Miracle-dz/UniFAR-FTUs huggingface dataset:
miR-26a/30d/152 are reliable reference genes for miRNA quantification in skin wound age estimation

Abstract MicroRNAs (miRNAs) are a class of small non-coding RNAs that exert their biological functions as negative regulators of gene expression. They are involved in the skin wound healing process with a dynamic expression pattern and can therefore potentially serve as biomarkers for skin wound age estimation. However, no reports have described any miRNAs as suitable reference genes (RGs) for miRNA quantification in wounded skin or samples with post-mortem changes. Here, we aimed to identify specific miRNAs as RGs for miRNA quantification to support further studies of skin wound age estimation. Overall, nine miRNAs stably expressed in mouse skin at certain posttraumatic intervals (PTIs) were preselected by next-generation sequencing as candidate RGs. These nine miRNAs and the commonly used reference genes (comRGs: U6, GAPDH, ACTB, 18S, 5S, LC-Ogdh) were quantitatively examined using quantitative real-time reverse-transcription polymerase chain reaction at different PTIs during skin wound healing in mice. The stabilities of these genes were evaluated using four independent algorithms: GeNorm, NormFinder, BestKeeper, and comparative Delta Ct. Stability was further evaluated in mice with different post-mortem intervals (PMIs). Overall, mmu-miR-26a-5p, mmu-miR-30d-5p, and mmu-miR-152-3p were identified as the most stable genes at both different PTIs and PMIs. These three miRNA RGs were additionally validated and compared with the comRGs in human samples. After assessing using one, two, or three miRNAs in combination for stability at different PTIs, PMIs, or in human samples, the set of miR-26a/30d/152 was approved as the best normalizer. In conclusion, our data suggest that the combination of miR-26a/30d/152 is recommended as the normalization strategy for miRNA qRT-PCR quantification in skin wound age estimation. Key points The small size of miRNAs makes them less susceptible to post-mortem autolysis or putrefaction, leading to their potential use in wound age estimation. Studying miRNAs as biological indicators of skin wound age estimation requires the selection and validation of stable reference genes because commonly used reference genes, such as U6, ACTB, GAPDH, 5S, 18S, and LC-Ogdh, are not stable. miR-26a/30d/152 are stable and reliable as reference genes and their use in combination is a recommended normalization strategy for miRNA quantitative analysis in wounded skin.
Cadmium accumulation dynamics in the rice endosperm during grain filling revealed by autoradiography

Abstract Cadmium (Cd) is one of the environmental pollutants contaminated in our food. Several previous reports showed that rice polishing cannot be efficient to reduce Cd content in white rice, implying the characteristic Cd distribution in rice grain. However, Cd distribution has not been fully elucidated so far. Herein, 109Cd radiotracer experiment was performed using the rice seedlings at various time points after flowering to obtain autoradiographs of the brown rice to visually understand the Cd transport and distribution during the grain‐filling process. It was shown that 109Cd accumulated in the outermost area of the brown rice, and also in the middle part of the starchy endosperm, resulting in the appearance of the double circle distribution pattern, which was not observed in the autoradiographs of 65Zn. The inner circle of 109Cd located around the center of the endosperm was developed particularly at around 8 and 10 days after flowering. After this period, 109Cd started to deposit at the outer part of the endosperm, which was also found in the autoradiograph of 14C‐sucrose. Considering the physiology of grain development, the contribution of water transport and protein synthesis in the endosperm on the characteristic Cd distribution pattern was hypothesized.
Protein modeling and in silico analysis to assess pathogenicity of ABCA4 variants in patients with inherited retinal disease

Purpose The retina-specific ABCA transporter, ABCA4, plays an essential role in translocating retinoids required by the visual cycle. ABCA4 genetic variants are known to cause a wide range of inherited retinal disorders, including Stargardt disease and cone-rod dystrophy. More than 1,400 ABCA4 missense variants have been identified; however, more than half of these remain variants of uncertain significance (VUS). The purpose of this study was to employ a predictive strategy to assess the pathogenicity of ABCA4 variants in inherited retinal diseases using protein modeling and computational approaches. Methods We studied 13 clinically well-defined patients with ABCA4 retinopathies and identified the presence of 10 missense variants, including one novel variant in the ABCA4 gene, by next-generation sequencing (NGS). All variants were structurally analyzed using AlphaFold2 models and existing experimental structures of human ABCA4 protein. The results of these analyses were compared with patient clinical presentations to test the effectiveness of the methods employed in predicting variant pathogenicity. Results We conducted a phenotype–genotype comparison of 13 genetically and phenotypically well-defined retinal disease patients. The in silico protein structure analyses we employed successfully detected the deleterious effect of missense variants found in this affected patient cohort. Our study provides American College of Medical Genetics and Genomics (ACMG)–defined supporting evidence of the pathogenicity of nine missense ABCA4 variants, aligning with the observed clinical phenotypes in this cohort. Conclusions In this report, we describe a systematic approach to predicting the pathogenicity of ABCA4 variants by means of three-dimensional (3D) protein modeling and in silico structure analysis. Our results demonstrate concordance between disease severity and structural changes in protein models induced by genetic variations. Furthermore, the present study suggests that in silico protein structure analysis can be used as a predictor of pathogenicity and may facilitate the assessment of genetic VUS.
An affordable Web-based Grant Management Software Designed to Support Romanian Scholarly Publications

: The rise of Web-based publishing and the increase of electronic usage has triggered profound changes in academic publishing and has determined national governments to take some forms of action designed to actively promote and support the publication of high-quality scientific literature produced in their own country. Considering the spread of ICT technologies nowadays, an online platform was developed in order to encourage participation in the grant competition for Romanian scholarly publications and establish a digital connection between the main actors involved in the process. In this context, the article presents the system architecture, development and outcomes. Building such a platform has required gathering and studying accurate information for data aggregation and user experience, having in mind a scalable design for requirements update or further developments. The system revolves around digitally connecting three major actors – publisher, evaluator, competition organizer. For ensuring the platform’s reliability and preventing failures, user-centric tests were developed and set to run automatically at specific triggers, such as code submission. The platform contributes to the transparency of the entire grant management process, substantial reduction of the time for submission, and streamlining of the evaluation procedures. The web platform has been effectively developed, implemented and regularly used by both publishers and reviewers in the latest Romanian grant competitions.
Cooperative Data Sharing for Mobile Cloudlets Under Heterogeneous Environments

As accessing remote cloud via cellular network is costly due to the lower bandwidth, higher wide area network (WAN) latency, and higher energy consumption, mobile cloudlet that formed by several edge mobile devices has become an emerging computing paradigm and attracted increasing attention recently. Being different from the existing studies that mainly focus on the issue of computation offloading among the peers, this paper investigates the problem of cooperative data sharing among peers to overcome the data dissymmetry, especially with the presence of dynamic network context. First, a publish/subscribe-based data sharing model is designed to cope with the unpredictable communication condition. Then, the data transmission scheduling within cooperative mobile devices is formulated as a utility maximization optimization considering the limited channel capacity, heterogeneous quality of experience (QoE) requirements, and incentive mechanism for participation. To encourage cooperation among mobile devices, a data downloading/uploading queuing mechanism is elegantly designed. Furthermore, an online algorithm without predicting the future information on request arrivals and network changes is developed to simultaneously optimize data transmission and communication interface selection in the long run. Theoretical analysis shows that the proposed algorithm is able to obtain a utility arbitrarily close to the offline optimum and guarantee the delay bound. Simulations demonstrate the effectiveness and the superiority of the proposed algorithm over some existing typical strategies.
Preoperative Patient Education: Perceptions and Actual Practice among Nurses Working in Surgical Units

Introduction Preoperative education is an essential nursing task that can be affected by the nurses’ perception. Patients may be receiving insufficient vital information before surgery. However, the essential information that should be provided to patients undergoing surgery is not fully addressed. Objective To assess the essential elements of preoperative information as perceived by the surgical nurses. Methods This was a cross-sectional study. A convenience sample of 224 registered nurses who were working at surgical units was recruited from two hospitals. A preoperative teaching questionnaire was used. Results Details about the operation (4.39 ± 0.61) and preoperative preparation (4.36 ± 0.61) were the most important domains of preoperative education as perceived by nurses. The results show significant differences between the perceived and actual preoperative educational practice across all domains except the preoperative preparation. Conclusions The delivery of preoperative education could be affected by nurses’ perceptions. Efforts to facilitate the implementation of effective education as perceived by nurses should be conducted by minimizing potential barriers.
Enhancement of the photocatalytic activity of rGO/NiO/Ag nanocomposite for degradation of methylene blue dye

The current study focuses on boosting the photocatalytic ability of reduced graphene oxide (rGO) by decorating the rGO nano-sheets with nickel oxide (NiOx) and silver (Ag) nanomaterials. The developed ternary nanomaterials were investigated using FTIR, XRD, FESEM, TEM, Raman, and UV-vis to evaluate the photo-degradation process. The rGO/NiOx/Ag ternary system showed promising photocatalytic dye degradation under simulated sunlight irradiance. The addition of NiOx and Ag nanomaterials widened the catalytic activity spectrum from the visible region to the UV-region. Besides, these materials hindered the electron–hole recombination, boosting the catalytic activity. The reusability results also clearly showed that the synthesized ternary nanomaterials have good reproducibility and stability for photocatalytic degradation of industrial wastewater.
World Journal of Gastrointestinal Surgery

BACKGROUND Carcinoembryonic antigen (CEA) is a broad-spectrum tumor marker for differential diagnosis, monitoring, and response assessment of a variety of malignancies. AIM To evaluate whether serum CEA could predict the prognosis in patients with colorectal cancer liver metastasis (CRCLM) before and after liver resection (LR).
Homogeneous region determination using linear and nonlinear techniques

Abstract Similarity between catchments in a region can be determined depending on catchment properties. This helps to understand the response behavior of the similar catchments more appropriately. Catchment classification plays a major role in the process of hydrological prediction in the case of ungauged catchments. The following categorization was carried out for 32 catchments of India. Principal Component Analysis (PCA) along with K-means clustering, was applied as linear classification; and Self-Organizing Map (SOM) and Kernel Principal Component Analysis (KPCA) were implemented as nonlinear classification methods on catchment attributes and daily streamflow time series. The classification established on streamflow signatures was taken as the reference classification. Results obtained from PCA, SOM, and KPCA were compared with results of the reference classification. The absence of discordant catchments from the clusters of SOM, based on catchment attributes, suggests homogeneity among SOM-derived clusters. Similarity index scores are 0.48 and 0.47, 0.46 and 0.42 for first, second, third and fourth clusters of SOM respectively with that of the reference classification technique. Nonlinear techniques with high similarity index values outperformed standard techniques. This study demonstrated the ability of classification based on catchment attributes to classify ungauged catchments.
Evolution and Spread of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus in Wild Birds, South Korea, 2022–2023

During October 2022–March 2023, highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3. 4.4b virus caused outbreaks in South Korea, including 174 cases in wild birds. To understand the origin and role of wild birds in the evolution and spread of HPAI viruses, we sequenced 113 HPAI isolates from wild birds and performed phylogenetic analysis. We identified 16 different genotypes, indicating extensive genetic reassortment with viruses in wild birds. Phylodynamic analysis showed that the viruses were most likely introduced to the southern Gyeonggi-do/northern Chungcheongnam-do area through whooper swans (Cygnus cygnus) and spread southward. Cross-species transmission occurred between various wild bird species, including waterfowl and raptors, resulting in the persistence of HPAI in wild bird populations and further geographic spread as these birds migrated throughout South Korea. Enhanced genomic surveillance was an integral part of the HPAI outbreak response, aiding in timely understanding of the origin, evolution, and spread of the virus.
Ability of three dairy feed evaluation systems to predict postruminal outflows of amino acids in dairy cows: A meta-analysis.

Adequate prediction of postruminal outflows of essential AA (EAA) is the starting point of balancing rations for EAA in dairy cows. The objective of this meta-analysis was to compare the performance of 3 dairy feed evaluation systems (National Research Council [NRC], Cornell Net Protein and Carbohydrate System version 6.5.5 [CNCPS], and National Academies of Sciences, Engineering and Medicine [NASEM]) to predict EAA outflows (Trp was not tested). The data set included a total of 354 treatment means from 70 duodenal and 24 omasal studies. To avoid Type I error, mean and linear biases were considered of concern if statistically significant and representing > 5.0% of the observed mean. Analyses were conducted on raw observed values and on observations adjusted for the random effect of study. The analysis on raw data indicates the ability of the feed evaluation system to predict absolute values whereas the analysis on adjusted values indicates its ability to predict responses of EAA outflows to dietary changes. For the prediction of absolute values (based on raw data), NRC underpredicted outflows of all EAA, from 5.3 to 8.6% of the observed mean (%obs.mean) except for Leu, Lys, and Val; NASEM overpredicted Lys (10.8%obs.mean); and CNCPS overpredicted Arg, His, Lys, Met, and Val (5.2 to 26.0%obs.mean). No EAA had a linear bias of concern with NASEM, followed by NRC for His (6.8%obs.mean), and CNCPS for all EAA (5.6 to 12.2%obs.mean) except Leu, Phe, and Thr. On the other hand, for the prediction of responses to dietary changes (based on adjusted data), NRC had 2 EAA presenting a linear bias of concern, followed by NASEM and CNCPS with 4 and 6 EAA, respectively. Predictions of His showed a linear bias of concern (5.3 to 9.6%obs.mean) with the 3 feed evaluation systems. Measured chemistry of crude protein and EAA were reported for 1 or more feed ingredients of the ration in 36% of the studies, and resulted in decreased linear biases in the 3 feed evaluation systems. The difference in mean biases of Met outflows was systematically positive when comparing omasal versus duodenal studies. Predictions of Met outflows with NRC had a higher concordance correlation coefficient in duodenal (used to develop NRC equations) versus omasal studies, whereas the opposite was observed with CNCPS, the latter showing the lowest mean bias for Met in omasal sampling studies. The 30% difference in Met mean biases between sampling sites appeared related to a similar difference found for observed Met versus NAN outflows between duodenal and omasal studies, which is independent of predictions. In conclusion, NRC and NASEM yielded accurate predictions of EAA outflows, with a small superiority of NASEM to predict absolute values, and slight superiority of NRC to predict the responses to dietary changes. In comparison, CNCPS may present mean and linear biases of concern for many EAA. Moreover, it remains to determine which sampling site is more representative of the true supply of EAA to the cows.
Model Based Trustworthiness Evaluation of Autonomous Cyber-Physical Production Systems: A Systematic Mapping Study

The fourth industrial revolution, i.e., Industry 4.0, is associated with Cyber-Physical Systems (CPS), which are entities integrating hardware (e.g., smart sensors and actuators connected through the Industrial Internet of Things) together with control and analytics software used to drive and support decisions at several levels. The latest developments in Artificial Intelligence (AI) and Machine Learning (ML) have enabled increased autonomy and closer human-robot cooperation in the production and manufacturing industry, thus leading to Autonomous Cyber-Physical Production Systems (ACPPS) and paving the way to the fifth industrial revolution (i.e., Industry 5.0). ACPPS are increasingly critical due to the possible consequences of their malfunctions on human co-workers, and therefore, evaluating their trustworthiness is essential. This paper reviews research trends, relevant attributes, modelling languages, and tools related to the model-based trustworthiness evaluation of ACPPS. As in many other engineering disciplines and domains, model-based approaches, including stochastic and formal analysis tools, are essential to master the increasing complexity and criticality of ACPPS and to prove relevant attributes such as system safety in the presence of intelligent behaviors and uncertainties.
In vivo anthelmintic potentials of Gongronema latifolium and Picralima nitida against gastrointestinal parasite (Heligmosomoides bakeri)

Summary Gastrointestinal parasites which are responsible for soil-transmitted helminthiases cause illness globally. The control of helminthiasis depends on mass distribution of anthelmintics which has been reported for its resistance, toxicity and low efficacy. In this study, anthelmintic potentials of Gongronema latifolium and Picralima nitida which have wide application in traditional medicine were determined in vivo using Heligmosomoides bakeri a naturally occurring gastro-intestinal parasite of rodents that is closely related to highly prevalent human nematode parasites. Extracts of P. nitida at 500 mg/kg had higher (p< 0.05) chemosuppression (92.45 %) than extracts of G. latifolium (65.82 %) and was highly comparable to albendazole (92.61 %). As the dose of the extracts increased from 300 to 500 mg/kg body weight, chemosuppression of 84.91 % and 92.45 % (P. nitida) and 43.54 % and 65.82 % (G. latifolium) respectively were produced. The extract of P. nitida gave deparasitization rates (p<0.05) of 72.60 % and 77.16 % at 300g/kg and 500mg/kg of body weight respectively. The glucose level and protein content reduced (p<0.05) in mice treated with extract of P. nitida when compared with extract of G. latifolium and untreated mice. Phytochemical screening revealed that P. nitida and G. latifolium contained flavonoids, alkaloids, saponins, tannins and polyphenols. Acute toxicity studies showed that Gongronema latifolium and Picralima nitida have no apparent toxic effect in mice even at the dose of 5000 mg/kg. Extracts of P. nitida and G. latifolium have anthelmintic properties that are dose-dependent, and this could offer potential lead for the development of safe, effective and affordable anthelmintics.
Stable isotopes and nanoSIMS single-cell imaging reveals soil plastisphere colonizers able to assimilate sulfamethoxazole

The presence and accumulation of both plastics and antibiotics in soils may lead to the colonization, selection and propagation of bacteria with certain metabolic traits e.g. antibiotic resistance, in plastisphere. However, the impact of plastic-antibiotic tandem on the soil ecosystem functioning, particularly on microbial function and metabolism remains currently unexplored. Herein, we investigated the competence of soil bacteria to colonize plastics and to mineralize/degrade 13C-labelled sulfamethoxazole (SMX). Using single cell imaging, isotope tracers, soil respiration and SMX mineralization bulk measurements we show that microbial colonization of polystyrene (PE) and polyethylene (PS) surfaces takes place within the first 30 days of incubation. Morphologically diverse, microorganisms were colonizing both plastic types, with a preference for PE substrate. Nano-scale Secondary Ion Mass Spectrometry measurements show that 13C enrichment was highest at 130 days with values up to 1.29 atom %, similar to those of the 13CO2 pool (up to 1.26 atom%, or 22.55 ‰). Our results provide direct evidence demonstrating, at single cell level, the capacity of bacterial colonizers of plastics to assimilate 13C from 13C-SMX. These findings expand our knowledge on the role of plastisphere microbiota in the ecological functioning of soils impacted by anthropogenic stressors.