Miracle-dz/UniFAR-FTUs huggingface dataset:
Simultaneous Fluorescent Identification of Odontoblasts and Ameloblasts

The tooth is mainly composed of dentin and enamel. Identification of dentin-producing odontoblasts and enamel-producing ameloblasts using reporter techniques is useful to study tooth development and regeneration with tissue engineering. Ameloblasts express Amelogenin, Ameloblastin, Enamelin, and Amelotin, whereas odontoblasts express Dentin sialophosphoprotein (Dspp) and Dentin matrix protein1 (Dmp1). Although there are several transgenic lines using promoter elements or bacterial artificial chromosomes (BACs) to label odontoblasts and ameloblasts, there is a possibility that the expression patterns vary from the endogenous genes. Here, we established 2 lines of mice where tdTomato was knocked into the second exon of X-chromosomal Amelogenin (Amelx), and green fluorescent protein (GFP) was knocked into the second exon of Dspp. tdTomato and GFP were highly expressed on secretory ameloblasts and secretory and fully differentiated odontoblasts, respectively. In addition, DSPP and AMELX were not produced in the dentin matrix and enamel matrix of Dspp GFP/GFP and Amelx tdTomato male mice (as representative of AmelxtdTomato/Y hemizygous male mice), respectively. Moreover, micro–computed tomography analysis of Amelx tdTomato male mice revealed a notable reduction in enamel volume but increased dentin mineral density. Dspp GFP/GFP mice had reduced dentin mineral density. To identify odontoblasts and ameloblasts from developing tooth, we examined the expression of mesenchymal cell surface molecules CD90, CD166 and epithelial cell surface molecules CD49f, Epcam1 with fluorescence on odontoblasts and ameloblasts in these mice. We found that GFP+ odontoblasts and tdTomato+ ameloblasts in tooth germ from 0.5-d-old DsppGFP/+ mice and Amelx tdTomato male mice were enriched in CD45−/Ter119−/Epcam1−/CD90+/Integrin α4+cell fractions and CD45−/Ter119−/Epcam1+/CD49f+/CD147+ cell fractions, respectively. By using antibodies against mesenchymal and epithelial cell surface molecules and fluorescence, we can easily distinguish odontoblasts from ameloblasts and isolate each cell for further studies. These mice would serve as useful models for tooth development and regeneration as well as provide concurrent observation for the differentiation processes of odontoblasts and ameloblasts in vivo and in vitro.
Ensuring seafood safe to spoon: a brief review of biosensors for marine biotoxin monitoring

Abstract With harmful algal blooms, marine food poisoning caused by marine biotoxins frequently occurs and is life-threatening if severe. However, the conventional detection methods of marine toxins have a few limitations: low sensitivity and high-cost. Therefore, it is necessary to establish a fast and sensitive on-site detection method for real seafood sample. Biosensors based on aptamers, antibodies, and cells have been applied in marine toxins monitoring. This review presents the classification and toxic effects of marine toxins, and recent biosensor for marine toxin detection. In addition, we have compared the superiority and limitation of these biosensors. Finally, challenges and opportunities of biosensors in food safety detection were discussed. Considering the excellent results achieved by the aptasensor in the field of detection, it seems ready to be put into practical applications.
Description and etiology of paleopathological lesions in the type specimen of Parasaurolophus walkeri (Dinosauria: Hadrosauridae), with proposed reconstructions of the nuchal ligament

Paleopathology, or the study of ancient injuries and diseases, can enable the ecology and life history of extinct taxa to be deciphered. Large‐bodied ornithopods are the dinosaurs with the highest frequencies of paleopathology reported to‐date. Among these, the crested hadrosaurid Parasaurolophus walkeri is one of the most famous, largely due to its dramatic elongated and tubular nasal crest. The holotype of Parasaurolophus walkeri at the Royal Ontario Museum, Canada, displays several paleopathologies that have not been discussed in detail previously: a dental lesion in the left maxilla, perhaps related to periodontal disease; callus formation associated with fractures in three dorsal ribs; a discoidal overgrowth above dorsal neural spines six and seven; a cranially oriented spine in dorsal seven, that merges distally with spine six; a V‐shaped gap between dorsal spines seven and eight; and a ventral projection of the pubic process of the ilium which covers, and is fused with, the lateral side of the iliac process of the pubis. These lesions suggest that the animal suffered from one or more traumatic events, with the main one causing a suite of injuries to the anterior aspect of the thorax. The presence of several lesions in a single individual is a rare observation and, in comparison with a substantial database of hadrosaur paleopathological lesions, has the potential to reveal new information about the biology and behavior of these ornithopods. The precise etiology of the iliac abnormality is still unclear, although it is thought to have been an indirect consequence of the anterior trauma. The discoidal overgrowth above the two neural spines also seems to be secondary to the severe trauma inflicted on the ribs and dorsal spines, and probably represents post‐traumatic ossification of the base of the nuchal ligament. The existence of this structure has previously been considered in hadrosaurs and dinosaurs more generally through comparison of origin and insertion sites in modern diapsids (Rhea americana, Alligator mississippiensis, Iguana iguana), but its presence, structure, and origin‐attachment sites are still debated. The V‐shaped gap is hypothesized as representing the point between the stresses of the nuchal ligament, pulling the anterior neural spines forward, and the ossified tendons pulling the posterior neural spines backward. Different reconstructions of the morphology of the structure based on the pathological conditions affecting the neural spines of ROM 768 are proposed. Finally, we review the history of reconstructions for Parasaurolophus walkeri showing how erroneous misconceptions have been perpetuated over time or have led to the development of new hypotheses, including the wide neck model supported in the current research.
The Arabidopsis Mitochondrial Glutaredoxin GRXS15 Provides [2Fe-2S] Clusters for ISCA-Mediated [4Fe-4S] Cluster Maturation

Iron-sulfur (Fe-S) proteins are crucial for many cellular functions, particularly those involving electron transfer and metabolic reactions. An essential monothiol glutaredoxin GRXS15 plays a key role in the maturation of plant mitochondrial Fe-S proteins. However, its specific molecular function is not clear, and may be different from that of the better characterized yeast and human orthologs, based on known properties. Hence, we report here a detailed characterization of the interactions between Arabidopsis thaliana GRXS15 and ISCA proteins using both in vivo and in vitro approaches. Yeast two-hybrid and bimolecular fluorescence complementation experiments demonstrated that GRXS15 interacts with each of the three plant mitochondrial ISCA1a/1b/2 proteins. UV-visible absorption/CD and resonance Raman spectroscopy demonstrated that coexpression of ISCA1a and ISCA2 resulted in samples with one [2Fe-2S]2+ cluster per ISCA1a/2 heterodimer, but cluster reconstitution using as-purified [2Fe-2S]-ISCA1a/2 resulted in a [4Fe-4S]2+ cluster-bound ISCA1a/2 heterodimer. Cluster transfer reactions monitored by UV-visible absorption and CD spectroscopy demonstrated that [2Fe-2S]-GRXS15 mediates [2Fe-2S]2+ cluster assembly on mitochondrial ferredoxin and [4Fe-4S]2+ cluster assembly on the ISCA1a/2 heterodimer in the presence of excess glutathione. This suggests that ISCA1a/2 is an assembler of [4Fe-4S]2+ clusters, via two-electron reductive coupling of two [2Fe-2S]2+ clusters. Overall, the results provide new insights into the roles of GRXS15 and ISCA1a/2 in effecting [2Fe-2S]2+ to [4Fe-4S]2+ cluster conversions for the maturation of client [4Fe-4S] cluster-containing proteins in plants.
A Cluster-Randomized Trial of Hydroxychloroquine for Prevention of Covid-19

Abstract Background Current strategies for preventing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are limited to nonpharmacologic interventions. Hydroxychloroquine has been proposed as a postexposure therapy to prevent coronavirus disease 2019 (Covid-19), but definitive evidence is lacking. Methods We conducted an open-label, cluster-randomized trial involving asymptomatic contacts of patients with polymerase-chain-reaction (PCR)–confirmed Covid-19 in Catalonia, Spain. We randomly assigned clusters of contacts to the hydroxychloroquine group (which received the drug at a dose of 800 mg once, followed by 400 mg daily for 6 days) or to the usual-care group (which received no specific therapy). The primary outcome was PCR-confirmed, symptomatic Covid-19 within 14 days. The secondary outcome was SARS-CoV-2 infection, defined by symptoms compatible with Covid-19 or a positive PCR test regardless of symptoms. Adverse events were assessed for up to 28 days. Results The analysis included 2314 healthy contacts of 672 index case patients with Covid-19 who were identified between March 17 and April 28, 2020. A total of 1116 contacts were randomly assigned to receive hydroxychloroquine and 1198 to receive usual care. Results were similar in the hydroxychloroquine and usual-care groups with respect to the incidence of PCR-confirmed, symptomatic Covid-19 (5.7% and 6.2%, respectively; risk ratio, 0.86 [95% confidence interval, 0.52 to 1.42]). In addition, hydroxychloroquine was not associated with a lower incidence of SARS-CoV-2 transmission than usual care (18.7% and 17.8%, respectively). The incidence of adverse events was higher in the hydroxychloroquine group than in the usual-care group (56.1% vs. 5.9%), but no treatment-related serious adverse events were reported. Conclusions Postexposure therapy with hydroxychloroquine did not prevent SARS-CoV-2 infection or symptomatic Covid-19 in healthy persons exposed to a PCR-positive case patient. (Funded by the crowdfunding campaign YoMeCorono and others; BCN-PEP-CoV2 ClinicalTrials.gov number, NCT04304053.)
Species sensitivities to a global pollutant: A meta‐analysis on acoustic signals in response to anthropogenic noise

Anthropogenically driven environmental changes affect our planet at an unprecedented rate. Among these changes are those in the acoustic environment caused by anthropogenic noise, which can affect both animals and humans. In many species, acoustic communication plays a crucial role to maintain social relationships by exchanging information via acoustic signals. However, how species relying on acoustic communication differ in their adjustments to anthropogenic noise is little understood. Yet, this is crucial because protecting species effectively depends on our capability to predict how species differ in their response to human‐induced environmental changes. Using a phylogenetically controlled meta‐analysis, we quantified differences in adjustments of acoustic signals to anthropogenic noise among species. The effect sizes included in the analysis were obtained from noise exposure experiments, as only carefully controlled experiments allow to establish cause‐and‐effect relationships. We found that animals changed acoustic signals when exposed to noise, but the magnitude and the direction of adjustments differed among species. Given the importance of communication in the animal kingdom, these adjustments can affect social relationships in many species. The diversity of responses among species highlights the necessity to assess the effect of environmental stressors not only for a few species, because an effect may be positive in one species but negative in another depending on the species’ biology. Thus, an effective conservation approach to protect different species is to preserve natural soundscapes of ecosystems to which species have adapted to by reducing or mitigating the emission of anthropogenic noise into the environment.
Associations of Relative Humidity and Lifestyles with Metabolic Syndrome among the Ecuadorian Adult Population: Ecuador National Health and Nutrition Survey (ENSANUT-ECU) 2012

The effects of the physical environment on metabolic syndrome (MetS) are still largely unexplained. This study aimed to analyze the associations of relative humidity of residence, lifestyles, and MetS among Ecuadorian adults. Data from 6024 people aged 20 to 60 years were obtained from an Ecuador national population-based health and nutrition survey (i.e., ENSANUT-ECU, 2012) and the mean annual relative humidity (%) from the Ecuador National Institute for Meteorology and Hydrology (2012). Odds ratio (OR) with 95% confidence intervals (CI) for MetS according to groups of relative humidity were calculated using multiple logistic regression. Living in high relative humidity (>80%) increased ORs of reduced high-density lipoprotein (HDL) cholesterol (1.25; 95 % CI, 1.06–1.56) and MetS (OR = 1.20; 95 % CI,1.01–1.42) in women. Furthermore, physically active men living in high relative humidity showed lower OR of elevated triglycerides (0.56; 95 % CI,0.37–0.85) while menopausal women living in high relative humidity showed increased ORs of MetS (5.42; 95 % CI, 1.92–15.27), elevated blood pressure (3.10; 95 % CI, 1.15–8.35), and increased waist circumference (OR = 1.34; 95 % CI, 1.09–1.63). Our results show that residence in high relative humidity and menopausal status increase ORs of MetS and its components in Ecuadorian women; however, physical activity significantly reduces the OR of elevated triglycerides in men. The obtained findings may help make public health policies regarding environmental humidity management, nutritional education, menopausal care, and physical activity promotion to prevent the onset of MetS among Ecuadorian adults.
Conceptualisations of masculinity and sexual development among boys and young men in Korogocho slum in Kenya

Abstract Youth and adolescence are times when young men negotiate their identity in relation to social and cultural expectations of being a man, with enduring implications for sexual health and wellbeing. This study explored how boys aged 10–14 years living in Korogocho slum in Nairobi, Kenya conceptualised masculinity, their perceptions of how masculinities are performed, and the linkage between conceptualisations of masculinity and sexual development. Three bases of gender socialisation were identified: (1) verbal messaging (mainly from parents and teachers); (2) observing the behaviours of older men in the community; and (3) information received from mainstream and social media. Masculinity conceptualisations focussed on financial stability, family life and responsibility, physical attributes, character and religion. Two contrasting portrayals of masculinity emerged in the form of idealised and dominant masculinities. A close linkage was found between masculinity conceptualisations and sexual development. Findings are important for programmes that aim to transform harmful gender norms and signal the need for longitudinal research exploring how gender beliefs may change over time.
A Tacholess Order Tracking Method Based on Inverse Short Time Fourier Transform and Singular Value Decomposition for Bearing Fault Diagnosis

Order tracking has been widely used to diagnose failures of variable speed rotating machines. The performance of the TOT (Time-Frequency Domain Tacholess Order Tracking) methods is based on the correct separation of the target component strictly related to the shaft rotation frequency. Currently, most of the methods have focused on obtaining the instantaneous frequency with accuracy. In this paper, a new TOT method has been proposed that combines the inverse short-time Fourier transform (ISTFT) with singular value decomposition (SVD). The target component closely related to the shaft rotation frequency is selected and filtered approximately in the time-frequency domain. Hence, the ISTFT is adopted to reverse the target component into the time domain. Next, SVD is used to refine the roughly filtered target component. Finally, the phase of the refined signal is extracted to resample the original signal. The performance of the method was tested using real vibration signals collected from a large-scale test rig of a high-speed train traction system.
Bifunctional Carbon Dots Derived From an Anaerobic Bacterium of Porphyromonas gingivalis for Selective Detection of Fe3+ and Bioimaging

In this study, for the first time, Porphyromonas gingivalis, an anaerobic bacterium, was selected to synthesize carbon dots. The achieved P. gingivalis–carbon dots (Pg‐CDs) exhibited strong fluorescence and high stability with capability for dual function as Fe3+ sensor and intracellular imaging agent. The detection limit for Fe3+ was as low as 1.85 µm. On the other hand, the prepared Pg‐CDs were an excellent candidate for biosensor with high biocompatibility.
The miRNA Content of Exosomes Released from the Glioma Microenvironment Can Affect Malignant Progression

Low-grade gliomas (LGG) are infiltrative primary brain tumors that in 70% of the cases undergo anaplastic transformation, deeply affecting prognosis. However, the timing of progression is heterogeneous. Recently, the tumor microenvironment (TME) has gained much attention either as prognostic factor or therapeutic target. Through the release of extracellular vesicles, the TME contributes to tumor progression by transferring bioactive molecules such as microRNA. The aim of the study was to take advantage of glioma-associated stem cells (GASC), an in vitro model of the glioma microenvironment endowed with a prognostic significance, and their released exosomes, to investigate the possible role of exosome miRNAs in favoring the anaplastic transformation of LGG. Therefore, by deep sequencing, we analyzed and compared the miRNA profile of GASC and exosomes obtained from LGG patients characterized by different prognosis. Results showed that exosomes presented a different signature, when compared to their cellular counterpart and that, although sharing several miRNAs, exosomes of patients with a bad prognosis, selectively expressed some miRNAs possibly responsible for the more aggressive phenotype. These findings get insights into the value of TME and exosomes as potential biomarkers for precision medicine approaches aimed at improving LGG prognostic stratification and therapeutic strategies.
Timing of Pulmonary Rehabilitation in Readmitted Patients with Severe Chronic Obstructive Pulmonary Disease: A Randomized Clinical Trial

Abstract Early pulmonary rehabilitation (PR), started during hospitalization or within the first month after discharge, has been shown to reduce exacerbations and improve health-related-quality of life (HRQoL) and exercise capacity. However, no randomized clinical trials (RCT) have compared the efficacy of PR started during hospitalization (DHPR) to PR initiated one month post-hospitalization (PHPR). We conducted an RCT to compare DHPR to PHPR in severe patients with COPD readmitted for exacerbations in a tertiary hospital setting. Patients were randomized to receive three months of DHPR or PHPR. Outcomes were assessed at completion of the PR programme and at months 3 and 9. A total of 53 patients (26 DHPR and 27 PHPR) were included. There were no between-group differences in the number of exacerbations (mean, 3.62 vs. 3.04 in the DHPR and PHPR groups, respectively; p = 0.403). Dyspnea in activities of daily living, exercise capacity, and all HRQoL parameters improved in the PHPR group. In the DHPR group, improvement was observed only for some HRQoL parameters. All gains in both groups were lost during follow-up. More adverse events were observed in the DHPR group (20 vs 5, p = 0.023), although none of these were clinically significant. In this sample of patients with severe COPD readmitted to the hospital for exacerbations, both approaches to PR were safe, but PHPR yielded better outcomes overall. These findings suggest that, PR should be initiated in patients with severe COPD only after hospital discharge when the patients’ clinical condition has stabilized.
CADE: Detecting and Explaining Concept Drift Samples for Security Applications

Concept drift poses a critical challenge to deploy machine learning models to solve practical security problems. Due to the dynamic behavior changes of attackers (and/or the benign counterparts), the testing data distribution is often shifting from the original training data over time, causing major failures to the deployed model. To combat concept drift, we present a novel system CADE aiming to 1) detect drifting samples that deviate from existing classes, and 2) provide explanations to reason the detected drift. Unlike traditional approaches (that require a large number of new labels to determine concept drift statistically), we aim to identify individual drifting samples as they arrive. Recognizing the challenges introduced by the high-dimensional outlier space, we propose to map the data samples into a low-dimensional space and automatically learn a distance function to measure the dissimilarity between samples. Using contrastive learning, we can take full advantage of existing labels in the training dataset to learn how to compare and contrast pairs of samples. To reason the meaning of the detected drift, we develop a distance-based explanation method. We show that explaining “distance” is much more effective than traditional methods that focus on explaining a “decision boundary” in this problem context. We evaluate CADE with two case studies: Android malware classification and network intrusion detection. We further work with a security company to test CADE on its malware database. Our results show that CADE can effectively detect drifting samples and provide semantically meaningful explanations.
Investigation of a Truncated Aptamer for Ofloxacin Detection Using a Rapid FRET-Based Apta-Assay

In this work, we describe the use of a new truncated aptamer for the determination of ofloxacin (OFL), being a principal quinolone commonly used in both human and animal healthcare. Since the affinity of a 72-mer ssDNA sequence has been previously described without further investigations, this paper demonstrates the first computational prediction of the binding motif between this aptamer and OFL through in silico molecular docking studies. Besides, we suggest the application of the characterized recognition mechanism in a simple FRET (Förster Resonance Energy Transfer) pattern for the rapid aptasensing of the quinolone of interest. Accordingly, our approach harnesses the fluorescence quenching of the fluorescein-tagged aptamer (FAM-APT) induced by its partial hybridization to a tetramethyl rhodamine-labelled complementary ssDNA (TAMRA-cDNA). In such a structure, dye labels brought into close proximity act as a FRET pair. Upon ofloxacin addition, an affinity competition occurs to form a more stable FAM-APT/OFL complex, thus unquenching the FAM-APT signal. Interestingly, the recovered fluorescence intensity was found to correlate well with the antibiotic’s concentrations in the range of 0.2–200 μM in HEPES buffer, with a linear response that ranged between 0.2 and 20 μM. The rapid apta-assay achieved limits of detection and quantification of 0.12 and 0.40 μM, respectively. The truncated aptamer has also shown an improved specificity toward OFL than other quinolones, compared to the original full-length aptamer described in previous works. Finally, the practical application of the developed apta-assay was successfully confirmed to detect OFL quinolone in spiked milk samples, with satisfactory recoveries ranging between 97.4% and 111.4%.