbutyric acid (PBA, an ER stress inhibitor). Besides, similar to PBA, D4F inhibited gly-HDL-induced ER stress response activation evaluated through the decreased PERK and eIF2α phosphorylation, together with reduced ATF6 nuclear translocation as well as the downregulation of GRP78 and CHOP. Interestingly, D4F facilitated gly-HDL-triggered activation of autophagy, measured as elevated levels of beclin-1, LC3-II, and ATG5 expressions in macrophages. Furthermore, the inhibition effect of D4F on gly-HDL-induced ER stress-CHOP-induced apoptosis of macrophages was restrained after beclin-1 siRNA and 3-methyladenine (3-MA, an inhibitor of autophagy) treatments, while this effect was further reinforced after rapamycin (Rapa, an inducer of autophagy) treatment. Furthermore, administering D4F or Rapa to T2DM mice upregulated LC3-II and attenuated CHOP expression, cell apoptosis, and atherosclerotic lesions. However, the opposite results were obtained when 3-MA was administered to these mice. These results support that D4F effectively protects macrophages against gly-HDL-induced ER stress-CHOP-mediated apoptosis by promoting autophagy.
A predictive model and survival analysis for local recurrence in differentiated thyroid carcinoma.

BACKGROUND Local recurrence (LR) is associated with poor outcome in patients with differentiated thyroid carcinoma (DTC). The aim of this study was to explore potential risk factors for LR and build a predictive model. METHODS The medical data of patients who were diagnosed with DTC after initial surgery in three medical centers (2000-2018) were reviewed. Detailed clinicopathologic characteristics of all cases were identified. RESULTS Multiple factors, including extrathyroidal extension (ETE), histology, symptoms, multifocality, and tumor diameter, were significantly different between the LR and no evidence of disease groups in univariate and multivariate analysis (P ˂ 0.05). Tumor diameter, symptoms, and ETE made the greatest contributions to prognosis according to decision tree analysis and random forest algorithm. The predictive model constructed from these data achieved 98.7% accuracy of classification. A five-fold cross-validation confirmed that the model has 84.7%-89.7% accuracy of classification. Additionally, symptoms and ETE were independent predictors on survival analysis (P ˂ 0.05). CONCLUSIONS This study optimized the weight of risk factors, including tumor diameter, symptoms, ETE, and multifocality, in predicting LR in patients with DTC. Our predictive model provides a strong tool to distinguish between high-risk and low-risk DTC.
Insights into anaerobic degradation of benzene and naphthalene

The dissertation shows that Pelotomaculum candidate BPL is the first member of the genus that can perform full dissimilatory sulfate reduction, besides its potential to degrade benzene. Results from physiological, genomic, and proteomic analyses are presented indicating that environmental Spirochaetes recycle detrital biomass and convert it into end products or electrons that support growth of associated degraders. Lastly, a novel reverse stable isotope labelling analysis is developed as a sensitive means to monitor biodegradation.
Glucosamine use, smoking and risk of incident chronic obstructive pulmonary disease: a large prospective cohort study

Abstract Chronic inflammation exerts pleiotropic effects in the aetiology and progression of chronic obstructive pulmonary disease (COPD). Glucosamine is widely used in many countries and may have anti-inflammatory properties. We aimed to prospectively evaluate the association of regular glucosamine use with incident COPD risk and explore whether such association could be modified by smoking in the UK Biobank cohort, which recruited more than half a million participants aged 40–69 years from across the UK between 2006 and 2010. Cox proportional hazards models with adjustment for potential confounding factors were used to calculate hazard ratios (HR) as well as 95 % CI for the risk of incident COPD. During a median follow-up of 8·96 years (interquartile range 8·29–9·53 years), 9016 new-onset events of COPD were documented. We found that the regular use of glucosamine was associated with a significantly lower risk of incident COPD with multivariable adjusted HR of 0·80 (95 % CI, 0·75, 0·85; P < 0·001). When subgroup analyses were performed by smoking status, the adjusted HR for the association of regular glucosamine use with incident COPD were 0·84 (0·73, 0·96), 0·84 (0·77, 0·92) and 0·71 (0·62, 0·80) among never smokers, former smokers and current smokers, respectively. No significant interaction was observed between glucosamine use and smoking status (P for interaction = 0·078). Incident COPD could be reduced by 14 % to 84 % through a combination of regular glucosamine use and smoking cessation.