Miracle-dz/UniFAR-FTUs huggingface dataset:
Mineralosphere Microbiome Leading to Changed Geochemical Properties of Sedimentary Rocks from Aiqigou Mud Volcano, Northwest China

The properties of rocks can be greatly affected by seepage hydrocarbons in petroleum-related mud volcanoes. Among them, the color of sedimentary rocks can reflect the changes of sedimentary environment and weathering history. However, little is known about the microbial communities and their biogeochemical significance in these environments. In this study, contrasting rock samples were collected from the Aiqigou mud volcano on the southern margin of the Junggar Basin in Northwest China as guided by rock colors indicative of redox conditions. The physicochemical properties and mineral composition are similar under the same redox conditions. For example, the content of chlorite, muscovite, quartz, and total carbon were higher, and the total iron was lower under reduced conditions compared with oxidized environments. High-throughput sequencing of 16S rRNA gene amplicons revealed that different functional microorganisms may exist under different redox conditions; microbes in oxidized conditions have higher diversity. Statistical analysis and incubation experiments indicated that the microbial community structure is closely related to the content of iron which may be an important factor for color stratification of continental sedimentary rocks in the Aiqigou mud volcano. The interactions between organics and iron-bearing minerals mediated by microorganisms have also been hypothesized.
The Creaming of Short Doughs and Its Impact on the Quality Attributes of Rotary-Molded Biscuits

Scant attention has been given to understanding the impact of creaming stability on the final structure of semi-sweet biscuits, an aspect that has traditionally concerned the biscuit industry. Accordingly, the aim of this study was to analyze the influence of the creaming phase stability on the quality attributes of rotary-molded biscuits. Doughs were formulated with 10.2% of fat (wet basis) and 16.3% of sucrose (w.b.), using two sucrose particle sizes, which were either added directly or after dilution in water at different concentrations. Additionally, the creaming phase was prepared using either a low-shear or a high-shear mixer. The results show that an aqueous-phase migration occurred when the creaming was blended in a low-shear mixer, when using either powdered sucrose or granular sucrose diluted in water at a high concentration. The phase separation was inhibited with the high-shear mixer, which provided a stable creaming. Notwithstanding the variation in creaming stability, no differences were observed in hardness, aeration, sweetness, color and noise intensity. Additionally, the micro-CT analysis revealed that biscuits had a similar microstructure (air porosity and thickness of biscuit walls) when they were prepared with either an unstable or a stable creaming phase. Consequently, creaming stability does not seem to affect the structure and the most relevant sensory attributes of rotary-molded biscuits under this set of experimental conditions, which are representative of those used by the industry for this product category.
Machine Learning Quantitation of Cardiovascular and Cerebrovascular Disease: A Systematic Review of Clinical Applications

Research into machine learning (ML) for clinical vascular analysis, such as those useful for stroke and coronary artery disease, varies greatly between imaging modalities and vascular regions. Limited accessibility to large diverse patient imaging datasets, as well as a lack of transparency in specific methods, are obstacles to further development. This paper reviews the current status of quantitative vascular ML, identifying advantages and disadvantages common to all imaging modalities. Literature from the past 8 years was systematically collected from MEDLINE® and Scopus database searches in January 2021. Papers satisfying all search criteria, including a minimum of 50 patients, were further analysed and extracted of relevant data, for a total of 47 publications. Current ML image segmentation, disease risk prediction, and pathology quantitation methods have shown sensitivities and specificities over 70%, compared to expert manual analysis or invasive quantitation. Despite this, inconsistencies in methodology and the reporting of results have prevented inter-model comparison, impeding the identification of approaches with the greatest potential. The clinical potential of this technology has been well demonstrated in Computed Tomography of coronary artery disease, but remains practically limited in other modalities and body regions, particularly due to a lack of routine invasive reference measurements and patient datasets.
Exosomes as Pleiotropic Players in Pancreatic Cancer

Pancreatic cancer (PC) incidence is rising and due to late diagnosis, combined with unsatisfactory response to current therapeutic approaches, this tumor has an extremely high mortality rate. A better understanding of the mechanisms underlying pancreatic carcinogenesis is of paramount importance for rational diagnostic and therapeutic approaches. Multiple lines of evidence have showed that exosomes are actively involved in intercellular communication by transferring their cargos of bioactive molecules to recipient cells within the tumor microenvironment and systemically. Intriguingly, exosomes may exert both protumor and antitumor effects, supporting or hampering processes that play a role in the pathogenesis and progression of PC, including shifts in tumor metabolism, proliferation, invasion, metastasis, and chemoresistance. They also have a dual role in PC immunomodulation, exerting immunosuppressive or immune enhancement effects through several mechanisms. PC-derived exosomes also induce systemic metabolic alterations, leading to the onset of diabetes and weight loss. Moreover, exosomes have been described as promising diagnostic and prognostic biomarkers for PC. Their potential application in PC therapy as drug carriers and therapeutic targets is under investigation. In this review, we provide an overview of the multiple roles played by exosomes in PC biology through their specific cargo biomolecules and of their potential exploitation in early diagnosis and treatment of PC.
Neuropathology of Animal Prion Diseases

Transmissible Spongiform Encephalopathies (TSEs) or prion diseases are a fatal group of infectious, inherited and spontaneous neurodegenerative diseases affecting human and animals. They are caused by the conversion of cellular prion protein (PrPC) into a misfolded pathological isoform (PrPSc or prion- proteinaceous infectious particle) that self-propagates by conformational conversion of PrPC. Yet by an unknown mechanism, PrPC can fold into different PrPSc conformers that may result in different prion strains that display specific disease phenotype (incubation time, clinical signs and lesion profile). Although the pathways for neurodegeneration as well as the involvement of brain inflammation in these diseases are not well understood, the spongiform changes, neuronal loss, gliosis and accumulation of PrPSc are the characteristic neuropathological lesions. Scrapie affecting small ruminants was the first identified TSE and has been considered the archetype of prion diseases, though atypical and new animal prion diseases continue to emerge highlighting the importance to investigate the lesion profile in naturally affected animals. In this report, we review the neuropathology and the neuroinflammation of animal prion diseases in natural hosts from scrapie, going through the zoonotic bovine spongiform encephalopathy (BSE), the chronic wasting disease (CWD) to the newly identified camel prion disease (CPD).
Broad Reactivity Single Domain Antibodies against Influenza Virus and Their Applications to Vaccine Potency Testing and Immunotherapy

The antigenic variability of influenza presents many challenges to the development of vaccines and immunotherapeutics. However, it is apparent that there are epitopes on the virus that have evolved to remain largely constant due to their functional importance. These more conserved regions are often hidden and difficult to access by the human immune system but recent efforts have shown that these may be the Achilles heel of the virus through development and delivery of appropriate biological drugs. Amongst these, single domain antibodies (sdAbs) are equipped to target these vulnerabilities of the influenza virus due to their preference for concave epitopes on protein surfaces, their small size, flexible reformatting and high stability. Single domain antibodies are well placed to provide a new generation of robust analytical reagents and therapeutics to support the constant efforts to keep influenza in check.
“You Can’t Go to the Park, You Can’t Go Here, You Can’t Go There”: Exploring Parental Experiences of COVID-19 and Its Impact on Their Children’s Movement Behaviours

Abstract: Background The COVID-19 outbreak and related public health guidelines have changed the daily lives of Canadians and restricted opportunities for healthy movement behaviours for children. The purpose of this study was to explore how parents experienced the pandemic-related restrictions and how they impacted their children’s movement behaviours. Methods: Twenty-nine semi-structured one-on-one interviews were conducted (June–July 2020) with parents of children (5–11 years old) in Ontario and British Columbia. Interviews lasted between 24–104 min, were audio-recorded, transcribed verbatim, and thematically analyzed. Results: Findings emphasized various individual (e.g., motivation), interpersonal (e.g., parent work schedule), built (e.g., closure of parks) and natural environment (e.g., weather) factors related to children’s movement behaviours. The findings highlighted the loss of structured activities and destinations for children’s physical activity, and restricted opportunities for outdoor play exacerbated by shrinking childhood independent mobility. Conclusion: Families are adapting to many pandemic-related challenges including adhering to public health restrictions, parents juggling multiple roles, conducting work and school from home, as well as exacerbating factors like weather. It will be important to continue to encourage outdoor time, support policies and practice that facilitate independent mobility, and develop centralized resources that help families in the maintenance of healthy movement behaviours.
Physical properties of ash from co-combustion of coal and biomass

This article presents the tests of fly ash properties which originated from co-combustion. The ash samples for testing came from Polish combined heat and power plants co-firing different types of biomass with hard coal in pulverized and fluidized beds. For comparison purposes, the properties of fly ash from coal combustion also were examined. Measured properties include grain composition, specific density, bulk density, and grain shape. Statistical analysis of results did not demonstrate the influence of biomass on the ash properties.
Newly Emerging Airborne Pollutants: Current Knowledge of Health Impact of Micro and Nanoplastics

Plastics are ubiquitous persistent pollutants, forming the most representative material of the Anthropocene. In the environment, they undergo wear and tear (i.e., mechanical fragmentation, and slow photo and thermo-oxidative degradation) forming secondary microplastics (MPs). Further fragmentation of primary and secondary MPs results in nanoplastics (NPs). To assess potential health damage due to human exposure to airborne MPs and NPs, we summarize the evidence collected to date that, however, has almost completely focused on monitoring and the effects of airborne MPs. Only in vivo and in vitro studies have assessed the toxicity of NPs, and a standardized method for their analysis in environmental matrices is still missing. The main sources of indoor and outdoor exposure to these pollutants include synthetic textile fibers, rubber tires, upholstery and household furniture, and landfills. Although both MPs and NPs can reach the alveolar surface, the latter can pass into the bloodstream, overcoming the pulmonary epithelial barrier. Despite the low reactivity, the number of surface area atoms per unit mass is high in MPs and NPs, greatly enhancing the surface area for chemical reactions with bodily fluids and tissue in direct contact. This is proven in polyvinyl chloride (PVC) and flock workers, who are prone to persistent inflammatory stimulation, leading to pulmonary fibrosis or even carcinogenesis.
Production of Bovine Equol-Enriched Milk: A Review

Simple Summary Milk and dairy products contain many substances beneficial to human health; moreover, the contents of some of these substances can be enhanced. This is also the case of isoflavones which are compounds of plant origin that can be ingested and metabolized by cattle and, subsequently, secreted into bovine milk. An especially healthful substance called equol is ranked among isoflavone metabolites, commonly produced in the digestive tract of cattle. Equol content in milk can be modified by using feedstuffs with different contents of isoflavones or by milk processing and storage. Abstract Milk and dairy products are important sources of nutrients in the human diet because they contain a number of essential substances and other biologically active components. Many of these substances can be modified, and thus offer opportunities to use milk and dairy products as functional food. Isoflavones are particularly important in human nutrition due to their diverse pharmacological and antioxidant properties. The clinical effectiveness of isoflavone-rich products is believed to be dependent on their ability to metabolize daidzein to equol, which may directly exert cancer preventive effects. However, only approximately 30–40% of humans are able to produce equol, while animals, in general, produce equol. Equol is the predominant product of bacterial metabolism of isoflavones and can be found in various amounts in some food of animal origin, especially in milk. Therefore, milk and dairy products can be considered to be sources of equol for humans who are not able to produce this metabolite. When the content of isoflavones in milk is to be modified, two groups of factors should be considered, i.e., dietary factors that include the source of isoflavones and the processing effects on feedstuffs and animal factors that include the intake of isoflavones, ruminal and postruminal changes, and the health and physiological status of animals. The approximate content of isoflavones in milk can be predicted using carry-over rates for different dietary sources or using a formula that describes the relationship between equol concentration in milk and formononetin intake. Processing and storage can affect the content and profile of isoflavones in milk and dairy products.
The Role of Mustelids in the Transmission of Sarcocystis spp. Using Cattle as Intermediate Hosts

Simple Summary Members of the genus Sarcocystis are worldwide distributed protozoan parasites. Sarcocystis infections cause great losses in economically important animals. There is a lack of studies on Sarcocystis in naturally infected wild predators, especially of the family Mustelidae which represent a presumably important group of definitive hosts of these parasites. The objective of the present study was to examine the small intestine samples of various mustelid species from Lithuania serving as a possible source of Sarcocystis spp. using cattle as intermediate hosts. Overall, 84 samples collected from five mustelid species were analyzed. Oocysts/sporocysts of Sarcocystis spp. were detected in 75 animals (89.3%). Using molecular methods four Sarcocystis spp. , S. bovifelis, S. cruzi, S. hirsuta and S. hominis were identified, with the first two being the most prevalent. These results indicate that mustelids are involved in the transmission of Sarcocystis spp. using cattle as intermediate hosts. The determined high prevalence of Sarcocystis spp. rates cause concerns about food safety issues. To control the spread of infection, further studies on the way carcasses of cattle or beef waste become accessible to mustelids are needed. Abstract There is a lack of research on the role of mustelids in the transmission of various Sarcocystis spp. In the present study we tested the hypothesis that widespread mustelids in Lithuania could be involved in the transmission of Sarcocystis spp. using cattle as intermediate hosts. In 2016–2020, intestinal samples of 84 mustelids were examined. Sarcocystis spp. were identified by species-specific PCR targeting the cox1 gene and subsequent sequencing. Under a light microscope, oocysts/sporocysts of Sarcocystis spp. were observed in 40 samples (47.6%), while using molecular methods, they were detected in 75 animals (89.3%). Four Sarcocystis spp. were identified in the intestinal samples of American mink (Neovison vison), Beech marten (Martes foina), European pine marten (Martes martes), European badger (Meles meles) and European polecat (Mustela putorius). The prevalence of predominant Sarcocystis spp. , S. bovifelis (89.3%) and S. cruzi (73.8%) was significantly higher than that of S. hirsuta (3.6%) and S. hominis (1.2%). In an individual sample, most frequently two Sarcocystis spp. were identified (69.0%), then a single species (15.5%) and three species (4.8%). The present study provides strong evidence that mustelids serve as definitive hosts for Sarcocystis spp. using cattle as intermediate hosts.
Resolving Differential Diagnostic Problems in von Willebrand Disease, in Fibrinogen Disorders, in Prekallikrein Deficiency and in Hereditary Hemorrhagic Telangiectasia by Next-Generation Sequencing

Diagnosis of rare bleeding disorders is challenging and there are several differential diagnostics issues. Next-generation sequencing (NGS) is a useful tool to overcome these problems. The aim of this study was to demonstrate the usefulness of molecular genetic investigations by summarizing the diagnostic work on cases with certain bleeding disorders. Here we report only those, in whom NGS was indicated due to uncertainty of diagnosis or if genetic confirmation of initial diagnosis was required. Based on clinical and/or laboratory suspicion of von Willebrand disease (vWD, n = 63), hypo-or dysfibrinogenemia (n = 27), hereditary hemorrhagic telangiectasia (HHT, n = 10) and unexplained activated partial thromboplastin time (APTT) prolongation (n = 1), NGS using Illumina platform was performed. Gene panel covered 14 genes (ACVRL1, ENG, MADH4, GDF2, RASA1, F5, F8, FGA, FGB, FGG, KLKB1, ADAMTS13, GP1BA and VWF) selected on the basis of laboratory results. We identified forty-seven mutations, n = 29 (6 novel) in vWD, n = 4 mutations leading to hemophilia A, n = 10 (2 novel) in fibrinogen disorders, n = 2 novel mutations in HHT phenotype and two mutations (1 novel) leading to prekallikrein deficiency. By reporting well-characterized cases using standardized, advanced laboratory methods we add new pieces of data to the continuously developing “bleeding disorders databases”, which are excellent supports for clinical patient management.
Improved Influenza Diagnostics through Thermal Contrast Amplification

Influenza poses a serious health threat and creates an economic burden for people around the world. The accurate diagnosis of influenza is critical to the timely clinical treatment of patients and the control of outbreaks to protect public health. Commercially available rapid influenza diagnostic tests (RIDTs) that are operated by visual readout are widely used in clinics to screen influenza infections, but RIDTs suffer from imperfect analytical sensitivity, especially when the virus concentration in the sample is low. Fortunately, the sensitivity can be simply improved through an add-on signal amplification step, i.e., thermal contrast amplification (TCA). To demonstrate the advantage of TCA for influenza diagnosis, we conducted a prospective cohort study on 345 clinical specimens collected for influenza A and B testing during the 2017–2018 influenza season. All samples were tested using the Quidel QuickVue Influenza A + B test, followed by a TCA readout, and then confirmatory polymerase chain reaction testing. Through the TCA detecting sub-visual weak positives, TCA reading improved the overall influenza sensitivity by 53% for influenza A and 33% for influenza B over the visual RIDTs readings. Even though the specificity was compromised slightly by the TCA protocol (relative decrease of 0.09% for influenza A and 0.01% for influenza B), the overall performance was still better than that achieved by visual readout based on comparison of their plots in receiver operating characteristic space and F1 scores (relative increase of 14.5% for influenza A and 12.5% for influenza B). Performing a TCA readout on wet RIDTs also improved the overall TCA performance (relative increase in F1 score of 48%). Overall, the TCA method is a simple and promising way to improve the diagnostic performance of commercial RIDTs for infectious diseases, especially in the case of specimens with low target analytes.
Additional Tissue Sampling Trials Did Not Change Our Thyroid Practice

Simple Summary Some studies have suggested that the use of additional tissue blocks to diagnose follicular thyroid carcinoma (FTC) could increase the accuracy of diagnosis and improve prognosis, and entire capsule sampling was recommended for a definitive diagnosis of borderline thyroid tumors in 2016. We conducted a study in 2016 to examine whether additional tissue sampling of the encapsulated follicular tumor increases the diagnosis of malignant cases in our patient cohort. Furthermore, the diagnosis was reclassified according to the 4th edition of the World Health Organization’s classification system. The additional tissue sampling only had a slight impact on our thyroid practice and resulted in no benefits to the patient; therefore, we decided to cease it. Abstract This study aimed to determine whether additional tissue sampling of encapsulated thyroid nodules would increase the frequency of follicular thyroid carcinoma (FTC) diagnoses. We examined thyroid tissue specimens from 86 patients suspected of FTC (84.9% female; mean age, 49.0 ± 17.8 years). The number of tissue blocks created for pathological assessments ranged from 3 to 20 (mean, 9.1 ± 4.1); the numbers in the previous method recommended by the Japanese General Rules for the Description of Thyroid Cancer and additional blocks ranged from 1 to 12 (mean, 6.0 ± 2.8) and from 1 to 8 (mean, 3.1 ± 2.0), respectively. The additional blocks were subsequently examined to determine whether any diagnoses changed from those based on the previous method. Five patients were diagnosed with FTC using the previous method; however, additional tissue blocks led to the diagnosis of FTC in 6 patients, as 1 diagnosis was revised from follicular adenoma to FTC. It has been reported that increasing the number of tissue blocks used for pathological assessments can increase the frequency of FTC diagnoses; however, this was not clinically significant in thyroid carcinoma, which requires completion thyroidectomy and radioactive iodine treatment. It resulted in no benefits to the patient because all minimally invasive FTCs, follicular tumors of uncertain malignant potential (FT-UMP), and follicular adenomas are treated with lobectomy alone in Japan. Additional tissue sampling only had a slight impact on our thyroid practice; therefore, we decided to cease it.