Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Relevant Biomarkers for the Diagnosis of Food Allergies: An Overview of the 2S Albumin Family

2S albumins are relevant and often major allergens from several tree nuts and seeds, affecting mainly children and young people. The present study aims to assess how the structural features of 2S albumins could affect their immunogenic capacity, which is essential to comprehend the role of these proteins in food allergy. For this purpose, twelve 2S albumins were isolated from their respective extracts by chromatographic methods and identified by MALDI-TOF mass-spectrometry. Their molecular and structural characterization was conducted by electrophoretic, spectroscopic and in silico methods, showing that these are small proteins that comprise a wide range of isoelectric points, displaying a general high structure stability to thermal treatment. Despite low amino acid sequence identity, these proteins share structural features, pointing conformational epitopes to explain cross-reactivity between them. Immunoblotting with allergic patients’ sera revealed those possible correlations between evolutionarily distant 2S albumins from different sources. The availability of a well-characterized panel of 2S albumins from plant-derived sources allowed establishing correlations between their structural features and their allergenic potential, including their role in cross-reactivity processes.
New Insights into Alterations in PL Proteins Affecting Their Binding to DNA after Exposure of Mytilus galloprovincialis to Mercury—A Possible Risk to Sperm Chromatin Structure?

Mercury (Hg) is a highly toxic and widespread pollutant. We previously reported that the exposure of Mytilus galloprovincialis for 24 h to doses of HgCl2 similar to those found in seawater (range 1–100 pM) produced alterations in the properties of protamine-like (PL) proteins that rendered them unable to bind and protect DNA from oxidative damage. In the present work, to deepen our studies, we analyzed PL proteins by turbidimetry and fluorescence spectroscopy and performed salt-induced release analyses of these proteins from sperm nuclei after the exposure of mussels to HgCl2 at the same doses. Turbidity assays indicated that mercury, at these doses, induced PL protein aggregates, whereas fluorescence spectroscopy measurements showed mercury-induced conformational changes. Indeed, the mobility of the PLII band changed in sodium dodecyl sulphate-polyacrylamide gel electrophoresis, particularly after exposure to 10-pM HgCl2, confirming the mercury-induced structural rearrangement. Finally, exposure to HgCl2 at all doses produced alterations in PL-DNA binding, detectable by DNA absorption spectra after the PL protein addition and by a decreased release of PLII and PLIII from the sperm nuclei. In conclusion, in this paper, we reported Hg-induced PL protein alterations that could adversely affect mussel reproductive activity, providing an insight into the molecular mechanism of Hg-related infertility.
Mercury Content in Three Edible Wild-Growing Mushroom Species from Different Environmentally Loaded Areas in Slovakia: An Ecological and Human Health Risk Assessment

Three edible mushroom species (Imlera badia, Boletus subtomentosus, Xerocomellus chrysenteron) sampled in 60 different localities of Slovakia were evaluated to determine health risks (associated with mercury content) arising from their consumption. Total content of mercury in soil and mushroom samples was determined by an AMA-254 analyzer. Soil pollution by mercury was evaluated by contamination factor (Cf), pollution load index (PLI), and geoaccumulation index (Igeo). Bioaccumulation factor (BAF), translocation factor (Qc/s), provisional tolerably weekly intake (%PTWI), estimated daily intake (EDI), and target hazard quotient (THQ) were used to describe and compare uptake and transition abilities of mushrooms, and the health risk arising from mushroom consumption. Mercury content in soil significantly influences the content of mercury in mushroom fruiting body parts. Caps and stipes of Boletus subtomentosus were found to be the best mercury accumulator. According to the EDI, consumption of the evaluated mushroom species represents a serious threat for adults and children. The lowest values of THQ were found for Xerocomellus chysenteron.
General Unified Microbiome Profiling Pipeline (GUMPP) for Large Scale, Streamlined and Reproducible Analysis of Bacterial 16S rRNA Data to Predicted Microbial Metagenomes, Enzymatic Reactions and Metabolic Pathways

General Unified Microbiome Profiling Pipeline (GUMPP) was developed for large scale, streamlined and reproducible analysis of bacterial 16S rRNA data and prediction of microbial metagenomes, enzymatic reactions and metabolic pathways from amplicon data. GUMPP workflow introduces reproducible data analyses at each of the three levels of resolution (genus; operational taxonomic units (OTUs); amplicon sequence variants (ASVs)). The ability to support reproducible analyses enables production of datasets that ultimately identify the biochemical pathways characteristic of disease pathology. These datasets coupled to biostatistics and mathematical approaches of machine learning can play a significant role in extraction of truly significant and meaningful information from a wide set of 16S rRNA datasets. The adoption of GUMPP in the gut-microbiota related research enables focusing on the generation of novel biomarkers that can lead to the development of mechanistic hypotheses applicable to the development of novel therapies in personalized medicine.
Greater higher order aberrations induced by toric orthokeratology versus soft toric multifocal contact lens wear

Spherical orthokeratology and soft multifocal contact lenses are commonly used for myopia control and correction, but have been shown to increase spherical aberration, coma and total higher order root mean square (HORMS) aberrations. There are limited myopia control contact lens options for patients with moderate to high astigmatism. The purpose of this study was to quantify changes in higher order aberrations (HOA) in myopic astigmatic eyes fitted with toric orthokeratology (TOK) and soft toric multifocal (STM) contact lenses.
Gut Microbiome and Metabolites in Patients with NAFLD and after Bariatric Surgery: A Comprehensive Review

The prevalence of non-alcoholic fatty liver disease (NAFLD) is increasing, as are other manifestations of metabolic syndrome such as obesity and type 2 diabetes. NAFLD is currently the number one cause of chronic liver disease worldwide. The pathophysiology of NAFLD and disease progression is poorly understood. A potential contributing role for gut microbiome and metabolites in NAFLD is proposed. Currently, bariatric surgery is an effective therapy to prevent the progression of NAFLD and other manifestations of metabolic syndrome such as obesity and type 2 diabetes. This review provides an overview of gut microbiome composition and related metabolites in individuals with NAFLD and after bariatric surgery. Causality remains to be proven. Furthermore, the clinical effects of bariatric surgery on NAFLD are illustrated. Whether the gut microbiome and metabolites contribute to the metabolic improvement and improvement of NAFLD seen after bariatric surgery has not yet been proven. Future microbiome and metabolome research is necessary for elucidating the pathophysiology and underlying metabolic pathways and phenotypes and providing better methods for diagnostics, prognostics and surveillance to optimize clinical care.
The Impact of Nutrition on the COVID-19 Pandemic and the Impact of the COVID-19 Pandemic on Nutrition

The coronavirus disease 2019 (COVID-19) pandemic has had significant morbidity, mortality, social and financial implications for the global population. Despite this knowledge, we still know very little about how COVID-19 infection affects quality of life resulting from changes in nutritional behaviour and, conversely, how nutrition could modulate the epidemiology of COVID-19. In addition, the social isolation most have experienced due to the regulations imposed by governments during the COVID-19 pandemic may have also had effects on our nutritional behaviour. It is possible that nutritional interventions may have effects on the incidence of COVID-19 infection and mortality rates. The purpose of this review is to evaluate the current status of research on the topic of nutrition as it relates to the COVID-19 pandemic.
Serum vitamin D levels in relation to type-2 diabetes and prediabetes in adults: a systematic review and dose–response meta-analysis of epidemiologic studies

Abstract Background Findings of observational studies that investigated the relationship between vitamin D deficiency and abnormal glucose homeostasis were contradictory. This meta-analysis of epidemiologic studies evaluated the association of vitamin D status and risk of type-2 diabetes (T2D) and prediabetes in adults. Methods A systematic search was conducted on all published articles in five electronic databases (including MEDLINE/PubMed, EMBASE, Institute for Scientific Information, Scopus and Google scholar), up to August 2020. Twenty-eight prospective cohort and nested case-control studies and 83 cross-sectional and case-control investigations that reported relative risks (RRs) or odds ratios (ORs) with 95% confidence intervals (CIs) for abnormal glucose homeostasis in relation to serum vitamin D levels in adults were included in the analysis. Results In prospective studies, high versus low level of vitamin D was respectively associated with significant 35%, 30% and 51% decrease in risk of T2D (RR:0.65; 95%CI: 0.55–0.76; 27 effect sizes), combined T2D and pre-diabetes (RR:0.70; 95%CI: 0.52–0.95; 9 effect sizes) and pre-diabetes (RR:0.49; 95%CI: 0.26–0.93; 2 effect sizes). These inverse associations were significant in almost all subgroups. Dose–response analysis in prospective studies showed that each 10 ng/ml increase in serum vitamin D levels resulted in 12% and 11% reduced risk of T2D (RR:0.88; 95%CI: 0.83–0.94) and combined T2D and prediabetes (RR:0.89; 95%CI: 0.87–0.92), respectively. In cross-sectional and case-control studies, highest versus lowest level of serum vitamin D was linked to reduced odds of T2D (OR:0.64; 95%CI: 0.57–0.72; 42 effect sizes) and combined T2D and pre-diabetes (OR:0.79; 95%CI: 0.74–0.85; 59 effect sizes); but not pre-diabetes (OR:0.64; 95%CI: 0.17–2.37; 11 effect sizes). Conclusion This meta-analysis of epidemiologic studies disclosed that serum vitamin D level was reversely associated with the risk of T2D and combined T2D and prediabetes in adults, in a dose–response manner. However, the association was not remarkable for pre-diabetes.
Multiple Mammarenaviruses Circulating in Angolan Rodents

Rodents are a speciose group of mammals with strong zoonotic potential. Some parts of Africa are still underexplored for the occurrence of rodent-borne pathogens, despite this high potential. Angola is at the convergence of three major biogeographical regions of sub-Saharan Africa, each harbouring a specific rodent community. This rodent-rich area is, therefore, strategic for studying the diversity and evolution of rodent-borne viruses. In this study we examined 290 small mammals, almost all rodents, for the presence of mammarenavirus and hantavirus RNA. While no hantavirus was detected, we found three rodent species positive for distinct mammarenaviruses with a particularly high prevalence in Namaqua rock rats (Micaelamys namaquensis). We characterised four complete virus genomes, which showed typical mammarenavirus organisation. Phylogenetic and genetic distance analyses revealed: (i) the presence of a significantly divergent strain of Luna virus in Angolan representatives of the ubiquitous Natal multimammate mouse (Mastomys natalensis), (ii) a novel Okahandja-related virus associated with the Angolan lineage of Micaelamys namaquensis for which we propose the name Bitu virus (BITV) and (iii) the occurrence of a novel Mobala-like mammarenavirus in the grey-bellied pygmy mouse (Mus triton) for which we propose the name Kwanza virus (KWAV). This high virus diversity in a limited host sample size and in a relatively small geographical area supports the idea that Angola is a hotspot for mammarenavirus diversity.
Pregnancy Outcome, Antibodies, and Placental Pathology in SARS-CoV-2 Infection during Early Pregnancy

There are reports that pregnant women infected with SARS-CoV-2 not only have increased morbidity but also increased complications and evidence of maternal and fetal vascular malperfusion on placental pathology. This was a retrospective study of pregnant women diagnosed with SARS-CoV-2 infection after March 2020. The results of reverse transcription polymerase chain reaction testing and IgM and IgG antibody testing of the amniotic fluid, cord blood, placenta, and maternal blood were confirmed at delivery. Placentas were evaluated histopathologically. The study included seven pregnant women diagnosed with SARS-CoV-2 infection during pregnancy at a mean gestational age of 14.5 weeks. Out of the seven women, five were infected during the first trimester. The mean gestational age at delivery was 38.4 weeks. The reverse transcription polymerase chain reaction results for maternal plasma, cord blood, placenta, and amniotic fluid were negative and IgG antibodies were detected in maternal plasma and cord blood. On placental pathology, maternal vascular malperfusion was found in only one case, fetal vascular malperfusion in four cases, and inflammatory changes were found in two cases. Pregnancy outcomes for women diagnosed with SARS-CoV-2 infection during early pregnancy are positive and it is likely that maternal antibodies are passed to the fetus, which results in a period of immunity.
Reproductive Outcomes in Lesbian Couples Undergoing Reception of Oocytes from Partner Versus Autologous In Vitro Fertilization/Intracytoplasmic Sperm Injection.

Purpose: This study aimed to compare reproductive outcomes after Reception of Oocytes from Partner (ROPA; also called reciprocal in vitro fertilization) with those after in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) with autologous oocytes, in lesbian couples. Methods: This was a retrospective matched cohort study of couples performing a first cycle of either ROPA (n = 60) or autologous IVF/ICSI (n = 120) between February 2012 and May 2018. Couples were matched 1:2 by age of the oocyte provider, day of embryo transfer (ET), and number of embryos transferred. Pregnancy and live birth rates after the first ET and cumulative results after all subsequent ETs performed until June 2019 were evaluated. Results: Reproductive outcomes were significantly better after ROPA at first ET: biochemical pregnancy 70.0% versus 47.5% (p = 0.004), clinical pregnancy 60.0% versus 40.0% (p = 0.011), ongoing pregnancy 60.0% versus 36.7% (p = 0.003), and live birth 57.1% versus 29.8% (p = 0.001). After adjusting for age, body mass index, and number of mature oocytes, we still observed a significant improvement across all outcomes in ROPA (live birth rate odds ratio [OR]: 3.05, 95% confidence interval [CI] 1.42-6.57). Cumulative pregnancy and live birth rates were also higher after ROPA (live birth 66.1% vs. 43.4% [p = 0.005]). The adjusted analysis result for cumulative live birth was OR: 2.51, 95% CI: 1.14-5.54. Conclusion: When medically indicated, ROPA can potentially improve reproductive outcomes for lesbian couples through the possibility of selecting the best combination between two oocyte providers and two gestational mothers, provided that both women wish to participate in the pregnancy plan.
The Validation of a Portable Functional NIRS System for Assessing Mental Workload

Portable functional near-infrared spectroscopy (fNIRS) systems have the potential to image the brain in naturalistic settings. Experimental studies are essential to validate such fNIRS systems. Working memory (WM) is a short-term active memory that is associated with the temporary storage and manipulation of information. The prefrontal cortex (PFC) brain area is involved in the processing of WM. We assessed the PFC brain during n-back WM tasks in a group of 25 college students using our laboratory-developed portable fNIRS system, WearLight. We designed an experimental protocol with 32 n-back WM task blocks with four different pseudo-randomized task difficulty levels. The hemodynamic response of the brain was computed from the experimental data and the evaluated brain responses due to these tasks. We observed the incremental mean hemodynamic activation induced by the increasing WM load. The left-PFC area was more activated in the WM task compared to the right-PFC. The task performance was seen to be related to the hemodynamic responses. The experimental results proved the functioning of the WearLight system in cognitive load imaging. Since the portable fNIRS system was wearable and operated wirelessly, it was possible to measure the cognitive load in the naturalistic environment, which could also lead to the development of a user-friendly brain–computer interface system.
A study on the homogeneous and surface initiated atom transfer radical polymerization of thermoresponsive polymers from regioselectively and non-regioselectively substituted cellulose derivatives

ii PREFACE . iii TABLE OF CONTENTS . iv LIST OF TABLES . viii LIST OF FIGURES . x LIST OF SCHEMES . xvi LIST OF EQUATIONS . xvii LIST OF ABREVIATIONS . xviii ACKNOWLEDGEMENTS. xxii DEDICATION . xxiii
UHPLC-ESI-QTOF-MS/MS Metabolite Profiling of the Antioxidant and Antidiabetic Activities of Red Cabbage and Broccoli Seeds and Sprouts

The antioxidant and antidiabetic properties and metabolite profiling of ethanol extracts of red cabbage (RC) and broccoli (BR) seeds and sprouts were investigated in this study. The total phenolic, flavonoid, and saponin contents were in the ranges of 385.4–480.4 mg FAE/100 g, 206.9–215.6 mg CE/100 g, and 17.8–27.0 mg soysaponin BE/100 g, respectively. BR seed had the highest total phenolic (480.4 mg FAE/100 g) and flavonoid (216.9 mg CE/100 g) contents, whereas BR sprout had the highest saponin content (27.0 soysaponin BE/100g). RC sprout demonstrated the highest antioxidant capacity, with DPPH and ABTS radical scavenging activity levels of 71.5% and 88.5%, respectively. Furthermore, BR and RC sprouts showed the most potent inhibition against α-glucosidase (91.32% and 93.11%, respectively) and pancreatic lipase (60.19% and 61.66%, respectively). BR seed (60.37%) demonstrated the lowest AGE inhibition. A total of 24 metabolites, predominantly amino acids and phenolic compounds, were characterized using UHPLC-QTOF-MS/MS. Germination not only improved the levels of metabolites but also resulted in the synthesis of new compounds. Therefore, these findings show that germination effectively enhanced the functional properties and metabolite profiles of broccoli and red cabbage seeds, making their sprouts more applicable as functional ingredients.
Analysis of the waiting time of the diagnosis for the first breast cancer treatment in southern Brazil

ABSTRACT This study aimed to determine the waiting time from the diagnosis to the first breast cancer treatment at the University Hospital in southern Brazil to verify if the law #12,732/12 is being respected and to identify the impact of this waiting time on breast cancer progression. A retrospective, quantitative, and indirect approach was carried out by reviewing the medical records of 118 patients who underwent oncologic breast surgery at the University Hospital, an exclusive public service, from January 1st 2012 to December 31st 2016. Data analysis revealed that the average waiting time was 104.4 days and the median was 92.5 days. Of the patients who started their treatment by surgery, 85.1% waited for more than 60 days. Meanwhile, 67.6% of the patients who underwent neoadjuvant chemotherapy, started the treatment within 60 days. In addition, the waiting time was not significant for relapse outcomes, metastatic disease, and death due to breast cancer. These results demonstrate the need for proposals that can reduce waiting times to the first treatment, especially if the indication is surgery.
Translational Studies on the Potential of a VEGF Nanoparticle-Loaded Hyaluronic Acid Hydrogel

Heart failure has a five-year mortality rate approaching 50%. Inducing angiogenesis following a myocardial infarction is hypothesized to reduce cardiomyocyte death and tissue damage, thereby preventing heart failure. Herein, a novel nano-in-gel delivery system for vascular endothelial growth factor (VEGF), composed of star-shaped polyglutamic acid-VEGF nanoparticles in a tyramine-modified hyaluronic acid hydrogel (nano-VEGF-HA-TA), is investigated. The ability of the nano-VEGF-HA-TA system to induce angiogenesis is assessed in vivo using a chick chorioallantoic membrane model (CAM). The formulation is then integrated with a custom-made, clinically relevant catheter suitable for minimally invasive endocardial delivery and the effect of injection on hydrogel properties is examined. Nano-VEGF-HA-TA is biocompatible on a CAM assay and significantly improves blood vessel branching (p < 0.05) and number (p < 0.05) compared to a HA-TA hydrogel without VEGF. Nano-VEGF-HA-TA is successfully injected through a 1.2 m catheter, without blocking or breaking the catheter and releases VEGF for 42 days following injection in vitro. The released VEGF retains its bioactivity, significantly improving total tubule length on a Matrigel® assay and human umbilical vein endothelial cell migration on a Transwell® migration assay. This VEGF-nano in a HA-TA hydrogel delivery system is successfully integrated with an appropriate device for clinical use, demonstrates promising angiogenic properties in vivo and is suitable for further clinical translation.
A Well-Structured Follow-Up Program is Required after Recovery from Coronavirus Disease 2019 (COVID-19); Release from Quarantine is Not the End of Treatment

During the Coronavirus Infection Disease-19 (COVID-19) pandemic, the number of patients released from quarantine is exceeding the number of newly diagnosed cases. This study is a retrospective cohort study in which consultation data were collected from a COVID-19 follow-up health consultation program. The studied population was selected from patients who recovered after quarantine and treatment for COVID-19 in Daegu City and in Gyeongsangbukdo province, Korea, from March to June 2020. The healthcare providers comprised 20 family-medicine specialists who consulted and educated the patients through phone calls in accordance with structured guidelines. Physical and mental status before and after recovery were compared among patients who received a single consultation and those who received two or more consultations. A total of 1604 subjects were selected for the final analysis. Of these, 1145 (71.4%) had one consultation and 459 (28.6%) had two or more. The group that had two or more consultations reported significantly more physical symptoms, more psychological symptoms (including depression), and more psychological stress. Multivariate forward selection logistic regression analysis showed that re-confirmed cases of COVID-19, physical symptoms after quarantine, feelings of depression, and psychological stress had a significant effect on the number of consultations received. In conclusion, COVID-19 has various physical and mental sequelae after discharge from quarantine. Therefore, a well-structured follow-up program is needed after recovery.