Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling pre-treatments effect on drying kinetics of garlic ( Allium sativum L.) slices in a convective hot air dryer

The study investigated the effect of different pretreatments such as citric-acid (CA), potassium-metabisulphite (KMS), and ethylenediamine-tetraacetic acid (EDTA) on the drying kinetics, allicin and colour of garlic slices in a convective hot-air dryer at temperatures of 45, 50 and 55°C. The allicin content of the fresh garlic slices compared with the dried slices increased non-linearly with increase in temperature from 8.6 to 23.5, 13.3 to 22.4, 11.9 to 23.4 and 12.3 to 24.1 µg/ml for the control, CA, KMS, and EDTA samples, respectively. The drying characteristics were evaluated against Page et al. (1949) mathematical models on the basis of the coefficient of determination (R2), reduced chi-square , and root mean square error (RMSE). The drying characteristics of garlic slices of the control were best described by the Midilli et al. (2002) model whilst the CA, KMS, and EDTA pretreated samples were best described by the Henderson and Pabis (2006) model within the confines of the experiments. The colour of the fresh and dried garlic slices were measured in Hunter parameters. The KMS pretreated samples showed greatest brightness (85.95) and least redness (1.36) in colour at 50°C and 45, respectively compared with the fresh, whereas the EDTA pretreated samples were yellower (17.43) at 45°C. Key words: Garlic slices, drying models, pre-treatments, allicin content, colour.
Evaluation of Live Bacterial Prophylactics to Decrease IncF Plasmid Transfer and Association With Intestinal Small RNAs

Chicken intestinal Escherichia coli are a reservoir for virulence and antimicrobial resistance (AMR) genes that are often carried on incompatibility group F (IncF) plasmids. The rapid transfer of these plasmids between bacteria in the gut contributes to the emergence of new multidrug-resistant and virulent bacteria that threaten animal agriculture and human health. Thus, the aim of the present study was to determine whether live bacterial prophylactics could affect the distribution of large virulence plasmids and AMR in the intestinal tract and the potential role of smRNA in this process. In this study, we tested ∼100 randomly selected E. coli from pullet feces (n = 3 per group) given no treatment (CON), probiotics (PRO), a live Salmonella vaccine (VAX), or both (P + V). E. coli isolates were evaluated via plasmid profiles and several phenotypic (siderophore production and AMR), and genotypic (PCR for virulence genes and plasmid typing) screens. P + V isolates exhibited markedly attenuated siderophore production, lack of AMR and virulence genes, which are all related to the loss of IncF and ColV plasmids (P < 0.0001). To identify a causal mechanism, we evaluated smRNA levels in the ceca mucus and found a positive association between smRNA concentrations and plasmid content, with both being significantly reduced in P + V birds compared to other groups (P < 0.01). To test this positive association between IncF plasmid transfer and host smRNA concentration, we evenly pooled smRNA per group and treated E. coli mating pairs with serial concentrations of smRNA in vitro. Higher smRNA concentrations resulted in greater rates of IncF plasmid transfer between E. coli donors (APEC O2 or VAX isolate IA-EC-001) and recipient (HS-4) (all groups; P < 0.05). Finally, RNAHybrid predictive analyses detected several chicken miRNAs that hybridize with pilus assembly and plasmid transfer genes on the IncF plasmid pAPEC-O2-R. Overall, we demonstrated P + V treatment reduced smRNA levels in the chicken ceca, which was associated with a reduction in potentially virulent E. coli. Furthermore, we propose a novel mechanism in which intestinal smRNAs signal plasmid exchange between E. coli. Investigations to understand the changes in bacterial gene expression as well as smRNAs responsible for this phenomenon are currently underway.
Integrative Analyses of mRNA Expression Profile Reveal SOCS2 and CISH Play Important Roles in GHR Mutation-Induced Excessive Abdominal Fat Deposition in the Sex-Linked Dwarf Chicken

Sex-linked dwarf (SLD) chicken, which is caused by a recessive mutation of the growth hormone receptor (GHR), has been widely used in the Chinese broiler industry. However, it has been found that the SLD chicken has more abdominal fat deposition than normal chicken. Excessive fat deposition not only reduced the carcass quality of the broilers but also reduced the immunity of broilers to diseases. To find out the key genes and the precise regulatory pathways that were involved in the GHR mutation-induced excessive fat deposition, we used high-fat diet (HFD) and normal diet to feed the SLD chicken and normal chicken and analyzed the differentially expressed genes (DEGs) among the four groups. Results showed that the SLD chicken had more abdominal fat deposition and larger adipocytes size than normal chicken and HFD can promote abdominal fat deposition and induce adipocyte hypertrophy. RNA sequencing results of the livers and abdominal fats from the above chickens revealed that many DEGs between the SLD and normal chickens were enriched in fat metabolic pathways, such as peroxisome proliferator-activated receptor (PPAR) signaling, extracellular matrix (ECM)-receptor pathway, and fatty acid metabolism. Importantly, by constructing and analyzing the GHR-downstream regulatory network, we found that suppressor of cytokine signaling 2 (SOCS2) and cytokine-inducible SH2-containing protein (CISH) may involve in the GHR mutation-induced abdominal fat deposition in chicken. The ectopic expression of SOCS2 and CISH in liver-related cell line leghorn strain M chicken hepatoma (LMH) cell and immortalized chicken preadipocytes (ICP) revealed that these two genes can regulate fatty acid metabolism, adipocyte differentiation, and lipid droplet accumulation. Notably, overexpression of SOCS2 and CISH can rescue the hyperactive lipid metabolism and excessive lipid droplet accumulation of primary liver cell and preadipocytes that were isolated from the SLD chicken. This study found some genes and pathways involved in abdominal fat deposition of the SLD chicken and reveals that SOCS2 and CISH are two key genes involved in the GHR mutation-induced excessive fat deposition of the SLD chicken.
Mercury-Tolerant Ensifer medicae Strains Display High Mercuric Reductase Activity and a Protective Effect on Nitrogen Fixation in Medicago truncatula Nodules Under Mercury Stress

Mercury (Hg) is extremely toxic for all living organisms. Hg-tolerant symbiotic rhizobia have the potential to increase legume tolerance, and to our knowledge, the mechanisms underlying Hg tolerance in rhizobia have not been investigated to date. Rhizobial strains of Ensifer medicae, Rhizobium leguminosarum bv. trifolii and Bradyrhizobium canariense previously isolated from severely Hg-contaminated soils showed different levels of Hg tolerance. The ability of the strains to reduce mercury Hg2+ to Hg0, a volatile and less toxic form of mercury, was assessed using a Hg volatilization assay. In general, tolerant strains displayed high mercuric reductase activity, which appeared to be inducible in some strains when grown at a sub-lethal HgCl2 concentration. A strong correlation between Hg tolerance and mercuric reductase activity was observed for E. medicae strains, whereas this was not the case for the B. canariense strains, suggesting that additional Hg tolerance mechanisms could be playing a role in B. canariense. Transcript abundance from merA, the gene that encodes mercuric reductase, was quantified in tolerant and sensitive E. medicae and R. leguminosarum strains. Tolerant strains presented higher merA expression than sensitive ones, and an increase in transcript abundance was observed for some strains when bacteria were grown in the presence of a sub-lethal HgCl2 concentration. These results suggest a regulation of mercuric reductase in rhizobia. Expression of merA genes and mercuric reductase activity were confirmed in Medicago truncatula nodules formed by a sensitive or a tolerant E. medicae strain. Transcript accumulation in nodules formed by the tolerant strain increased when Hg stress was applied, while a significant decrease in expression occurred upon stress application in nodules formed by the Hg-sensitive strain. The effect of Hg stress on nitrogen fixation was evaluated, and in our experimental conditions, nitrogenase activity was not affected in nodules formed by the tolerant strain, while a significant decrease in activity was observed in nodules elicited by the Hg-sensitive bacteria. Our results suggest that the combination of tolerant legumes with tolerant rhizobia constitutes a potentially powerful tool in the bioremediation of Hg-contaminated soils.
Different Machine Learning and Deep Learning Methods for the Classification of Colorectal Cancer Lymph Node Metastasis Images

The classification of colorectal cancer (CRC) lymph node metastasis (LNM) is a vital clinical issue related to recurrence and design of treatment plans. However, it remains unclear which method is effective in automatically classifying CRC LNM. Hence, this study compared the performance of existing classification methods, i.e., machine learning, deep learning, and deep transfer learning, to identify the most effective method. A total of 3,364 samples (1,646 positive and 1,718 negative) from Harbin Medical University Cancer Hospital were collected. All patches were manually segmented by experienced radiologists, and the image size was based on the lesion to be intercepted. Two classes of global features and one class of local features were extracted from the patches. These features were used in eight machine learning algorithms, while the other models used raw data. Experiment results showed that deep transfer learning was the most effective method with an accuracy of 0.7583 and an area under the curve of 0.7941. Furthermore, to improve the interpretability of the results from the deep learning and deep transfer learning models, the classification heat-map features were used, which displayed the region of feature extraction by superposing with raw data. The research findings are expected to promote the use of effective methods in CRC LNM detection and hence facilitate the design of proper treatment plans.
Reverberant Shear Wave Elastography: A Multi-Modal and Multi-Scale Approach to Measure the Viscoelasticity Properties of Soft Tissues

There are a variety of approaches used to create elastography images. Techniques based on shear wave propagation have received significant attention. However, there remain some limitations and problems due to shear wave reflections, limited penetration in highly viscous media, requirements for prior knowledge of wave propagation direction, and complicated propagation in layers where surface acoustic waves and guided waves are dominant. To overcome these issues, reverberant shear wave elastography (RSWE) was proposed as an alternative method which applies the concept of a narrow-band diffuse field of shear waves within the tissue. Since 2017, the RSWE approach has been implemented in ultrasound (US) and optical coherence tomography (OCT). Specifically, this approach has been implemented in these imaging modalities because they are similar in image formation principles and both share several approaches to estimate the biomechanical properties in tissues. Moreover, they cover different spatial-scale and penetration depth characteristics. RSWE has shown promising results in the elastic and viscoelastic characterization of multiple tissues including liver, cornea, and breast. This review summarizes the 4-year progress of the RSWE method in US and OCT. Theoretical derivations, numerical simulations, and applications in ex vivo and in vivo tissues are shown. Finally, we emphasize the current challenges of RSWE in terms of excitation methods and estimation of biomechanical parameters for tissue-specific cases and discuss future pathways for the in vivo and in situ clinical implementations.
Immune System Effects of Insulin-Like Peptide 5 in a Mouse Model

Introduction Insulin-like peptide 5 (INSL5) is a peptide hormone with proposed actions in glucose homeostasis and appetite regulation via its cognate receptor, relaxin family peptide receptor 4 (RXFP4). Here, we look for evidence for their involvement in the immune system using a mouse model. Methods In silico analyses: we queried public databases for evidence of expression of INSL5-RXFP4 in immune system tissues/cells (NCBI’s SRA and GeoProfiles) and disorders (EMBO-EBI) and performed phylogenetic footprinting to look for evidence that they are regulated by immune-associated transcription factors (TFs). Experimental analyses: We characterized the expression and correlation of INSL5/RXFP4 and other immune system markers in central and peripheral immune organs from C57/bl6 mice in seven cohorts. We tested whether fluctuations in circulating INSL5 induce an immune response, by injecting mice with 30 μg/kg of INSL5 peptide in the peritoneum, and examining levels of immune markers and metabolic peptides in plasma. Lastly, we quantified the expression of Rxfp4 in T-cells, dendritic cells and cell lines derived from human and mouse and tested the hypothesis that co-incubation of ANA-1 cells in INSL5 and LPS alters cytokine expression. Results We find Insl5 expression only in thymus (in addition to colon) where its expression was highly correlated with Il-7, a marker of thymocyte development. This result is consistent with our in silico findings that Insl5 is highly expressed in thymic DP, DN thymocytes and cortical TEC’s, and with evidence that it is regulated by thymocyte-associated TF’s. We find Rxfp4 expression in all immune organs, and moderately high levels in DCs, particularly splenic DCs, and evidence that it is regulated by immune-associated TF’s, such as STAT’s and GATA. Systemic effects: We observed significantly elevated concentrations of blood GLP-1, GIP, GCG and PYY following intraperitoneal injection of INSL5, and significantly altered expression of cytokines IL-5, IL-7, M-CSF, IL-15, IL-27 and MIP-2. Immune cell effects: Incubation of ANA-1 cells with INSL5 impeded cell growth and led to a transient elevation of IL-15 and sustained reduction in IL-1β, IL-6 and TNFα. Conclusion We propose that INSL5-RXFP4 play a novel role in both central and peripheral immune cell signaling.
Effects of Betaine Supplementation on Live Performance, Selected Blood Parameters, and Expression of Water Channel and Stress-Related mRNA Transcripts of Delayed Placement Broiler Chicks

This study examined the effect of supplemental betaine on live performance, selected blood parameters, and gene expression of water channel proteins (Aquaporins, AQP) of broiler chicks delayed in placement for 48 h post-hatch. In total, 540 newly-hatched male broiler chicks were obtained from a local hatchery and were randomly allotted to one of five treatments with nine replicates per treatment (12 chicks per replicate). Chicks were either placed immediately, control; held for 48 h post-hatch with no access to feed or water, Holdnull; held for 48 h with free access to drinking water only, HoldW; held for 48 h with free access to drinking water supplemented with 1 ml per L of betaine solution (40% betaine), HoldB1; or held for 48 h with free access to drinking water supplemented with 2 ml per L of betaine solution (40% betaine), HoldB2 group. The results showed that post-hatch holding for 48 h depressed feed intake and body weight gain during the entire 15 d study period with no beneficial effect of supplemental betaine. Chicks in the HoldB2 group had elevated serum glucose, triglycerides, and aspartate aminotransferase 48 h post-hatch. Early water deprivation directly affected the brain proopiomelanocortin (POMC) and hepatic glucocorticoid receptors (GR) expression and induced significant changes in various aquaporins (AQP1, AQP2, AQP4, and AQP9). In conclusion, betaine supplementation to chicks held for 48 h post-hatch resulted in some changes in blood biochemical indices with no effects on performance during the first 15 days of life. The results suggest that betaine supplementation could ameliorate the stressful effects of water deprivation on POMC and GR expression and maintain cellular osmosis through interactions with variable aquaporins expression, particularly the AQP1 and AQP2. Further investigations are required to investigate the molecular mechanisms underlying the selective regulatory expression of different aquaporins in relation to betaine supplementation.
A Weight of Evidence Analysis of the Chronic Ecotoxicity of Nonylphenol Ethoxylates, Nonylphenol Ether Carboxylates, and Nonylphenol

ABSTRACT Nonylphenol ethoxylates (NPE) are widely used surfactant compounds with many domestic and industrial applications. Due to the nature of their use in down-the-drain applications, spent NPE are discharged to septic systems or to wastewater treatment plants. Biodegradation of parent material during treatment is often incomplete, leading to release of NPE and their degradation intermediates into the environment. Considerable aquatic toxicity research has occurred on NPE and particularly on nonylphenol (NP). Available data were subjected to a quality review and all studies of acceptable quality were used in a weight of evidence hazard assessment. Data for NP were further analyzed using a Species Sensitivities Distribution (SSD) approach. About 90 chronic values are available (ChVs, geometric mean of the no-observed effect concentration and lowest-observed effect concentration for each endpoint reported), which may be reduced to average ChVs for each tested species. Higher mole NPE (NPE ≥ 9) had ChVs ranging from 900 to 14,100 μg/L, ChVs for the low mole nonylphenol ether carboxylate (NPEC1) ranged from 3200 to 12,000 μg/L, ChVs for lower mole NPE (NPE1,2) ranged from 11 to 500 μg/L, and ChVs for NP ranged from 5 to 3500 μg/L. Using the SSD analysis for NP with higher quality study results, the 10th percentile chronic effect value is 5.7 μg/L, which supports the draft USEPA criteria on NP of 5.9 μg/L.
Diffusion Entropy vs. Multiscale and Rényi Entropy to Detect Progression of Autonomic Neuropathy

We review the literature to argue the importance of the occurrence of crucial events in the dynamics of physiological processes. Crucial events are interpreted as short time intervals of turbulence, and the time distance between two consecutive crucial events is a waiting time distribution density with an inverse power law (IPL) index μ, with μ < 3 generating non-stationary behavior. The non-stationary condition is characterized by two regimes of the IPL index: (a) perennial non-stationarity, with 1 < μ < 2 and (b) slow evolution toward the stationary regime, with 2 < μ < 3. Human heartbeats and brain dynamics belong to the latter regime, with healthy physiological processes tending to be closer to the border with the perennial non-stationary regime with μ = 2. The complexity of cognitive tasks is associated with the mental effort required to address a difficult task, which leads to an increase of μ with increasing task difficulty. On this basis we explore the conjecture that disease evolution leads the IPL index μ moving from the healthy condition μ = 2 toward the border with Gaussian statistics with μ = 3, as the disease progresses. Examining heart rate time series of patients affected by diabetes-induced autonomic neuropathy of varying severity, we find that the progression of cardiac autonomic neuropathy (CAN) indeed shifts μ from the border with perennial variability, μ = 2, to the border with Gaussian statistics, μ = 3 and provides a novel, sensitive index for assessing disease progression. We find that at the Gaussian border, the dynamical complexity of crucial events is replaced by Gaussian fluctuation with long-time memory.
The Functional Impact of Alternative Splicing on the Survival Prognosis of Triple-Negative Breast Cancer

Purpose Triple-negative breast cancer (TNBC) is a type of breast cancer (BC) showing a high recurrence ratio and a low survival probability, which requires novel actionable molecular targets. The involvement of alternative splicing (AS) in TNBC promoted us to study the potential roles of AS events in the survival prognosis of TNBC patients. Methods A total of 150 TNBC patients from The Cancer Genome Atlas (TCGA) were involved in this work. To study the effects of AS in the recurrence-free survival (RFS) prognosis of TNBC, we performed the analyses as follows. First, univariate Cox regression model was applied to identify RFS-related AS events. Their host genes were analyzed by Metascape to discover the potential functions and involved pathways. Next, least absolute shrinkage and selection operator (LASSO) method was used to select the most informative RFS-related AS events to constitute an AS risk factor for RFS prognosis, which was evaluated by Kaplan–Meier (KM) and receiver operating characteristic (ROC) curves in all the data and also in different clinical subgroups. Furthermore, we analyzed the relationships between splicing factors (SFs) and these RFS-related AS events to seek the possibility that SFs regulated AS events to influence RFS. Then, we evaluated the potential of these RFS-related AS events in the overall survival (OS) prognosis from all the above aspects. Results We identified a total of 546 RFS-related AS events, which were enriched in some splicing and TNBC-associated pathways. Among them, seven RFS-related events were integrated into a risk factor, exhibiting satisfactory RFS prognosis alone and even better performance when combined with clinical tumor–node–metastasis stages. Furthermore, the correlation analysis between SFs and the seven AS events revealed the hypotheses that SRPK3 might upregulate PCYT2_44231_AA to have an effect on RFS prognosis and that three other SFs may work together to downregulate FLAD1_7874_RI to influence RFS prognosis. In addition, the seven RFS-related AS events were validated to be promising in the OS prognosis of TNBC as well. Conclusion The abnormal AS events regulated by SFs may act as a kind of biomarker for the survival prognosis of TNBC.
Regulating T Cell Population Alleviates SLE by Inhibiting mTORC1/C2 in MRL/lpr Mice

It’s well known that the mammalian target of rapamycin (mTOR) exerts a critical role in the regulator of immune cells and is associated with T cells dysfunction in patients with systemic lupus erythematosus (SLE). Antigen-induced T-cell proliferation via mTORC1 suppressed by Rapamycin has been used to improve SLE primarily. Previously it has showed that INK128, a highly potent, specific orally inhibitor of mTORC1 and mTORC2, significantly attenuates SLE in pristine-induced lupus mice. Herein we compared the cure effects of INK128 and rapamycin on lupus mice. We treated MRL/lpr mice with INK128 or rapamycin at 12 weeks-age. The effect of the two inhibitors on the lupus mice was determined by immunohistochemistry. The effect of the two inhibitors on T cell populations was investigated by flow cytometry. The mTOR signaling was measured by Western Blot. INK128 remarkably alleviated SLE by reducing splenomegaly, renal inflammation and damage, and resuming T-cell dysfunction. The more effective of INK128 on SLE than rapamycin. INK128 effectively suppressed mTORC1 and mTORC2 activity in T cells, but rapamycin just suppressed mTORC1 activity. Thus, our results show that INK128 is can effectively alleviate SLE and be used as one of the potential clinical therapeutic candidates for SLE.