Miracle-dz/UniFAR-FTUs huggingface dataset:
Management of the Most Common Functional Gastrointestinal Disorders in Infancy: The Middle East Expert Consensus

The occurrence of functional gastrointestinal disorders (FGIDs) is a formidable challenge for infants, parents, and healthcare professionals. Although data from the Middle East are scarce, experts consider FGIDs a prevalent condition in everyday clinical practice. The new Rome IV criteria revisited the definitions from a clinical perspective to provide a practical and consistent diagnostic protocol for FGIDs. However, the treatment practices for functional disorders vary considerably among Middle Eastern countries, often resulting in mismanagement with unnecessary investigations and treatments. In addition, the role of various treatment modalities, including probiotics such as Lactobacillus reuteri DSM 17938, in FGIDs requires further discussion and evaluation. During a consensus meeting, a locally relevant approach for treating common FGIDs such as infant regurgitation, infant colic, and functional constipation was discussed and approved by regional experts. The participants suggested a simplified treatment plan and protocol for general pediatricians and other primary care physicians managing FGIDs. This easy-to-follow standardized protocol will help streamline the initial management of this complex disorder in the Middle East region and even globally.
Specific characteristics of essential oils of four Artemisia species from the Mongolian Trans-Altai Gobi

The essential oil compositions of four Artemisia species in Mongolian Trans-Altai Gobi were studied by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS). The oil from A.macrocephala Jacq and A.dracunculus Ledeb. were characterized by the presence of monoterpene hydrocarbons and oxygenated monoterpeneoids predominately. E-nerolidol (26.95%), methyleugenol (23.29%) and sabinene (13.21%) were found as main components in the essential oils of A.dracunculus. A.macrocephalla was characterized by the presence of chamazulene (13.8%), cineol (11.7%), myrcene (9.0%), germacrene-D (7.1%). A.anethifolia Web was characterized by the presence of fragrant compounds as camphor (26.05%), α-thujone (10.1%), borneol (5.1%). Davanone and davanone derivatives were also detected in the sample in amount of 7.7% in total. A.scoparia Waldst differed by domination of monoterpene hydrocarbons (78.9%) with (Z)- β-ocimene (29.24%), α-pinene (15.19%), limonene (10.27%) and myrcene (9.61%). Mongolian Journal of Chemistry 16 (42), 2015, 34-38
Gene expression during THP-1 differentiation is influenced by vitamin D3 and not vibrational mechanostimulation

Background In injury or infection, monocytes migrate into the affected tissues from circulation and differentiate into macrophages which are subsequently involved in the inflammatory responses. Macrophage differentiation and activation have been studied in response to multiple chemokines and cytokines. However, mechanical, and physical stimuli can also influence macrophage differentiation, activation, cytokine production, and phagocytic activity. Methods In this study the macrophage differentiation from THP-1 monocytes was assessed upon the stimulation with 1,25-dihydroxyvitamin D3 and 1,000 Hz vibrations, using qPCR for quantification of transcript expression. Vitamin D binds the vitamin D receptor (VDR) and subsequently modulates the expression of a variety of genes in monocytes. The effects of the 1,000 Hz vibrational stimulation, and the combined treatment of vitamin D3 and 1000 Hz vibrations were unknown. The differentiation of macrophages was assessed by looking at transcription of macrophage markers (e.g., CD14, CD36), antigen presenting molecules (e.g., HLA-DRA), transcription factors (e.g., LEF-1, TCF7L2), and mechanosensors (e.g., PIEZO1 and PKD2). Results The results showed that vitamin D3 induced THP-1 macrophage differentiation, which was characterized by upregulation of CD14 and CD36, downregulation of HLA-DRA, upregulation of the PKD2 (TRPP2), and an inverse relationship between TCF7L2 and LEF-1, which were upregulated and downregulated respectively. The 1,000 Hz vibrations were sensed from the cells which upregulated PIEZO1 and TCF3, but they did not induce expression of genes that would indicate macrophage differentiation. The mRNA transcription profile in the cells stimulated with the combined treatment was comparable to that of the cells stimulated by the vitamin only. The 1,000 Hz vibrations slightly weakened the effect of the vitamin for the regulation of CD36 and HLA-DMB in the suspension cells, but without causing changes in the regulation patterns. The only exception was the upregulation of TCF3 in the suspension cells, which was influenced by the vibrations. In the adherent cells, the vitamin D3 cancelled the upregulating effect of the 1,000 Hz vibrations and downregulated TCF3. The vitamin also cancelled the upregulation of PIEZO1 gene by the 1,000 Hz vibrations in the combined treatment. Conclusion The mechanical stimulation with 1,000 Hz vibrations resulted in upregulation of PIEZO1 in THP-1 cells, but it did not affect the differentiation process which was investigated in this study. Vitamin D3 induced THP-1 macrophage differentiation and could potentially influence M2 polarization as observed by upregulation of CD36 and downregulation of HLA-DRA. In addition, in THP-1 cells undergoing the combined stimulation, the gene expression patterns were influenced by vitamin D3, which also ablated the effect of the mechanical stimulus on PIEZO1 upregulation.
A novel class of inhibitors that target SRSF10 and promote p53-mediated cytotoxicity on human colorectal cancer cells

Abstract The elevated expression of the splicing regulator SRSF10 in metastatic colorectal cancer (CRC) stimulates the production of the pro-tumorigenic BCLAF1-L splice variant. We discovered a group of small molecules with an aminothiazole carboxamide core (GPS167, GPS192 and others) that decrease production of BCLAF1-L. While additional alternative splicing events regulated by SRSF10 are affected by GPS167/192 in HCT116 cells (e.g. in MDM4, WTAP, SLK1 and CLK1), other events are shifted in a SRSF10-independent manner (e.g. in MDM2, NAB2 and TRA2A). GPS167/192 increased the interaction of SRSF10 with the CLK1 and CLK4 kinases, leading us to show that GPS167/192 can inhibit CLK kinases preferentially impacting the activity of SRSF10. Notably, GPS167 impairs the growth of CRC cell lines and organoids, inhibits anchorage-independent colony formation, cell migration, and promotes cytoxicity in a manner that requires SRSF10 and p53. In contrast, GPS167 only minimally affects normal colonocytes and normal colorectal organoids. Thus, GPS167 reprograms the tumorigenic activity of SRSF10 in CRC cells to elicit p53-dependent apoptosis.
Dairy management practices associated with multi-drug resistant fecal commensals and Salmonella in cull cows: a machine learning approach

Background Understanding the effects of herd management practices on the prevalence of multidrug-resistant pathogenic Salmonella and commensals Enterococcus spp. and Escherichia coli in dairy cattle is key in reducing antibacterial resistant infections in humans originating from food animals. Our objective was to explore the herd and cow level features associated with the multi-drug resistant, and resistance phenotypes shared between Salmonella, E. coli and Enterococcus spp. using machine learning algorithms. Methods Randomly collected fecal samples from cull dairy cows from six dairy farms in central California were tested for multi-drug resistance phenotypes of Salmonella, E. coli and Enterococcus spp. Using data on herd management practices collected from a questionnaire, we built three machine learning algorithms (decision tree classifier, random forest, and gradient boosting decision trees) to predict the cows shedding multidrug-resistant Salmonella and commensal bacteria. Results The decision tree classifier identified rolling herd average milk production as an important feature for predicting fecal shedding of multi-drug resistance in Salmonella or commensal bacteria. The number of culled animals, monthly culling frequency and percentage, herd size, and proportion of Holstein cows in the herd were found to be influential herd characteristics predicting fecal shedding of multidrug-resistant phenotypes based on random forest models for Salmonella and commensal bacteria. Gradient boosting models showed that higher culling frequency and monthly culling percentages were associated with fecal shedding of multidrug resistant Salmonella or commensal bacteria. In contrast, an overall increase in the number of culled animals on a culling day showed a negative trend with classifying a cow as shedding multidrug-resistant bacteria. Increasing rolling herd average milk production and spring season were positively associated with fecal shedding of multidrug- resistant Salmonella. Only six individual cows were detected sharing tetracycline resistance phenotypes between Salmonella and either of the commensal bacteria. Discussion Percent culled and culling rate reflect the increase in culling over time adjusting for herd size and were associated with shedding multidrug resistant bacteria. In contrast, number culled was negatively associated with shedding multidrug resistant bacteria which may reflect producer decisions to prioritize the culling of otherwise healthy but low-producing cows based on milk or beef prices (with respect to dairy beef), amongst other factors. Using a data-driven suite of machine learning algorithms we identified generalizable and distant associations between antimicrobial resistance in Salmonella and fecal commensal bacteria, that can help develop a producer-friendly and data-informed risk assessment tool to reduce shedding of multidrug-resistant bacteria in cull dairy cows.
LncRNA AC007255.1, an immune-related prognostic enhancer RNA in esophageal cancer

Background Growing evidence has suggested that enhancer RNAs (eRNAs), a set of long non-coding RNAs (lncRNAs) that were derived from active enhancer regions, play critical roles in regulating gene expression in human cancers. Nevertheless potential functions of eRNAs in esophageal cancer ESCA have not yet been expounded. Here, this study aimed to explore key prognostic eRNAs in ESCA. Methods LncRNAs that were transcribed from active enhancer regions were analyzed utilizing the PreSTIGE algorithm, followed by prediction of their target genes. Based on the ESCA RNA-seq data from the TANRIC database, overall survival (OS)-related eRNAs were determined. The correlation between AC007255.1 expression and various clinical traits of ESCA was calculated. Functional enrichment analysis was presented based on its co-expressed genes. Based on the TIMER database, we analyzed correlations between AC007255.1 expression and immune infiltration levels. qRT-PCR was utilized to validate the expression of AC007255.1 and PRR15 in ESCA and normal tissues. Results Totally, 2,695 lncRNAs were transcribed from active enhancer regions. Among them, 33 were significantly related to OS. AC007255.1 was a key eRNA. PRR15 was a target gene of AC007255.1 (correlation coefficient r = 0.936). Patients with high AC007255.1 expression indicated poor OS time. There were significant correlations between AC007255.1 expression and clinical characteristics like pathological TNM, grade and stage. AC007255.1 was closely related to tight junction and neutrophil activation involved in immune response. Moreover, AC007255.1 expression was related to the infiltration levels of B cell, dendritic cell and neutrophil. qRT-PCR results confirmed that AC007255.1 and PRR15 were both up-regulated in ESCA tissues, and there was a positive correlation between the two. Conclusion Our findings identified a novel immune-related eRNA AC007255.1 in ESCA, which could be a promising prognostic factor for ESCA.
Inhibition of Melanosis in Whiteleg Shrimp (Litopenaeus vannamei) during Refrigerated Storage Using Extracts of Different Avocado (Persea americana Mill.) By-Products

Melanosis in shrimp usually leads to reduction in its shelf life and quality, which causes a significant loss in economic value of shrimp products. This study reports potential applications of nine ethanolic extracts of by-products, i.e., peel and/or seed from three Vietnamese avocado varieties as effective inhibitors of melanosis in whiteleg shrimp. Six out of nine shrimp samples treated with the prepared extracts (0.025%, w/v) reduced melanosis and lipid oxidation more significantly as compared to those treated with sodium metabisulfite (SMS, 1.25%, w/v) and control groups (treated with water) during 8-day storage at 4°C (P<0.05). These six extracts had mean gray values ranging from 47.0±0.7 to 57.3±0.4% were lower than those treated with SMS (mean gray of 39.8±0.4%). The inhibition of melanosis and lipid oxidation in shrimp for these extracts could be attributed to their high content of polyphenols [total phenolic content (TPC) from 44.5±1.1 to 144.7±1.9 mg gallic acid equivalents/g dried weight] and strong antioxidant activities [including 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, ferric reducing antioxidant power (FRAP), and tyrosinase enzyme inhibition]. Pearson statistical analysis showed strong correlation for melanosis inhibition to TPC and DPPH scavenging (r>0.80) followed by tyrosinase inhibition and FRAP (r>0.50). The findings obtained from this study suggest potential utilization of avocado by-product extracts as safe and cheap natural alternatives to traditional sulfites for anti-melanosis and shelf life extension of whiteleg shrimp.
Chances and risks of sodium-glucose cotransporter 2 inhibitors in solid organ transplantation: A review of literatures

Solid organ transplantation offers life-saving treatment for patients with end-organ dysfunction. Patient survival and quality of life have improved over the past few decades as a result of pharmacological development, expansion of the donor pool, technological advances and standardization of practices related to transplantation. Still, transplantation is associated with cardiovascular complications, of which post-transplant diabetes mellitus (PTDM) is one of the most important. PTDM increases mortality, which is best documented in patients who have received kidney and heart transplants. PTDM results from traditional risk factors seen in patients with type 2 diabetes mellitus, but also from specific post-transplant risk factors such as metabolic side effects of immunosuppressive drugs, post-transplant viral infections and hypomagnesemia. Oral hypoglycaemic agents are the first choice for the treatment of type 2 diabetes mellitus in non-transplanted patients. However, the evidence on the safety and efficacy of oral hypoglycaemic agents in transplant recipients is limited. The favourable risk/benefit ratio, which is suggested by large-scale and long-term studies on new glucose-lowering drug classes such as glucagon-like peptide 1 receptor agonists and sodium-glucose cotransporter 2 inhibitors, makes studies warranted to assess the potential role of these agents in the management of PTDM.
Artemisia annua and artemisinins are ineffective against human Babesia microti and six Candida sp

Background: Artemisia annua L.is a well-established medicinal herb used for millennia to treat parasites and fever-related ailments caused by various microbes. Although effective against many infectious agents, the plant is not a miracle cure and there are infections where it has proved ineffective or limited. It is important to report those failures. Methods: Here artemisinin, artesunate and dried leaf slurries of A. annua were used daily for 6 days in vivo against Babesia microti in mice 2 days post infection at 100 µg artemisinin/kg body weight. Parasitemia was measure before and 15 days days post treatment. Artemisinin and extracts of A. annua also were tested in vitro against six Candida sp. at artemisinin concentrations up to 180 µM and growth measured after cultures were fed drugs once at different stages of growth and also after repeated dosing. Results: A. annua, artesunate, and artemisinin were ineffective in reducing or eliminating parasitemia in B. microti-infected mice treated at 100 µg artemisinin/kg body weight. Although the growth of exponential cultures of many of the tested Candida sp. was inhibited, the response was not sustained and both artemisinin and Artemisia were essentially ineffective at concentrations of artemisinin at up to 180 µM of artemisinin. Conclusions: Together these results show that artemisinin, its derivatives, and A. annua are ineffective against B. microti and at least six species of Candida.
Identification of miR-203a, mir-10a, and miR-194 as predictors for risk of lymphovascular invasion in head and neck cancers

Lymphovascular invasion (LVI) is an important prognostic indicator of lymph node metastasis and disease aggressiveness but clear molecular mechanisms mediating this in head and neck cancers (HNSC) remain undefined. To identify important microRNAs (miRNAs) in HNSC that associate with and are also predictive of increased risk of LVI, we used a combination of clustering algorithms, multiple regression analyses and machine learning approaches and analyzed miRNA expression profiles in the TCGA HNSC database. As the first step, we identified miRNAs with increased association with LVI as a binary variable. In order to determine whether the identified miRNAs would show functional clusters that are also indicative of increased risk for LVI, we carried out unsupervised as well as supervised clustering. Our results identified distinct clusters of miRNAs that are predictive of increased LVI. We further refined these findings using a Random forest approach, and miR-203a-3p, mir-10a-5p, and miR-194-5p to be most strongly associated with LVI. Pathway enrichment analysis showed these miRNAs targeted genes involved in Hippo signaling and fatty acid oxidation pathways that are mediators of lymph node metastasis. Specific association was also identified between the miRNAs associated with LVI and expression of several lymphangiogenic genes that could be critical for determination of therapeutic strategies.
Phenotypic characterization and principal component analyses of indigenous chicken breeds in Indonesia

Background and Aim: Understanding the phenotypic characteristics of indigenous livestock breeds is essential for their utilization and conservation. This study aimed to characterize indigenous chicken breeds in Indonesia based on phenotypic traits. Materials and Methods: Data on eight qualitative and 12 quantitative traits were recorded for 250 chickens from six breeds: Black Kedu, Gaga, Merawang, Nunukan, Pelung, and Sentul. Data were analyzed using descriptive statistics and one-way analysis of variance to test the effect of breed on observed traits. Moreover, principal component analysis (PCA) was conducted separately for each chicken breed. Data on quantitative traits were subjected to Kaiser-Meyer-Olkin, which was computed to test the sampling adequacy and the pattern of correlation among the traits, and Bathlett’s tests were used to assess the validity of the factor analysis of each of the datasets and determine whether the partial correlations among traits were small. Results: We found considerable phenotypic variation in both qualitative and quantitative traits among indigenous chicken breeds. Multicolored plumage (96.40%), wild plumage (39.20%), gold feather flick (51.20%), yellow shank (36.80%), single comb (80.80%), red comb (94.80%), red earlobe (77.60%), and orange eyes (61.60%) were the most common features in the indigenous chickens. In addition, breed had a significant effect on all the quantitative traits that were analyzed (p<0.05). There were higher mean values for all quantitative traits for Pelung chickens than other chickens. In addition, the overall mean values for all quantitative traits in Merawang chicken were intermediate between Pelung chickens and Black Kedu, Gaga, and Nunukan chickens. The PCA showed two principal factors extracted that accounted for 77.80% and 78.38% of the total variance in the original variables for males and females, respectively. Conclusion: In general, body weight and body measurements, except wattle length, were loaded in PC1 as the primary factors responsible for the variation. The phenotypic variation observed in indigenous chickens in Indonesia could provide valuable basic information for the design of selection and genetic improvement programs.
Molecular phylogenetic assessment of Spirobranchus kraussii-complex (Annelida: Serpulidae) from the Japanese Archipelago

Spirobranchus kraussii (Annelida: Serpulidae) was recognized as being widely distributed both in the Pacific and Atlantic Oceans. However, the sampling records far from its type locality (South Africa) have been questioned. Actually, recent molecular phylogenetic studies showed that S. kraussii contains genetically distinct species. In this study, we performed molecular phylogenetic analyses of S. cf. kraussii collected from Japan using the nucleotide sequences of a mitochondrial gene and two nuclear genes. Three lineages were recovered within Spirobranchus kraussii-complex in Japan, and one (Spirobranchus sp. 6) showed moderate genetic difference (approximately 4%) in the mitochondrial cytb gene sequence from Spirobranchus sp. 1, an undescribed sequenced species from Honshu Island, Japan. However, the nucleotide sequences of the 18S rRNA gene and ITS2 region were nearly indistinguishable. The other lineage was clearly distinct from the other previously sequenced species and is thus considered to be another distinct species of this species complex (Spirobranchus sp. 5). Although detailed morphological assessment of these lineages is necessary to define their taxonomic status, the present study provided further implications for the species diversity within the S. kraussii-complex.
Feasibility and Outcomes of Multivisceral Resection in Locally Advanced Colorectal Cancer: Experience of a Tertiary Cancer Center in North-East India

Purpose Locally advanced colorectal cancer may require an en bloc resection of surrounding organs or structures to achieve complete tumor removal. This decision must weigh the risk of complications of multivisceral resection against the potential survival benefit. The purpose of this study is to review a single-center experience of feasibility of en bloc multivisceral resections for locally advanced colorectal carcinoma and to examine the effect of surgical experience on immediate outcome and rate of R0 resections. Methods This is a study of 27 patients who underwent multivisceral resection for locally advanced colorectal carcinoma which was performed at our institute from January 2016 to December 2019. Among the 27 patients aged between 21 and 76 years (mean age, 48.67±7.3 years), 13 were males and 14 were females. Overall 18 patients had primary colon carcinoma and 9 had primary rectal carcinoma. All rectal cancer patients received neoadjuvant chemoradiation. All patients underwent surgery with curative intent. All patients underwent open surgery of which 66.7% underwent colectomy, 14.8% underwent anterior resection, 11.1% underwent Miles procedure, and 7.4% underwent pelvic exenteration. Results The mean operative time was 268.14±72.2 minutes and the median amount of blood units transfused was 2.07 units. The mean hospital stay was 13.67±3.4 days. Histologically, 44.4% of patients had well-differentiated adenocarcinoma and 55.6% had moderately differentiated adenocarcinoma. The final histopathological examinatio n revealed malignant infiltration of the adjacent organs in 19/27 patients (70.4%). Pathological complete response was seen in 2 patients. R0 resection rate achieved was 96.3%. Lymph node metastasis was seen in 66.7% of patients with colon cancer and 11.1% with rectal cancer with overall mean number of harvested lymph nodes being 12.44±3.01. Postoperative complications were identified in 7 patients (25.9%), while mortality was seen in 2 (7.4%). Conclusion Multivisceral resection for advanced colorectal cancer invading into the adjacent organ may be performed with acceptable morbidity and mortality.