Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of process conditions on the microbial community dynamics and metabolite production kinetics of teff sourdough fermentations under bakery and laboratory conditions

Abstract Teff and teff sourdoughs are promising ingredients for bread production. Therefore, this study aimed at the characterization of spontaneous and flour‐native starter culture‐initiated teff sourdough productions under bakery and laboratory conditions. Backslopped laboratory and bakery teff sourdough productions were characterized by different lactic acid bacteria (LAB) and yeast species, but were both characterized by a pH below 4.0 after five backslopping steps. The sourdough‐associated Lactobacillus sanfranciscensis was isolated for the first time from backslopped spontaneous teff sourdoughs. The autochthonous strain L. sanfranciscensis IMDO 150101 was tested as starter culture during laboratory teff sourdough fermentations. Its prevalence could be related to the process conditions applied, in particular the ambient temperature (below 30°C). Breads made with 20% teff sourdough (on flour basis) displayed interesting features compared with all‐wheat‐based reference breads. Teff sourdoughs were characterized as to their pH evolution, microbial community dynamics, and microbial species composition. Representative strains of the LAB species isolated from these sourdoughs, in particular L. sanfranciscensis, may be selected as starter cultures for the production of stable teff sourdoughs and flavorful breads, provided they are adapted to the environmental conditions applied.
Receptors and Signaling Pathways for Recognition of Bacteria in Livestock and Crops: Prospects for Beneficial Microbes in Healthy Growth Strategies

Modern animal and crop production practices are associated with the regular use of antimicrobials, potentially increasing selection pressure on bacteria to become resistant. Alternative approaches are needed in order to satisfy the demands of the growing human population without the indiscriminate use of antimicrobials. Researchers have brought a different perspective to solve this problem and have emphasized the exploitation of animal- and plant-associated microorganisms that are beneficial to their hosts through the modulation of the innate immune system. There is increasing evidence that plants and animals employ microbial perception and defense pathways that closely resemble each other. Formation of pattern recognition receptor (PRR) complexes involving leucine-rich repeat (LRR)-containing proteins, mitogen-activated protein kinase (MAPK)-mediated activation of immune response genes, and subsequent production of antimicrobial products and reactive oxygen species (ROS) and nitric oxide (NO) to improve defenses against pathogens, add to the list of similarities between both systems. Recent pioneering work has identified that animal and plant cells use similar receptors for sensing beneficial commensal microbes that are important for the maintenance of the host's health. Here, we reviewed the current knowledge about the molecular mechanisms involved in the recognition of pathogenic and commensal microbes by the innate immune systems of animal and plants highlighting their differences and similarities. In addition, we discuss the idea of using beneficial microbes to modulate animal and plant immune systems in order to improve the resistance to infections and reduce the use of antimicrobial compounds.
Characterization of Diarrheagenic Enteroaggregative Escherichia coli in Danish Adults—Antibiotic Treatment Does Not Reduce Duration of Diarrhea

Enteroaggregative Escherichia coli (EAEC) is frequently isolated from sporadic cases of diarrhea and in outbreaks of gastroenteritis in several regions of the world. The pathophysiology of EAEC continues to be enigmatic, and the efficacy of antibiotic treatment in EAEC-associated diarrhea has been discussed. Since the level of antibiotic resistance is increasing, it is essential to restrict the use of antibiotics to prevent further resistance development. We aimed to investigate EAEC strains in adult Danish patients suffering from diarrhea and from healthy controls. We examined the antibiotic resistance in EAEC strains, the clinical response to antibiotic treatment in EAEC diarrheal cases, and the distribution of virulence genes in diarrheal cases. The EAEC strains were collected from patients suffering from diarrhea in a Danish multicenter study. A medical doctor interviewed the patients by using a questionnaire regarding gastrointestinal symptoms, exposures, and use of antibiotic and over-the-counter antidiarrheal drugs. Follow-up was performed after 3–5 months to inquire about differential diagnosis to gastrointestinal disease. A multiplex polymerase chain reaction characterized virulence genes in diarrheal cases. Finally, the level of antibiotic resistance was examined by using the disc diffusion method. Asymptomatic carriage of EAEC in the adult Danish population was rare, in contrast to findings in healthy Danish children. The duration of diarrhea was not shortened by antibiotic treatment, specifically ciprofloxacin treatment, or by over-the-counter antidiarrheal drugs. Follow-up revealed no pathology in diarrheal patients apart from irritable bowel syndrome in two patients. A high number of patients suffered from long-term diarrhea, which was associated with the enterotoxin EAST-1 and a high virulence factor score. A high level of antibiotic resistance was observed and 58% of the EAEC strains were multidrug resistant. Multidrug resistance was most pronounced in cases of travelers' diarrhea, and it was seen that antibiotic treatment did not reduce the duration of diarrhea.
Effects of aging on liver microcirculatory function and sinusoidal phenotype

The socioeconomic and medical improvements of the last decades have led to a relevant increase in the median age of worldwide population. Although numerous studies described the impact of aging in different organs and the systemic vasculature, relatively little is known about liver function and hepatic microcirculatory status in the elderly. In this study, we aimed at characterizing the phenotype of the aged liver in a rat model of healthy aging, particularly focusing on the microcirculatory function and the molecular status of each hepatic cell type in the sinusoid. Moreover, major findings of the study were validated in young and aged human livers. Our results demonstrate that healthy aging is associated with hepatic and sinusoidal dysfunction, with elevated hepatic vascular resistance and increased portal pressure. Underlying mechanisms of such hemodynamic disturbances included typical molecular changes in the cells of the hepatic sinusoid and deterioration in hepatocyte function. In a specific manner, liver sinusoidal endothelial cells presented a dysfunctional phenotype with diminished vasodilators synthesis, hepatic macrophages exhibited a proinflammatory state, while hepatic stellate cells spontaneously displayed an activated profile. In an important way, major changes in sinusoidal markers were confirmed in livers from aged humans. In conclusion, our study demonstrates for the first time that aging is accompanied by significant liver sinusoidal deregulation suggesting enhanced sinusoidal vulnerability to chronic or acute injuries.
Carotid Webs: Radiographic Appearance and Significance

First identified and named in 1973, carotid webs are nonatherosclerotic fibrous bands that arise along the posterior margin of the carotid bulb. [1][1],[2][2] Histopathologically, these entities are characterized by fibroelastic thickening of the arterial intima. They appear on imaging modalities as
Exposure to tobacco smoke increases bone loss in spontaneously hypertensive rats

Abstract Purpose: To define if exposure to tobacco smoke (TS) could induce reduction of bone mass and impairment of bone architecture, features observed in osteoporosis in normotensive rats and the influence of TS exposure on the osteoporotic features exhibited in the spontaneously hypertensive (SH) rats. Methods: Normotensive Wistar Kyoto (WKY) and SH rats were exposed to filtered air or TS for 8 weeks, then their proximal femurs were extracted for micro-computed tomography (micro-CT) assessment, histological and immune-histological examinations to quantify the adverse influence of TS exposure on the bone mass and density, as well as bone architecture. Results: We found that TS exposure not only induced significant decreases in bone mineral density (BMD), bone volume (BV), cortical and trabecular thickness (Ct.Th and Tb.Th), trabecular surface area (Tb.Ar), expression of hypoxia-inducible factor-1α (HIF-1α) in the trabecular marrow, delayed ossification of cartilage, as well as statistical increases in trabecular separation (Tb.SP) and the number of trabecular marrow adipocytes in both WKY and SH rats, but also exacerbated multiple features of osteoporosis exhibited in SH rats, including decreased BMD, Ct.Th, Tb.Ar, HIF-1α expression, delayed cartilage ossification, and increased Tb.SP. Conclusions: Our results show that TS exposure can reduce bone mass and impair bone architecture and exacerbate multiple features of osteoporosis exhibited in SH rats.
Noise Thresholds for Amplification: From Quantum Foundations to Classical Fault-Tolerant Computation

We revisit an old question—fault-tolerant computation by noisy circuits—in a new light. More precisely, we investigate noise thresholds in fault-tolerant computation for new classes of noisy gates inspired by foundational questions in quantum mechanics. Our main technical result is that, perhaps surprisingly, noiseless XOR gates are not more helpful than noisy ones in read-once formulas that have noisy AND gates for the task of building ampliﬁers. We also formalize a connection between fault-tolerant computation and ampliﬁcation, and highlight new directions and open questions in fault-tolerant computation with noisy circuits.
Relationship between 50-g glucose challenge test and large for gestational age infants among pregnant women without gestational diabetes

Abstract The study aimed to compare the incidence of large for gestational age (LGA) infants between women with a false positive and normal glucose challenge test (GCT), and to evaluate the factors associated with LGA. A total of 480 pregnant women at risk for gestational diabetes mellitus (GDM); 160 with a false positive GCT and 320 with normal GCT results were included. The incidence of LGA and other pregnancy outcomes were compared between the two groups. Possible associated factors for LGA were also evaluated. Women with a false positive GCT were significantly older and more likely to be multiparous. The incidence of LGA was comparable between the false positive and normal GCT groups (15.6% vs. 13.1%, p = .456). Other pregnancy outcomes were also comparable. Logistic regression analysis showed that pre-pregnancy underweight significantly reduced the risk of LGA (adjusted OR 0.25, 95% CI 0.07–0.87, p = .029) while a second trimester weight gain >7 kg significantly increased the risk of LGA (adjusted OR 3.13, 95% CI 1.67–5.89, p < .001). Impact Statement What is already known on this subject? Women with a false-positive GCT (abnormal GCT but normal OGTT) can be considered as having an early form of glucose intolerance which similar adverse outcomes to GDM could develop. Previous studies have reported that a mild maternal hyperglycaemia in the absence of GDM is associated with LGA, macrosomia, shoulder dystocia and a caesarean delivery. There is no current recommendation for any intervention or treatment among women with a false positive GCT. What the results of this study add? The results of this study showed that an incidence of LGA was not significantly increased in the false positive GCT groups and that other pregnancy outcomes were comparable. A pre-pregnancy underweight significantly reduced the risk of LGA while a second trimester weight gain >7 kg significantly increased the risk of LGA. What the implications are of these findings for clinical practice and/or further research? As a gestational weight gain is modifiable, behavioural and a dietary intervention as well as a close monitoring of the weight gain could help in lowering the risk of LGA, even in the absence of GDM. Further studies which are more widely generalisable are needed to elucidate the relationship between 50 g GCT and the adverse outcomes and to investigate the benefits of a specific intervention among this specific group of women.
Spirituality, depression and quality of life in medical students in KwaZulu-Natal

Background The majority of studies on spirituality demonstrate its positive association with mental health. Despite the increasing number of studies, there remains a dearth of studies emanating from African countries looking at the relationship between mental illness, quality of life and measures of spirituality. The present study evaluates the role of spirituality in relation to current depression and quality of life in medical students, who are known to be at high risk for depression. Objectives The aim of this study was to determine the prevalence of moderate and severe depressive symptoms in this population and explore potential correlations between spirituality, depression and quality of life. Methods 230 medical students were surveyed at the University of KwaZulu-Natal Medical School, using the Zung Self-Rating Depression Scale (Zung SDS), Spiritual Involvement and Beliefs Scale (SIBS), WHO Quality of Life Scale (WHOQOL) and a demographic data sheet. Results There was a high prevalence of depressive symptoms in the medical students, with a significant proportion (15.6%) showing evidence of severe depressive symptoms (indicating likely depressive illness). Those with a history of mental illness or of having attended traditional, complementary or alternate medical practitioners showed higher levels of depression. Lower spirituality was associated with non-adherence to a major religion and a history of mental illness. Quality of life was better in second and fifth year students and poorer in those with a history of mental illness. Conclusion Medical students’ experiences of depression (most probably due to stress) and its relationship with spirituality and quality of life merit further investigation with a view to establishing policy guidelines for dealing with this issue.
Effects of ball milling treatment on physicochemical properties and digestibility of Pacific oyster (Crassostrea gigas) protein powder

Abstract The oyster protein was ball milling treated in this work, and the effects on particle size, conformation, physicochemical properties, and in vitro protein digestibility (IVPD) were investigated. After ball milling treatment, the particle size obviously decreased, and the protein powder became denser and more homogeneous. The ball milling treatment could not change the primary structure of oyster protein. However, it could affect the secondary structure and physicochemical properties. The disulfide bond increased from 8.18 to 9.14 μmol/g protein, while the protein surface hydrophobicity index increased from 0.088 to 0.176. The decreasing water‐holding capacity from 390% to 226% and the increasing oil‐binding capacity from 91.2% to 189.1% were related to the alterations of conformation and physicochemical properties. Ball milling could also improve the IVPD from 54.6% to 82.4%. These results provided theoretical basis for the application of ball milling treatment in the utilization of oyster protein in the food industry.
Pharmacological bypass of NAD+ salvage pathway protects neurons from chemotherapy-induced degeneration

Significance Axon degeneration is caused by multiple chemotherapeutic agents and is a hallmark of chemotherapy-induced peripheral neuropathy (CIPN). CIPN is associated with the loss of the essential metabolite nicotinamide adenine dinucleotide (NAD+), a vital metabolite involved in energy homeostasis, but whether NAD+ loss or the accumulation of an NAD+ precursor, nicotinamide mononucleotide (NMN), is responsible for axon degeneration is controversial. We found that axon degeneration caused by vincristine, a widely used chemotherapeutic agent, could be ameliorated by forcing peripheral neurons to use an NAD+ biosynthetic pathway that bypasses NMN formation. This strategy provides an approach for preventing CIPN. Axon degeneration, a hallmark of chemotherapy-induced peripheral neuropathy (CIPN), is thought to be caused by a loss of the essential metabolite nicotinamide adenine dinucleotide (NAD+) via the prodegenerative protein SARM1. Some studies challenge this notion, however, and suggest that an aberrant increase in a direct precursor of NAD+, nicotinamide mononucleotide (NMN), rather than loss of NAD+, is responsible. In support of this idea, blocking NMN accumulation in neurons by expressing a bacterial NMN deamidase protected axons from degeneration. We hypothesized that protection could similarly be achieved by reducing NMN production pharmacologically. To achieve this, we took advantage of an alternative pathway for NAD+ generation that goes through the intermediate nicotinic acid mononucleotide (NAMN), rather than NMN. We discovered that nicotinic acid riboside (NAR), a precursor of NAMN, administered in combination with FK866, an inhibitor of the enzyme nicotinamide phosphoribosyltransferase that produces NMN, protected dorsal root ganglion (DRG) axons against vincristine-induced degeneration as well as NMN deamidase. Introducing a different bacterial enzyme that converts NAMN to NMN reversed this protection. Collectively, our data indicate that maintaining NAD+ is not sufficient to protect DRG neurons from vincristine-induced axon degeneration, and elevating NMN, by itself, is not sufficient to cause degeneration. Nonetheless, the combination of FK866 and NAR, which bypasses NMN formation, may provide a therapeutic strategy for neuroprotection.
Changes in the balance between proliferation and apoptosis during the progression of malignancy in thyroid tumours

The aim of this study was to gain better insight into molecular changes which reflect disturbances in the balance between proliferation and apoptosis during progression of thyroid malignancy from papillary microcarcinoma (PMC) via clinically manifest papillary carcinoma (PTC) to anaplastic carcinoma (ATC). The apoptosis related molecules (Bcl-2, Bax) and proliferation related marker (PCNA) were analysed immunohistochemically in 120 archival cases comprising PMC (n=34), PTC (n=52) and ATC (n=34). In addition, in situ apoptotic cell death was analysed by the TUNEL method. The average Bcl-2 staining score did not differ between PMC and PTC (p>0.05), but was significantly lower in ATC (p<0.05). The Bax score was higher in PTCs and ATCs than in PMCs (p<0.05). Due to these changes, the Bcl-2/Bax ratio showed a marked decrease from PMC to ATC (p<0.05), while proliferation activity increased significantly from PTC to ATC (p<0.05). Despite high Bax expression, the rate of apoptotic cell death was low in the investigated carcinomas, especially in ATC, i.e. the increase in proliferative activity was not counterbalanced with appropriate cell death. Differences were found in the expression of apoptotic molecules (Bcl-2 and Bax), their ratio (Bcl-2 /Bax) and in the rate of apoptotic cell death and proliferative activity between PMC, PTC and ATC, indicating that disturbances in the balance between apoptosis and proliferation, in favour of the latter, occur gradually during the progression of malignancy in thyroid tumours.
Reduced Insulin Receptor Expression and Altered DNA Methylation in Fat Tissues and Blood of Women With GDM and Offspring

Context Altered expression of the insulin receptor (IR) in adipose tissue (AT) could contribute to gestational diabetes mellitus (GDM) etiopathogenesis. Transcriptional regulation via epigenetic mechanisms (e.g., DNA methylation) may play a critical role. However, the human IR promoter DNA methylation patterns and involvement in gene expression are unknown. Objective We evaluated IR mRNA and protein expression accompanied by targeted DNA methylation analyses in AT and blood cells of women with GDM and their offspring. Design Prospective observational study. Setting Academic clinic and research unit. Participants GDM-affected (n = 25) and matched control (n = 30) mother-child dyads. Main Outcome Measures Maternal IR gene and protein expression in paired subcutaneous (SAT) and visceral adipose tissue samples (VAT). DNA methylation levels in IR promoter and intronic regions in maternal AT and blood cells of mother-offspring pairs. Results In SAT and VAT, IR mRNA/protein expressions were significantly reduced in women with GDMs (P < 0.05). The decrease in VAT was more pronounced and independent of maternal body mass index. VAT IR protein levels were inversely associated with key maternal and neonatal anthropometric and metabolic parameters (P < 0.05). DNA methylation patterns were similar across tissues, with significant yet small size alterations between groups in mothers and offspring (P < 0.05). Conclusion Decreased IR levels in AT may be a relevant pathogenic factor in GDM, affecting materno-fetal metabolism. Further investigation of causal factors for IR dysregulation is necessary, especially in VAT. Potential functional and/or clinical roles of altered DNA methylation also should be evaluated.
Comparison of circulating metabolite concentrations in dogs and cats when allowed to freely choose macronutrient intake

ABSTRACT Food intake changes circulating metabolite concentrations. Thus, a comparison of circulating metabolites between dogs and cats is necessarily confounded by the composition of foods offered. The objective of this study was to determine differences between dogs and cats when given the opportunity to choose their own macronutrient intake. Four experimental foods with similar palatability, but varying in macronutrient content were prepared for dogs, and four for cats. Foods were available to dogs (n=17) for food intake once a day and to cats (n=27) at all times. Food 1 was high protein; Food 2 was high fat; Food 3 was high carbohydrates and Food 4 was balanced for macronutrients. By choosing a combination of foods, each animal could individually set its own macronutrient intake. Plasma metabolomics were determined after pets had consumed their food intake of choice for 28 days. Cats had higher concentrations of the essential amino acids histidine, isoleucine, phenylalanine and valine, but lower concentrations of lysine, methionine and threonine compared with dogs. Overall, non-essential amino acids were higher in cats. Regarding lipids, cats had increased concentrations of highly polyunsaturated fatty acids (PUFA) after 28 days, although arachidonic acid (AA) was consistently higher in dogs. Regarding circulating microbial metabolites, there was more stability for dogs compared with cats (none changed over time in dogs versus 42% changed in cats; P<0.01). Concentrations of urea cycle intermediates, antioxidants and methylated compounds were also different between species. In conclusion, metabolite differences between dogs and cats reflected differences in species and food choices. Summary: Dogs and cats offered foods with different macronutrient composition, but equivalent palatability, have different circulating metabolite concentrations that reflect differences in species and food choices.