Miracle-dz/UniFAR-FTUs huggingface dataset:
Amino acid and nucleotide metabolism shape the selection of trophic levels in animals

What an animal eats determines its trophic level (TL) in the food web. The diet of high-TL animals is thought to contain more energy because it contains higher levels of lipids. This however has not been systematically examined in the context of comprehensive metabolic networks of different animals. Here, we reconstruct species-specific genome-scale metabolic models (GEMs) of 32 animals, and calculate the maximum ATP production per unit of food for each animal. Surprisingly, we find that ATP production is closely associated with metabolic flux through central carbon metabolism and amino acid metabolism, while correlation with lipid metabolism is low. Further, metabolism of specific amino acids and nucleotides underlie maximum ATP production from food. Our analyses indicate that amino acid and nucleotide metabolism, rather than lipid metabolism, are major contributors to the selection of animal trophic levels, demonstrating that species-level metabolic flux plays key roles in trophic interactions and evolution.
Adsorption of Organic Pollutants by Modified Chitosan Microspheres

Modified chitosan microspheres were prepared by reverse phase suspension method,and adsorption of organic pollutants by modified chitosan microspheres was detected by high performance liquid chromatography.Factors that affected the adsorption including adsorption time,pH and organic pollutant concentration were studied.Results indicated that under the condition of similar concentration of organic pollutants,the modified chitosan microspheres can remove aqueous 2,4-dinitrophenol to the most.
Diversity and distribution of sulfur metabolism in the human gut microbiome and its association with colorectal cancer

Microbial sulfidogenesis produces genotoxic hydrogen sulfide (H2S) in the human gut using inorganic (sulfate) and organic (taurine/cysteine/methionine) substrates, however the majority of studies have focused on sulfate reduction using dissimilatory sulfite reductases (Dsr). Recent evidence implicates microbial sulfidogenesis as a potential trigger of colorectal cancer (CRC), highlighting the need for comprehensive knowledge of sulfur metabolism within the human gut. Here we show that microbial sulfur metabolism is more abundant and diverse than previously studied and is statistically associated with CRC. Using ~17,000 bacterial genomes from publicly available stool metagenomes, we studied the diversity of sulfur metabolic genes in 667 participants across different health statuses: healthy, adenoma, and carcinoma. Sulfidogenic genes were harbored by 142 bacterial genera and both organic and inorganic sulfidogenic genes were associated with carcinoma. Significantly, anaerobic sulfite reductases were twice as abundant as dsr. We identified twelve potential pathways for reductive taurine metabolism including novel pathways, and prevalence of organic sulfur metabolic genes indicate these substrates may be the most abundant source of microbially derived H2S. Our findings significantly expand knowledge of microbial sulfur metabolism in the human gut, and highlight key gaps that limit understanding of its potential contributions to the pathogenesis of CRC.
Wild lab: A naturalistic free viewing experiment reveals previously unknown EEG signatures of face processing

Neural mechanisms of face perception are predominantly studied in well-controlled experimental settings that involve random stimulus sequences and fixed eye positions. While powerful, the employed paradigms are far from what constitutes natural vision. Here, we demonstrate the feasibility of ecologically more valid experimental paradigms using natural viewing behavior, by combining a free viewing paradigm on natural scenes, free of photographer bias, with advanced data processing techniques that correct for overlap effects and co-varying nonlinear dependencies of multiple eye movement parameters. We validate this approach by replicating classic N170 effects in neural responses, triggered by fixation onsets (fERPs). Importantly, our more natural stimulus paradigm yielded smaller variability between subjects than the classic setup. Moving beyond classic temporal and spatial effect locations, our experiment furthermore revealed previously unknown signatures of face processing. This includes modulation of early fERP components, as well as category-specific adaptation effects across subsequent fixations that emerge even before fixation onset.
PEPSDI: Scalable and flexible inference framework for stochastic dynamic single-cell models

Mathematical modelling is an invaluable tool to describe dynamic cellular processes and to rationalise cell-to-cell variability within the population. This requires statistical methods to infer unknown model parameters from dynamic, multi-individual data accounting for heterogeneity caused by both intrinsic and extrinsic noise. Here we present PEPSDI, a scalable and flexible framework for Bayesian inference in state-space mixed-effects stochastic dynamic single-cell models. Unlike previous frameworks, PEPSDI imposes a few modelling assumptions when inferring unknown model parameters from time-lapse data. Specifically, it can infer model parameters when intrinsic noise is modelled by either exact or approximate stochastic simulators, and when extrinsic noise is modelled by either time-varying, or time-constant parameters that vary between cells. This allowed us to identify hexokinase activity as a source of extrinsic noise, and to deduce that sugar availability dictates cell-to-cell variability in the budding yeast Saccharomyces cerevisiae SNF1 nutrient sensing pathway.
Building resilience in transcultural adults: investigating the effect of a strength-based programme

ABSTRACT Objective: The current study used a mixed-method approach to evaluate the effect of Building Resilience in Transcultural Adults programme (BRiTA), a strength-based preventative intervention developed by Queensland Transcultural Mental Health Centre (QTMHC), on the acculturation and resilience of culturally and linguistically diverse (CALD) adults from migrant background. QTMHC, as a part of their services, train facilitators to execute this programme in a range of community settings. Method: CALD individuals, from migrant background, attended the programme at community centres and organisations. They completed a demographic form, scale that measured their acculturation and resilience pre and post intervention and open-ended questions about each session at the end of the sessions. Facilitators of the programme also recorded their observations. Results: Quantitative data and qualitative feedback, were collected from every BRiTA programme run from 2012 to 2017. Paired T-Test indicated that the CALD migrant sample (N = 192) showed a significant self-reported increase in their acculturation and resilience levels after completing the BRiTA futures programme. Thematic analysis of the participants’ comments after every session indicated that they found the programme relevant, helpful, and enjoyable. Conclusions: The findings illustrate the benefits of the preventative BRiTA programme and the role it can play in promoting CALD migrant’s wellbeing and integration in Australia. Implications and future directions are discussed. Key Points What is already known about this topic: (1) Migrants have to acculturate to their new relocated country, which can be stressful. (2) Preventative programmes can promote the acculturation and wellbeing of migrants. (3) Building resilience in transcultural adults and parents (BRiTA) is one of the preventative group programmes. What this paper adds: (1) BRiTA can positively affect the acculturation and resilience of those who attend this programme. (2) It can be delivered in different languages to different ethnic groups. (3) It can be used successfully in community settings.
Feel-Good Requirements: Neurophysiological and Psychological Design Criteria of Affective Touch for (Assistive) Robots

Previous research has shown the value of the sense of embodiment, i.e., being able to integrate objects into one's bodily self-representation, and its connection to (assistive) robotics. Especially, tactile interfaces seem essential to integrate assistive robots into one's body model. Beyond functional feedback, such as tactile force sensing, the human sense of touch comprises specialized nerves for affective signals, which transmit positive sensations during slow and low-force tactile stimulations. Since these signals are extremely relevant for body experience as well as social and emotional contacts but scarcely considered in recent assistive devices, this review provides a requirement analysis to consider affective touch in engineering design. By analyzing quantitative and qualitative information from engineering, cognitive psychology, and neuroscienctific research, requirements are gathered and structured. The resulting requirements comprise technical data such as desired motion or force/torque patterns and an evaluation of potential stimulation modalities as well as their relations to overall user experience, e.g., pleasantness and realism of the sensations. This review systematically considers the very specific characteristics of affective touch and the corresponding parts of the neural system to define design goals and criteria. Based on the analysis, design recommendations for interfaces mediating affective touch are derived. This includes a consideration of biological principles and human perception thresholds which are complemented by an analysis of technical possibilities. Finally, we outline which psychological factors can be satisfied by the mediation of affective touch to increase acceptance of assistive devices and outline demands for further research and development.
Mutual Relationship Between Sleep Disorders, Quality of Life and Psychosocial Aspects in Patients With Psoriasis

Psoriasis is a chronic, autoimmune skin disease affecting about 2–4% of the worldwide population. It is now perceived as a systemic disease because of the complex pathogenesis and multiple comorbidities. It leads to decreased quality of life and productivity of patients. Nowadays, sleep disorders are investigated as well in relation to psoriasis as another possible comorbidity. This review focuses on possible negative effects of sleep deprivation, decreased quality of life, and psychosocial status in patients with psoriasis and highlights their mutual, complex relationship of divergent consequences. The relationship between sleep disorders and psychosocial status in patients with psoriasis is bidirectional and resembles a vicious circle, one abnormality triggering the other. Sleep disorders additionally increase the risk of metabolic and psychiatric diseases in psoriatic patients who are already at increased risk of developing such disorders. There should be measures taken to screen patients with psoriasis for sleep disorders in order to diagnose early and treat.
HIV-1-Specific CAR-T Cells With Cell-Intrinsic PD-1 Checkpoint Blockade Enhance Anti-HIV Efficacy in vivo

Adoptive cellular immunotherapy therapy using broadly neutralizing antibody-based chimeric antigen receptor-T cells (bNAb-based CAR-T) has shown great potency and safety for the functional cure of HIV. The efficacy of bNAb-based CAR-T cells could be compromised by adaptive resistance during HIV chronic infection according to the phenomenon that cellular exhaustion was observed in endogenous cytotoxic T-lymphocytes (CTLs) along with upregulated expression of PD−1. Here, we created HIV-specific CAR-T cells using human peripheral blood mononuclear cells (PBMCs) and a 3BNC117-DNR CAR (3BD CAR) construct that enables the expression of PD-1 dominant negative receptor (DNR) and the single-chain variable fragment of the HIV-1-specific broadly neutralizing antibody 3BNC117 to target native HIV envelope glycoprotein (Env). Compared with HIV CAR expression alone, 3BD CAR-T cells displayed potent lytic and functional responses to Env-expressing cell lines and HIV-infected CD4+ T cells. Moreover, 3BD CAR-T cells can kill HIV-latently-infected cell lines, which are reactivated by the secretory cytokines of effector cells followed by contact with initial HIV-expressing fraction. Furthermore, bioluminescence imaging indicated that 3BD CAR-T cells displayed superior anti-HIV function in an HIV NCG mouse model of transplanting Env+/PD-L1+ cells (LEL6). These studies suggested that our proposed combinational strategy of HIV CAR-T therapy with PD-1 blockade therapy is feasible and potent, making it a promising therapeutic candidate for HIV functional cure.
Phytoplankton Photophysiology Utilities: A Python Toolbox for the Standardization of Processing Active Chlorophyll-a Fluorescence Data

The uptake and application of single turnover chlorophyll fluorometers to the study of phytoplankton ecosystem status and microbial functions has grown considerably in the last two decades. However, standardization of measurement protocols, processing of fluorescence transients and quality control of derived photosynthetic parameters is still lacking and makes community goals of large global databases of high-quality data unrealistic. We introduce the Python package Phytoplankton Photophysiology Utilities (PPU), an adaptable and open-source interface between Fast Repetition Rate and Fluorescence Induction and Relaxation instruments and python. The PPU package includes a variety of functions for the loading, processing and quality control of single turnover fluorescence transients from many commercially available instruments. PPU provides the user with greater flexibility in the application of the Kolber-Prasil-Falkowski model; tools for plotting, quality control, correcting instrument biases and high-throughput processing with ease; and a greater appreciation for the uncertainties in derived photosynthetic parameters. Using data from three research cruises across different biogeochemical regimes, we provide example applications of PPU to fit raw active chlorophyll-a fluorescence data from three commercial instruments and demonstrate tools which help to reduce uncertainties in the final fitted parameters.
A Promising Anticancer Agent Dimethoxycurcumin: Aspects of Pharmacokinetics, Efficacy, Mechanism, and Nanoformulation for Drug Delivery

Curcumin is a well-known anticancer natural product with various significant bioactivities that has been well documented, but its widespread use is mainly hindered by insufficient ADME properties such as poor solubility and low metabolic stability. Dimethoxycurcumin (DiMC) is a kind of lipophilic compound derived from curcumin that maintains its anticancer potency and has greatly improved systematic bioavailability. Therefore, DiMC is regarded as a promising plant-derived anticancer agent that deserves to be well developed. Herein, we concentrate on the published work by those from original research groups concerned with the pharmacokinetics, efficacy, and mechanism of DiMC involved in the treatment of various tumors, as well as the nanoformulations for effective drug delivery.
CAM-DR: Mechanisms, Roles and Clinical Application in Tumors

Despite the continuous improvement of various therapeutic techniques, the overall prognosis of tumors has been significantly improved, but malignant tumors in the middle and advanced stages still cannot be completely cured. It is now evident that cell adhesion-mediated resistance (CAM-DR) limits the success of cancer therapies and is a great obstacle to overcome in the clinic. The interactions between tumor cells and extracellular matrix (ECM) molecules or adjacent cells may play a significant role in initiating the intracellular signaling pathways that are associated with cell proliferation, survival upon binding to their ligands. Recent studies illustrate that these adhesion-related factors may contribute to the survival of cancer cells after chemotherapeutic therapy, advantageous to resistant cells to proliferate and develop multiple mechanisms of drug resistance. In this review, we focus on the molecular basis of these interactions and the main signal transduction pathways that are involved in the enhancement of the cancer cells’ survival. Furthermore, therapies targeting interactions between cancer cells and their environment to enhance drug response or prevent the emergence of drug resistance will also be discussed.
Association of the CPT1A p.P479L Metabolic Gene Variant With Childhood Respiratory and Other Infectious Illness in Nunavut

Objective: Infectious illness, including lower respiratory tract infection (LRTI), is a leading cause of childhood morbidity and infant mortality in Inuit children in Nunavut Canada. The carnitine palmitoyltransferase 1A (CPT1A) p.P479L variant is common in arctic Indigenous populations of Alaska, Canada, and Greenland. CPT1A is a fatty acid oxidation enzyme expressed in the liver, immunocytes and other tissues, and is needed to use fats for energy during fasting. Previous association of the variant with early childhood infectious illness and infant death has been challenged because of sample size and limited adjustment for confounders. We evaluated whether the p.P479L variant is associated with infectious illness in Inuit children of Nunavut, Canada. Methods: We conducted a retrospective clinical chart review of 2,225 Inuit children (0–5 years) for infectious illness (including otitis media, gastroenteritis, and hospital admission for LRTI), prenatal, perinatal, and socioeconomic indicators, subsequently linking to CPT1A genotype. Multivariable logistic regression adjusted for birth characteristics, breastfeeding, maternal smoking, food insecurity, and socioeconomic indicators. Results: Overall, 27% of children were hospitalized for LRTI, 86% had otitis media and 50% had gastroenteritis. The p.P479L allele frequency was 0.82. In multivariable analysis, p.P479L homozygosity was associated with LRTI admission (aOR:2.88 95%CI:1.46–5.64), otitis media (aOR:1.83, 95%CI:1.05–3.21), and gastroenteritis (aOR:1.74, 95%CI:1.09–2.77), compared to non-carriers. Conclusion: Children homozygous for the p.P479L variant were more likely to experience infectious illness than non-carriers, including hospitalization for respiratory tract infections. Given the role of CPT1A in immunocytes, our findings indicate that more study is needed to determine if there is a role of the variant in immune response. Continued Inuit involvement is essential when considering next steps.
A Systematic Review of the Predictive Value of Plasma D-Dimer Levels for Predicting Stroke Outcome

Background: Stroke is a leading cause of morbidity and mortality. Over the past decade, plasma D-dimer levels have emerged as a biomarker for predicting stroke outcome. However, no consensus in the literature currently exists concerning its utility for predicting post-stroke functional outcome and mortality. Objective: To systematically review the effectiveness of plasma D-dimer levels for predicting functional outcome and mortality following stroke. Methods: Five academic databases were screened according to PRISMA guidelines for eligible studies. With these studies, we conducted a random-effect meta-analysis to evaluate the impact of plasma D-dimer levels for predicting functional outcome and mortality post-stroke. We also conducted subgroup analyses to evaluate differences in predictive capacity for different stroke subtypes. Results: Nineteen studies were included, containing data on 5,781 stroke patients (mean age: 65.26 ± 6.4 years). Overall methodological quality for the included studies was high. Meta-analysis showed that increased D-dimer levels were predictive of worsened functional outcomes (Hazard ratio: 2.19, 95% CI: 1.63–2.93) and elevated overall mortality (2.29, 1.35–3.88). Subgroup analysis showed that plasma D-dimer levels were more predictive of poorer functional outcomes for ischemic (2.08, 1.36–3.18) stroke as compared to intracerebral hemorrhage (2.62, 1.65–4.17). We also noted that predictive capacity was similar when it came to mortality in patients with cryptogenic ischemic stroke (2.65, 0.87–8.08) and intracerebral hemorrhage (2.63, 1.50–4.59). Conclusion: The study provides preliminary evidence concerning the capacity of plasma D-dimer levels for predicting functional outcomes and mortality following stroke and reports that higher D-dimer levels of are associated with poorer functional outcomes and higher mortality.
STYK1/NOK Promotes Metastasis and Epithelial-Mesenchymal Transition in Non-small Cell Lung Cancer by Suppressing FoxO1 Signaling

Aims Serine/threonine/tyrosine kinase 1 (STYK1) has been previously shown to have oncogenic properties, and emerging evidence suggests that STYK1 expression correlates with epithelial-mesenchymal transition (EMT). However, the mechanism of STYK1 involvement in oncogenesis remains unknown. The present study aimed to elucidate how STYK1 expression level relates to the metastasis, migration, invasion, and EMT in non-small cell lung cancer (NSCLC) and to determine the molecular mechanism of STYK1 effects. Methods Serine/threonine/tyrosine kinase 1 (STYK1) expression level and its relationship with the prognosis of NSCLC were determined using the ONCOMINE database and clinical cases. Non-small cell lung cancer cell lines with the overexpression or knockdown of STYK1 were established to determine whether STYK1 promotes cell migration, invasion, and EMT in vitro and in vivo. In addition, a constitutively active FoxO1 mutant (FoxO1AAA) was used to examine the role of FoxO1 in the STYK1-mediated upregulation of metastasis and EMT in NSCLC. Results Serine/threonine/tyrosine kinase 1 (STYK1) was upregulated in NSCLC tissues and cell lines, and its overexpression correlated with poor prognosis in patients with NSCLC after surgery. Enhanced expression of STYK1 potentiated the migration, invasion, and EMT in SW900 cells, thereby promoting metastasis, whereas knockdown of STYK1 inhibited these cellular phenomena in Calu-1 cells. Furthermore, STYK1 expression was positively related to the level of phosphorylated-FoxO1, whereas the constitutively active FoxO1 mutant protected against the positive effect of STYK1 overexpression on cell migration, invasion, and EMT. Conclusion Serine/threonine/tyrosine kinase 1 (STYK1) was upregulated in NSCLC and correlated with poor clinical outcomes. In addition, STYK1 suppressed FoxO1 functions, thereby promoting metastasis and EMT in NSCLC.