Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth Patterns of Indonesian Infants with Cow's Milk Allergy and Fed with Soy-Based Infant Formula

Purpose The use of soy-based infant formula has increased widely in infants with cow's milk allergy (CMA). This study aimed to provide evidence on the growth pattern of CMA infants fed with soy-based infant formula in an Indonesian setting. Methods A multi-site, intervention study was conducted among full-term and normal birth weight CMA infants. Within six months, the subjects were provided with a soy-based infant formula. Weight, height, and head circumference were measured at baseline, weeks 4, 8, 12, 16, 20, and 24. Adverse events were recorded by scoring atopic dermatitis and symptom-based clinical scores. Results Based on the World Health Organization growth chart, we found that most of subjects had normal nutritional status for weight-for-age, length-for-age, weight-for-length, and head-circumference-for-age. There were statistically significant differences between baseline and end-line for weight-for-age, length-for-age, weight-for-length, and head circumference-for-age nutritional status. No allergic symptoms or intolerance toward soy formula were observed at the end of the intervention period. Conclusion These results show that infants fed with soy-based infant formula have a normal pattern of growth.
Frequency of CDH1 Germline Mutations in Non-Gastric Cancers

Simple Summary Diffuse gastric cancer is the hallmark of the hereditary diffuse gastric cancer syndrome related with the E-cadherin germline mutations. Other cancers (non-gastric) are described in association with the CDH1 gene germline alterations. In this study, we aimed to assess the overall frequency of CDH1 mutations in non-gastric tumors reported in literature so far. Abstract Hereditary Diffuse Gastric Cancer (HDGC) is a complex inherited syndrome caused by CDH1 germline mutations. DGC is the hallmark cancer of this genetic predisposition, but several other cancers are associated with these CDH1 mutations. In this review, we revised all studies reporting CDH1 mutations in non-GC patients. The selected studies included: (a) families aggregating with GC and other cancers, both, and (b) families presenting only non-gastric tumors association. Among non-gastric tumors, our results show that CDH1 mutations are most frequently identified in breast cancer. The frequency of missense mutations is higher in the non-GC group, as the age at diagnosis in this group. Moreover, the predominant CDH1 mutation affects the extracellular domain. Our data suggest that CDH1 genetic testing should be considered also in other cancers, especially breast tumors.
Dietary Bioactive Peptide Alanyl-Glutamine Attenuates Dextran Sodium Sulfate-Induced Colitis by Modulating Gut Microbiota

Inflammatory bowel disease (IBD) is a chronic intestinal disorder threatening human health. Di-peptide alanyl-glutamine (Ala-Gln) has various beneficial effects on gut health. However, its role and functional mechanism in treating IBD are still not clear. Therefore, the protective effects of Ala-Gln and glutamine (Gln) on dextran sulfate sodium- (DSS-) induced colitic mice were investigated in this study. The results showed that oral supplementation of Ala-Gln or Gln significantly attenuated the colitis symptoms in mice, including body weight loss, colon length, disease activity index, histological scores, and tissue apoptosis. The concentrations of interleukin- (IL-) 1β, IL-6, tumor necrosis factor-α, and myeloperoxidase were significantly decreased, while the concentrations of immunoglobulins (IgA, IgG, and IgM) and superoxide dismutase were significantly increased by Ala-Gln or Gln supplementation. The expression of occludin and peptide transporter 1 (PepT1) was significantly increased by Ala-Gln or Gln. Interestingly, Ala-Gln had better beneficial effects than Gln in alleviating colitis. In addition, 16S rDNA sequencing showed that the DSS-induced shifts of the microbiome (community diversity, evenness, richness, and composition) in the mouse colon were restored by Gln and Ala-Gln, including Lactobacillus, Bacteroides_acidifaciens, Bacteroidales, Firmicutes, Clostridia, Helicobacter, and Bacteroides. Correspondingly, the functions of the microflora metabolism pathways were also rescued by Ala-Gln, including fatty acid metabolism, membrane transporters, infectious diseases, and immune system. In conclusion, the results revealed that Ala-Gln can prevent colitis through PepT1, enhancing the intestinal barrier and modulating gut microbiota and microflora metabolites.
MiR-378b Modulates Chlamydia-Induced Upper Genital Tract Pathology

Genital Chlamydia trachomatis infection causes severe reproductive pathologies such as salpingitis and pelvic inflammatory disease that can lead to tubal factor infertility. MicroRNAs (miRNAs) are evolutionarily conserved regulators of mammalian gene expression in development, immunity and pathophysiologic processes during inflammation and infection, including Chlamydia infection. Among the miRNAs involved in regulating host responses and pathologic outcome of Chlamydia infection, we have shown that miR-378b was significantly differentially expressed during primary infection and reinfection. In this study, we tested the hypothesis that miR-378b is involved in the pathological outcome of Chlamydia infection. We developed miR-378b knockout mice (miR-378b−/−) using Crispr/Cas and infected them along with their wild-type (WT) control with Chlamydia to compare the infectivity and reproductive pathologies. The results showed that miR-378b−/− mice were unable to clear the infection compared to WT mice; also, miR-378b−/− mice exhibited a relatively higher Chlamydia burden throughout the duration of infection. However, gross pathology results showed that miR-378b−/− mice had significantly reduced uterine dilatations and pathologic lesions after two infections compared to WT mice. In addition, the pregnancy and fertility rates for infected miR-378b−/− mice showed protection from Chlamydia-induced infertility with fertility rate that was comparable to uninfected WT mice. These results are intriguing as they suggest that miR-378b is important in regulating host immune responses that control Chlamydial replication and drive the inflammation that causes complications such as infertility. The finding has important implications for biomarkers of Chlamydial complications and targets for prevention of disease.
Treatment of Rare Mutations in Patients with Lung Cancer

Lung cancer is a worldwide prevalent malignancy. This disease has a low survival rate due to diagnosis at a late stage challenged by the involvement of metastatic sites. Non-small-cell lung cancer (NSCLC) is presented in 85% of cases. The last decade has experienced substantial advancements in scientific research, leading to a novel targeted therapeutic approach. The newly developed pharmaceutical agents are aimed towards specific mutations, detected in individual patients inflicted by lung cancer. These drugs have longer and improved response rates compared to traditional chemotherapy. Recent studies were able to identify rare mutations found in pulmonary tumors. Among the gene alterations detected were mesenchymal epithelial transition factor (MET), human epidermal growth factor 2 (HER2), B-type Raf kinase (BRAF), c-ROS proto-oncogene (ROS1), rearranged during transfection (RET) and neurotrophic tyrosine kinase (NTRK). Ongoing clinical trials are gaining insight onto possible first and second lines of medical treatment options intended to enable progression-free survival to lung cancer patients.
Aqueous Blackcurrant Extract Improves Insulin Sensitivity and Secretion and Modulates the Gut Microbiome in Non-Obese Type 2 Diabetic Rats

This study was undertaken to determine whether aqueous blackcurrant extracts (BC) improve glucose metabolism and gut microbiomes in non-obese type 2 diabetic animals fed a high-fat diet and to identify the mechanism involved. Partially pancreatectomized male Sprague–Dawley rats were provided a high-fat diet containing 0% (control), 0.2% (L-BC; low dosage), 0.6% (M-BC; medium dosage), and 1.8% (H-BC; high dosage) blackcurrant extracts; 0.2% metformin (positive-C); plus 1.8%, 1.6%, 1.2%, 0%, and 1.6% dextrin, specifically indigestible dextrin, daily for 8 weeks. Daily blackcurrant extract intakes were equivalent to 100, 300, and 900 mg/kg body weight (bw). After a 2 g glucose or maltose/kg bw challenge, serum glucose and insulin concentrations during peak and final states were obviously lower in the M-BC and H-BC groups than in the control group (p < 0.05). Intraperitoneal insulin tolerance testing showed that M-BC and H-BC improved insulin resistance. Hepatic triglyceride deposition, TNF-α expression, and malondialdehyde contents were lower in the M-BC and H-BC groups than in the control group. Improvements in insulin resistance in the M-BC and H-BC groups were associated with reduced inflammation and oxidative stress (p < 0.05). Hyperglycemic clamp testing showed that insulin secretion capacity increased in the acute phase (2 to 10 min) in the M-BC and H-BC groups and that insulin sensitivity in the hyperglycemic state was greater in these groups than in the control group (p < 0.05). Pancreatic β-cell mass was greater in the M-BC, H-BC, and positive-C groups than in the control group. Furthermore, β-cell proliferation appeared to be elevated and apoptosis was suppressed in these three groups (p < 0.05). Serum propionate and butyrate concentrations were higher in the M-BC and H-BC groups than in the control group. BC dose-dependently increased α-diversity of the gut microbiota and predicted the enhancement of oxidative phosphorylation-related microbiome genes and downregulation of carbohydrate digestion and absorption-related genes, as determined by PICRUSt2 analysis. In conclusion, BC enhanced insulin sensitivity and glucose-stimulated insulin secretion, which improved glucose homeostasis, and these improvements were associated with an incremental increase of the α-diversity of gut microbiota and suppressed inflammation and oxidative stress.
Upregulation of Chemoresistance by Mg2+ Deficiency through Elevation of ATP Binding Cassette Subfamily B Member 1 Expression in Human Lung Adenocarcinoma A549 Cells

Several anticancer drugs including cisplatin (CDDP) induce hypomagnesemia. However, it remains fully uncertain whether Mg2+ deficiency affects chemosensitivity of cancer cells. Here, we investigated the effect of low Mg2+ concentration (LM) on proliferation and chemosensitivity using human lung adenocarcinoma A549 cells. Cell proliferation was reduced by continuous culture with LM accompanied with the elevation of G1 phase proportion. The amounts of reactive oxygen species (ROS) and stress makers such as phosphorylated-ataxia telangiectasia mutated and phosphorylated-p53 were increased by LM. Cell injury was dose-dependently increased by anticancer drugs such as CDDP and doxorubicin (DXR), which were suppressed by LM. Similar results were obtained by roscovitine, a cell cycle inhibitor. These results suggest that LM induces chemoresistance mediated by ROS production and G1 arrest. The mRNA and protein levels of ATP binding cassette subfamily B member 1 (ABCB1) were increased by LM and roscovitine. The LM-induced elevation of ABCB1 and nuclear p38 expression was suppressed by SB203580, a p38 MAPK inhibitor. PSC833, an ABCB1 inhibitor, and SB203580 rescued the sensitivity to anticancer drugs. In addition, cancer stemness properties were suppressed by SB203580. We suggest that Mg2+ deficiency reduces the chemotherapy sensitivity of A549 cells, although it suppresses cell proliferation.
Characterization of Kefir Produced in Household Conditions: Physicochemical and Nutritional Profile, and Storage Stability

Kefir, a traditional fermented food, has numerous health benefits due to its unique chemical composition, which is reflected in its excellent nutritional value. Physicochemical and microbial composition of kefir obtained from fermented milk are influenced by the type of the milk, grain to milk ratio, time and temperature of fermentation, and storage conditions. It is crucial that kefir characteristics are maintained during storage since continuous metabolic activities of residual kefir microbiota may occur. This study aimed to examine the nutritional profile of kefir produced in traditional in use conditions by fermentation of ultra-high temperature pasteurized (UHT) semi-skimmed cow milk using argentinean kefir grains and compare the stability and nutritional compliance of freshly made and refrigerated kefir. Results indicate that kefir produced under home use conditions maintains the expected characteristics with respect to the physicochemical parameters and composition, both after fermentation and after refrigerated storage. This work further contributes to the characterization of this food product that is so widely consumed around the world by focusing on kefir that was produced in a typical household setting.
Properties of Silicone Rubber-Based Composites Reinforced with Few-Layer Graphene and Iron Oxide or Titanium Dioxide

The increasing demand for polymer composites with novel or improved properties requires novel fillers. To meet the challenges posed, nanofillers such as graphene, carbon nanotubes, and titanium dioxide (TiO2) have been used. In the present work, few-layer graphene (FLG) and iron oxide (Fe3O4) or TiO2 were used as fillers in a room-temperature-vulcanized (RTV) silicone rubber (SR) matrix. Composites were prepared by mixing RTV-SR with nanofillers and then kept for vulcanization at room temperature for 24 h. The RTV-SR composites obtained were characterized with respect to their mechanical, actuation, and magnetic properties. Fourier-transform infrared spectroscopy (FTIR) analysis was performed to investigate the composite raw materials and finished composites, and X-ray photoelectron spectroscopy (XPS) analysis was used to study composite surface elemental compositions. Results showed that mechanical properties were improved by adding fillers, and actuation displacements were dependent on the type of nanofiller used and the applied voltage. Magnetic stress-relaxation also increased with filler amount and stress-relaxation rates decreased when a magnetic field was applied parallel to the deformation axes. Thus, this study showed that the inclusion of iron oxide (Fe3O4) or TiO2 fillers in RTV-SR improves mechanical, actuation, and magnetic properties.
Landscape Enhancements in Apple Orchards: Higher Bumble Bee Queen Species Richness, but No Effect on Apple Quality

Simple Summary Pollinators are essential to produce fruits in apple production. Bumble bees are among the most effective pollinators in orchards during the blooming season, yet they are often threatened by the high levels of pesticide use in apple production. Hedgerows and flower strips are infrequently sprayed by pesticides and are thus potentially good shelter for bumble bees. This study evaluated the influence of landscaping in the form of hedgerows and flower strips on the abundance and number of bumble bee species found in apple orchards. The number of bumble bee species found in orchards with hedgerows or flower strips was higher than in orchards without such landscape enhancements. Similarly, three species were more abundant in orchards with landscaping than orchards without those enhancements. Our work provides additional evidence that landscaping in the form of hedgerows and/or flower strips improves bumble bee presence in apple orchards and should therefore be considered as a means to enhance and ensure pollination within farms. Abstract Bumble bees are among the most effective pollinators in orchards during the blooming period, yet they are often threatened by the high levels of pesticide use in apple production. This study aimed to evaluate the influence of landscape enhancements (e.g., hedgerows, flower strips) on bumble bee queens in apple orchards. Bumble bee queens from 12 orchards in southern Québec (Canada) were marked, released, and recaptured in the springs and falls of 2017 to 2019. Half of the 12 orchards had landscape enhancements. Apples were harvested in 2018 and 2019 to compare their quality (weight, diameter, sugar level, and seed number) in sites with and without landscape enhancements. Species richness, as well as the occurrence of three species out of eight, was higher in orchards with landscape enhancements than in orchards without such structures. The occurrence of Bombus ternarius was lower in orchards with high levels of pesticide use. Apples had fewer seeds when collected in orchards with landscape enhancements and were heavier in orchards that used more pesticides. Our work provides additional evidence that landscape enhancements improve bumble bee presence in apple orchards and should therefore be considered as a means to enhance pollination within farms.
Update on Metabolic Bariatric Surgery for Morbidly Obese Adolescents

Despite worldwide public attention and intense medical efforts, the prevalence of severe morbid obesity in children and adolescents is still rising. Similar to adults, excess adipose tissue triggers multiple immunological and metabolic pathways leading to serious co-morbidities such as impaired glucose tolerance or even type 2 diabetes (T2D), dyslipidemia, arterial hypertension, non-alcoholic fatty liver disease, and hyperuricemia. The management of severe childhood obesity requires a life-long multidisciplinary approach with a combination of lifestyle changes, nutrition, and medications. Standardized life-style intervention programs remain the first-line treatment for morbid obese children and adolescents, but unfortunately reveal limited long-term success. In such cases, metabolic bariatric surgery (MBS) has evolved from being a controversial issue to being included in distinct recommendations. According to the American Society for Metabolic and Bariatric Surgery (ASMBS) Pediatric Committee, indications for bariatric surgery in adolescence must follow very strict criteria. Adolescents with class II obesity (BMI > 120% of the 95th percentile) and a diagnosed co-morbidity or with class III obesity (BMI ≥ 140% of the 95th percentile) should be considered for MBS. These interventions represent high-risk operations, and adolescents should be treated in specialized, multidisciplinary high-volume obesity centers with long-term follow-up programs. The Roux-en-Y gastric bypass (RYGB) remains the gold standard of all malabsorptive procedures. Laparoscopic sleeve gastrectomy (LSG), which the authors pioneered as a stand-alone procedure in morbidly obese adolescents in 2008, has become the most commonly performed operation in morbidly obese adolescents at present. Recent literature proves that MBS is safe and effective in morbidly obese adolescents. Mid-term data have revealed significant improvement or even resolution of major co-morbidities. Thus, MBS for the treatment of morbidly obese adolescents has evolved from being a controversial issue to being included in distinct recommendations by several medical societies as a therapeutic strategy to reduce severe co-morbidities potentially causing end-organ damage in adulthood.
Percutaneous Endoscopic Gastrostomy Tube Insertion in Patient With Situs Inversus Totalis

Situs inversus totalis (SIT) is a rare congenital condition in which the abdominal and thoracic organs are completely reversed from right to left, and their diagnosis is usually incidental. However, patients with SIT need a comprehensive radiological evaluation before undertaking any invasive procedures. Percutaneous endoscopic gastrostomy (PEG) insertion is an effective procedure for enteral feeding in patients with difficulty swallowing. Many post-procedural complications have been reported after the PEG procedure. We performed PEG insertion in an 85-year-old Qatari SIT patient, who was admitted to the hospital as a case of aspiration pneumonia and on nasogastric feeding tube (NGT). The procedure was started while the patient was in left lateral decubitus position as in normal anatomy patients after careful examination and in accordance with the general principles of PEG insertion. No complications were seen, neither intraoperative nor postoperative in two months follow-up. We suggest that in a patient with SIT, PEG insertion can be performed while the patient is in left decubitus position with no additional risk or extra intraoperative time if the pre-operative anatomical position of vital organs is carefully evaluated.
Cross-Predicting Essential Genes between Two Model Eukaryotic Species Using Machine Learning

Experimental studies of Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular and cellular processes in metazoans at large. Since the publication of their genomes, functional genomic investigations have identified genes that are essential or non-essential for survival in each species. Recently, a range of features linked to gene essentiality have been inferred using a machine learning (ML)-based approach, allowing essentiality predictions within a species. Nevertheless, predictions between species are still elusive. Here, we undertake a comprehensive study using ML to discover and validate features of essential genes common to both C. elegans and D. melanogaster. We demonstrate that the cross-species prediction of gene essentiality is possible using a subset of features linked to nucleotide/protein sequences, protein orthology and subcellular localisation, single-cell RNA-seq, and histone methylation markers. Complementary analyses showed that essential genes are enriched for transcription and translation functions and are preferentially located away from heterochromatin regions of C. elegans and D. melanogaster chromosomes. The present work should enable the cross-prediction of essential genes between model and non-model metazoans.
The Effect of Ageing on Clinical, Hormonal and Sonographic Features Associated with PCOS—A Long-Term Follow-Up Study

The knowledge of polycystic ovary syndrome (PCOS) natural history is limited. Our objective was to assess the effect of aging on clinical, hormonal and sonographic ovarian PCOS features and additionally to identify parameters that impact the course of PCOS. A secondary aim was to supply additional information on the reproductive outcome in women with previously diagnosed PCOS. A longitudinal cohort study with a median follow-up of 120.9 months was conducted, and 31 Caucasian women previously diagnosed with PCOS according to the Rotterdam criteria were re-examined at a median age of 35. Clinical examinations; transvaginal ultrasound scans; and lipid, E-selectin and sex hormone assessments were performed at the beginning and at the end of the follow-up. It was observed that menstrual cycles became regular and sonographic morphology of ovaries was normalized in 55% and 49% of the participants, respectively (all p < 0.05). At the final assessment, 55% of the women no longer met the criteria for PCOS (p < 0.05). The age, follicle-stimulating hormone (FSH) and E-selectin assessed at the baseline were the most important predictors of the PCOS persistence into later years (respectively, OR = 0.84, OR = 0.39, OR = 1.08, all p < 0.05). Ninety-five percent of the patients who had ever been trying to conceive became pregnant a minimum of once. The women with persistent PCOS had worse metabolic and reproductive parameters compared to the women with resolved PCOS. Positive correlations were found between the number of miscarriages and ovarian volume, LH, androstenedione, 17-hydroxyprogesterone and an increase in E-selectin during the follow-up (R = 0.46, R = 0.59, R = 0.54, R = 0.49, R = 0.47, all p < 0.05). In conclusion, progressing from the third to the fourth decade is connected with a reduction in PCOS features, which seems to have a great impact on fertility of women with a previous diagnosis of PCOS. FSH and E-selectin, as determined at the initial PCOS diagnosis, had an impact on the disappearance of the syndrome years after.