Miracle-dz/UniFAR-FTUs huggingface dataset:
Insights from Bacteroides Species in Children with Type 1 Diabetes

In our previous study the enrichment of the intestinal proteome of type 1 diabetes (T1D) children with Bacteroides proteins was observed, which led us to our current study that aimed to isolate and characterize Bacteroides species from fecal samples of T1D and control children. Repetitive sequence-based PCR (rep-PCR) was used for typing the isolated Bacteroides species. The antibiotic susceptibility and mucinolytic activity of the isolates was determined. The quantification of specific bacterial groups in the fecal samples was determined by qPCR. The ability to adhere and invade the human colonic cell line HT29-MTX-E12 of strains of P. dorei, B. uniformis and P. distasonis was determined and their whole genome sequencing was performed. The results showed similar numbers of Bacteroides species in T1D and control samples, but unique Bacteroides species and a higher recovery of P. distasonis from T1D samples was observed. Rep-PCR grouped the different Bacteroides species, but no discrimination by origin was achieved. T1D children showed a significant increase in Proteobacteria and a depletion in Lactobacillus sp. All tested P. dorei, B. uniformis and P. distasonis were able to adhere to HT29-MTX-E12 cells but significant differences (p < 0.05) in the ability to invade was observed. The highest ability to invade was exhibited by P. distasonis PtF D14MH1 and P. dorei PtFD16P1, while B. uniformis strains were unable to invade. The damage to tight junctions was also observed. The presence of Lactobacillus sp. inhibited the invasion ability of P. distasonis PtF D14MH1 but not P. dorei PtFD16P1. Sequences of agonist peptides of the human natural preproinsulin and the insulin B chain insB:9-23 peptide mimics were identified. The results reported in our study stresses the continued efforts required to clarify the link between T1D and gut microbiota.
Associations between Maternal Iron Supplementation in Pregnancy and Changes in Offspring Size at Birth Reflect Those of Multiple Micronutrient Supplementation

It was previously observed that in a population of a high-income country, dietary multiple micronutrient supplementation in pregnancy was associated with an increased risk of gestational diabetes (GDM) and increased offspring size at birth. In this follow-up study, we investigated whether similar changes are observed with dietary iron supplementation. For this we used the prospective Cambridge Baby Growth Study with records of maternal GDM status, nutrient supplementation, and extensive offspring birth size measurements. Maternal iron supplementation in pregnancy was associated with GDM development (risk ratio 1.67 (1.01–2.77), p = 0.048, n = 677) as well as offspring size and adiposity (n = 844–868) at birth in terms of weight (β’ = 0.078 (0.024–0.133); p = 0.005), head circumference (β’ = 0.060 (0.012–0.107); p = 0.02), body mass index (β’ = 0.067 (0.014–0.119); p = 0.01), and various skinfold thicknesses (β’ = 0.067–0.094; p = 0.03–0.003). In a subset of participants for whom GDM statuses were available, all these associations were attenuated by adjusting for GDM. Iron supplementation also attenuated the associations between multiple micronutrient supplementation and these same measures. These results suggest that iron supplementation may mediate the effects associated with multiple micronutrient supplementation in pregnancy in a high-income country, possibly through the increased risk of developing GDM.
Effect of Low FODMAPs Diet on Irritable Bowel Syndromes: A Systematic Review and Meta-Analysis of Clinical Trials

We conducted a meta-analysis exploring the effect of a low fermentable oligo-, di-, monosaccharides, and polyols diet (LFD) on the overall symptoms, quality of life, and stool habits of irritable bowel syndrome (IBS) patients. The meta-analysis was performed using a random-effects method. The effect size was presented as weighted standardized mean difference (SMD) and 95% confidence interval (CI). Subgroup analyses were conducted to determine the potential effects of covariates on the outcome. Twenty-two papers were included. The LFD group showed a moderate reduction in symptom severity and a slight improvement in quality of life compared to the control group (SMD, −0.53 and 0.24; 95% CI, −0.68, −0.38 and 0.02, 0.47, respectively). IBS symptom improvement was consistent between subgroups stratified according to proportions of female patients, study durations, IBS subtypes, assessment methods, and control interventions. Three studies regarding stool habits change in IBS-D patients showed a significant decrease in stool frequency (mean differences [MD], −5.56/week; 95% CI, −7.40, −3.72) and a significant improvement in stool consistency (MD, −0.86; 95% CI, −1.52, −0.19) in the LFD group compared to the control group. This is the most updated meta-analysis including studies that adopted diverse control interventions such as dietary interventions, supplementation, habitual diets, and lifestyle changes.
Molecular Diagnosis of Leishmaniasis: Quantification of Parasite Load by a Real-Time PCR Assay with High Sensitivity

Real-time PCR was developed to quantify Leishmania infantum kinetoplast DNA and optimized to achieve a sensitivity of 1 parasite/mL. For this purpose, we cloned the conserved kDNA fragment of 120 bp into competent cells and correlated them with serial dilutions of DNA extracted from reference parasite cultures calculating that a parasite cell contains approximately 36 molecules of kDNA. This assay was applied to estimate parasite load in clinical samples from visceral, cutaneous leishmaniasis patients and infected dogs and cats comparing with conventional diagnosis. The study aimed to propose a real-time PCR for the detection of Leishmania DNA from clinical samples trying to solve the diagnostic problems due to the low sensitivity of microscopic examination or the low predictive values of serology and resolve problems related to in vitro culture. The quantitative PCR assay in this study allowed detection of Leishmania DNA and quantification of considerably low parasite loads in samples that had been diagnosed negative by conventional techniques. In conclusion, this quantitative PCR can be used for the diagnosis of both human, canine and feline Leishmaniasis with high sensitivity and specificity, but also for evaluating treatment and the endpoint determination of leishmaniasis.
Multiple Human Papilloma Virus (HPV) Infections Are Associated with HSIL and Persistent HPV Infection Status in Korean Patients

Infections with multiple human papilloma virus (HPV) types have been reported, but their role in cervical carcinogenesis has not been fully elucidated. In this study, 236 cases with multiple HPV infection were examined and compared to 180 cases with single HPV infection. HPV genotyping was performed with cervico-vaginal swab specimens using multiplex (real-time) polymerase chain reaction (PCR). In multiple HPV infection, the most prevalent HPV genotype was HPV 53, followed by HPV 16, 58, 52, and 68. HPV 33, 35, 39, 51, 52, 53, 58, and 68 were high-risk-HPV (HR-HPV) genotypes that were more frequently detected in multiple HPV infection compared to that in single HPV infection. The association between multiple HPV infection and high-grade SIL (HSIL) was significantly stronger compared to that of single HPV infection and HSIL (p = 0.002). Patients with multiple HPV infection displayed persistent and longer duration of the HPV infection compared to patients with single HPV infection. Multiple HPV infections have distinct clinicopathologic characteristics. Since it is associated with persistent HPV infection, HSIL, and different HR-HPV strains in contrast to single HPV infection, the presence of multiple HPV infection should be reported; close follow up is warranted.
Molecular Detection of Soil-Transmitted Helminths and Enteric Protozoa Infection in Children and Its Association with Household Water and Sanitation in Manhiça District, Southern Mozambique

Intestinal parasite infections can have detrimental health consequences in children. In Mozambique, soil-transmitted helminth (STH) infections are controlled through mass drug administration since 2011, but no specific control program exists for enteric protozoa. This study evaluates STH and protozoan infections in children attending healthcare in Manhiça district, Southern Mozambique, and its association with water and sanitation conditions. We conducted a cross-sectional study in children between 2 and 10 years old in two health centers (n = 405). A stool sample and metadata were collected from each child. Samples were analyzed by multi-parallel real-time quantitative PCR (qPCR). We fitted logistic regression-adjusted models to assess the association between STH or protozoan infection with household water and sanitation use. Nineteen percent were infected with at least one STH and 77.5% with at least one enteric protozoon. qPCR detected 18.8% of participants with intestinal polyparasitism. Protected or unprotected water well use showed a higher risk for at least one protozoan infection in children (OR: 2.59, CI: 1.01–6.65, p-value = 0.010; OR: 5.21, CI: 1.56–17.46, p-value = 0.010, respectively) compared to household piped water. A high proportion of children had enteric protozoan infections. Well consumable water displayed high risk for that.
Characterization of RIN Isoforms and Their Expression in Tomato Fruit Ripening

Ripening of tomato fleshy fruit is coordinated by transcription factor RIN, which triggers ethylene and carotenoid biosynthesis, sugar accumulation, and cell wall modifications. In this study, we identified and characterized complete sequences of the RIN chromosomal locus in two tomato Solanum lycopersicum cultivars, its rin/RIN genotype, and three wild green-fruited species differing in fruit color and composition. The results reveal that S. lycopersicum cultivars and some wild species (S. pennellii, S. habrochaites, and S. huaylasense) had a 3′-splicing site enabling the transcription of RIN1i and RIN2i isoforms. The other wild species (S. arcanum, S. chmielewskii, S. neorickii, and S. peruvianum) had a 3′-splicing site only for RIN2i, which was consistent with RIN1i and RIN2i expression patterns. The genotype rin/RIN, which had an extended 3′-terminal deletion in the rin allele, mainly expressed the chimeric RIN–MC transcript, which was also found in cultivars (RIN/RIN). The RIN1, but not RIN2, protein is able to induce the transcription of the reporter gene in the Y2H system, which positively correlated with the transcription profile of RIN1i and RIN target genes. We suggest that during fruit ripening, RIN1 activates ripening-related genes, whereas RIN2 and RIN–MC act as modulators by competing for RIN-binding sites in gene promoters, which should be confirmed by further studies on the association between RIN-splicing mechanisms and tomato fruit ripening.
Accuracy of Dose Administered to Children Using Off-Labelled or Unlicensed Oral Dosage Forms

The pediatric population suffers from a lack of age-appropriate medicines leading to unsafe situations when off-labelled or unlicensed drugs are used. Assessing the best option to administrate medicines when manipulations are required is essential in order to improve child care. This study aimed to compare the accuracy of the administered dose provided by three dosage forms and their techniques of administration. Different techniques of administration were assessed, covering three oral dosage forms (commercially available tablets, capsules, oral suspensions) using two APIs not available in a children-adapted dosage form. Techniques of administration were simulated and administered doses were determined using HPLC-UV. Means were compared to the target dose while distributions of doses were compared between each technique. For both APIs, mean administered doses obtained with capsules and tablets were significantly different from the target dose, whereas there was no statistical difference with oral suspensions. Distributions of doses showed significant difference between the three dosage forms. This study demonstrates that manipulations of solid oral dosage forms provide dramatic underdosing leading to unsafe situations. Compounded oral suspension is the best option to avoid underdosing and dose variation. This solution should be prioritized when age-appropriate commercial medicines are not available.
Experimental Setting for Applying Mechanical Stimuli to Study the Endothelial Response of Ex Vivo Vessels under Realistic Pathophysiological Environments

This paper describes the design, construction and testing of an experimental setting, making it possible to study the endothelium under different pathophysiological conditions. This novel experimental approach allows the application of the following stimuli to an ex vivo vessel in a physiological bath: (a) a realistic intravascular pressure waveform defined by the user; (b) shear stress in the endothelial layer since, in addition to the pressure waveform, the flow through the vessel can be independently controlled by the user; (c) conditions of hypo/hyperoxia and hypo/hypercapnia in an intravascular circulating medium. These stimuli can be applied alone or in different combinations to study possible synergistic or antagonistic effects. The setting performance is illustrated by a proof of concept in an ex vivo rabbit aorta. The experimental setting is easy to build by using very low-cost materials widely available. Online Supplement files provide all the technical information (e.g., circuits, codes, 3D printer drivers) following an open-source hardware approach for free replication.
Retrospective Study of the Seroprevalence of HIV, HCV, and HBV in Blood Donors at a Blood Bank of Western Mexico

Obtaining blood which is safe for transfusions is one of the principal challenges in the health systems of developing countries. Supply of contaminated blood increases morbidity, mortality, and the costs of patient care. In Mexico, serological screening is mandatory, but only a few of the main blood banks routinely perform a nucleic acid test (NAT). Data from 80,391 blood donations processed between August 2018 and December 2019 at the Central Blood Bank of the Western National Medical Center of the Mexican Social Security Institute (IMSS) were analyzed. All donors were screened for serological markers and NAT was performed. Reactive donors were followed-up to confirm their results. The number of reactive donors and seroprevalence rates for HIV, HCV, and HBV were 152 (18.91/10,000), 385 (47.89/10,000), and 181 (22.51/10,000), respectively; however, these rates decreased when NAT-confirmed reactive results were considered. Male donors were found to have a higher seroprevalence than females, and younger donors higher than older donors. The present study shows that HIV, HCV, and HBV seroprevalence in blood donors in Western Mexico is low. We propose that Mexico should establish future strategies, including pathogen reduction technologies (PRTs), in order to improve blood safety and reduce transfusion-transmissible infections (TTIs).
Texturization of a Blend of Pea and Destarched Oat Protein Using High-Moisture Extrusion

Grain protein fractions have great potential as ingredients that contain high amounts of valuable nutritional components. The aim of this study was to study the rheological behavior of destarched oat and pea proteins and their blends in extrusion-like conditions with a closed cavity rheometer. Additionally, the possibility of producing fibrous structures with high-moisture extrusion from a blend of destarched oat and pea protein was investigated. In the temperature sweep measurement (60–160 °C) of the destarched oat protein concentrate and pea protein isolate blend, three denaturation and polymerization sections were observed. In addition, polymerization as a function of time was recorded in the time sweep measurements. The melting temperature of grain proteins was an important factor when producing texturized structures with a high-moisture extrusion. The formation of fibrillar structures was investigated with high-moisture extrusion from the destarched oat and pea protein blend at temperatures ranging from 140 to 170 °C. The protein–protein interactions were significantly influenced in the extruded samples. This was due to a decrease in the amount of extractable protein in selective buffers. In particular, there was a decrease in non-covalent and covalent bonds due to the formation of insoluble protein complexes.
Coffee Consumption and Prostate Cancer Risk: Results from National Health and Nutrition Examination Survey 1999–2010 and Mendelian Randomization Analyses

The aim of this study was to examine the association between coffee and prostate cancer. Firstly, we conducted an observational study using data from National Health and Nutrition Examination Survey (NHANES) 1999–2010. Coffee intake was derived from 24 h dietary recalls. Weighted multivariable-adjusted logistic regression was applied to evaluate the association. Then, we performed Mendelian randomization (MR) to explore the possible causal effect of coffee on prostate cancer risk. Primary and secondary genetic instruments were obtained from genome-wide association studies among 375,833 and 91,462 individuals separately. Prostate cancer summary statistics were extracted from Prostate Cancer Association Group to Investigate Cancer-Associated Alterations in the Genome (PRACTICAL) (79,194 cases and 61,112 controls) and FinnGen project (4754 cases and 63,465 controls). Inverse variance weighted (IVW) was the primary analytical method. Through selection, we enrolled 8336 individuals (weighted number = 58,796,070) for our observational study in NHANES. Results suggested that there was no association between coffee and prostate cancer. MR analyses with primary genetic instruments also did not support a causal association between coffee intake and prostate cancer risk, whether using summary data from PRACTICAL (IVW: OR 1.001, 95% CI 0.997–1.005) or FinnGen (IVW: OR 1.005, 95% CI 0.998–1.012). Similar results were observed when using secondary genetic instruments. Therefore, our study did not support a causal association between coffee intake and prostate cancer risk. Further studies with a larger sample size are needed to examine if an association exists by different coffee bean types, roasting procedures, and brewing methods.
Positive Rate of Tests for Group a Streptococcus and Viral Features in Children with Acute Pharyngitis

Group A streptococcus (GAS) is an important cause of acute pharyngitis. We investigated the positive rate of GAS tests and clinical viral features in children with acute pharyngitis. A retrospective review was conducted for patients <15 years old with both rapid antigen detection test (RADT) and throat culture results. Patients were excluded if they were diagnosed with influenza or had received antibiotics within two weeks before these tests. A total of 377 patients were eligible. The median age of patients was 3.5 years, and 45.4% of total patients were <3 years old. Among all patients, 68.7% had at least one viral feature, and 39% had more than two. The overall positiv rate for GAS was 11.4%. The GAS positive rate was significantly lower in patients <3 years old than in older patients (1.8% vs. 19.4%, p < 0.0001). The overall sensitivity and specificity of RADT were 75.0% (95% CI: 57.8–87.9) and 97.9% (95% CI: 95.8–99.2), respectively. The GAS positive rate was not significantly different between patients with and without viral features (12.4% vs. 9.3%, p = 0.4854). In patients aged 3–14 years, the GAS positive rate was not associated with the modified Centor score or the frequency of clinical viral features. Despite a low prevalence of GAS pharyngitis, testing for GAS was frequently performed in children <3 years old in this study. Appropriate use of laboratory testing for GAS pharyngitis and judicious prescription of antibiotics were imperative.
Diversity and Biocontrol Potential of Cultivable Endophytic Bacteria Associated with Halophytes from the West Aral Sea Basin

Endophytes associated with halophytes may contribute to the host’s adaptation to adverse environmental conditions through improving their stress tolerance and protecting them from various soil-borne pathogens. In this study, the diversity and antifungal activity of endophytic bacteria associated with halophytic samples growing on the shore of the western Aral Sea in Uzbekistan were investigated. The endophytic bacteria were isolated from the nine halophytic samples by using the culture-dependent method and identified according to their 16S rRNA gene sequences. The screening of endophytic bacterial isolates with the ability to inhibit pathogenic fungi was completed by the plate confrontation method. A total of 289 endophytic bacterial isolates were isolated from the nine halophytes, and they belong to Firmicutes, Actinobacteria, and Proteobacteria. The predominant genera of the isolated endophytic bacteria were Bacillus, Staphylococcus, and Streptomyces, accounting for 38.5%, 24.7%, and 12.5% of the total number of isolates, respectively. The comparative analysis indicated that the isolation effect was better for the sample S8, with the highest diversity and richness indices. The diversity index of the sample S7 was the lowest, while the richness index of samples S5 and S6 was the lowest. By comparing the isolation effect of 12 different media, it was found that the M7 medium had the best performance for isolating endophytic bacteria associated with halophytes in the western Aral Sea Basin. In addition, the results showed that only a few isolates have the ability to produce ex-enzymes, and eight and four endophytic bacterial isolates exhibited significant inhibition to the growth of Valsa mali and Verticillium dahlia, respectively. The results of this study indicated that halophytes are an important source for the selection of microbes that may protect plant from soil-borne pathogens.
Exogenous Methyl Jasmonate Improves Cold Tolerance with Parallel Induction of Two Cold-Regulated (COR) Genes Expression in Triticum aestivum L.

Methyl jasmonate (MJ) is an important plant growth regulator that plays a key role in tolerance to biotic and abiotic stresses. In this research, the effects of exogenous MJ on cold tolerance, photosynthesis, activity and gene expression of antioxidant enzymes, proline accumulation, and expression of cold-regulated (COR) genes in wheat seedlings under low temperature (4 °C) were investigated. Exogenous MJ treatment (1 µM) promoted wheat cold tolerance before and during cold exposure. Low temperature significantly decreased photosynthetic parameters, whereas MJ application led to their partial recovery under cold exposure. Hydrogen peroxide (H2O2) and malondialdehyde (MDA) levels increased in response to low temperature, and this was counteracted by MJ application. Exogenous MJ significantly enhanced the activities of antioxidant enzymes and upregulated the expression of MnSOD and CAT during cold exposure. MJ application also led to enhanced proline content before 4 °C exposure, whereas the P5CS gene expression was upregulated by MJ’s presence at both normal (22 °C) and low (4 °C) temperatures. It was also shown that MJ tended to upregulate the expression of the COR genes WCS19 and WCS120 genes. We conclude that exogenous MJ can alleviate the negative effect of cold stress thus increasing wheat cold tolerance.