Miracle-dz/UniFAR-FTUs huggingface dataset:
Uncovering the Fungal Diversity Colonizing Limestone Walls of a Forgotten Monument in the Central Region of Portugal by High-Throughput Sequencing and Culture-Based Methods

Fungal organisms are considered one of the most relevant stone colonizers, and biodeteriogens. They are ubiquitous heterotrophs, metabolically versatile, ranging from generalist to extremophiles. Limestone, a sedimentary rock characterized by high levels of calcium carbonate, has low compressive strength and hardness and high porosity. These features make it highly susceptible to fungal colonization and an exceptional target for biodeterioration. Understanding the mycobiome composition associated with different biodeterioration scenarios is key for the development of effective guidelines and strategies for preventive conservation and viable maintenance of our cultural heritage. In this work, a thorough analysis of the fungal community composition on the Lemos Pantheon, a limestone-built artwork located in Portugal, was performed using high-throughput sequencing complemented with culture-based methods. The combined results allowed a detailed characterization of the fungal communities of each analyzed spot, revealing highly diverse and dissimilar communities according to the type of biodeterioration observed. In addition, we verified that both cultivation and metagenomics methodologies should be employed synergistically to tackle inherent limitations.
Pre-Conceptual Guidelines for Men: A Review of Male Infertility Experience, including Nutrition and Lifestyle Factors

Male fertility is declining and affects approximately one in seven couples. Reasons for this are multi-factorial and the subject of on-going research, though environmental contaminants (such xenoestrogens) are believed to be contributory factors. Semen parameters can be improved through a healthy diet and nutritional supplementation has also been shown to improve semen parameters, clinical pregnancy and live birth rates significantly. Despite this, in medical care dietary modification beyond alcohol reduction is rarely recommended. The aim of this review was to consider the psychosocial impacts of infertility in males whilst assessing other nutritional and lifestyle interventions that can be used in personalized nutrition care. More tailored nutrition care needs to consider this and the taboo surrounding the male infertility experience. A systematic approach was used. Three electronic databases (CINAHL, Medline and Academic Search Complete) were searched using predetermined Boolean search terms and identified 125 papers for review. Hand searches were undertaken to ensure recent evidence was included. Duplicates were removed and predefined inclusion and exclusion criteria were applied. Narrative synthesis was used for review and to develop preconceptual guidelines. Review data indicates dietary modification or supplementation with antioxidants such as vitamin C, vitamin E, coenzyme Q10, selenium, carnitine and zinc have been shown to improve markers of male fertility and reduce markers of seminal oxidative damage. Also, a Mediterranean style diet is also associated with higher quality sperm counts. Weight loss is beneficial in terms of normalizing endocrine profiles but at present it is not possible to determine if this is the effect of weight loss alone, or the combined effect of weight loss alongside other dietary improvement. Further research is therefore needed to understand the role of the many potential confounding factors. Despite this, infertility is emotionally challenging for men and nutrition, and personalised nutrition and lifestyle therapies have potential to support men trying to conceive. Pre-conceptual nutrition and lifestyle guidelines for men have been developed from this review and the use should be considered as the basis for more tailored nutrition care in practice.
Residual Information in Deep Speaker Embedding Architectures

Speaker embeddings represent a means to extract representative vectorial representations from a speech signal such that the representation pertains to the speaker identity alone. The embeddings are commonly used to classify and discriminate between different speakers. However, there is no objective measure to evaluate the ability of a speaker embedding to disentangle the speaker identity from the other speech characteristics. This means that the embeddings are far from ideal, highly dependent on the training corpus and still include a degree of residual information pertaining to factors such as linguistic content, recording conditions or speaking style of the utterance. This paper introduces an analysis over six sets of speaker embeddings extracted with some of the most recent and high-performing deep neural network (DNN) architectures, and in particular, the degree to which they are able to truly disentangle the speaker identity from the speech signal. To correctly evaluate the architectures, a large multi-speaker parallel speech dataset is used. The dataset includes 46 speakers uttering the same set of prompts, recorded in either a professional studio or their home environments. The analysis looks into the intra- and inter-speaker similarity measures computed over the different embedding sets, as well as if simple classification and regression methods are able to extract several residual information factors from the speaker embeddings. The results show that the discriminative power of the analyzed embeddings is very high, yet across all the analyzed architectures, residual information is still present in the representations in the form of a high correlation to the recording conditions, linguistic contents and utterance duration. However, we show that this correlation, although not ideal, could still be useful in downstream tasks. The low-dimensional projections of the speaker embeddings show similar behavior patterns across the embedding sets with respect to intra-speaker data clustering and utterance outlier detection.
The Potential Neuroprotective Effect of Cyperus esculentus L. Extract in Scopolamine-Induced Cognitive Impairment in Rats: Extensive Biological and Metabolomics Approaches

The aim of the present study is to investigate the phytochemical composition of tiger nut (TN) (Cyperus esculentus L.) and its neuroprotective potential in scopolamine (Scop)-induced cognitive impairment in rats. The UHPLC-ESI-QTOF-MS analysis enabled the putative annotation of 88 metabolites, such as saccharides, amino acids, organic acids, fatty acids, phenolic compounds and flavonoids. Treatment with TN extract restored Scop-induced learning and memory impairments. In parallel, TN extract succeeded in lowering amyloid beta, β-secretase protein expression and acetylcholine esterase (AChE) activity in the hippocampus of rats. TN extract decreased malondialdehyde levels, restored antioxidant levels and reduced proinflammatory cytokines as well as the Bax/Bcl2 ratio. Histopathological analysis demonstrated marked neuroprotection in TN-treated groups. In conclusion, the present study reveals that TN extract attenuates Scop-induced memory impairments by diminishing amyloid beta aggregates, as well as its anti-inflammatory, antioxidant, anti-apoptotic and anti-AChE activities.
Lactic Acid Bacteria: A Promising Tool for Menopausal Health Management in Women

Menopause is a period during which women undergo dramatic hormonal changes. These changes lead to physical and mental discomfort, are greatly afflictive, and critically affect women’s lives. However, the current safe and effective management measures for women undergoing menopause are insufficient. Several probiotic functions of lactic acid bacteria (LAB) have been recognized, including alleviation of lactose intolerance, protection of digestive tract health, activation of the immune system, protection against infections, improvement of nutrient uptake, and improvement of the microbiota. In this review, we highlight the currently available knowledge of the potential protective effects of LAB on preventing or mitigating menopausal symptoms, particularly in terms of maintaining balance in the vaginal microbiota, reducing bone loss, and regulating the nervous system and lipid metabolism. Given the increasing number of women entering menopause and the emphasis on the management of menopausal symptoms, LAB are likely to soon become an indispensable part of clinical/daily care for menopausal women. Herein, we do not intend to provide a comprehensive analysis of each menopausal disorder or to specifically judge the reliability and safety of complementary therapies; rather, we aim to highlight the potential roles of LAB in individualized treatment strategies for the clinical management of menopause.
High-Dimensional Cytometry Dissects Immunological Fingerprints of Idiopathic Inflammatory Myopathies

Chronic inflammation of skeletal muscle is the common feature of idiopathic inflammatory myopathies (IIM). Given the rarity of the disease and potential difficulty of routinely obtaining target tissue, i.e., standardized skeletal muscle, our understanding of immune signatures of the IIM spectrum remains incomplete. Further insight into the immune topography of IIM is needed to determine specific treatment targets according to clinical and immunological phenotypes. Thus, we used high-dimensional flow cytometry to investigate the immune phenotypes of anti-synthetase syndrome (ASyS), dermatomyositis (DM) and inclusion-body myositis (IBM) patients as representative entities of the IIM spectrum and compared them to healthy controls. We studied the CD8, CD4 and B cell compartments in the blood aiming to provide a contemporary overview of the immune topography of the IIM spectrum. ASyS was characterized by altered CD4 composition and expanded T follicular helper cells supporting B cell-mediated autoimmunity. For DM, unsupervised clustering identified expansion of distinct B cell subtypes highly expressing immunoglobulin G4 (IgG4) and CD38. Lastly, terminally differentiated, cytotoxic CD8 T cells distinguish IBM from other IIM. Interestingly, these terminally differentiated CD8 T cells highly expressed the integrin CD18 mediating cellular adhesion and infiltration. The distinct immune cell topography of IIM might provide the framework for targeted treatment approaches potentially improving therapeutic outcomes.
Total Mass of Ordinary Chondrite Matter Originally Present in the Solar System

Recently, I reported the discovery of a new fundamental relationship of the major elements (Fe, Mg, Si) of chondrites that admits the possibility that ordinary chondrite meteorites are derived from two components, a relatively oxidized and undifferentiated, primitive component and a somewhat differentiated, planetary component, with oxidation state like the highly reduced enstatite chondrites, which I suggested was identical to Mercury's complement of lost elements. Subsequently, on the basis of that relationship, I derived expressions, as a function of the mass of planet Mercury and the mass of its core, to estimate the mass of Mercury's lost elements, the mass of Mercury's alloy and rock protoplanetary core, and the mass of Mercury's gaseous protoplanet. Here, on the basis of the supposition that Mercury's complement of lost elements is in fact identical to the planetary component of ordinary chondrite formation, I estimate, as a function of Mercury's core mass, the total mass of ordinary chondrite matter originally present in the Solar System. Although Mercury's mass is well known, its core mass is not, being widely believed to be in the range of 70 to 80 percent of the planet mass. For a core mass of 75 percent, the calculated total mass of ordinary chondrite matter originally present in the Solar System amounts to 1.83E24 kg, about 5.5 times the mass of Mercury. That amount of mass is insufficient in itself to form a planet as massive as the Earth, but may have contributed significantly to the formation of Mars, as well as adding to the veneer of other planets, including the Earth. Presently, only about 0.1 percent of that mass remains in the asteroid belt.
Predictors of Adherence to Cancer-Related mHealth Apps in Cancer Patients Undergoing Oncological or Follow-Up Treatment—A Scoping Review

mHealth interventions in cancer care are being increasingly applied in various settings. Nevertheless, there is a phenomenon wherein individuals show different usage patterns, which could affect the effectiveness of the intervention. In general, it is important to know the predictors of app adherence and usage patterns to improve the design and content (i.e., tailoring). The aim of this scoping review was to provide an overview of predictors of adherence to cancer-related mHealth apps in cancer patients. A systematic literature search was conducted in March 2021 in the electronic databases PubMed, CINAHL, and PsychINFO without limitation in year, focusing on cancer patients undergoing oncological or follow-up treatment using mHealth apps. The initial database search yielded a total of N = 8035 records. After title, abstract, and full-text screening, 10 articles met inclusion criteria. Studies were published between 2013 and 2020. Studies focused on children and adolescents (2/10) as well as adults (8/10). The predictors identified could be categorized into sociodemographic variables, cancer-related factors and others. This study provides an initial insight into relevant predictors of app adherence in cancer patients. However, no clear predictor of increased app adherence was found. Further research of usage patterns is therefore needed so that mHealth interventions can be tailored during development.
The cosmic evolution of dust-corrected metallicity in the neutral gas

Interpreting abundances of Damped Ly-$\alpha$ Absorbers (DLAs) from absorption-line spectroscopy has typically been a challenge because of the presence of dust. Nevertheless, because DLAs trace distant gas-rich galaxies regardless of their luminosity, they provide an attractive way of measuring the evolution of the metallicity of the neutral gas with cosmic time. This has been done extensively so far, but typically not taking proper dust corrections into account. The aims of this paper are to: $i)$ provide a simplified way of calculating dust corrections, based on a single observed [$X$/Fe], $ii)$ assess the importance of dust corrections for DLA metallicities and their evolution, and $iii)$ investigate the cosmic evolution of iron for a large DLA sample. We derive dust corrections based on the observed [Zn/Fe], [Si/Fe], or [S/Fe], and confirm their robustness. We present dust-corrected metallicities in a scale of [Fe/H]$_{\rm tot}$ for 266 DLAs over a broad range of $z$, and assess the extent of dust corrections for different metals at different metallicities. Dust corrections in DLAs are important even for Zn (typically of 0.1-0.2, and up to 0.45 dex), which is often neglected. Finally, we study the evolution of the dust-corrected metallicity with $z$. The DLA metallicities decrease with redshift, by a factor of 50-100 from today to $\sim$ 12.6 billions ago ($z=$ 5). When including dust corrections, the metallicity evolution is more steep than previously thought. At low $z$, the average DLA metallicities are $\sim$ 0.3 dex higher than without corrections. The upper envelope of the relation between metallicity and $z$ reaches solar metallicity at $z\lesssim$ 0.5, although some systems can have solar metallicity already out to $z\sim$ 3.
Potential value of cerebrospinal fluid α-synuclein in the identification of postoperative delirium undergoing knee/hip arthroplasty: The perioperative neurocognitive disorder and biomarker lifestyle study

Objective Postoperative delirium (POD) is a common postoperative complication, which may be associated with α-synuclein (α-syn). The purpose of this study was to explore the association between the expression level of α-syn in cerebrospinal fluid (CSF) and POD. Methods We conducted a prospective observational cohort study, which involved in 740 participants (mean age of 61.86 years, range 40–90 years; 40% female) from the Perioperative Neurocognitive Disorder And Biomarker Lifestyle (PNDABLE) study in the final analysis. POD was diagnosed using the Confusion Assessment Scale (CAM), and its severity was measured using the Memorial Delirium Assessment Scale (MDAS). Enzyme-linked immune-sorbent assay (ELISA) was used to detect the concentrations of α-syn, Aβ40, Aβ42, T-tau, and P-tau in CSF. Results The incidence of POD was 11.22% (83/740). The logistic regression analysis showed that the increased concentrations of CSF α-syn (OR = 1.005, 95%CI 1.004–1.006, P < 0.001), P-tau (OR = 1.093, 95%CI 1.071–1.115, P < 0.001), and T-tau (OR = 1.008, 95%CI 1.006–1.009, P < 0.001) were risk factors of POD. Linear regression showed that CSF α-syn had positive correlations with P-tau (β = 0.480, P < 0.001), T-tau (β = 0.334, P < 0.001), while negative correlations with Aβ40 (β = –0.378 P < 0.001), Aβ42 (β = -0.800, P = 0.001) in POD patients. Mediation analyses showed the association between α-syn and POD was partially mediated by tau pathologies (proportion: 16–17%). Conclusion CSF α-syn is one of the preoperative risk factors for POD, which may be mediated through tau pathologies. Clinical trial registration [www.ClinicalTrials. gov], identifier [ChiCTR20 00033439].
Physical Fitness, Screen Time and Sleep Habits According to Obesity Levels in Schoolchildren: Findings from the Health Survey of the Extreme South of Chile

Obesity is a worry because it is associated with a greater burden of disease, and it has been shown to be related to the health habits and physical condition of children and adolescents. Objective: To associate physical fitness, screen time, and sleep habits with the different categories of obesity in schoolchildren from the extreme south of Chile. Methods: 583 schoolchildren were included in this cross-sectional analysis. The screen time and sleep habits were measured with the Sleep Self-Report questionnaire, while the physical fitness was assessed with the Alpha Fitness test battery. The Body Mass Index/age (BMI/age) and the Waist-to-Height ratio (WtHr) were used to define adiposity using the following categories: healthy weight/low-risk waist-to-height ratio (H/LR), healthy weight/high-risk waist-to-height ratio (H/HR), overweight/low-risk waist to height ratio (O/LR), and overweight/high-risk waist to height ratio (O/HR). Results: A considerable number of schoolchildren (23.2%) presented sleep problems, while the mean screen time was 9.3 (95% CI: 8.4; 10.1) hours/day. Schoolchildren classified as H/HR showed better physical fitness than the O/HR group but worse physical fitness than the H/LR group. Conclusions: Significant differences were evidenced in the physical fitness between the adiposity categories, which could open future lines of research concerning the characterization of the healthy weight-obese adiposity categories in children.
Autoimmune Pancreatitis: From Pathogenesis to Treatment

Autoimmune pancreatitis (AIP) is a rare disease. The diagnosis of AIP is difficult and should be made by a comprehensive evaluation of clinical, radiological, serological, and pathological findings. Two different types of AIP have been identified: autoimmune pancreatitis type 1 (AIP-1), which is considered a pancreatic manifestation of multiorgan disease related to IgG4, and autoimmune pancreatitis type 2 (AIP-2), which is considered a pancreas-specific disease not related to IgG4. Although the pathophysiological conditions seem to differ between type 1 and type 2 pancreatitis, both respond well to steroid medications. In this review, we focused on the pathogenesis of the disease to develop a tool that could facilitate diagnosis and lead to the discovery of new therapeutic strategies to combat autoimmune pancreatitis and its relapses. The standard therapy for AIP is oral administration of corticosteroids. Rituximab (RTX) has also been proposed for induction of remission and maintenance therapy in relapsing AIP-1. In selected patients, immunomodulators such as azathioprine are used to maintain remission. The strength of this review, compared with previous studies, is that it focuses on the clear difference between the two types of autoimmune pancreatitis with a clearly delineated and separate pathogenesis. In addition, the review also considers various therapeutic options, including biologic drugs, such as anti-tumor necrosis factor (TNF) therapy, a well-tolerated and effective second-line therapy for AIP type 2 relapses or steroid dependence. Other biologic therapies are also being explored that could provide a useful therapeutic alternative to corticosteroids and immunosuppressants, which are poorly tolerated due to significant side effects.
Envelopes and refinements in categories, with applications to functional analysis

An envelope in a category is a construction that generalizes the operations of "exterior completion", like completion of a locally convex space, or Stone-\v{C}ech compactification of a topological space, or universal enveloping algebra of a Lie algebra. Dually, a refinement generalizes operations of "interior enrichment", like bornologification (or saturation) of a locally convex space, or simply connected covering of a Lie group. In this paper we define envelopes and refinements in abstract categories and discuss the conditions under which these constructions exist and are functors. The aim of the exposition is to build a fundament for duality theories of non-commutative groups based on the idea of envelope. The advantage of this approach is that in the arising theories the analogs of group algebras are Hopf algebras. At the same time the classical Fourier and Gelfand transforms are interpreted as envelopes with respect to the prearranged classes of algebras.
On the origin of thigh-frequency radiation in experimental earthquakes

We monitor dynamic rupture propagation during laboratory stick-slip experiments performed on saw-cut Westerly granite under upper crustal conditions (10-90 MPa). Spectral analysis of high-frequency acoustic waveforms provided evidence that energy radiation is enhanced with stress conditions and rupture velocity. Using acoustic recordings bandpass filtered to 400-800 kHz (7-14 mm wavelength) and highpass filtered above 800 kHz, we back projected high-frequency energy generated during rupture propagation. Our results show that the high-frequency radiation originates behind the rupture front during propagation and propagates at a speed close to that obtained by our rupture velocity inversion. From scaling arguments, we suggest that the origin of high-frequency radiation lies in the fast dynamic stress-drop in the breakdown zone together with off-fault co-seismic damage propagating behind the rupture tip. The application of the back-projection method at the laboratory scale provides new ways to locally investigate physical mechanisms that control high-frequency radiation.