Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhancing egg production and quality by the supplementation of probiotic strains (Clostridium and Brevibacillus) via improved amino acid digestibility, intestinal health, immune response, and antioxidant activity

This study focused on evaluating the influence of Clostridium butyricum and Brevibacillus strains on egg production, egg quality, immune response and antioxidant function, apparent fecal amino acid digestibility, and jejunal morphology when supplemented as probiotics in the diets of laying hens in the peak phase. A total of 288 healthy 30-week-old Hy-Line Brown laying hens were arbitrarily assigned to four dietary groups, which included control diet and control diet supplemented with 0.02% C. butyricum zlc-17, C. butyricum lwc-13, or Brevibacillus zlb-z1, for 84 days. The results showed that dietary C. butyricum and Brevibacillus sp. exerted a positively significant influence (P ≤ 0.05) compared to the control group on the performance, egg quality, and physiological response of the birds. The diets could reduce mortality rate and enhance (P ≤ 0.05) egg weight and egg mass, egg production rate, and feed efficiency. Further analysis suggested that the probiotic strains can enhance (P ≤ 0.05) eggshell quality, Haugh unit, thick albumen content, and albumen height. Also, probiotics enhanced (P ≤ 0.05) the antioxidant status via increased antioxidant enzymes and jejunal morphology as evidenced by increased villi surface area (VSA), the ratio of villi height to crypt depth, villi width, and villi height, and a significant reduction in crypt depth. Besides, nutrient absorption and retention were enhanced, as apparent fecal amino acid digestibility of key essential amino acids was substantially improved in the diet-based group. The concentrations of immunoglobulin M and A (IgM and IgA) increased significantly (P ≤ 0.05) in the probiotics group and the same effect was notable for complement proteins (C3) and immune organ (Spleen). Conclusively, the supplementation of Clostridium butyricum zlc-17 in comparison to Clostridium butyricum lwc-13 and Brevibacillus zlb-z1 strains significantly (P ≤ 0.05) promoted the antioxidant status, modulated the intestinal structure, enhanced amino acid digestibility, and regulated the immunity index of the laying hens, which finally improves the laying performance and egg quality of the laying hens.
Dynamic Modelling of DNA Repair Pathway at the Molecular Level: A New Perspective

DNA is the genetic repository for all living organisms, and it is subject to constant changes caused by chemical and physical factors. Any change, if not repaired, erodes the genetic information and causes mutations and diseases. To ensure overall survival, robust DNA repair mechanisms and damage-bypass mechanisms have evolved to ensure that the DNA is constantly protected against potentially deleterious damage while maintaining its integrity. Not surprisingly, defects in DNA repair genes affect metabolic processes, and this can be seen in some types of cancer, where DNA repair pathways are disrupted and deregulated, resulting in genome instability. Mathematically modelling the complex network of genes and processes that make up the DNA repair network will not only provide insight into how cells recognise and react to mutations, but it may also reveal whether or not genes involved in the repair process can be controlled. Due to the complexity of this network and the need for a mathematical model and software platform to simulate different investigation scenarios, there must be an automatic way to convert this network into a mathematical model. In this paper, we present a topological analysis of one of the networks in DNA repair, specifically homologous recombination repair (HR). We propose a method for the automatic construction of a system of rate equations to describe network dynamics and present results of a numerical simulation of the model and model sensitivity analysis to the parameters. In the past, dynamic modelling and sensitivity analysis have been used to study the evolution of tumours in response to drugs in cancer medicine. However, automatic generation of a mathematical model and the study of its sensitivity to parameter have not been applied to research on the DNA repair network so far. Therefore, we present this application as an approach for medical research against cancer, since it could give insight into a possible approach with which central nodes of the networks and repair genes could be identified and controlled with the ultimate goal of aiding cancer therapy to fight the onset of cancer and its progression.
Comparative effectiveness of electroacupuncture VS neuromuscular electrical stimulation in the treatment of chronic low back pain in active-duty personals: A single-center, randomized control study

Introduction Low back pain (LBP) is the most prevalent form of chronic pain in active-duty military personnel worldwide. Electroacupuncture (EA) and neuromuscular electrical stimulation (NMES) are the two most widely used treatment methods in the military, while evidence for their benefits is lacking. The aim of this randomized clinical trial is to investigate the effectiveness of EA vs. NMES in reducing pain intensity among active-duty navy personals with chronic LBP. Methods The study is designed as a single-center, randomized controlled trial. The primary outcome is a positive categorical response for treatment success in the first-time follow-up, which is predesignated as a two-point or greater decrease in the NRS score and combined with a score > 3 on the treatment satisfaction scale. The secondary outcomes include pain intensity, rate of treatment success, and Oswestry Disability Index (ODI) fear-avoidance beliefs questionnaire (FABQ) score along with muscular performance. The first follow-up starts on the first day after completing the last treatment session, and then the 4-weeks and 12-weeks follow-up are applied via telephone visit. Results Eighty-five subjects complete the treatment diagram and are included in the analysis. For the primary outcome, no difference has been found between EA and NMES, with 65.1% (28 in 43) individuals reporting a positive response to EA treatment, while 53.5% (23 in 43) in NMES. However, for longer follow-ups, superiority in positive response of EA has been found in 4-weeks (26 in 39, 66.7% vs. 16 in 40, 40%; P = 0.018) and 12-weeks (24 in 36, 66.7% vs. 12 in 36, 33.3%; P = 0.005) follow-up. In the regression analysis, baseline pain intensity and FABQ score are identified to be highly associated with positive treatment outcomes. Finally, the subgroup analysis suggests that EA treatment is associated with better long-term outcomes in patients with LBP with a severe pain score (NRS score >4, Figure 4B) and stronger fear-avoidance beliefs. Conclusion Both the EA and NMES are associated with a positive response in treating military LBP, and the former offers lasting benefits in the later follow-ups. Thus, electroacupuncture is a more recommended treatment for military LBP. A lot of research is needed to verify an efficient and standardized treatment session, with more information and evidence about indications for these treatments. Trial registration ChiCTR, (ChiCTR2100043726); registered February 27, 2021.
A clustering-based sampling method for miRNA-disease association prediction

More and more studies have proved that microRNAs (miRNAs) play a critical role in gene expression regulation, and the irregular expression of miRNAs tends to be associated with a variety of complex human diseases. Because of the high cost and low efficiency of identifying disease-associated miRNAs through biological experiments, scholars have focused on predicting potential disease-associated miRNAs by computational methods. Considering that the existing methods are flawed in constructing negative sample set, we proposed a clustering-based sampling method for miRNA-disease association prediction (CSMDA). Firstly, we integrated multiple similarity information of miRNA and disease to represent miRNA-disease pairs. Secondly, we performed a clustering-based sampling method to avoid introducing potential positive samples when constructing negative sample set. Thirdly, we employed a random forest-based feature selection method to reduce noise and redundant information in the high-dimensional feature space. Finally, we implemented an ensemble learning framework for predicting miRNA-disease associations by soft voting. The Precision, Recall, F1-score, AUROC and AUPR of the CSMDA achieved 0.9676, 0.9545, 0.9610, 0.9928, and 0.9940, respectively, under five-fold cross-validation. Besides, case study on three cancers showed that the top 20 potentially associated miRNAs predicted by the CSMDA were confirmed by the dbDEMC database or literatures. The above results demonstrate that the CSMDA can predict potential disease-associated miRNAs more accurately.
Modified nanofat grafting: Stromal vascular fraction simple and efficient mechanical isolation technique and perspectives in clinical recellularization applications

Background: Nanofat grafting (NG) is a simple and cost-effective method of lipoaspirates with inter-syringe passages, to produce stromal vascular fraction (SVF) and isolate adipose-derived stem cells (ASCs). This represents a tremendous interest in the future clinical needs of tissue engineering. In this study, we optimized the NG technique to increase the yield of ASC extractions. Methods: We analyzed three groups of SVF obtained by 20, 30, and 40 inter-syringe passages. The control group was an SVF obtained by enzymatic digestion with Celase. We studied their cell composition by flow cytometry, observed their architecture by confocal microscopy, and observed immunomodulatory properties of the ASCs from each of the SVFs by measuring inflammatory markers of macrophages obtained by an ASC monocyte co-culture. Results: We have established the first cell mapping of the stromal vascular fraction of adipose tissue. The results showed that SVF obtained by 20 inter-syringe passages contains more statistically significant total cells, more cells expressing the ASC phenotype, more endothelial cells, and produces more CFU-F than the SVF obtained by 30 and 40 passages and by enzymatic digestion. Confocal microscopy showed the presence of residual adipocytes in SVF obtained by inter-syringe passages but not by enzymatic digestion. The functional study indicates an orientation toward a more anti-inflammatory profile and homogenization of their immunomodulatory properties. Conclusion: This study places mechanically dissociated SVF in the center of approaches to easily extract ASCs and a wide variety and number of other progenitor cells, immediately available in a clinical setting to provide both the amount and quality of cells required for decellularized tissues.
Association between kinking of the cervical carotid or vertebral artery and ischemic stroke/TIA

Introduction Kinking of the cervical carotid or vertebral artery is a common structural abnormality in patients with cerebrovascular disease. However, there is no consensus about the relationship between kinking and ischemic stroke/TIA. We aim to determine the effect of arterial kinking on ischemic stroke/TIA. Methods A retrospective study was performed on patients who underwent cerebral angiography with DSA between January 2014 and December 2018. Demographic information and comorbidities were recorded. Each anatomical circulation system was defined as an observation unit. Kinking and stenosis of each circulation unit were recorded. Ischemia stroke or TIA within 6 months and its location were assessed as an outcome. Logistic regression with a generalized estimating equation approach was used for the analysis. Results A total of 1,062 patients (mean age 57.9 ± 14.5 years, 740 males and 322 females) were included in the study. Of the patients, 369 (35%) had kinking and 771 (73%) had ischemic stroke/TIA. There were 110 left anterior, 90 right anterior, and 308 posterior circulation units, among which 343 had mild, 160 had moderate, and 243 had severe kinking. Multivariate regression analysis showed that ischemic stroke/TIA was associated with severe kinking (OR 1.39, 95% CI 1.03–1.88, P = 0.03). Posterior circulation was more vulnerable to acute ischemia than left anterior and right anterior circulation (OR 3.58, 95% CI 2.81–4.56, P < 0.0001). Conclusion Severe kinking of the cervical carotid or vertebral artery may be associated with a higher risk of ischemic stroke/TIA, especially when the kinking is located in the posterior circulation.
Effects of long-term climate trends on the methane and CO2 exchange processes of Toolik Lake, Alaska

Methane and carbon dioxide effluxes from aquatic systems in the Arctic will affect and likely amplify global change. As permafrost thaws in a warming world, more dissolved organic carbon (DOC) and greenhouse gases are produced and move from soils to surface waters where the DOC can be oxidized to CO2 and also released to the atmosphere. Our main study objective is to measure the release of carbon to the atmosphere via effluxes of methane (CH4) and carbon dioxide (CO2) from Toolik Lake, a deep, dimictic, low-arctic lake in northern Alaska. By combining direct eddy covariance flux measurements with continuous gas pressure measurements in the lake surface waters, we quantified the k 600 piston velocity that controls gas flux across the air–water interface. Our measured k values for CH4 and CO2 were substantially above predictions from several models at low to moderate wind speeds, and only converged on model predictions at the highest wind speeds. We attribute this higher flux at low wind speeds to effects on water-side turbulence resulting from how the surrounding tundra vegetation and topography increase atmospheric turbulence considerably in this lake, above the level observed over large ocean surfaces. We combine this process-level understanding of gas exchange with the trends of a climate-relevant long-term (30 + years) meteorological data set at Toolik Lake to examine short-term variations (2015 ice-free season) and interannual variability (2010–2015 ice-free seasons) of CH4 and CO2 fluxes. We argue that the biological processing of DOC substrate that becomes available for decomposition as the tundra soil warms is important for understanding future trends in aquatic gas fluxes, whereas the variability and long-term trends of the physical and meteorological variables primarily affect the timing of when higher or lower than average fluxes are observed. We see no evidence suggesting that a tipping point will be reached soon to change the status of the aquatic system from gas source to sink. We estimate that changes in CH4 and CO2 fluxes will be constrained with a range of +30% and −10% of their current values over the next 30 years.
A unified bus voltage regulation and MPPT control for multiple PV sources based on modified MPC in the DC microgrid

This study proposes a unified voltage regulation and maximum power point tracking (MPPT) method for photovoltaic (PV) sources in islanded direct current (DC) microgrids based on modified model predictive control (MPC). The method enables the PV sources to track the maximum power and serve as voltage sources for DC-bus voltage regulation when their available power is sufficient. Based on the proposed modified predictive model, the desired duty cycles can be calculated and directly applied to the PV sources in a constant switching frequency without a modulator. Real-time laboratory tests show that the PV sources can support the DC-bus voltage without energy storage (ES) and can proportionally share the load. Moreover, power oscillations and voltage ripples of the modified MPC get greatly attenuated compared with the traditional MPC under the same sampling frequency.
Deep learning for screening primary osteopenia and osteoporosis using spine radiographs and patient clinical covariates in a Chinese population

Purpose Many high-risk osteopenia and osteoporosis patients remain undiagnosed. We proposed to construct a convolutional neural network model for screening primary osteopenia and osteoporosis based on the lumbar radiographs, and to compare the diagnostic performance of the CNN model adding the clinical covariates with the image model alone. Methods A total of 6,908 participants were collected for analysis, including postmenopausal women and men aged 50–95 years, who performed conventional lumbar x-ray examinations and dual-energy x-ray absorptiometry (DXA) examinations within 3 months. All participants were divided into a training set, a validation set, test set 1, and test set 2 at a ratio of 8:1:1:1. The bone mineral density (BMD) values derived from DXA were applied as the reference standard. A three-class CNN model was developed to classify the patients into normal BMD, osteopenia, and osteoporosis. Moreover, we developed the models integrating the images with clinical covariates (age, gender, and BMI), and explored whether adding clinical data improves diagnostic performance over the image mode alone. The receiver operating characteristic curve analysis was performed for assessing the model performance. Results As for classifying osteoporosis, the model based on the anteroposterior+lateral channel performed best, with the area under the curve (AUC) range from 0.909 to 0.937 in three test cohorts. The models with images alone achieved moderate sensitivity in classifying osteopenia, in which the highest AUC achieved 0.785. The performance of models integrating images with clinical data shows a slight improvement over models with anteroposterior or lateral images input alone for diagnosing osteoporosis, in which the AUC increased about 2%–4%. Regarding categorizing osteopenia and the normal BMD, the proposed models integrating images with clinical data also outperformed the models with images solely. Conclusion The deep learning-based approach could screen osteoporosis and osteopenia based on lumbar radiographs.
Characterization and application of a novel xylanase from Halolactibacillus miurensis in wholewheat bread making

The presence of arabinoxylan in wholewheat flour affects its quality significantly. Here, an efficient arabinoxylan hydrolytic enzyme, Hmxyn, from Halolactibacillus miurensis was identified and heterologously expressed in pichia pastoris. Moreover, its relevant properties, including potential application in the wholewheat bread were evaluated. Recombinant Hmxyn exhibited maximal activity at 45°C and pH 6.5, and was stable at mid-range temperature (<55°C) and pH (5.5–8.0) conditions. Hmxyn had a clear hydrolysis effect on wheat arabinoxylan in dough and caused the degradation of the water-unextractable arabinoxylan, which increased the content of wheat soluble arabinoxylan of dough. The fermentation characteristics results and microstructure analysis revealed that Hmxyn improved the organizational structure and air holding capacity of fermented dough, thus promoting the dough expansion. Baking experiments further showed that Hmxyn significantly increased specific volume- and texture-linked properties of wholewheat breads. This study indicates the application potential of Hmxyn in the preparation of wholewheat bread.
Simple new technique for macular pucker peel without forceps

Purpose This study aimed to describe the effectiveness and evaluate the anatomical and functional results of surgery for macular pucker (MP) peel using a 25-gauge pars plana vitrectomy (PPV) cutter without forceps. Methods This study assessed a prospective consecutive case series of 14 eyes of 14 patients who underwent 25-gauge PPV for MP. The surgical procedure was performed using the new peeling technique. The edge of the membrane was engaged at the opening of the cutter by gradually increasing the vacuum. The peeling process was finished by holding a stable vacuum or regrasping the membrane in the same manner. Results The study included six women and eight men patients with a mean age of 72.3 (range 59–84) years. MP peel was achieved in all cases without the need for microforceps. Patients were followed for at least 6 months. Visual acuity and retinal thickness were obtained 6 months after the surgery. Best corrected visual acuity improved from a mean pre-operative 0.6 on a logMAR scale to post-operative 0.23 (P < 0.001). Mean pre-operative Central Retinal Thickness was significantly reduced from 489.7 to 377.6 μm post-operatively (P < 0.001). There were no intra- or post-operative complications. Conclusion MP peel with a 25-gauge vitrectomy probe could be an alternative simple and safe technique. The technique does not require extra instrumentation. It results in anatomic and functional improvement in all cases.
miR-21-5p/PRKCE axis implicated in immune infiltration and poor prognosis of kidney renal clear cell carcinoma

Kidney renal clear cell carcinoma (KIRC or ccRCC) is the most notorious subtype of renal cell carcinoma for its poor prognosis. Mounting evidence has highlighted the key role of PRKCE in the initiation and development of several types of human cancer, including kidney renal clear cell carcinoma (KIRC). However, the mechanism of PRKCE aberrant expression and the specific clinical correlation of PRKCE expression with immune cell infiltration in KIRC remains elusive. Therefore, we analyzed the relationship between PRKCE and KIRC using many databases, including Oncomine, TCGA, GTEx, TIMER, and GEO. We found that PRKCE decreased in KIRC tumor tissue compared to normal tissue. The Kaplan-Meier Plotter analysis and Univariate and Multivariate Cox analyses were used to evaluate the association between PRKCE and clinicopathological variables and prognosis. Low PRKCE expression was associated with poor survival and histologic grade, T stage, pathologic stage, and M stage. Besides, the C-indexes and calibration plots of the nomogram based on multivariate analysis showed an effective predictive performance for KIRC patients. In addition, PRKCE may be positively correlated with inflammation and negatively correlated with proliferation, metastasis, and invasion as identified by CancerSEA. Moreover, overexpression of PRKCE suppressed ACHN and Caki-1 cell proliferation, migration, and invasion in vitro. Additionally, methylation level data acquired from UALCAN, DiseaseMeth, CCLE, LinkedOmics, and MEXPRESS was used to investigate the relationship between PRKCE expression and PRKCE methylation level. Furthermore, upstream potential miRNA predictions were further performed to explore the mechanism of PRKCE decreased expression in KIRC using multiple online databases available on publicly assessable bioinformatics platforms. High PRKCE methylation levels and hsa-miR-21-5p may contribute to PRKCE low expression in KIRC. Finally, an analysis of immune infiltration indicated that PRKCE was associated with immune cell infiltration. Importantly, PRKCE may affect prognosis partially by regulating immune infiltration in KIRC. In summary, PRKCE may serve as a novel prognostic biomarker reflecting immune infiltration level and a novel therapeutic target in KIRC.