Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Environmental Variables and Carbon Input on Soil Microbiome, Metabolome and Disease Control Efficacy in Strawberry Attributable to Anaerobic Soil Disinfestation

Charcoal rot and Fusarium wilt, caused by Macrophomina phaseolina and Fusarium oxysporum f. sp. fragariae, respectively, are major soil-borne diseases of strawberry that have caused significant crop losses in California. Anaerobic soil disinfestation has been studied as an industry-level option to replace soil fumigants to manage these serious diseases. Studies were conducted to discern whether Gramineae carbon input type, incubation temperature, or incubation duration influences the efficacy of this disease control tactic. In experiments conducted using ‘low rate’ amendment applications at moderate day/night temperatures (24/18 °C), and carbon inputs (orchard grass, wheat, and rice bran) induced an initial proliferation and subsequent decline in soil density of the Fusarium wilt pathogen. This trend coincided with the onset of anaerobic conditions and a corresponding generation of various anti-fungal compounds, including volatile organic acids, hydrocarbons, and sulfur compounds. Generation of these metabolites was associated with increases in populations of Clostridium spp. Overall, carbon input and incubation temperature, but not incubation duration, significantly influenced disease suppression. All Gramineae carbon inputs altered the soil microbiome and metabolome in a similar fashion, though the timing and maximum yield of specific metabolites varied with input type. Fusarium wilt and charcoal rot suppression were superior when anaerobic soil disinfestation was conducted using standard amendment rates of 20 t ha−1 at elevated temperatures combined with a 3-week incubation period. Findings indicate that anaerobic soil disinfestation can be further optimized by modulating carbon source and incubation temperature, allowing the maximum generation of antifungal toxic volatile compounds. Outcomes also indicate that carbon input and environmental variables may influence treatment efficacy in a target pathogen-dependent manner which will require pathogen-specific optimization of treatment protocols.
Sagittal Integral Morphotype of Competitive Amateur Athletes and Its Potential Relation with Recurrent Low Back Pain

Athletes have higher thoracic and lumbar curvature in standing than the reference values of the non-athletic population. The sagittal integral morphotype method (SIM) assessment has not previously been applied to competitive amateur athletes (CAA). The propose of the present study was to determine the SIM of CAA treated at a sports-medicine center and to identify spinal misalignments associated with recurrent low back pain (LBP). An observational analysis was developed to describe the SIM in 94 CAA. The thoracic and lumbar curvatures of the CAA were measured in standing, sitting, and trunk forward flexion. Association analysis (Pearson’s chi-square and Cramér’s V tests) was then performed to identify the SIM misalignments associated with LBP. Effect size was analyzed based on Hedges’ g. The most common thoracic SIMs in CAA were total hyperkyphosis (male = 59.02%; female = 42.42%) and static hyperkyphosis (male = 11.48%; female = 6.06%). Hyperlordotic attitude (female = 30.30%; male = 4.92%), static-functional hyperkyphosis (male = 16.39%; female = 3.03%), and structured hyperlordosis (female = 21.21%; male = 1.64%) were the most common lumbar SIMs. Hyperlordotic attitude, static functional lumbar hyperkyphosis, and structured hyperlordosis were associated with LBP in male and female athletes.
Factors Influencing the Surgical Decision in Dystonia Patients Referred for Deep Brain Stimulation

There is no available data on the journey of dystonia patients once referred to a tertiary center to undergo deep brain stimulation (DBS). We hypothesized that some patients might be incorrectly diagnosed while others might decline the procedure or experience significant benefit with switching to a different botulinum neurotoxin (BoNT). This is a single-center, retrospective study of dystonia patients who were referred to the DBS program between January 2014 and December 2018. We collected data on the surgical decision as well as factors influencing this decision. Sixty-seven patients were included (30 males, mean age: 48.3 ± 20.1 years, disease duration: 16.9 ± 15.3 years). Thirty-three (49%) patients underwent DBS. Four (6%) patients were awaiting the procedure while the remaining 30 patients (45%) did not undergo DBS. Reasons for DBS decline were patient refusal (17, 53%), functional dystonia (6, 20%), and successful use of AbobotulinumtoxinA (3, 10%) in patients who had failed other BoNTs. Our study highlights the importance of structured patient education to increase acceptance of DBS, as well as careful patient evaluation, particularly with respect to functional dystonia. Finally, changing BoNT formulation might be beneficial in some patients.
Association between Lifestyle Changes and at-Home Hours during and after the State of Emergency Due to the COVID-19 Pandemic in Japan

Lifestyle changes during the coronavirus disease (COVID-19) lockdown have been previously examined, but there is limited understanding about changes after such restrictions were lifted. This study examines changes in lifestyle habits and body weight among the Japanese population with regard to the length of at-home hours both during (April to May) and after (September) the nationwide stay-at-home request compared to those before the COVID-19 pandemic (January 2020). An online survey was conducted in September 2020 involving 10,000 Japanese survey monitors, selected according to population distribution. During the stay-at-home request, 34% participants extended their at-home hours. More respondents in the group with extended at-home hours experienced an increase or decrease in total physical activity, snacking, food intake, alcohol drinking, and body weight than those in the group with nonextended at-home hours. Some of these changes had a trend according to age. The prevalence of most of these changes decreased when at-home hours returned to normal after the stay-at-home request period; however, increased alcohol consumption and increased or decreased body weight persisted. Our findings suggest that close monitoring for further health outcomes and age-appropriate measures to encourage favorable health behaviors is needed.
Anti-Cancer Activity and Phenolic Content of Extracts Derived from Cypriot Carob (Ceratonia siliqua L.) Pods Using Different Solvents

Extracts derived from the Ceratonia siliqua L. (carob) tree have been widely studied for their ability to prevent many diseases mainly due to the presence of polyphenolic compounds. In this study, we explored, for the first time, the anti-cancer properties of Cypriot carobs. We produced extracts from ripe and unripe whole carobs, pulp and seeds using solvents with different polarities. We measured the ability of the extracts to inhibit proliferation and induce apoptosis in cancer and normal immortalized breast cells, using the MTT assay, cell cycle analysis and Western Blotting. The extracts’ total polyphenol content and anti-oxidant action was evaluated using the Folin–Ciocalteu method and the DPPH assay. Finally, we used LC-MS analysis to identify and quantify polyphenols in the most effective extracts. Our results demonstrate that the anti-proliferative capacity of carob extracts varied with the stage of carob maturity and the extraction solvent. The Diethyl-ether and Ethyl acetate extracts derived from the ripe whole fruit had high Myricetin content and also displayed specific activity against cancer cells. Their mechanism of action involved caspase-dependent and independent apoptosis. Our results indicate that extracts from Cypriot carobs may have potential uses in the development of nutritional supplements and pharmaceuticals.
Treatment of Critical-Size Femoral Bone Defects with Chitosan Scaffolds Produced by a Novel Process from Textile Engineering

The purpose of this study was to investigate, in vitro and in vivo, the suitability of chitosan (CHS) scaffolds produced by the net-shape-nonwoven (NSN) technology, for use as bone graft substitutes in a critical-size femoral bone defect in rats. For in vitro investigations, scaffolds made of CHS, mineralized collagen (MCM), or human cancellous bone allograft (CBA) were seeded with human telomerase-immortalized mesenchymal stromal cells (hTERT-MSC), incubated for 14 days, and thereafter evaluated for proliferation and osteogenic differentiation. In vivo, CHS, MCM and CBA scaffolds were implanted into 5 mm critical-size femoral bone defects in rats. After 12 weeks, the volume of newly formed bone was determined by microcomputed tomography (µCT), while the degree of defect healing, as well as vascularization and the number of osteoblasts and osteoclasts, was evaluated histologically. In vitro, CHS scaffolds showed significantly higher osteogenic properties, whereas treatment with CHS, in vivo, led to a lower grade of bone-healing compared to CBA and MCM. While chitosan offers a completely new field of scaffold production by fibers, these scaffolds will have to be improved in the future, regarding mechanical stability and osteoconductivity.
Melatonin, a Potential Therapeutic Agent for Preeclampsia, Reduces the Extrusion of Toxic Extracellular Vesicles from Preeclamptic Placentae

Preeclampsia, characterised by maternal endothelial cell activation, is triggered by toxic factors, such as placental extracellular vesicles (EVs) from a dysfunctional placenta. The increased oxidative stress seen in the preeclamptic placenta links to endoplasmic reticulum (ER) stress. The ER regulates protein folding and trafficking. When the ER is stressed, proteins are misfolded, and misfolded proteins are toxic. Misfolded proteins can be exported from cells, via EVs which target to other cells where the misfolded proteins may also be toxic. Melatonin is a hormone and antioxidant produced by the pineal gland and placenta. Levels of melatonin are reduced in preeclampsia. In this study we investigated whether melatonin treatment can change the nature of placental EVs that are released from a preeclamptic placenta. EVs were collected from preeclamptic (n = 6) and normotensive (n = 6) placental explants cultured in the presence or absence of melatonin for 18 h. Misfolded proteins were measured using a fluorescent compound, Thioflavin-T (ThT). Endothelial cells were exposed to placental EVs overnight. Endothelial cell activation was measured by the quantification of cell-surface ICAM-1 using a cell-based ELISA. EVs from preeclamptic placentae carried significantly (p < 0.001) more misfolded proteins than normotensive controls. Incubating preeclamptic placental explants in the presence of melatonin (1 µM and 10 µM) significantly (p < 0.001) reduced the misfolded proteins carried by EVs. Culturing endothelial cells in the presence of preeclamptic EVs significantly increased the expression of ICAM-1. This increased ICAM-1 expression was significantly reduced when the endothelial cells were exposed to preeclamptic EVs cultured in the presence of melatonin. This study demonstrates that melatonin reduces the amount of misfolded proteins carried by EVs from preeclamptic placentae and reduces the ability of these EVs to activate endothelial cells. Our study provides further preclinical support for the use of melatonin as a treatment for preeclampsia.
Diets for Dairy Cows with Different Proportions of Crude Protein Originating from Red Clover Silage versus Soybean Meal: Ruminal Degradation and Intestinal Digestibility of Amino Acids

Simple Summary The purpose was to assess the effect of exchanging crude protein of soybean meal with red clover silage (RCS) in total mixed rations (TMR) on ruminal degradation and intestinal digestibility (ID) of essential amino acids (EAA). Increasing proportions of RCS in the TMR increased the ruminal degradation and reduced the ID of EAA. The ruminal degradation of EAA of the TMR followed that of CP, but the ID of EAA differed from that of CP at higher levels of RCS in the diet. In conclusion, increasing proportions of RCS in TMR reduced the extent of EAA flow into the small intestine, reduced the ID of EAA, and consequently the intestinal absorbable EAA. Abstract The purpose was to assess the effect of exchanging crude protein (CP) of soybean meal (SBM) with red clover silage (RCS) in total mixed rations (TMR) on ruminal degradation and intestinal digestibility (ID) of essential amino acids (EAA). Four TMR and their individual feed components were studied. The TMR were composed of forage and concentrates (75:25), with proportions of RCS in TMR of 0.15, 0.30, 0.45, and 0.60 on a dry matter basis, resulting in diet groups RCS15, RCS30, RCS45, and RCS60, respectively. The ruminal degradation of EAA was determined using the nylon bag technique. For this, samples of TMR and their individual feed components were ruminally incubated for 16 h. The feed residues of TMR obtained after 16 h of incubation were used for the determination of ID of EAA using the mobile-bag technique. Increasing RCS and reducing SBM proportions linearly increased (p < 0.01) the in situ ruminal degradation of individual EAA from 75.5% to 83.5%. The degradation of EAA followed the trend of CP degradation among TMR, except for Cys that was lower (p < 0.05) than that of CP in RCS60 (79.7% vs. 86.3%). The degradation of EAA in individual feed ingredients not always corresponded to the degradation of CP and was feed dependent. Increasing the proportions of RCS in the TMR linearly reduced (p < 0.001) the ID of EAA (except for Ile) from 78.2% to 67.3%. However, the ID of EAA did not always reflect the ID of CP, and in general, the differences between the ID of CP and EAA increased as RCS increased in the TMR. The ID values of most of the EAA were similar (p > 0.05) to ID of CP in RCS15 and RCS30, while they mostly differed (p < 0.05) in RCS45 and RCS60, and being higher for EAA than CP (except for Cys that was lower than CP, p < 0.05). Similar trends were observed for intestinal absorbable AA, resulting in higher values (p < 0.05) of intestinal absorbable for all EAA than of CP in diet RCS60. In conclusion, increasing levels of RCS in TMR reduced the extent of EAA flow into the small intestine, the ID of EAA, and consequently the intestinal absorbable EAA. Therefore, accurate determination of metabolizable AA must be considered for optimal diet formulation when including high proportions of RCS in diets of high-producing dairy cows.
2′O-Ribose Methylation of Ribosomal RNAs: Natural Diversity in Living Organisms, Biological Processes, and Diseases

Recent findings suggest that ribosomes, the translational machineries, can display a distinct composition depending on physio-pathological contexts. Thanks to outstanding technological breakthroughs, many studies have reported that variations of rRNA modifications, and more particularly the most abundant rRNA chemical modification, the rRNA 2′O-ribose methylation (2′Ome), intrinsically occur in many organisms. In the last 5 years, accumulating reports have illustrated that rRNA 2′Ome varies in human cell lines but also in living organisms (yeast, plant, zebrafish, mouse, human) during development and diseases. These rRNA 2′Ome variations occur either within a single cell line, organ, or patient’s sample (i.e., intra-variability) or between at least two biological conditions (i.e., inter-variability). Thus, the ribosomes can tolerate the absence of 2′Ome at some specific positions. These observations question whether variations in rRNA 2′Ome could provide ribosomes with particular translational regulatory activities and functional specializations. Here, we compile recent studies supporting the heterogeneity of ribosome composition at rRNA 2′Ome level and provide an overview of the natural diversity in rRNA 2′Ome that has been reported up to now throughout the kingdom of life. Moreover, we discuss the little evidence that suggests that variations of rRNA 2′Ome can effectively impact the ribosome activity and contribute to the etiology of some human diseases.
Functions of the Thyroid-Stimulating Hormone on Key Developmental Features Revealed in a Series of Zebrafish Dyshormonogenesis Models

The hypothalamic–pituitary–thyroid (HPT) axis regulates many critical features in vertebrates. Utilizing TALENs and CRISPR/Cas9 techniques, thyroid-stimulating hormone subunit beta a (tshba), thyroglobulin (tg), and solute carrier family 16 member 2 (slc16a2) mutant zebrafish lines were generated. Among the three mutants, the earliest time point for the significantly altered T3 contents was observed in tshba mutants, which resulted in the most severe defects, including typical defects such as the retardation of inflated anterior swimming bladder (aSB), proper formation of fin ray and posterior squamation (SP), the larval-to-juvenile transition (LTJT) process, juvenile growth retardation, and mating failure. In tg mutants, which are actually compensated with an alternative splicing form, growth retardation was observed in the juvenile stage without LTJT and reproductive defects. The evident goiter phenotype was only observed in tg- and slc16a2 mutants, but not in tshba mutants. Other than goiters being observed, no other significant developmental defects were found in the slc16a2 mutants. Regarding the reproductive defects observed in tshba mutants, the defective formation of the secondary sex characteristics (SSCs) was observed, while no obvious alterations during gonad development were found. Based on our analyses, zebrafish at the 6–12 mm standard length or 16–35 days post-fertilization (dpf) should be considered to be in their LTJT phase. Using a series of zebrafish dyshormonogenesis models, this study demonstrated that the TSH function is critical for the proper promotion of zebrafish LTJT and SSC formation. In addition, the elevation of TSH levels appears to be essential for goiter appearance in zebrafish.
Genome-Wide Association Study Using Whole-Genome Sequence Data for Fertility, Health Indicator, and Endoparasite Infection Traits in German Black Pied Cattle

This genome-wide association study (GWAS) aimed to identify sequence variants (SVs) and candidate genes associated with fertility and health in endangered German Black Pied cattle (DSN) based on whole-genome sequence (WGS) data. We used 304 sequenced DSN cattle for the imputation of 1797 genotyped DSN to WGS. The final dataset included 11,413,456 SVs of 1886 cows. Cow traits were calving-to-first service interval (CTFS), non-return after 56 days (NR56), somatic cell score (SCS), fat-to-protein ratio (FPR), and three pre-corrected endoparasite infection traits. We identified 40 SVs above the genome-wide significance and suggestive threshold associated with CTFS and NR56, and three important potential candidate genes (ARHGAP21, MARCH11, and ZNF462). For SCS, most associations were observed on BTA 25. The GWAS revealed 61 SVs, a cluster of 10 candidate genes on BTA 13, and 7 pathways for FPR, including key mediators involved in milk fat synthesis. The strongest associations for gastrointestinal nematode and Dictyocaulus viviparus infections were detected on BTA 8 and 24, respectively. For Fasciola hepatica infections, the strongest associated SVs were located on BTA 4 and 7. We detected 200 genes for endoparasite infection traits, related to 16 pathways involved in host immune response during infection.
Genetic Interaction of SEEDSTICK, GORDITA and AUXIN RESPONSE FACTOR 2 during Seed Development

Seed development is under the control of complex and coordinated molecular networks required for the formation of its different components. The seed coat development largely determines final seed size and shape, in addition to playing a crucial role in protecting the embryo and promoting germination. In this study, we investigated the role of three transcription factors known to be active during seed development in Arabidopsis thaliana: SEEDSTICK (STK) and GORDITA (GOA), two MADS-domain proteins, and AUXIN RESPONSE FACTOR 2 (ARF2), belonging to the ARF family. Through a reverse genetic approach, we characterized the seed phenotypes of all the single, double and triple loss-of-function mutants in relation to seed size/shape and the effects on metabolic pathways occurring in the seed coat. This approach revealed that dynamic networks involving these TFs are active throughout ovule and seed development, affecting the formation of the seed coat. Notably, while the genetic interaction among these genes results in synergies that control the promotion of cell expansion in the seed coat upon pollination and production of proanthocyanidins, functional antagonists arise in the control of cell proliferation and release of mucilage.
Non-Canonical Role of PDK1 as a Negative Regulator of Apoptosis through Macromolecular Complexes Assembly at the ER–Mitochondria Interface in Oncogene-Driven NSCLC

Simple Summary Co-targeting of glucose metabolism and oncogene drivers in patients with non-small cell lung cancer (NSCLC) has been proposed as a potentially effective therapeutic strategy. Here, we demonstrate that downregulation of pyruvate dehydrogenase kinase 1 (PDK1), an enzyme of glycolytic cascade, enhances maximal respiration of cancer cells by upregulating mitochondrial complexes of oxidative phosphorylation (OXPHOS) and improves tumor response to tyrosine kinase inhibitors by promoting apoptosis. Furthermore, we provided consistent evidence that PDK1 drives the formation of macromolecular complexes at the ER–mitochondria interface involving PKM2, Bcl-2 and Bcl-xL and serves as an indirect anchorage of anti-apoptotic proteins to the mitochondrial membrane. Our findings taken together highlighted a non-canonical role of PDK1 as a negative regulator of apoptosis, thus coupling the glycolytic phenotype to drug resistance. The major translational relevance of this study is to provide a rational basis for combined therapeutic strategies targeting PDK1 and oncogene drivers in NSCLC patients. Abstract Here, we tested whether co-targeting of glucose metabolism and oncogene drivers may enhance tumor response to tyrosine kinase inhibitors (TKIs) in NSCLC. To this end, pyruvate dehydrogenase kinase 1 (PDK1) was stably downregulated in oncogene-driven NSCLC cell lines exposed or not to TKIs. H1993 and H1975 cells were stably transfected with scrambled (shCTRL) or PDK1-targeted (shPDK1) shRNA and then treated with MET inhibitor crizotinib (1 µM), double mutant EGFRL858R/T790M inhibitor WZ4002 (1 µM) or vehicle for 48 h. The effects of PDK1 knockdown on glucose metabolism and apoptosis were evaluated in untreated and TKI-treated cells. PDK1 knockdown alone did not cause significant changes in glycolytic cascade, ATP production and glucose consumption, but it enhanced maximal respiration in shPDK1 cells when compared to controls. When combined with TKI treatment, PDK1 downregulation caused a strong enhancement of OXPHOS and a marked reduction in key glycolytic enzymes. Furthermore, increased levels of apoptotic markers were found in shPDK1 cells as compared to shCTRL cells after treatment with TKIs. Co-immunoprecipitation studies showed that PDK1 interacts with PKM2, Bcl-2 and Bcl-xL, forming macromolecular complexes at the ER–mitochondria interface. Our findings showed that downregulation of PDK1 is able to potentiate the effects of TKIs through the disruption of macromolecular complexes involving PKM2, Bcl-2 and Bcl-xL.