Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Candidate Genes for Root Traits Using Genotype–Phenotype Association Analysis of Near-Isogenic Lines in Hexaploid Wheat (Triticum aestivum L.)

Global wheat (Triticum aestivum L.) production is constrained by different biotic and abiotic stresses, which are increasing with climate change. An improved root system is essential for adaptability and sustainable wheat production. In this study, 10 pairs of near-isogenic lines (NILs)—targeting four genomic regions (GRs) on chromosome arms 4BS, 4BL, 4AS, and 7AL of hexaploid wheat—were used to phenotype root traits in a semi-hydroponic system. Seven of the 10 NIL pairs significantly differed between their isolines for 11 root traits. The NIL pairs targeting qDSI.4B. 1 GR varied the most, followed by the NIL pair targeting qDT.4A. 1 and QHtscc.ksu-7A GRs. For pairs 5–7 targeting qDT.4A. 1 GR, pair 6 significantly differed in the most root traits. Of the 4 NIL pairs targeting qDSI.4B. 1 GR, pairs 2 and 4 significantly differed in 3 and 4 root traits, respectively. Pairs 9 and 10 targeting QHtscc.ksu-7A GR significantly differed in 1 and 4 root traits, respectively. Using the wheat 90K Illumina iSelect array, we identified 15 putative candidate genes associated with different root traits in the contrasting isolines, in which two UDP-glycosyltransferase (UGT)-encoding genes, TraesCS4A02G185300 and TraesCS4A02G442700, and a leucine-rich repeat receptor-like protein kinase (LRR-RLK)-encoding gene, TraesCS4A02G330900, also showed important functions for root trait control in other crops. This study characterized, for the first time, that these GRs control root traits in wheat, and identified candidate genes, although the candidate genes will need further confirmation and validation for marker-assisted wheat breeding.
Calibration of Visible Light Positioning Systems with a Mobile Robot

Most indoor positioning systems require calibration before use. Fingerprinting requires the construction of a signal strength map, while ranging systems need the coordinates of the beacons. Calibration approaches exist for positioning systems that use Wi-Fi, radio frequency identification or ultrawideband. However, few examples are available for the calibration of visible light positioning systems. Most works focused on obtaining the channel model parameters or performed a calibration based on known receiver locations. In this paper, we describe an improved procedure that uses a mobile robot for data collection and is able to obtain a map of the environment with the beacon locations and their identities. Compared to previous work, the error is almost halved. Additionally, this approach does not require prior knowledge of the number of light sources or the receiver location. We demonstrate that the system performs well under a wide range of lighting conditions and investigate the influence of parameters such as the robot trajectory, camera resolution and field of view. Finally, we also close the loop between calibration and positioning and show that our approach has similar or better accuracy than manual calibration.
Osteogenic Peptides and Attachment Methods Determine Tissue Regeneration in Modified Bone Graft Substitutes

The inclusion of biofunctional molecules with synthetic bone graft substitutes has the potential to enhance tissue regeneration during treatment of traumatic bone injuries. The clinical use of growth factors has though been associated with complications, some serious. The use of smaller, active peptides has the potential to overcome these problems and provide a cost-effective, safe route for the manufacture of enhanced bone graft substitutes. This review considers the design of peptide-enhanced bone graft substitutes, and how peptide selection and attachment method determine clinical efficacy. It was determined that covalent attachment may reduce the known risks associated with growth factor-loaded bone graft substitutes, providing a predictable tissue response and greater clinical efficacy. Peptide choice was found to be critical, but even within recognised families of biologically active peptides, the configurations that appeared to most closely mimic the biological molecules involved in natural bone healing processes were most potent. It was concluded that rational, evidence-based design of peptide-enhanced bone graft substitutes offers a pathway to clinical maturity in this highly promising field.
Recent Advances in Anti-Metastatic Approaches of Herbal Medicines in 5 Major Cancers: From Traditional Medicine to Modern Drug Discovery

Metastasis is the main cause of cancer-related death. Despite its high fatality, a comprehensive study that covers anti-metastasis of herbal medicines has not yet been conducted. The aim of this study is to investigate and assess the anti-metastatic efficacies of herbal medicines in the five major cancers, including lung, colorectal, gastric, liver, and breast cancers. We collected articles published within five years using PubMed, Google Scholar, and Web of Science with “cancer metastasis” and “herbal medicine” as keywords. Correspondingly, 16 lung cancer, 23 colorectal cancer, 10 gastric cancer, 10 liver cancer, and 18 breast cancer studies were systematically reviewed. The herbal medicines attenuated metastatic potential targeting various mechanisms such as epithelial mesenchymal transition (EMT), reactive oxygen species (ROS), and angiogenesis. Specifically, the drugs regulated metastasis related factors such as matrix metalloproteinase (MMP), serine-threonine protein kinase/extracellular regulated protein kinase (AKT/ERK), angiogenic factors, and chemokines. Overall, the present study is the first review, comprehensively investigating the anti-metastasis effect of herbal medicines on five major cancers, providing the experimental models, doses and durations, and mechanisms. Herbal medicines could be a potent candidate for anti-metastatic drugs.
Polyphenol Diversity and Antioxidant Activity of European Cistus creticus L. (Cistaceae) Compared to Six Further, Partly Sympatric Cistus Species

This investigation focused on the qualitative and quantitative composition of polyphenolic compounds of Mediterranean northern shore Cistus creticus and six further, partly sympatric Cistus species (C. albidus, C. crispus, C. ladanifer, C. monspeliensis, C. parviflorus, C. salviifolius). Aqueous extracts of 1153 individual plants from 13 countries were analyzed via high performance liquid chromatography (HPLC). The extracts of C. creticus were primarily composed of two ellagitannins (punicalagin and punicalagin gallate) and nine flavonol glycosides (myricetin and quercetin glycosides, with m-3-O-rhamnoside as the dominant main compound). Differences in the proportions of punicalagin derivatives and flavonol glycosides allowed the classification into two chemovariants. Plants containing punicalagin derivatives and flavonol glycosides were especially abundant in the western and central Mediterranean areas and in Cyprus. From Albania eastwards, punicalagin and punicalagin gallate were of much lesser importance and the predominant chemovariant there was a nearly pure flavonol type. With its two chemovariants, C. creticus takes a central position between the flavonol-rich, purple-flowered clade (besides C. creticus, here represented by C. albidus and C. crispus) and the more ellagitannin-rich, white- or whitish-pink-flowered clade (here represented by C. ladanifer, C. monspeliensis, C. parviflorus and C. salviifolius). The median antioxidative capacity of C. creticus plant material was, with 166 mg Trolox equivalents/g dry wt, about half of the antioxidative capacity of C. ladanifer (301 mg te/g dry wt), the species with the highest antioxidative potential.
Improvements in the Resistance of the Banana Species to Fusarium Wilt: A Systematic Review of Methods and Perspectives

The fungus Fusarium oxysporum f. sp. cubense (FOC), tropical race 4 (TR4), causes Fusarium wilt of banana, a pandemic that has threatened the cultivation and export trade of this fruit. This article presents the first systematic review of studies conducted in the last 10 years on the resistance of Musa spp. to Fusarium wilt. We evaluated articles deposited in different academic databases, using a standardized search string and predefined inclusion and exclusion criteria. We note that the information on the sequencing of the Musa sp. genome is certainly a source for obtaining resistant cultivars, mainly by evaluating the banana transcriptome data after infection with FOC. We also showed that there are sources of resistance to FOC race 1 (R1) and FOC TR4 in banana germplasms and that these data are the basis for obtaining resistant cultivars, although the published data are still scarce. In contrast, the transgenics approach has been adopted frequently. We propose harmonizing methods and protocols to facilitate the comparison of information obtained in different research centers and efforts based on global cooperation to cope with the disease. Thus, we offer here a contribution that may facilitate and direct research towards the production of banana resistant to FOC.
High Mobility Group Box 1 Promotes Lung Cancer Cell Migration and Motility via Regulation of Dynamin-Related Protein 1

High mobility group box 1 (HMGB1) has been demonstrated to promote the migration and invasion of non-small cell lung cancer (NSCLC). However, the mechanism of action of HMGB1 in regulating tumor mobility remains unclear. Therefore, we aimed to investigate whether HMGB1 affects mitochondria distribution and regulates dynamin-related protein 1 (DRP1)-mediated lamellipodia/filopodia formation to promote NSCLC migration. The regulation of mitochondrial membrane tension, dynamics, polarization, fission process, and cytoskeletal rearrangements in lung cancer cells by HMGB1 was analyzed using confocal microscopy. The HMGB1-mediated regulation of DRP1 phosphorylation and colocalization was determined using immunostaining and co-immunoprecipitation assays. The tumorigenic potential of HMGB1 was assessed in vivo and further confirmed using NSCLC patient samples. Our results showed that HMGB1 increased the polarity and mobility of cells (mainly by regulating the cytoskeletal system actin and microtubule dynamics and distribution), promoted the formation of lamellipodia/filopodia, and enhanced the expression and phosphorylation of DRP1 in both the nucleus and cytoplasm. In addition, HMGB1 and DRP1 expressions were positively correlated and exhibited poor prognosis and survival in patients with lung cancer. Collectively, HMGB1 plays a key role in the formation of lamellipodia and filopodia by regulating cytoskeleton dynamics and DRP1 expression to promote lung cancer migration.
Cloning, Characterization, and RNA Interference Effect of the UDP-N-Acetylglucosamine Pyrophosphorylase Gene in Cnaphalocrocis medinalis

The rice leaf folder, Cnaphalocrocis medinalis is a major pest of rice and is difficult to control. UDP-N-acetylglucosamine pyrophosphorylase (UAP) is a key enzyme in the chitin synthesis pathway in insects. In this study, the UAP gene from C. medinalis (CmUAP) was cloned and characterized. The cDNA of CmUAP is 1788 bp in length, containing an open reading frame of 1464 nucleotides that encodes 487 amino acids. Homology and phylogenetic analyses of the predicted protein indicated that CmUAP shared 91.79%, 87.89%, and 82.75% identities with UAPs of Glyphodes pyloalis, Ostrinia furnacalis, and Heortia vitessoides, respectively. Expression pattern analyses by droplet digital PCR demonstrated that CmUAP was expressed at all developmental stages and in 12 tissues of C. medinalis adults. Silencing of CmUAP by injection of double-stranded RNA specific to CmUAP caused death, slow growth, reduced feeding and excretion, and weight loss in C. medinalis larvae; meanwhile, severe developmental disorders were observed. The findings suggest that CmUAP is essential for the growth and development of C. medinalis, and that targeting the CmUAP gene through RNAi technology can be used for biological control of this insect.
Comparative Study on Pale, Soft and Exudative (PSE) and Red, Firm and Non-Exudative (RFN) Pork: Protein Changes during Aging and the Differential Protein Expression of the Myofibrillar Fraction at 1 h Postmortem

In this paper, the protein changes during aging and the differences in the myofibrillar protein fraction at 1 h postmortem of pale, soft and exudative (PSE), and red, firm and non-exudative (RFN) pork longissimus thoracis (LT) were comparatively studied. The PSE and RFN groups were screened out based on the differences in their pH and lightness (L*) at 1 h, and their purge loss at 24 h postmortem. Based on the measured MFI, desmin degradation, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis, PSE meat presented more significant changes in the myofibrillar protein fraction compared to RFN meat during postmortem aging. Through liquid chromatograph-mass spectrometer/mass spectrometer (LC-MS/MS) analysis, a total of 172 differential proteins were identified, among which 151 were up-regulated and 21 were down-regulated in the PSE group. The differential proteins were muscle contraction, motor proteins, microfilaments, microtubules, glycolysis, glycogen metabolism, energy metabolism, molecular chaperones, transport, and enzyme proteins. The AMP activated protein kinase (AMPK) signaling pathway, HIF-1 signaling pathway, calcium signaling pathway, and PI3K-Akt signaling pathway were identified as the significant pathways related to meat quality. This study suggested that the different changes of the myofibrillar protein fraction were involved in the biochemical metabolism in postmortem muscle, which may contribute to the molecular understanding of PSE meat formation.
Expression Pattern of α-Tubulin, Inversin and Its Target Dishevelled-1 and Morphology of Primary Cilia in Normal Human Kidney Development and Diseases

The spatiotemporal expression of α-tubulin, inversin and dishevelled-1 (DVL-1) proteins associated with the Wnt-signaling pathway, and primary cilia morphology were analyzed in developing kidneys (14th–38th developmental weeks), healthy postnatal (1.5- and 7-years old) and pathologically changed human kidneys, including multicystic dysplastic kidneys (MCDK), focal segmental glomerulosclerosis (FSGS) and nephrotic syndrome of the Finnish type (CNF). The analysis was performed by double immunofluorescence, electron microscopy, semiquantitative and statistical methods. Cytoplasmic co-expression of α-tubulin, inversin and DVL-1 was observed in the proximal convoluted tubules (pct), distal convoluted tubules (dct) and glomeruli (g) of analyzed tissues. During kidney development, the overall expression of α-tubulin, inversin and DVL-1 decreased, while in the postnatal period slightly increased. The highest expressions of α-tubulin and inversin characterized dct and g, while high DVL-1 characterized pct. α-tubulin, inversin and DVL-1 expression pattern in MCDK, FSGS and CNF kidneys significantly differed from the healthy control. Compared to healthy kidneys, pathologically changed kidneys had dysmorphic primary cilia. Different expression dynamics of α-tubulin, inversin and DVL-1 during kidney development could indicate that switch between the canonical and noncanonical Wnt-signaling is essential for normal kidney morphogenesis. In contrast, their disturbed expression in pathological kidneys might be associated with abnormal primary cilia, leading to chronic kidney diseases.
Airway Surface Liquid pH Regulation in Airway Epithelium Current Understandings and Gaps in Knowledge

Knowledge on the mechanisms of acid and base secretion in airways has progressed recently. The aim of this review is to summarize the known mechanisms of airway surface liquid (ASL) pH regulation and their implication in lung diseases. Normal ASL is slightly acidic relative to the interstitium, and defects in ASL pH regulation are associated with various respiratory diseases, such as cystic fibrosis. Basolateral bicarbonate (HCO3−) entry occurs via the electrogenic, coupled transport of sodium (Na+) and HCO3−, and, together with carbonic anhydrase enzymatic activity, provides HCO3− for apical secretion. The latter mainly involves CFTR, the apical chloride/bicarbonate exchanger pendrin and paracellular transport. Proton (H+) secretion into ASL is crucial to maintain its relative acidity compared to the blood. This is enabled by H+ apical secretion, mainly involving H+/K+ ATPase and vacuolar H+-ATPase that carry H+ against the electrochemical potential gradient. Paracellular HCO3− transport, the direction of which depends on the ASL pH value, acts as an ASL protective buffering mechanism. How the transepithelial transport of H+ and HCO3− is coordinated to tightly regulate ASL pH remains poorly understood, and should be the focus of new studies.
Rejection of wastewater‐derived micropollutants in high‐pressure membrane applications leading to indirect potable reuse

The rejection of emerging organic micropollutants is an important issue where sources impaired by wastewater discharge are used to augment drinking water supplies. Because previous findings from bench- and laboratory-scale membrane experiments indicated that nanofiltration and to a lesser extent reverse osmosis (RO) membranes can incompletely reject organic micropollutants, this study investigated the efficiency of reverse osmosis membranes in rejecting these compounds at conditions simulating full-scale installations. Compounds investigated were classified by their physicochemical properties. Rejection of solutes was studied using a two-stage laboratory membrane skid and two full-scale RO trains. Full-scale studies did not reveal any quantifiable detects of any target compound, except for low concentrations of caffeine in permeate samples of the second and third stages of one facility. In general, hydrophilic ionic compounds were efficiently removed by steric and electrostatic exclusion. Although there was no evidence that hydrophobic solutes such as steroid hormones partition into permeates, the rejection of chloroform at one facility was rather poor, confirming findings from laboratory-scale experiments. Findings suggest that fouling layers present on membranes in full-scale installations result in an improved rejection of hydrophilic nonionic and especially hydrophobic solutes. © 2005 American Institute of Chemical Engineers Environ Prog, 2005
Bluetooth Low Energy Interference Awareness Scheme and Improved Channel Selection Algorithm for Connection Robustness

Bluetooth Low Energy (BLE) is a popular wireless communication protocol heavily used in Internet of Things applications. Nowadays, robustness is considered a key requirement in wireless communication. However, radio interference from various sources may affect the performance of BLE devices, leading to channel congestion. Therefore, there is a broadly recognized need of methodologies capable of sensing and avoiding interference. In this paper, two improvements at the data link layer for interference detection and channel selection are proposed to enhance the BLE connection robustness. This paper also presents a wide range of experimental evaluations aiming at validating the improvements and providing insights on both these improvements. Particularly, the communication performance of the BLE link layer is assessed in terms of channel usage distribution, supervision timeout ratio (STR) and packet loss rate (PLR) under different interference environments. Results from these experiments (reliability over 97% and 99% under two different harsh environments) highlight the effects of both improvements on the BLE robustness. Meanwhile, the authority of scheduling the whole mechanism is given to the link layer and even the higher application layer. This paper provides a set of solutions for BLE confronting interference in link layer.
The relationship between vitamin D status, intake and exercise performance in UK University-level athletes and healthy inactive controls

The potential ergogenic effects of vitamin D (vitD) in high performing athletes has received considerable attention in the literature and media. However, little is known about non-supplemented university athletes and students residing at a higher latitude. This study aimed to investigate the effects of vitD (biochemical status and dietary intake) on exercise performance in UK university athletes and sedentary students. A total of 34 athletes and 16 sedentary controls were studied during the spring and summer months. Serum vitD status and sunlight exposure were assessed using LC-MS/MS and dosimetry, respectively. Muscular strength of the upper and lower body was assessed using handgrip and knee extensor dynamometry (KE). Countermovement jump (CMJ) and aerobic fitness were measured using an Optojump and VO2max test, respectively. Statistical analysis was performed using paired/ independent t-tests, ANCOVA and Pearson/ Spearman correlations, depending on normality. VitD status increased significantly over the seasons, with athletes measuring higher status both in spring (51.7±20.5 vs. 37.2±18.9 nmol/L, p = 0.03) and summer (66.7±15.8 vs 55.6±18.8 nmol/L, p = 0.04) when compared to controls, respectively. Notably, 22% of the subjects recruited were vitD deficient during the spring term only (<25nmol/L, n 9). Subjects with ‘insufficient’ vitD status (<50nmol/L) elicited significantly lower CMJ when contrasted to the vitD ‘sufficient’ (>50nmol/l) group (p = 0.055) and a lower VO2 max (p = 0.05) in the spring and summer term (p = 0.05 and p = 0.01, respectively). However, an ANCOVA test showed no significant difference detected for either CMJ or VO2max following adjustments for co-variates. In conclusion, we provide novel information on the vitD status, dietary intake, physical fitness and sunlight exposure of UK young adults across two separate seasons, for which there is limited data at present.
COVID-19, Chikungunya, Dengue and Zika Diseases: An Analytical Platform Based on MALDI-TOF MS, IR Spectroscopy and RT-qPCR for Accurate Diagnosis and Accelerate Epidemics Control

COVID-19 and arboviruses (ARBOD) epidemics co-occurrence is a great concern. In tropical and subtropical regions, ARBOD diseases such as chikungunya, dengue, and Zika are frequent. In both COVID-19 and ARBOD cases, an accurate diagnosis of infected patients is crucial to promote adequate treatment and isolation measures in COVID-19 cases. Overlap of clinical symptoms and laboratory parameters between COVID-19 and ARBOD present themselves as an extra challenge during diagnosis. COVID-19 diagnosis is mainly performed by quantitative reverse polymerase chain reaction (RT-qPCR), while ARBOD diagnosis is performed by serology, detection of antigen or antibody, and molecular diagnosis. In this review, the epidemiologic profile of arboviruses and SARS-CoV-2 is analyzed, and potential risks of symptom overlap is addressed. The implementation of an analytical platform based on infrared (IR) spectroscopy, MALDI-TOF mass spectrometry, and RT-qPCR is discussed as an efficient strategy for a fast, robust, reliable, and cost-effective diagnosis system even during the co-occurrence of virus outbreaks. The spectral data of IR spectroscopy and MALDI-TOF MS obtained from COVID-19 infected and recovered patients can be used to build up an integrated spectral database. This approach can enable us to determine quickly the groups that have been exposed and have recovered from COVID-19 or ARBOD, avoiding misdiagnoses.