Miracle-dz/UniFAR-FTUs huggingface dataset:
Bobolink (Dolichonyx oryzivorus) Declines Follow Bison (Bison bison) Reintroduction on Private Conservation Grasslands

Simple Summary North American grassland birds evolved with American bison (Bison bison), until overhunting drove bison to near-extinction > 150 years ago. Bison have now been reintroduced to many areas that provide important nesting habitat for grassland birds, which are now among the most rapidly declining birds in North America. However, little is known about bison interactions with birds such as Bobolinks (Dolichonyx oryzivorus), obligate grassland nesting songbirds of conservation concern. Using data collected over an 18-year period, we assessed the effects of bison reintroduction, together with other land management and climate factors, on Bobolinks in a private conservation area comprising 24 km2 of native grasslands in the North American Great Plains. In grasslands where bison were reintroduced, Bobolink abundance (adult numbers) declined by 62%, and productivity (juvenile numbers) declined by 84%. By contrast, Bobolink populations remained stable over the same time period in adjacent grasslands where bison were not reintroduced. Bobolink abundance and productivity increased in years following warmer and wetter winters, but nevertheless declined over time in grasslands where the bison population doubled. Where bison are reintroduced and confined in high densities, overgrazing, trampling, and related impacts may drive severe declines in Bobolinks and other grassland birds of conservation concern. Abstract Among the most rapidly declining birds in continental North America, grassland birds evolved with American bison (Bison bison) until bison nearly became extinct due to overhunting. Bison populations have subsequently rebounded due to reintroductions on conservation lands, but the impacts of bison on grassland nesting birds remain largely unknown. We investigated how bison reintroduction, together with other land management and climate factors, affected breeding populations of a grassland bird species of conservation concern, the Bobolink (Dolichonyx oryzivorus). We quantified population changes in Bobolinks over an 18-year period in conservation grasslands where bison were reintroduced, compared with adjacent grasslands grazed by cattle and where hay was harvested after the bird breeding season. Four years after bison reintroduction, the bison population in the study area had doubled, while Bobolink abundance declined 62% and productivity declined 84%. Our findings suggest that bison reintroduction as a conservation strategy may be counterproductive in grassland fragments where overgrazing, trampling, and other negative impacts drive declines in grassland breeding birds. Where bird conservation is an objective, small grassland reserves may therefore be inappropriate sites for bison reintroduction. To maximize conservation benefits to birds, land managers should prioritize protecting grassland birds from disturbance during the bird breeding season.
Somatic Disease in Survivors of Childhood Malignant Bone Tumors in the Nordic Countries

Simple Summary The treatment of osteosarcoma and Ewing sarcoma, the two major types of malignant bone tumors in children, has progressed considerably during the last decades, with more patients becoming long-term survivors. This improvement has resulted in an increasing number of patients with long-term adverse health consequences from the life-saving treatment. The aim of this study was to provide a detailed, comprehensive overview of somatic diseases that require hospitalization in long-term survivors of osteosarcoma and Ewing sarcoma. This study contributes new insights into the risk of somatic late effects in survivors of osteosarcoma and Ewing sarcoma which are urgently requested by pediatric oncologists, researchers, and by survivors and their families. The study provides an essential basis for the development of preventive intervention strategies and for optimal patient counseling and follow-up care, which all contribute to improving the health and quality of life in survivors. Abstract Survivors of malignant bone tumors in childhood are at risk of long-term adverse health effects. We comprehensively reviewed cases of somatic diseases that required a hospital contact in survivors of osteosarcoma and Ewing sarcoma. In a population-based cohort study, 620 five-year survivors of osteosarcoma (n = 440) or Ewing sarcoma (n = 180), diagnosed before the age of 20 years in Denmark, Finland, Iceland, and Sweden during 1943–2008, were followed in the national hospital registers. Overall rates of hospital contacts for any somatic disease and for 12 main diagnostic groups and 120 specific disease categories were compared with those in a matched comparison cohort (n = 3049) randomly selected from the national population registers. The rate of hospital contact for any somatic disease was 80% higher in survivors of malignant bone tumors than in comparisons and remained elevated up to 30 years after diagnosis. The rate of hospital contacts was higher after Ewing sarcoma (rate ratio (RR) 2.24; 95% confidence interval (CI) 1.76–2.85) than after osteosarcoma (RR 1.67; 95% CI 1.41–1.98). Elevated rates were observed for 11 main diagnostic groups, including infections, second malignant neoplasms, and diseases of the skin, bones, and circulatory, digestive, endocrine, and urinary systems. Survivors of malignant bone tumors in childhood are at increased risk of somatic diseases many years after diagnosis. This comprehensive study contributes new insight into the risk of late effects in survivors of osteosarcoma and Ewing sarcoma, which is an essential basis for optimal patient counseling and follow-up care.
Development and Validation of an LC-MS/MS Based Method for the Determination of Deoxynivalenol and Its Modified Forms in Maize

The Fusarium mycotoxin deoxynivalenol (DON) is a common contaminant of cereals and is often co-occurring with its modified forms DON-3-glucoside (D3G), 3-acetyl-DON (3ADON) or 15-acetyl-DON (15ADON). A stable-isotope dilution liquid chromatography-tandem mass spectrometry (LC-MS/MS) based method for their determination in cereals was developed and validated for maize. Therefore, 13C-labelled D3G was enzymatically produced using 13C-DON and [13C6Glc]-sucrose and used as an internal standard (IS) for D3G, while uniformly 13C labelled IS was used for the other mycotoxins. Baseline separation was achieved for the critical peak pair DON/D3G, while 3ADON/15ADON could not be fully baseline separated after testing various reversed phase, fluorinated phase and chiral LC columns. After grinding, weighing and extracting the cereal samples, the raw extract was centrifuged and a mixture of the four 13C-labelled ISs was added directly in a microinsert vial. The subsequent analytical run took 7 min, followed by negative electrospray ionization and selected reaction monitoring on a triple quadrupole MS. Maize was used as a complex cereal model matrix for validation. The use of the IS corrected the occurring matrix effects efficiently from 76 to 98% for D3G, from 86 to 103% for DON, from 68 to 100% for 15ADON and from 63 to 96% for 3ADON.
Expression Patterns of DNA Methylation and Demethylation Genes during Plant Development and in Response to Phytohormones

DNA methylation and demethylation precisely and effectively modulate gene expression during plant growth and development and in response to stress. However, expression profiles of genes involved in DNA methylation and demethylation during plant development and their responses to phytohormone treatments remain largely unknown. We characterized the spatiotemporal expression patterns of genes involved in de novo methylation, methyl maintenance, and active demethylation in roots, shoots, and reproductive organs using β-glucuronidase (GUS) reporter lines. Promoters of DNA demethylases were generally more highly active at the mature root tissues, whereas the promoters of genes involved in DNA methylation were more highly active at fast-growing root tissues. The promoter activity also implies that methylation status in shoot apex, leaf primordia, floral organs, and developing embryos is under tight equilibrium through the activity of genes involved in DNA methylation and demethylation. The promoter activity of DNA methylation and demethylation-related genes in response to various phytohormone treatments revealed that phytohormones can alter DNA methylation status in specific and redundant ways. Overall, our results illustrate that DNA methylation and demethylation pathways act synergistically and antagonistically in various tissues and in response to phytohormone treatments and point to the existence of hormone-linked methylome regulation mechanisms that may contribute to tissue differentiation and development.
Plasma Concentrations of Lysophosphatidic Acid and Autotaxin in Abstinent Patients with Alcohol Use Disorder and Comorbid Liver Disease

Lysophosphatidic acid (LPA) is an endogenous lysophospholipid and a bioactive lipid that is synthesized by the enzyme autotaxin (ATX). The ATX–LPA axis has been associated with cognitive dysfunction and inflammatory diseases, mainly in a range of nonalcoholic liver diseases. Recently, preclinical and clinical evidence has suggested a role of LPA signaling in alcohol use disorder (AUD) and AUD-related cognitive function. However, the ATX–LPA axis has not been sufficiently investigated in alcoholic liver diseases. An exploratory study was conducted in 136 participants, 66 abstinent patients with AUD seeking treatment for alcohol (alcohol group), and 70 healthy control subjects (control group). The alcohol group was divided according to the presence of comorbid liver diseases (i.e., fatty liver/steatosis, alcoholic steatohepatitis, or cirrhosis). All participants were clinically evaluated, and plasma concentrations of total LPA and ATX were measured using enzyme-linked immunosorbent assays. Data were primarily analyzed using analysis of covariance (ANCOVA) while controlling for age, body mass index, and sex. Logistic regression models were created to assess the association of the ATX–LPA axis and AUD or liver disease. LPA and ATX were log10-transformed to fit the assumptions of parametric testing.The main results were as follows: total LPA and ATX concentrations were dysregulated in the alcohol group, and patients with AUD had significantly lower LPA (F(1,131) = 10.677, p = 0.001) and higher ATX (F(1,131) = 8.327, p = 0.005) concentrations than control subjects; patients with AUD and liver disease had significantly higher ATX concentrations (post hoc test, p < 0.05) than patients with AUD but not liver disease; significant correlations between AUD-related variables and concentrations of LPA and ATX were only found in the non-liver disease subgroup (the duration of alcohol abstinence with LPA and ATX (r = +0.33, p < 0.05); and the severity of AUD with ATX (rho = −0.33, p < 0.05)); and a logistic regression model with LPA, ATX, and AUD-related variables showed an excellent discriminative power (area under the curve (AUC) = 0.915, p < 0.001) for distinguishing patients with AUD and comorbid liver disease. In conclusion, our data show that the ATX–LPA axis is dysregulated in AUD and suggest this lipid signaling, in combination with relevant AUD-related variables, as a reliable biomarker of alcoholic liver diseases.
Cold Atmospheric Pressure Microplasma Pipette for Disinfection of Methicillin-Resistant Staphylococcus aureus

Microbial infections should be controlled and prevented for successful wound healing and tissue regeneration. Various disinfection methods exist that use antibiotics, ultraviolet (UV), heat, radiation, or chemical disinfectants; however, cold atmospheric pressure plasma has exhibited a unique and effective antibacterial ability that is not affected by antibiotic resistance or pain. This study develops a cold atmospheric pressure microplasma pipette (CAPMP) that outputs an Ar plasma plume through a tube with an inner radius of 180 μm for disinfection in a small area. The CAPMP was evaluated using Staphylococcus aureus and methicillin-resistant Staphylococcus aureus diluted in liquid media, spread on solid agar, or covered by dressing gauze. An increase in the treatment time of CAPMP resulted in a decrease in the number of colonies of the grown microorganism (colony forming unit) and an increase in the disinfected area for both bacteria. The disinfection ability of CAPMP was observed when the bacteria were covered with dressing gauze and was dependent on the number of gauze layers.
Molecular and Enzymatic Characterization of Flavonoid 3′-Hydroxylase of Malus × domestica

Malus × domestica (apple) accumulates particularly high amounts of dihydrochalcones in various tissues, with phloridzin (phloretin 2′-O-glucoside) being prevalent, although small amounts of 3-hydroxyphloretin and 3-hydroxyphloridzin are also constitutively present. The latter was shown to correlate with increased disease resistance of transgenic M. × domestica plants. Two types of enzymes could be involved in 3-hydroxylation of dihydrochalcones: polyphenol oxidases or the flavonoid 3′-hydroxylase (F3′H), which catalyzes B-ring hydroxylation of flavonoids. We isolated two F3′H cDNA clones from apple leaves and tested recombinant Malus F3′Hs for their substrate specificity. From the two isolated cDNA clones, only F3′HII encoded a functionally active enzyme. In the F3′HI sequence, we identified two putatively relevant amino acids that were exchanged in comparison to that of a previously published F3′HI. Site directed mutagenesis, which exchanged an isoleucine into methionine in position 211 restored the functional activity, which is probably because it is located in an area involved in interaction with the substrate. In contrast to high activity with various flavonoid substrates, the recombinant enzymes did not accept phloretin under assay conditions, making an involvement in the dihydrochalcone biosynthesis unlikely.
RNA-Seq Provides New Insights into the Gene Expression Changes in Azoarcus olearius BH72 under Nitrogen-Deficient and Replete Conditions beyond the Nitrogen Fixation Process

Azoarcus olearius BH72 is an endophyte capable of biological nitrogen fixation (BNF) and of supplying nitrogen to its host plant. Our previous microarray approach provided insights into the transcriptome of strain BH72 under N2-fixation in comparison to ammonium-grown conditions, which already indicated the induction of genes not related to the BNF process. Due to the known limitations of the technique, we might have missed additional differentially expressed genes (DEGs). Thus, we used directional RNA-Seq to better comprehend the transcriptional landscape under these growth conditions. RNA-Seq detected almost 24% of the annotated genes to be regulated, twice the amount identified by microarray. In addition to confirming entire regulated operons containing known DEGs, the new approach detected the induction of genes involved in carbon metabolism and flagellar and twitching motility. This may support N2-fixation by increasing energy production and by finding suitable microaerobic niches. On the other hand, energy expenditures were reduced by suppressing translation and vitamin biosynthesis. Nonetheless, strain BH72 does not appear to be content with N2-fixation but is primed for alternative economic N-sources, such as nitrate, urea or amino acids; a strong gene induction of machineries for their uptake and assimilation was detected. RNA-Seq has thus provided a better understanding of a lifestyle under limiting nitrogen sources by elucidating hitherto unknown regulated processes.
Comparison of Nutritional Knowledge, Attitudes and Practices between Urban and Rural Secondary School Students: A Cross-Sectional Study in Sabah, East Malaysia

Nutritional knowledge, attitudes and practice (KAP) may guide healthy meal choices. Here, nutritional KAP was compared across school students in Sabah based on locality and gender. A cross-sectional survey of students aged 15–19 years was conducted using multistage sampling. Nutritional KAP was measured via questionnaire. Anthropometric measures of weight and height were taken in person to calculate body mass index (BMI). Among the 994 participants, 80% were urban and 60% were female (mean age 16.5 ± 0.6 yr). Most were of Kadazan-Dusun (23%) ethnicity. Measured height for age Z score (HAZ) and BMI for age Z score (BAZ) differed between urban and rural students (−1.2 ± 0.8 versus −1.5 ± 0.7 for HAZ; p < 0.001; 0.2 ± 1.4 versus −0.1 ± 1.3; p = 0.02, respectively). No difference in nutritional knowledge was found, although urban students prioritized having a healthy/balanced diet (59.55% versus 48.50%, p = 0.03) and ate daily breakfast (57.4% versus 10.2%, p < 0.001) compared to rural. Females scored higher on nutritional knowledge than males (18.9 ± 2.8 vs. 18.1 ± 3.4, respectively, p = 0.0001), yet males selected more healthy/balanced foods (63.3% versus 53.3%, p = 0.041). The gap remains between nutritional KAP and translating this to healthy eating among adolescents, related to locality and gender.
Artificial Intelligence in Capsule Endoscopy: A Practical Guide to Its Past and Future Challenges

Artificial intelligence (AI) has revolutionized the medical diagnostic process of various diseases. Since the manual reading of capsule endoscopy videos is a time-intensive, error-prone process, computerized algorithms have been introduced to automate this process. Over the past decade, the evolution of convolutional neural network (CNN) enabled AI to detect multiple lesions simultaneously with increasing accuracy and sensitivity. Difficulty in validating CNN performance and unique characteristics of capsule endoscopy images make computer-aided reading systems in capsule endoscopy still on a preclinical level. Although AI technology can be used as an auxiliary second observer in capsule endoscopy, it is expected that in the near future, it will effectively reduce the reading time and ultimately become an independent, integrated reading system.
LC-MS/MS Proteomic Study of MCF-7 Cell Treated with Dox and Dox-Loaded Calcium Carbonate Nanoparticles Revealed Changes in Proteins Related to Glycolysis, Actin Signalling, and Energy Metabolism

Simple Summary This work revealed that DOX-Ar-CC-NPs have the ability to promote cell death in MCF-7 cells, showing high potency in drug delivery. DOX-Ar-CC-NPs prompts cell death of MCF-7 cancer cells in vivo. LC-MS/MS Proteomic experemnt showed alteration on the expression of proteins linked to actine signaling, carbohydrate metabolisim. Abstract One of the most prevalent death causes among women worldwide is breast cancer. This study aimed to characterise and differentiate the proteomics profiles of breast cancer cell lines treated with Doxorubicin (DOX) and Doxorubicin-CaCO3-nanoparticles (DOX-Ar-CC-NPs). This study determines the therapeutic potential of doxorubicin-loaded aragonite CaCO3 nanoparticles using a Liquid Chromatography/Mass Spectrometry analysis. In total, 334 proteins were expressed in DOX-Ar-CC-NPs treated cells, while DOX treatment expressed only 54 proteins. Out of the 334 proteins expressed in DOX-CC-NPs treated cells, only 36 proteins showed changes in abundance, while in DOX treated cells, only 7 out of 54 proteins were differentially expressed. Most of the 30 identified proteins that are differentially expressed in DOX-CC-NPs treated cells are key enzymes that have an important role in the metabolism of carbohydrates as well as energy, including: pyruvate kinase, ATP synthase, enolase, glyceraldehyde-3-phosphate dehydrogenase, mitochondrial ADP/ATP carrier, and trypsin. Other identified proteins are structural proteins which included; Keratin, α- and β-tubulin, actin, and actinin. Additionally, one of the heat shock proteins was identified, which is Hsp90; other proteins include Annexins and Human epididymis protein 4. While the proteins identified in DOX-treated cells were tubulin alpha-1B chain and a beta chain, actin cytoplasmic 1, annexin A2, IF rod domain-containing protein, and 78 kDa glucose-regulated protein. Bioinformatics analysis revealed the predicted canonical pathways linking the signalling of the actin cytoskeleton, ILK, VEGF, BAG2, integrin and paxillin, as well as glycolysis. This research indicates that proteomic analysis is an effective technique for proteins expression associated with chemotherapy drugs on cancer tumours; this method provides the opportunity to identify treatment targets for MCF-7 cancer cells, and a liquid chromatography-mass spectrometry (LC-MS/MS) system allowed the detection of a larger number of proteins than 2-DE gel analysis, as well as proteins with maximum pIs and high molecular weight.
Rational Design of Cellulose Nanofibrils Separator for Sodium-Ion Batteries

Cellulose nanofibrils (CNF) with high thermal stability and excellent electrolyte wettability attracted tremendous attention as a promising separator for the emerging sodium-ion batteries. The pore structure of the separator plays a vital role in electrochemical performance. CNF separators are assembled using the bottom-up approach in this study, and the pore structure is carefully controlled through film-forming techniques. The acid-treated separators prepared from the solvent exchange and freeze-drying demonstrated an optimal pore structure with a high electrolyte uptake rate (978.8%) and Na+ transference number (0.88). Consequently, the obtained separator showed a reversible specific capacity of 320 mAh/g and enhanced cycling performance at high rates compared to the commercial glass fiber separator (290 mAh/g). The results highlight that CNF separators with an optimized pore structure are advisable for sodium-ion batteries.
A Novel Hybrid Approach Based on Deep CNN Features to Detect Knee Osteoarthritis

In the recent era, various diseases have severely affected the lifestyle of individuals, especially adults. Among these, bone diseases, including Knee Osteoarthritis (KOA), have a great impact on quality of life. KOA is a knee joint problem mainly produced due to decreased Articular Cartilage between femur and tibia bones, producing severe joint pain, effusion, joint movement constraints and gait anomalies. To address these issues, this study presents a novel KOA detection at early stages using deep learning-based feature extraction and classification. Firstly, the input X-ray images are preprocessed, and then the Region of Interest (ROI) is extracted through segmentation. Secondly, features are extracted from preprocessed X-ray images containing knee joint space width using hybrid feature descriptors such as Convolutional Neural Network (CNN) through Local Binary Patterns (LBP) and CNN using Histogram of oriented gradient (HOG). Low-level features are computed by HOG, while texture features are computed employing the LBP descriptor. Lastly, multi-class classifiers, that is, Support Vector Machine (SVM), Random Forest (RF), and K-Nearest Neighbour (KNN), are used for the classification of KOA according to the Kellgren–Lawrence (KL) system. The Kellgren–Lawrence system consists of Grade I, Grade II, Grade III, and Grade IV. Experimental evaluation is performed on various combinations of the proposed framework. The experimental results show that the HOG features descriptor provides approximately 97% accuracy for the early detection and classification of KOA for all four grades of KL.