Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome Profiling across Five Tissues of Giant Panda

Gene differential expression studies can serve to explore and understand the laws and characteristics of animal life activities, and the difference in gene expression between different animal tissues has been well demonstrated and studied. However, for the world-famous rare and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood and spleen has been reported separately. Here, in order to explore the transcriptome differences between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 platform. The comparative analysis of the intertissue gene expression patterns was carried out based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network were performed according to the identified differentially expressed genes (DEGs). We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 18,701 genes, including 3492 novel genes. With corrected p value <0.05 and |log2FoldChange| >2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI network. The results of the analyses showed a similar gene expression pattern between the spleen and lung. This study provided for the first time the heart, liver, lung, and kidney's transcriptome resources of the giant panda, and it provided a valuable resource for further genetic research or other potential research.
The Role of Interleukin-6 and Inflammatory Cytokines in Pancreatic Cancer-Associated Depression

Pancreatic cancer is historically known for representing a challenge for both diagnosis and treatment. Despite the advances in medicine, science, and technology, it remains the third leading cause of cancer-related deaths in the United States. The association between pancreatic cancer and major depression preceding the diagnosis is well known; however, it is still poorly understood, being considered an obscure piece of the puzzle the disease represents. It has been characterized as a paraneoplastic syndrome caused by the dysregulation of inflammatory cytokines, especially interleukin-6 (IL-6). Despite many types of studies describing the association, researchers have been reluctant to recommend it as a screening tool or early marker of the disease, mainly because of the non-specific nature of depression and anxiety in the studied patients. In this literature review, we aim to better understand the relationship between pancreatic cancer and major depression and characterize the immunologic mechanism of action behind the association.
Cross-Cultural Adaptation of the Greek Versions of the Lysholm Knee Scoring Scale and Tegner Activity Scale

Purpose The Lysholm Knee Scoring Scale (LKSS) and the Tegner Activity Scale (TAS) are widely used instruments for assessing knee function and activity level in various knee pathologies, especially knee ligament injuries. The purpose of this study was to translate and cross-culturally adapt the Greek versions of the Lysholm Knee Scoring Scale (Gr-LKSS) and Tegner Activity Scale (Gr-TAS) and assess their reliability and validity in Greek patients suffering from various knee problems. Materials and methods Translation of the LKSS and TAS questionnaires was done according to established international guidelines. Fifty-five patients (32 males and 23 females; mean age: 24 ±7 years; range: 17-54 years) with various knee pathologies completed the Gr-LKSS and Gr-TAS along with the Greek versions of International Knee Documentation Committee (IKDC) Subjective Knee Evaluation Form, the Knee Outcome Survey Activities of Daily Living Scale (KOS-ADLS) and the Oxford Knee Score (OKS). Test-retest reliability was evaluated with the intraclass correlation coefficient (ICC) in 53 (96%) individuals, who completed the questionnaires again after 48-72 hours while abstaining from all forms of treatment. Internal consistency for the Gr-LKSS was measured using Cronbach’s alpha and criterion-related validity was evaluated with the Pearson's correlation coefficient (r) in relation to control questionnaires (IKDC, KOS-ADLS, OKS). The distribution of floor and ceiling effects were also determined. Results There were no problems during the forward-backward translation and cultural adaptation of the Gr-LKSS and Gr-TAS. Criterion-related validity was confirmed with moderate to high associations of Gr-LKSS and Gr-TAS (after injury) with the IKDC and KOS-ADLS (Pearson’s r ranging between 0.61-0.71 and 0.64-0.73, respectively). However, weak correlations were yielded between both questionnaires with the OKS (r=0.14-0.19). The internal consistency for Gr-LKSS was high (Cronbach's alpha: 0.779) and the test-retest reliability was high for both questionnaires (Gr-LKSS: ICC=0.950; Gr-TAS before and after injury: ICCs of 0.877 and 0.876, respectively). Conclusion The cultural adaptation and validity of Gr-LKSS and Gr-TAS were successfully accomplished. These questionnaires are recommended for use in the evaluation of soft tissue knee disorders in both clinical practice and research.
The relationship between oxidative stress and preeclampsia. The serum ischemia-modified albumin levels and thiol/disulfide homeostasis

Objective: Preeclampsia (PE) is a dangerous complication of pregnancy and still a major cause of maternal-fetal morbidity and mortality. Its etiology remains largely unknown, but researchers have suggested oxidative stress-mediated inflammation for the same. The purpose of this study is to investigate the relationship between oxidative stress and PE as well as the usability of oxidative stress indicators such as serum ischemia-modified albumin (IMA) levels and thiol/disulfide balance in the prediction of PE. Materials and Methods: The study included 47 pregnant women with PE and 57 healthy pregnant women. We measured their serum IMA, native thiol, total thiol, and disulfide levels. Additionally, we determined the optimal cutoff values via the receiver operating characteristic curve analysis. Results: There were no differences between the two groups with respect to the maternal age, body mass index, gravida, and parity. The native and total thiol levels were found to be low when the disulfide and IMA levels were high in the patients with PE (p<0.05). When the IMA level was corrected by the albumin level (IMAR), the significant difference between the two groups disappeared. We also found that the native and total thiol concentrations were correlated with the systolic and diastolic blood pressures. The optimal cut-off values calculated for the prediction of PE were as follows: 178.45 µmol/L (with sensitivity of 72% and specificity of 83%) for native thiol, 232.55 µ mol/L (with a sensitivity of 75% and specificity of 85%) for total thiol, and 29.05 µmol/L (with sensitivity of 65% and specificity of 72%) for disulfide. Conclusion: The balance of thiol/disulfide may play a role in the pathogenesis of PE and could be used as a biological marker for PE.
Cinnamomum burmannii (Nees & T. Nees) Blume and Eleutherine palmifolia (L.) Merr. extract combination ameliorate lipid profile and heart oxidative stress in hyperlipidemic mice

Background and Aim: Hyperlipidemia is an important risk factor for cardiovascular disease. The use of statins has adverse side effects that result in oxidative stress disorders. The objective of this study was to investigate the antihyperlipidemic effect of a combination of Cinnamomum burmannii and Eleutherine palmifolia extract in high-fat diet (HFD)-induced hyperlipidemia mice. Materials and Methods: Mice were divided into eight groups (n=4): Control group or healthy mice (normal), HFD-induced hyperlipidemic mice without any treatment (CE0), HFD-induced hyperlipidemic mice treated with 3.6 mg/kg body weight (BW) atorvastatin (atorvastatin), and HFD-induced hyperlipidemic mice treated with a combination of C. burmannii and E. palmifolia in the following ratios: 300:0 (C300), 225:75 (C225), 150:150 (CE150), 75:225 (E225), and 0:300 (E300). Mice were fed a HFD for 4 months to induce hyperlipidemia. Total cholesterol, cholesterol oxidase-peroxidase aminophenazone (CHOD-PAP), triglyceride-glycerine, and fat serum were analyzed with colorimetric method. The measurement of superoxide dismutase was done with the xanthine oxidase method and malondialdehyde measurement was done with the thiobarbituric acid method. Results: Results showed an increase in antihyperlipidemic characteristics as the concentration of E. palmifolia extract (p<0.05) increased. Duncan’s multiple range test also showed an increase in anti-stress oxidation as the concentration of C. burmannii extract (p<0.05) increased. Conclusion: The E225 group showed the most potential as a safe, antihyperlipidemic agent characterized by improvement in lipid profile and antioxidant balance.
Current Status and Future Perspectives of Immunotherapy in Middle-Income Countries: A Single-Center Early Experience

Background Immunotherapy agents offer novel treatment options in advanced cancers. However, their use is limited in developing countries lacking unifying guidelines and can be followed by a financial burden. In this study, we aimed to provide an overview regarding the use of immunotherapy and the overall response to treatment in patients with metastatic disease in relation to cost-effectiveness. Methods This was a retrospective study involving adult metastatic cancer patients, treated with programmed cell death-1 (PD-1) inhibitors at American University of Beirut Medical Center (AUBMC), a tertiary cancer center in Lebanon. Study enrollment began on January 1, 2014 and ended on January 12, 2016. Baseline demographics, epidemiological and clinical data were collected from the patients’ records. Results Our study consisted of 34 patients. Fifteen patients self-financed the treatment. The patients were prescribed immunotherapy without programmed cell death-ligand 1 (PD-L1) testing as it was not part of the guidelines at the time. Twenty-two patients were treated with nivolumab and 12 patients with pembrolizumab. Thirteen patients showed partial response or stable disease, while 21 patients showed progression. Conclusion Improvement in terms of overall survival and progression-free survival has been undercut by the lack of availability of these drugs and their cost. Considering that a large percentage of patients do not respond to immunotherapy, there is a need to use guidelines such as a preset PD-L1 level that ensure cost-effectiveness and prevent resource waste.
Surface Damaging of Brass and Steel Pins when Sliding over Nitrided Samples Cut by Finishing and Roughing EDM Conditions

In the forging industry, surface quality and surface treatments of dies are crucial parameters to extend their life. These components are usually machined by milling or by Electrical Discharge Machining (EDM), and the final surface roughness depends on the machining techniques and operational conditions used in its fabrication. After milling, a nitriding treatment is widely applied to extend its service life. Nevertheless, no scientific report that informs about nitriding after EDM has been found. Accordingly, this work focuses on the wear and friction behavior of pins made of brass and medium carbon steel sliding over AISI H13 discs, made by wire EDM in the conditions of finishing and roughing. The discs are plasma nitride, and their effect on the wear during pin-on-disc tests is evaluated. In this sense, the analysis of the surface damage for the different pins will help us to understand the service life and wear evolution of the forging dies. The results show that plasma nitride reduces the friction and prevents the degradation of the pin, independently of the material of the pin, when sliding over finishing and roughing EDM conditions.
Effect of Lb. plantarum BFE 5092 Fermentation on Antinutrient and Oligosaccharide Composition of Whole Red Haricot Bean (Phaseolus vulgaris L)

Common beans are a leguminous plant of the genus Phaseolus. They are rich in protein, energy, and minerals. They confer a wide range of health benefits when consumed. Utilization of common bean has however been poor due to high antinutrient content that results in reduced nutrient digestibility and mineral bioavailability. Flatulence after consumption is also a huge deterrent to common bean consumption. Lactic acid fermentation is the most common form of food fermentation with the Lactobacilli spp dominating most spontaneous fermentations. The objective of this study was to determine the effect of lactic acid bacteria (LAB) on the antinutrient and flatulence causing oligosaccharide composition of red haricot bean. A factorial research design was used in the study. Red haricot beans were sorted and soaked for 15 h. The soaked beans were fermented in 2% salt-sugar solutions for 120 h. Experimental batch was inoculated with Lb. plantarum BFE 5092 (IF), and the control batch was spontaneously fermented (SF). Microbial growth and pH were monitored every 24 h during fermentation. After fermentation, the beans were dried and milled, and the flours were subjected to biochemical analysis. ANOVA was done using SPSS statistics 23. The pH decreased significantly (P < 0.05) from 6.06 to 3.9 in both batches at the end of fermentation. The LAB counts significantly increased (P < 0.05) in both batches, whereas coliform counts decreased significantly (P < 0.05). Fungi were not detected in both batches. Soaking lowered tannins and phytates and raffinose concentrations significantly but had no significant effect on stachyose concentration. At the end of 120 h of fermentation, the tannin content was 109.50 and 54.04 mg/100 g in IF and SF, respectively. Phytates were at 242.52 and 163.43 mg/100 g in IF and SF, respectively. Raffinose content was 32.85 and 32.58 mg/100 g in IF and SF, respectively, while stachyose content was 593.33 and 467.49 mg/100 g in IF and SF, respectively. This research showed that LAB is able to ferment soaked whole red haricot and lower the tannin, phytate, raffinose, and stachyose content significantly. Spontaneous fermentation lowered these antinutrients and oligosaccharides better than inoculation with Lb. plantarum BFE 5092.
Genome selection in fruit breeding: application to table grapes

Genomic selection (GS) has recently been proposed as a new selection strategy which represents an innovative paradigm in crop improvement, now widely adopted in animal breeding. Genomic selection relies on phenotyping and high-density genotyping of a sufficiently large and representative sample of the target breeding population, so that the majority of loci that regulate a quantitative trait are in linkage disequilibrium with one or more molecular markers and can thus be captured by selection. In this study we address genomic selection in a practical fruit breeding context applying it to a breeding population of table grape obtained from a cross between the hybrid genotype D8909-15 (Vitis rupestris × Vitis arizonica/girdiana), which is resistant to dagger nematode and Pierce’s disease (PD), and ‘B90-116’, a susceptible Vitis vinifera cultivar with desirable fruit characteristics. Our aim was to enhance the knowledge on the genomic variation of agronomical traits in table grape populations for future use in marker-assisted selection (MAS) and GS, by discovering a set of molecular markers associated with genomic regions involved in this variation. A number of Quantitative Trait Loci (QTL) were discovered but this method is inaccurate and the genetic architecture of the studied population was better captured by the BLasso method of genomic selection, which allowed for efficient inference about the genetic contribution of the various marker loci. The technology of genomic selection afforded greater efficiency than QTL analysis and can be very useful in speeding up the selection procedures for agronomic traits in table grapes.
Pulmonary Fibrosis in COVID-19 Survivors: Predictive Factors and Risk Reduction Strategies

Although pulmonary fibrosis can occur in the absence of a clear-cut inciting agent, and without a clinically clear initial acute inflammatory phase, it is more commonly associated with severe lung injury. This may be due to respiratory infections, chronic granulomatous diseases, medications, and connective tissue disorders. Pulmonary fibrosis is associated with permanent pulmonary architectural distortion and irreversible lung dysfunction. Available clinical, radiographic, and autopsy data has indicated that pulmonary fibrosis is central to severe acute respiratory distress syndrome (SARS) and MERS pathology, and current evidence suggests that pulmonary fibrosis could also complicate infection by SARS-CoV-2. The aim of this review is to explore the current literature on the pathogenesis of lung injury in COVID-19 infection. We evaluate the evidence in support of the putative risk factors for the development of lung fibrosis in the disease and propose risk mitigation strategies. We conclude that, from the available literature, the predictors of pulmonary fibrosis in COVID-19 infection are advanced age, illness severity, length of ICU stay and mechanical ventilation, smoking and chronic alcoholism. With no proven effective targeted therapy against pulmonary fibrosis, risk reduction measures should be directed at limiting the severity of the disease and protecting the lungs from other incidental injuries.
CT Findings in a Novel Coronavirus Disease (COVID-19) Pneumonia at Initial Presentation

Background COVID-19 first broke out in China and spread rapidly over the world. Objectives To describe the CT features of COVID-19 pneumonia and to share our experience at initial diagnoses. Patients and Methods. Data from 53 patients (31 men, 22 women; mean age, 53 years; age range, 16-83 years) with confirmed COVID-19 pneumonia were collected. Their complete clinical data was reviewed, and their CT features were recorded and analyzed. Results The average time between onset of illness and the initial CT scan was six days (range, 1-42 days). A total of 399 segments were involved and distributed bilaterally (left lung: 186 segments [46.6%], right lung: 213 segments [53.4%]) and peripherally (38 [71.7%] patients). Multiple lobes (45 [84.9%]) and bilateral lower lobes (left lower lobe: 104 [26.1%], right lower lobe: 107 [26.8%], and total: 211 [52.9%]) were the most commonly involved. Ground-glass opacity with consolidation (24 [45.3%]) and pure ground-glass opacity (28 [52.8%]) were the main findings. The other findings were crazy-paving (14 [26.4%]), bronchiectasis (12 [22.6%]), atelectasis (7 [13.2%]), parenchymal bands (6 [11.3%]), air bronchogram (6 [11.3%]), interlobular thickening (5 [9.4%]), reticular pattern (1 [1.9%]), and pleural effusion (1 [1.9%]). Conclusions Most COVID-19 pneumonia patients had abnormalities on chest CT images at initial presentation. Imaging features combined with patient's exposure history and onset symptoms could facilitate the identification of the suspected patient for further examinations.
Adult attachment styles, self-esteem, and quality of life in women with fibromyalgia

Recently, the research on pain-related disability has increasingly paid attention to the psychological and social factors that may influence the biological condition. In the current study, we aimed to explore attachment styles, self-esteem, and quality of life in individuals with a diagnosis of fibromyalgia. Participants were 371 diagnosed women, with a mean age of 42.7 years (standard deviation = 10.6). The average number of years since diagnosis was 7.4 years (standard deviation = 2.4) years. To assess attachment, quality of life, and self-esteem, women responded, respectively, to the Relationship Questionnaire, the World Health Organization Quality of Life Questionnaire, and the Rosenberg Self-Esteem Inventory. Our results showed that secure attachment relationships and high self-esteem represent protective factors for quality of life of women with fibromyalgia, while the contrary emerged for insecure attachments and low self-esteem. The understanding of the psychological components that contribute to fibromyalgia may improve the effectiveness of interventions.
Risk Factors for Lymph Node Metastasis and Survival Outcomes in Colorectal Neuroendocrine Tumors

Objective The aim of our study was to analyze the factors affecting lymph node metastasis (LNM) and the prognosis of colorectal neuroendocrine tumors (NETs). Patients and Methods A retrospective analysis was conducted to collect the clinical data of 135 patients with colorectal NETs from January 2000 to December 2018, including clinical manifestations, pathological results, treatment methods, etc. Follow-up was regularly performed to observe the recurrence and metastasis of tumors and to identify the clinical and pathological features of colorectal NETs, risk factors for LNM and survival outcomes. Results Among 135 patients, there were 57 (42.2) patients with LNM, and the independent risk factors for LNM in the multivariable analyses were tumor diameter ≥2 cm (P= 0.040) and tumor grade G3 (P=0.001). Patients were followed up for 1 to 190 months, and of the 133 patients who were successfully followed up, the 5-year OS was 71.7%, and the 5-year PFS was 69.0%. The multivariate analysis for survival outcomes showed that age ≥65 years (P=0.002/<0.001) and lymph node metastasis (P=0.018/0.025) were independent risk factors affecting 5-year PFS and OS in colorectal neuroendocrine tumors. Tumors in the colon (P=0.022), moderately positive (++) CgA (P=0.010) and strongly positive (+++) CgA (P=0.007) were independent risk factors for poor 5-year PFS in patients with colorectal NETs. Conclusion Rectal NETs have a better prognosis than colonic neuroendocrine tumors. Tumor diameter and tumor grade are independent risk factors for LNM in colorectal neuroendocrine tumors. Age, tumor location, lymph node status and a positive level of the neuroendocrine marker CgA are independent risk factors that affect the prognosis of colorectal NETs.
Clinical Effects of Mercury in Conservative Dentistry: A Systematic Review, Meta-Analysis, and Trial Sequential Analysis of Randomized Controlled Trials

Methods A systematic literature search was conducted in four electronic databases (Ovid via PubMed, Web of Science, Scopus, and CENTRAL) including all available randomised controlled trials published in the last 15 years comparing the use of dental amalgam with composite resins in humans with a follow-up period of at least one year. The primary outcome was the Hg concentration in biological fluids (urine, hair, blood, and saliva) with the aim of assessing their reliability as biomarkers of Hg exposure. The risk of bias was assessed through the Cochrane Collaboration tool and the overall quality of evidence through the Grading of Recommendations, Assessment, Development and Evaluations (GRADE) system. The results of the meta-analysis were expressed using a random-effects model, and their power was assessed through the trial sequential analysis (TSA). Results From the initial 2555 results, only 6 publications were included in the review: five were considered as having high risk of bias, whereas one as having moderate risk. Only two articles were eligible for quantitative analysis. The meta-analysis gathered data from 859 patients but was nevertheless not significant (p = 0.12). The TSA confirmed this evidence revealing that it was due to a lack of statistical power since the required information size (RIS) threshold is not reached. Conclusions The existing evidence revealed that there are not enough data to support the hypothesis that restorations with dental amalgam can cause nephrotoxicity when compared with composite resins restorations.