Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of the PRA1 Genes in Cotton Identifies the Role of GhPRA1.B1-1A in Verticillium dahliae Resistance

Verticillium wilt in cotton (Gossypium hirsutum) is primarily caused by Verticillium dahliae. Previous data suggest that prenylated RAB acceptors (PRAs) play essential roles in environmental plant adaptation, although the potential roles of PRA1 in cotton are unclear. Therefore, in this study, PRA1 family members were identified in G. hirsutum, and their roles in biotic and abiotic stresses were analyzed. Thirty-seven GhPRA1 family members were identified in upland cotton, which were divided into eight groups. Gene structure and domain analyses revealed that the sequences of GhPRA1 members in each group were highly conserved. Many environmental stress-related and hormone-response cis-acting elements were identified in the GhPRA1 promoter regions, indicating that they may respond to biotic and abiotic stresses. Expression analysis revealed that GhPRA1 members were widely expressed in upland cotton. The GhPRA1 genes responded to abiotic stress: drought, cold, salt, and heat stress. GhPRA1.B1-1A expression increased after V. dahliae infection. Furthermore, the functional role of GhPRA1.B1-1A was confirmed by overexpression in Arabidopsis thaliana, which enhanced the resistance to V. dahliae. In contrast, V. dahliae resistance was significantly weakened via virus-induced gene silencing of GhPRA1.B1-1A in upland cotton. Simultaneously, reactive oxygen species accumulation; the H2O2, salicylic acid, and jasmonic acid contents; and callose deposition were significantly decreased in cotton plants with GhPRA1.B1-1A silencing. These findings contribute to a better understanding of the biological roles of GhPRA1 proteins and provide candidate genes for cotton breeders for breeding V. dahliae-resistant cultivars.
Minimization of MEDA Biochip-Size in Droplet Routing

With the increasing demand for fast, accurate, and reliable biological sensor systems, miniaturized systems have been aimed at droplet-based sensor systems and have been promising. A micro-electrode dot array (MEDA) biochip, which is one kind of the miniaturized systems for biochemical protocols such as dispensing, dilutions, mixing, and so on, has become widespread due to enabling dynamical control of the droplets in microfluidic manipulations. In MEDA biochips, the electrowetting-on-dielectric (EWOD) technique stands out since it can actuate droplets with nano/picoliter volumes. Microelectrode cells on MEDA actuate multiple droplets simultaneously to route locations for the purpose of the biochemical operations. Taking advantage of the feature, droplets are often routed in parallel to achieve high-throughput outcomes. Regarding parallel manipulation of multiple droplets, however, the droplets are known to be initially placed at a distant position to avoid undesirable mixing. The droplets thus result in traveling a long way for a manipulation, and the required biochip size for routing is also enlarged. This paper proposes a routing method for droplets to reduce the biochip size on a MEDA biochip with the allowance of splitting during routing operations. We mathematically derive the routing problem, and the experiments demonstrate that our proposal can significantly reduce the biochip size by 70.8% on average, compared to the state-of-the-art method.
Effective Enrichment of Plasmonic Hotspots for SERS by Spinning Droplets on a Slippery Concave Dome Array

Surface-enhanced Raman scattering (SERS) detection requires dense hotspots and a uniform distribution of analytes to obtain a stable signal with good repeatability. However, due to the coffee-ring effect on the hydrophilic substrate, and the difficulty of droplet manipulation on the superhydrophobic substrate, few substrates can ensure that the analytes are evenly distributed. In this work, we develop a method that can efficiently enrich plasmonic hotspots for SERS measurement on the superhydrophobic concave dome array (SCDA). The SCDA is formed by spraying hydrophobic silica nanoparticles onto a polydimethylsiloxane (PDMS) slab with a concave dome array that can physically confine the droplets and overcome the coffee-ring effect. During droplet evaporation, the SCDA is driven by a horizontal spinner, and the droplets spin on the SCDA, enabling the plasmonic nanoparticles to become closely packed to form the SERS hotspots. The limit of detection (LOD) of the dynamic-enriched SERS hotspots for crystal violet and methylene blue can reach up to 10−11 M. Moreover, the LOD for melamine in milk can reach 5 × 10−7 M, which is lower than the safety threshold defined by the Food and Drug Administration (FDA). Based on this SERS platform, an effective, low-cost, and simple method for SERS detection in analytical chemistry and food safety is highly expected.
Protective Effects of Nuciferine in Middle Cerebral Artery Occlusion Rats Based on Transcriptomics

Middle cerebral artery occlusion (MCAO), with the characteristics of high morbidity, high recurrence rate, high mortality, and disability rate, is a typical manifestation of ischemic stroke and has become a hot research topic in the clinical field. The protective effects of nuciferine on brain injury MCAO rats were investigated and its mechanisms of actions were revealed. The MCAO rats were established by the suture method. The pathological staining of the rat brain was processed and observed, the pharmacodynamics assay of nuciferine were studied, and the gene expression regulation by nuciferine was detected by transcriptome technology. The results showed that nuciferine significantly alleviated brain damage in MCAO rats, and the transcriptomic results suggested that nuciferine could exert therapeutic effects through the regulation of lipid metabolism, including arachidonic acid metabolism, sphingolipid metabolism, the PPAR signaling pathway and other related pathways. This finding provided new perspectives on the treatment of MCAO with nuciferine and facilitates the development of novel drugs for this disease.
Polylactide-Based Films with the Addition of Poly(ethylene glycol) and Extract of Propolis—Physico-Chemical and Storage Properties

Polymeric films based on polylactide (PLA) with the addition of poly(ethylene glycol) (PEG) and a chloroformic extract of propolis were obtained. In the case of the studied films, polylactide (PLA) played the role of polymeric matrix and poly(ethylene glycol) was used as a plasticizer, while the extract of propolis was incorporated as a compound that could significantly affect the properties of the obtained materials, especially the water vapour permeation rate and the stability of the food products. Moreover, changes in structure, morphology, mechanical and storage properties as well as differences in colour, thickness and transparency after introducing propolis into the PLA–PEG system were determined. Based on the obtained results, it was established that the addition of the chloroformic extract of propolis significantly influences the most important properties taken into account during food packaging. It was also noticed that films with incorporated propolis were characterised by a significant improvement in the water vapour barrier property. Moreover, the obtained results prove that packaging containing a chloroformic propolis extract allow for the maintenance of the quality of the fruit stored for an extended period of time. To summarise, the application of a chloroformic propolis extract enables the formation of packaging materials that extend the shelf life of stored food products.
Effectiveness of Different Chemotherapeutic Agents for Decontamination of Infected Dental Implant Surface: A Systematic Review

Aim: To evaluate the most effective chemotherapeutic agent for decontamination of infected dental implants. Material and methods: A systematic electronic literature search in MEDLINE (PubMed) and Google scholar between January 2010 to December 2021 was carried out by using the PRISMA guidelines. A total of five studies related to chemical decontamination of the dental implant were evaluated. The search strategy was based on the PICOS framework. Randomized controlled trials (RCT’s) and cohort studies evaluating the effectiveness of different chemotherapeutic agents for the decontamination of dental implants were included in the study. The outcome variable examined was the most effective chemotherapeutic agent(s) for dental implant surface decontamination after comparing the chemotherapeutic agents used in the qualifying studies. Result: Out of the basic database of 1564 records, 1380 articles were excluded due to irrelevance, unavailability, and repetition. Furthermore, 134 articles were excluded from 184 studies for various reasons. After further filtration, 13 studies were shortlisted. Two investigators (SSA and SA) appraised the quality of the selected studies using the risk of bias assessment tool. After excluding eight studies, five articles were finally included in the present systematic review. Conclusion: The data reported for the efficacy of chemotherapeutic agents in cleaning contaminated titanium surfaces are scarce, thus it is not possible to draw a definite conclusion. However, chlorhexidine (CHX) (0.2%, 0.12%), citric acid (40%) and sodium hypochlorite (1%) are the most commonly used chemotherapeutic agents; amongst them, citric acid showed the highest potential for biofilm removal from the contaminated implant surface. All three agents [CHX (0.2%, 0.12%), citric acid (40%), and sodium hypochlorite (1%)] can be recommended as therapeutic agents along with their curbs.
Comparison of Two Kinds of Two-Dimensional Shear Wave Elastography Techniques in the Evaluation of Jaundiced Infants Suspected of Biliary Atresia

Purpose: To compare the reliability and performance of Supersonic shear wave elastography (S-SWE) and Toshiba shear wave elastography (T-SWE) in the diagnosis of biliary atresia (BA) and assessment of liver fibrosis among jaundiced infants suspected of BA. Material and Methods: A total of 35 patients with suspected BA who underwent both S-SWE and T-SWE examinations were prospectively included. Diagnostic performances of S-SWE and T-SWE in identifying BA were evaluated. The correlation between two types of SWE values and histological liver fibrosis stages by Metavir scores were investigated in 21 patients with pathology results. The intraclass correlation coefficients (ICCs) were calculated in 16 patients for inter- and intra-observer agreement. The area under the receiver operating characteristic curve (AUC) analysis was compared using a DeLong test. Results: There were 22 patients with BA and 13 patients without BA. The diagnostic performance of S-SWE was comparable to that of T-SWE (AUC 0.895 vs. 0.822, p = 0.071) in diagnosing BA. The AUCs of S-SWE in predicting liver fibrosis stages were from 0.676 to 1.000 and showed no statistical differences from that of T-SWE (from 0.704 to 1.000, all p > 0.05). T-SWE provided higher inter-operator agreement (ICC 0.990) and intra-operator agreement (ICCs 0.966–0.993), compared with that of S-SWE in a previous study (ICC 0.980 for inter-operator and 0.930–0.960 for intra-operator). Conclusions: For infants suspected of BA, T-SWE had good performances in the diagnosis of BA and the assessment of liver fibrosis compared with S-SWE. Furthermore, T-SWE showed higher measurement reproducibility than S-SWE.
Heracleum persicum Essential Oil Nanoemulsion: A Nanocarrier System for the Delivery of Promising Anticancer and Antioxidant Bioactive Agents

Essential oils are important compounds for the prevention and/or treatment of various diseases in which solubility and bio-accessibility can be improved by nanoemulsion systems. Heracleum persicum oil nanoemulsion (HAE-NE) was prepared and biological properties were investigated against human breast cancer cells and normal human fibroblasts foreskin. Particle size, zeta potential and poly dispersity index were 153 nm, −47.9 mV and 0.35, respectively. (E)anethole (57.9%), terpinolene (13.8%), ɣ-terpinene (8.1%), myrcene (6.8%), hexyl butyrate (5.2%), octyl butanoate (4.5%) and octyl acetate (3.7%) was detected in nanoemulsion. Proliferation of cancer cells at IC50 = 2.32 μg/mL was significantly (p < 0.05) inhibited, and cell migration occurred at 1.5 μL/mL. The HAE-NE at 1.5, 2.5 and 3.5 µg/concentration up-regulated caspase 3 and enhanced sub-G1 peak of cell cycle with nil cytotoxic effects in the liver, kidney and jejunum of mice. Villus height, villus width, crypt depth and goblet cells in mice group fed with 10 and 20 mg/kg body weight of HAE-NE improved. Cellular redox state in the liver indicated 10 and 20 mg/kg body weight of nanoemulsion significantly up-regulated the expression of SOD, CAT and GPx genes. Heracleum persicum oil nanoemulsion could be an eco-friendly nanotherapeutic option for pharmaceutical, cosmetological and food applications.
Hyaluronidase 6 Does Not Affect Cumulus–Oocyte Complex Dispersal and Male Mice Fertility

Glycosylphosphatidylinositol-anchored sperm hyaluronidases (HYAL) assist sperm penetration through the cumulus–oocyte complex (COC), but their role in mammalian fertilization remains unclear. Previously, we demonstrated that sperm from HYAL 5 and 7 double-knockout (dKO) mice produced significantly less offspring than sperm from wild-type mice due to defective COC dispersal. However, the HYAL6 gene remained active in the sperm from the dKO mice, indicating that they were not entirely infertile. This study explored the role of HYAL6 in fertilization by analyzing HYAL6-mutant mice. In this mouse model, HYAL5 and HYAL7 were present in the HYAL6-knockout sperm, and they could disperse hyaluronic acid. We found that HYAL6 was present on the surface of sperm. However, male mice lacking the HYAL6 gene had normal fertility, testicular integrity, and sperm characteristics. Furthermore, in vitro fertilization assays demonstrated that HYAL6-deficient epididymal sperm functioned normally. Therefore, HYAL6 is dispensable for fertilization.
Osteocalcin Alleviates Lipopolysaccharide-Induced Acute Inflammation via Activation of GPR37 in Macrophages

The G protein-coupled receptor 37 (GPR37) has been reported to be expressed in macrophages and the activation of GPR37 by its ligand/agonist, and it can regulate macrophage-associated functions and inflammatory responses. Since our previous work identified that osteocalcin (OCN) acts as an endogenous ligand for GPR37 and can elicit various intracellular signals by interacting with GPR37, we thus hypothesized that OCN may also play a functional role in macrophage through the activation of GPR37. To verify the hypothesis, we conducted a series of in vivo and in vitro studies in lipopolysaccharide (LPS)-challenged mice and primary cultured macrophages. Our results reveal that the OCN gene deletion (OCN−/−) and wild type (WT) mice showed comparable death rates and inflammatory cytokines productions in response to a lethal dose of LPS exposure. However, the detrimental effects caused by LPS were significantly ameliorated by exogenous OCN treatments in both WT and OCN−/− mice. Notably, the protective effects of OCN were absent in GPR37−/− mice. In coordination with the in vivo results, our in vitro studies further illustrated that OCN triggered intracellular responses via GPR37 in peritoneal macrophages by regulating the release of inflammatory factors and macrophage phagocytic function. Finally, we exhibited that the adoptive transfer of OCN-treated macrophages from WT mice significantly inhibits the release of pro-inflammatory cytokines in GPR37−/− mice exposed to LPS. Taken together, these findings suggest a protective role of OCN against LPS-caused acute inflammation, by the activation of GPR37 in macrophages, and provide a potential application of the activation of the OCN/GPR37 regulatory axis as a therapeutic strategy for inflammatory diseases.
Diagnostics of HNSCC Patients: An Analysis of Cell Lines and Patient-Derived Xenograft Models for Personalized Therapeutical Medicine

Head and neck squamous cell carcinomas (HNSCC) are very frequent worldwide, and smoking and chronic alcohol use are recognized as the main risk factors. For oropharyngeal cancers, HPV 16 infection is known to be a risk factor as well. By employing next-generation sequencing, both HPV-positive and negative HNSCC patients were detected as positive for PI3K mutation, which was considered an optimal molecular target. We analyzed scientific literature published in the last 5 years regarding the newly available diagnostic platform for targeted therapy of HNSCC HPV+/−, using HNSCC-derived cell lines cultures and HNSCC pdx (patient-derived xenografts). The research results are promising and require optimal implementation in the management of HNSCC patients.
FLAIRectomy: Resecting beyond the Contrast Margin for Glioblastoma

The standard of care for isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GBM) is maximal resection followed by chemotherapy and radiation. Studies investigating the resection of GBM have primarily focused on the contrast enhancing portion of the tumor on magnetic resonance imaging. Histopathological studies, however, have demonstrated tumor infiltration within peri-tumoral fluid-attenuated inversion recovery (FLAIR) abnormalities, which is often not resected. The histopathology of FLAIR and local recurrence patterns of GBM have prompted interest in the resection of peri-tumoral FLAIR, or FLAIRectomy. To this point, recent studies have suggested a significant survival benefit associated with safe peri-tumoral FLAIR resection. In this review, we discuss the evidence surrounding the composition of peri-tumoral FLAIR, outcomes associated with FLAIRectomy, future directions of the field, and potential implications for patients.
The Prevalence and Characteristics of Diffuse Idiopathic Skeletal Hyperostosis (DISH): A Cross-Sectional Study of 1519 Japanese Individuals

Background: Diffuse idiopathic skeletal hyperostosis (DISH) is a pathology characterized by enthesis ossification, but there have been few reports on epidemiological surveys. This report presents a cross-sectional survey of DISH from thoracic to sacral spine in patients at the tertiary emergency medical center. Methods: The patients were divided into DISH (+) group and DISH (−) group for a retrospective comparative study. The primary outcome measures were the frequency of DISH and the patient demographic data, the secondary outcome measures were the previous medical history (diabetes mellitus, cardiovascular disease), the extent of aortic calcification, the frequency of hyperostosis around the costovertebral joint and the mortality rate within 3 months of the initial examination. Results: This survey examined a total of 1519 patients. There were 265 cases (17.4%) in the DISH (+) group and 1254 cases in DISH (−) group. The prevalence of DISH was concentrated at the thoracolumbar junction, particularly at T9. The mean age, ratio of male and hyperostosis around the costovertebral joint were significantly higher in the DISH (+) group (p < 0.001), but there was no significant difference in other variables. Conclusions: The pathology of DISH might involve the effects of age-related changes or biomechanical effects.
Inferring Potential Cancer Driving Synonymous Variants

Synonymous single nucleotide variants (sSNVs) are often considered functionally silent, but a few cases of cancer-causing sSNVs have been reported. From available databases, we collected four categories of sSNVs: germline, somatic in normal tissues, somatic in cancerous tissues, and putative cancer drivers. We found that screening sSNVs for recurrence among patients, conservation of the affected genomic position, and synVep prediction (synVep is a machine learning-based sSNV effect predictor) recovers cancer driver variants (termed proposed drivers) and previously unknown putative cancer genes. Of the 2.9 million somatic sSNVs found in the COSMIC database, we identified 2111 proposed cancer driver sSNVs. Of these, 326 sSNVs could be further tagged for possible RNA splicing effects, RNA structural changes, and affected RBP motifs. This list of proposed cancer driver sSNVs provides computational guidance in prioritizing the experimental evaluation of synonymous mutations found in cancers. Furthermore, our list of novel potential cancer genes, galvanized by synonymous mutations, may highlight yet unexplored cancer mechanisms.
Autism Children and English Vocabulary Learning: A Qualitative Inquiry of the Challenges They Face in Their English Vocabulary Learning Journey

Language learning is one of the most important aspects of an individual’s life development and growth. Normal learners’ English language acquisition differs depending on their preferences and learning styles. Children with autism, on the other hand, appear to have different learning methods and routines. There has been a lot of previous work on the language learning styles of normal learners, but not much on the language learning path of children with autism. Due to that, this study aims at investigating the challenges children with autism face in their English vocabulary learning. Observations and focus group discussions were conducted with 45 children with autism, 4 autism education teachers, 2 occupational therapists and a parent of children with mild autism children to investigate the challenges autism children face in their vocabulary learning. The findings have gathered that autistic children encounter a few challenges occasionally in their English vocabulary learning journey. The data were gathered and arranged thematically. Further recommendations and suggestions are discussed in this study.
Looking for the Holy Grail—Drug Candidates for Glioblastoma Multiforme Chemotherapy

Glioblastoma multiforme (GBM) is the deadliest and the most heterogeneous brain cancer. The median survival time of GBM patients is approximately 8 to 15 months after initial diagnosis. GBM development is determined by numerous signaling pathways and is considered one of the most challenging and complicated-to-treat cancer types. Standard GBM therapy consist of surgery followed by radiotherapy or chemotherapy, and combined treatment. Current standard of care (SOC) does not offer a significant chance for GBM patients to combat cancer, and the selection of available drugs is limited. For almost 20 years, there has been only one drug, Temozolomide (TMZ), approved as a first-line GBM treatment. Due to the limited efficacy of TMZ and the high rate of resistant patients, the implementation of new chemotherapeutics is highly desired. However, due to the unique properties of GBM, many challenges still need to be overcome before reaching a ‘breakthrough’. This review article describes the most recent compounds introduced into clinical trials as drug candidates for GBM chemotherapy.