Miracle-dz/UniFAR-FTUs huggingface dataset:
Circular RNA circRNA_0082835 promotes progression and lymphatic metastasis of primary melanoma by sponging microRNA miRNA-429

ABSTRACT To identify how circular RNA circRNA_0082835 impacts melanoma cells and lymphatic metastasis to observe whether it exerts effects through its action mechanism of sponging microRNA miR-429. Clinical baseline information was collected, and clinical samples were used for detection on circRNA_0082835 and EZH2. The expression of circRNA_0082835, EZH2, and miR-429 was detected by quantitative real-time PCR (RT-qPCR). Cell proliferation was tested with cell counting kit-8 (CCK-8). Flow cytometry was applied to examination of cell cycle levels. Cell invasion and migration were observed by transwell and wound healing. The expression of Wnt/β-catenin pathway, cell cycle and epithelial–mesenchymal transition (EMT) marker proteins was analyzed by western blot. Dual-luciferase determined the binding of miR-429 and circ_0082835. As a result, the expression of circRNA_0082835 was increased and that of miR-429 was decreased with the increase in lymphatic metastasis level. CircRNA_0082835 expression was downregulated by circ_0082835 interference, upregulated by EZH2 interference and also downregulated after transfection of both shRNA-circ_0082835 and shRNA-EZH2. Inhibiting circ_0082835 and EZH2 suppressed the proliferation, invasion and migration, regulated the cell cycle levels, inhibited Wnt/β-catenin and attenuated EMT in melanoma cells. Inhibition of circ_0082835 and/or EZH2 elevated miR-429 expression. The binding among miR-429 and circ_0082835 was verified. MiR-429 inhibitor reversed the effect of circ_0082835 interference while having no significant impact on EZH2. In conclusion, circRNA_0082835 sponges miR-429 to affect the anti-tumor effect of miR-429 in primary melanoma and lymphatic metastasis. Graphical Abtstract
Phonological variations in typically-developing Italian-speaking children aged 3;0-4;11

ABSTRACT Normative data on phonological acquisition of a language are a prerequisite for evaluating children’s speech sound competences. To date, these data are not sufficiently available for Italian. This study, therefore, aimed to describe the phonological development of 183 typically developing monolingual Italian-speaking children aged 3;0–4;11 (four 6-months age bands). Participants were assessed through a picture naming task, and performances analysed in terms of number of phonological variations (Tokens), Types and percentage of occurrence of patterns, and number of infrequent variants (InfrVar) as a measure of stability in speech production. Two cut-off criteria to distinguish InfrVar from phonological patterns were applied. Results showed a gradual reduction of all measures with increasing age. Twenty-two patterns generally in line with previous Italian and cross-linguistic studies were observed, with only five patterns and two phonetic distortions occurring across all age groups. Eight patterns only emerged when applying the lower cut-off criterion, while further seven patterns only occurred with very low frequency or in isolated age groups. These findings highlight the influence of the selected cut-off criterion on the identification of patterns and raise the question of whether some patterns should rather be considered InfVar. Data on younger children are still needed to clarify whether low-frequency patterns are patterns of younger typically developing children that have almost resolved in the age groups assessed. At least half of the phonological variation Tokens fell into the category of InfrVar, indicating a need to pay more attention to this so far ignored measure.
Kinematic gait characteristics of straight line walk in clinically sound dairy cows

The aim of this study is to describe the kinematic gait characteristics of straight line walk in clinically sound dairy cows using body mounted Inertial Measurement Units (IMUs) at multiple anatomical locations. The temporal parameters used are speed and non-speed normalized stance duration, bipedal and tripedal support durations, maximal protraction and retraction angles of the distal limbs and vertical displacement curves of the upper body. Gait analysis was performed by letting 17 dairy cows walk in a straight line at their own chosen pace while equipped with IMU sensors on tubera sacrale, left and right tuber coxae (LTC and RTC), back, withers, head, neck and all four lower limbs. Data intervals with stride by stride regularity were selected based on video data. For temporal parameters, the median was calculated and 95% confidence intervals (CI) were estimated based on linear mixed model (LMM) analysis, while for limb and vertical displacement curves, the median and most typical curves were calculated. The temporal parameters and distal limb angles showed consistent results with low variance and LMM analysis showed non-overlapping CI for all temporal parameters. The distal limb angle curves showed a larger and steeper retraction angle range for the distal front limbs compared with the hind limbs. The vertical displacement curves of the sacrum, withers, LTC and RTC showed a consistent sinusoidal pattern while the head, back and collar curves were less consistent and showed more variation between and within cows. This kinematic description might allow to objectively differentiate between normal and lame gait in the future and determine the best anatomical location for sensor attachment for lameness detection purposes.
Recessive/dominant model: Alternative choice in case-control-based genome-wide association studies

An additive genetic model is usually employed in case-control-based genome-wide association studies. The model usually encodes "AA", "Aa" and "aa" ("a" represents the minor allele) as three different numbers, implying the contribution of genotype "Aa" to the phenotype is different from "AA" and "aa". From the perspective of biological phenomena, the coding is reasonable since the phenotypes of lives are not "black and white". A case-control based study, however, has only two phenotypes, case and control, which means that the phenotypes are "black and white". It suggests that a recessive/dominant model may be an alternative to the additive model. In order to investigate whether the alternative is feasible, we conducted comparative experiments on several models used in those studies through chi-square test and logistic regression. Our simulation experiments demonstrate that a recessive model is better than the additive model. The area under the curve of the former has increased by 5% compared with the latter, the discrimination of identifying risk single nucleotide polymorphisms has been improved by 61%, and the precision has also reached 1.10 times that of the latter. Furthermore, the real data experiments show that the precision and area under the curve of the former are 16% and 20% higher than the latter respectively, and the area under the curve of dominant model of the former is 13% higher than the latter. The results indicate a recessive/dominant model may be an alternative to the additive model and suggest a new route for case-control-based studies.
Draft Genome Sequence of Aeromonas popoffii ID682, Isolated from a Natural Water Source in Idaho

A draft genome sequence of Aeromonas popoffii ID682, isolated from a natural water source in Idaho, is presented here. A. popoffii is a relatively understudied species within a diverse, expanding freshwater genus of bacteria. Here, we describe only the second genome published for this species to date. ABSTRACT A draft genome sequence of Aeromonas popoffii ID682, isolated from a natural water source in Idaho, is presented here. A. popoffii is a relatively understudied species within a diverse, expanding freshwater genus of bacteria. Here, we describe only the second genome published for this species to date.
Coleofasciculaceae, a Monophyletic Home for the Microcoleus steenstrupii Complex and Other Desiccation‐tolerant Filamentous Cyanobacteria

Cyanobacteria classified as Microcoleus steenstrupii play a significant role as pioneers of biological soil crusts (biocrusts), but this taxon is recognized to constitute a diverse complex of strains and field populations. With the aim of clarifying its systematics, we conducted a polyphasic characterization of this and allied taxa. A 16S ribosomal gene meta‐analysis of published environmental sequences showed that the complex encompasses a variety of well supported genus‐level clades with clade‐specific environmental preferences, indicating significant niche differentiation. Fifteen strains in the M. steenstrupii complex were selected as representative of naturally occurring clades and studied using 16S rRNA gene phylogeny, morphology, and niche delineation with respect to temperature and rainfall. Bayesian phylogenetic reconstructions within a comprehensive, curated database of long 16S rRNA cyanobacterial sequences (1,000 base pairs or more) showed that they all belonged in a monophyletic, family‐level clade (91.4% similarity) that included some other known genera of desiccation‐resistant, largely terrestrial, filamentous, nonheterocystous cyanobacteria, including Coleofasciculus, the type genus for the family Coleofasciculaceae. To accommodate this biodiversity, we redescribe the Coleofasciculaceae, now composed of 11 genera, among which six are newly described herein (Funiculus, Parifilum, Arizonema, Crassifilum, Crustifilum, and Allocoleopsis), and five were previously recognized (Porphyrosiphon, Coleofasciculus, Pycnacronema, Potamolinea, and Wilmottia). We provide an evaluation of their respective niches and global distributions within biocrusts based on published molecular data. This new systematics treatment should help simplify and improve our understanding of the biology of terrestrial cyanobacteria.
Sepsis in patients hospitalized with coronavirus disease 2019: how often and how severe?

Purpose of review To discuss why severe COVID-19 should be considered sepsis and how co-infection and secondary infection can aggravate this condition and perpetuate organ dysfunction leading to high mortality rates. Recent findings In severe COVID-19, there is both direct viral toxicity and dysregulated host response to infection. Although both coinfection and/or secondary infection are present, the latest is of greater concern mainly in resource-poor settings. Patients with severe COVID-19 present a phenotype of multiorgan dysfunction that leads to death in an unacceptable high percentage of the patients, with wide variability around the world. Similarly to endemic sepsis, the mortality of COVID-19 critically ill patients is higher in low-income and middle-income countries as compared with high-income countries. Disparities, including hospital strain, resources limitations, higher incidence of healthcare-associated infections (HAI), and staffing issues could in part explain this variability. Summary The high mortality rates of critically ill patients with severe COVID-19 disease are not only related to the severity of patient disease but also to modifiable factors, such as the ICU strain, HAI incidence, and organizational aspects. Therefore, HAI prevention and the delivery of best evidence-based care for these patients to avoid additional damage is important. Quality improvement interventions might help in improving outcomes mainly in resource-limited settings.
Development of a protocol and a clinical tool to assess the audiological needs of younger and older adults with hearing loss

Abstract Objective To develop a protocol and a clinical tool to assess the audiological needs of younger and older adults with hearing loss. Design A needs assessment protocol was developed based on recommendations of an expert panel, existing literature, the International Classification of Functioning, Disability and Health, client-centered care and goal setting. The protocol was reviewed by the expert panel. Semi-structured interviews were conducted with clinical audiologists to validate its content and explore its clinical applicability. A clinical tool was developed to make the administration of the protocol more uniform. Study sample 15 experts and 14 clinical audiologists. Results Feedback received from the participants (experts and clinicians) supported the content validity of the needs assessment protocol and clinical tool. The topics covered within the protocol and tool include: Audiological needs (activity limitations, participation restrictions, environmental factors), Living conditions (social networks, living environment), Personal factors, Discussion with the client to define the intervention plan, and Recommendations. Conclusions A protocol and a clinical tool were developed to help audiologists and clients undertake a comprehensive audiological needs assessment. The content validity of the protocol and tool were demonstrated. Their use can facilitate the delivery of a client-centered assessment using a uniform and comprehensive approach.
EasyNAT MTC assay: A simple, rapid, and low-cost cross-priming amplification method for the detection of mycobacterium tuberculosis suitable for point-of-care testing

ABSTRACT More sensitive, rapid, and affordable diagnostic tools for pulmonary tuberculosis (PTB) are urgently needed. This study aimed to assess the performance of EasyNAT MTC (abbreviation: EasyNAT) (Ustar Biotechnologies, China), a novel isothermal amplification method with a turnaround time of less than two hours that requires a few manual steps to process the sputum. Sputum samples from 249 patients with suspected PTB were subjected to smear, culture, Xpert MTB/RIF (Cepheid, USA) and EasyNAT assay testing. Of the 169 PTB patients, EasyNAT detected more PTB patients than Xpert (72.19% vs. 61.54%, P < 0.05, χ2 = 4.326). Both the Xpert assay and EasyNAT assay detected almost all the culture-positive sputa successfully, but EasyNAT yielded more positive results among the smear-negative and culture-negative PTB cases (44.59% (33/74) vs. 22.97% (17/74), P < 0.01, χ2 = 7.732). Although the specificity of EasyNAT was lower in contrast to Xpert [95.00% (76/80) vs. 98.75% (79/80)], the difference was not significant (P = 0.363, χ2 = 0.826). EasyNAT could be used as an initial test for PTB diagnosis due to its simplicity, rapid turnaround time, high sensitivity, and low cost.
Predicting Writing Styles of Web-Based Materials for Children’s Health Education Using the Selection of Semantic Features: Machine Learning Approach

Background Medical writing styles can have an impact on the understandability of health educational resources. Amid current web-based health information research, there is a dearth of research-based evidence that demonstrates what constitutes the best practice of the development of web-based health resources on children’s health promotion and education. Objective Using authoritative and highly influential web-based children’s health educational resources from the Nemours Foundation, the largest not-for-profit organization promoting children’s health and well-being, we aimed to develop machine learning algorithms to discriminate and predict the writing styles of health educational resources on children versus adult health promotion using a variety of health educational resources aimed at the general public. Methods The selection of natural language features as predicator variables of algorithms went through initial automatic feature selection using ridge classifier, support vector machine, extreme gradient boost tree, and recursive feature elimination followed by revision by education experts. We compared algorithms using the automatically selected (n=19) and linguistically enhanced (n=20) feature sets, using the initial feature set (n=115) as the baseline. Results Using five-fold cross-validation, compared with the baseline (115 features), the Gaussian Naive Bayes model (20 features) achieved statistically higher mean sensitivity (P=.02; 95% CI −0.016 to 0.1929), mean specificity (P=.02; 95% CI −0.016 to 0.199), mean area under the receiver operating characteristic curve (P=.02; 95% CI −0.007 to 0.140), and mean macro F1 (P=.006; 95% CI 0.016-0.167). The statistically improved performance of the final model (20 features) is in contrast to the statistically insignificant changes between the original feature set (n=115) and the automatically selected features (n=19): mean sensitivity (P=.13; 95% CI −0.1699 to 0.0681), mean specificity (P=.10; 95% CI −0.1389 to 0.4017), mean area under the receiver operating characteristic curve (P=.008; 95% CI 0.0059-0.1126), and mean macro F1 (P=.98; 95% CI −0.0555 to 0.0548). This demonstrates the importance and effectiveness of combining automatic feature selection and expert-based linguistic revision to develop the most effective machine learning algorithms from high-dimensional data sets. Conclusions We developed new evaluation tools for the discrimination and prediction of writing styles of web-based health resources for children’s health education and promotion among parents and caregivers of children. User-adaptive automatic assessment of web-based health content holds great promise for distant and remote health education among young readers. Our study leveraged the precision and adaptability of machine learning algorithms and insights from health linguistics to help advance this significant yet understudied area of research.
Thermoregulation is not impaired in breast cancer survivors during moderate‐intensity exercise performed in warm and hot environments

This study aimed to assess how female breast cancer survivors (BCS) respond physiologically, hematologically, and perceptually to exercise under heat stress compared to females with no history of breast cancer (CON). Twenty‐one females (9 BCS and 12 CON [age; 54 ± 7 years, stature; 167 ± 6 cm, body mass; 68.1 ± 7.62 kg, and body fat; 30.9 ± 3.8%]) completed a warm (25℃, 50% relative humidity, RH) and hot (35℃, 50%RH) trial in a repeated‐measures crossover design. Trials consisted of 30 min of rest, 30 min of walking at 4 metabolic equivalents, and a 6‐minute walk test (6MWT). Physiological measurements (core temperature (Tre), skin temperature (Tskin), heart rate (HR), and sweat analysis) and perceptual rating scales (ratings of perceived exertion, thermal sensation [whole body and localized], and thermal comfort) were taken at 5‐ and 10‐min intervals throughout, respectively. Venous blood samples were taken before and after to assess; IL‐6, IL‐10, CRP, IFN‐γ, and TGF‐β1. All physiological markers were higher during the 35 versus 25℃ trial; Tre (~0.25℃, p = 0.002), Tskin (~3.8℃, p < 0.001), HR (~12 beats·min−1, p = 0.023), and whole‐body sweat rate (~0.4 L·hr−1, p < 0.001), with no difference observed between groups in either condition (p > 0.05). Both groups covered a greater 6MWT distance in 25 versus 35℃ (by ~200 m; p = 0.003). Nevertheless, the control group covered more distance than BCS, regardless of environmental temperature (by ~400 m, p = 0.03). Thermoregulation was not disadvantaged in BCS compared to controls during moderate‐intensity exercise under heat stress. However, self‐paced exercise performance was reduced for BCS regardless of environmental temperature.
Stabilization and structural changes of 2D DNA origami by enzymatic ligation

Abstract The low thermal stability of DNA nanostructures is the major drawback in their practical applications. Most of the DNA nanotubes/tiles and the DNA origami structures melt below 60°C due to the presence of discontinuities in the phosphate backbone (i.e., nicks) of the staple strands. In molecular biology, enzymatic ligation is commonly used to seal the nicks in the duplex DNA. However, in DNA nanotechnology, the ligation procedures are neither optimized for the DNA origami nor routinely applied to link the nicks in it. Here, we report a detailed analysis and optimization of the conditions for the enzymatic ligation of the staple strands in four types of 2D square lattice DNA origami. Our results indicated that the ligation takes overnight, efficient at 37°C rather than the usual 16°C or room temperature, and typically requires much higher concentration of T4 DNA ligase. Under the optimized conditions, up to 10 staples ligation with a maximum ligation efficiency of 55% was achieved. Also, the ligation is found to increase the thermal stability of the origami as low as 5°C to as high as 20°C, depending on the structure. Further, our studies indicated that the ligation of the staple strands influences the globular structure/planarity of the DNA origami, and the origami is more compact when the staples are ligated. The globular structure of the native and ligated origami was also found to be altered dynamically and progressively upon ethidium bromide intercalation in a concentration-dependent manner.
Dose-adjusted EPOCH and rituximab for the treatment of double expressor and double-hit diffuse large B-cell lymphoma: impact of TP53 mutations on clinical outcome

Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease, including one-third of cases overexpressing MYC and BCL2 proteins (double expressor lymphoma, DEL) and 5-10% of patients with chromosomal rearrangements of MYC, BCL2 and/or BCL-6 (double/triple-hit lymphomas, DH/TH). TP53 mutations are detected in 20-25% of DEL. We report the efficacy of dose-adjusted EPOCH and rituximab (DA-EPOCH-R) in a series of 122 consecutive patients, including DEL (n=81, 66%), DEL-MYC (n=9, 7%), DEL-BCL2 (n=13, 11%), or high-grade lymphomas (DH/TH) (n=19, 16%). Central nervous system (CNS) prophylaxis included intravenous methotrexate (n=66), intrathecal chemotherapy (IT) (n=40) or no prophylaxis (n=16). Sixty-seven patients (55%) had highintermediate or high International Prognostic Index (IPI) and 30 (25%) had high CNS-IPI. The 2-year progression-free survival (PFS) and overall survival (OS) for the entire study population were 74% and 84%, respectively. There was a trend for inferior OS for DH/TH (2-year OS: 66%, P=0.058) as compared to all the others. The outcome was significantly better for the IPI 0-2 versus IPI 3-5 (OS: 98% vs. 72%, P=0.002). DA-EPOCH-R did not overcome the negative prognostic value of TP53 mutations: 2-year OS of 62% versus 88% (P=0.036) were observed for mutated as compared to wild-type cases, respectively. Systemic CNS prophylaxis conferred a better 2-year OS (94%) as compared to IT or no prophylaxis (76% and 65%, respectively; P=0.008). DA-EPOCH-R treatment resulted in a favorable outcome in patients with DEL and DEL with single rearrangement, whereas those with multiple genetic alterations such as DEL-DH/TH and TP53 mutated cases still have an inferior outcome.