Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitrogen Pulse and Competition Affects Nitrogen Metabolism in Invasive Weed (Amaranthus retroflexus) and Native Crop (Glycine max)

Nitrogen (N) pulse is a frequent event in agroecosystems caused by fertilization. Understanding the responses of nitrogen metabolisms in native crops and invasive weeds to N pulses is essential in investigating the invasive mechanism of invasive weeds. A pot experiment was carried out to study the impacts of N pulse and the interspecific competition on nitrogen metabolism of an invasive weed (Amaranthus retroflexus) and a native crop (Glycine max); the plants were applied with an equal amount of N in three N pulse treatments, i.e., sole-summit treatment (SS) with N only applied on the seeding date, double-summit treatment (DS) with twice N applied (the fertilizer was applied on both the seeding date and the flowering date), and no-summit treatment (NS) in which N was applied evenly during the experiment. The results showed that A. retroflexus increased the nitrate reductase (NR) activity more than G. max (except for the roots) in the early growing stage, and increased the glutamine synthetase (GS) and glutamate dehydrogenase (GDH) activities in stem more than G. max in SS and DS treatments during the last two growing stages, however, the advantages were far weaker in the NS treatment. Interspecific competition had negative effects on the nitrogen metabolism of the two species among most of the sample times, and the effects of interspecific competition exerted a tissue-specific influence on nitrogen metabolism in the two species. A. retroflexus switched to reproductive growth earlier in SS treatment than in the DS and NS treatments when it was grown in mixed planting, and its height was the lowest in the NS treatment, so the competitive ability of A. retroflexus was higher in the SS and DS treatments than in the NS treatment, while SS treatment was the common application method of N fertilizer in the G. max farmland in China. Thus, the results of this study suggest that, if the farmer changed the N fertilizer application mode to a constant multiple fertilization mode, the competitive capacity of A. retroflexus will be reduced.
Characteristics and Outcomes Among Patients With Autoimmune Rheumatic Diseases Requiring a Higher Level of Care

Objective Patients with autoimmune rheumatic diseases (ARDs) have a higher risk of developing organ failure, and they may require admission to the intensive care unit (ICU). The aim of our study is to determine the reasons for admission to the ICU, identify potential risk factors associated with mortality, and assess the outcomes of patients with ARD diseases admitted to the ICU. Methods We conducted a medical records review study of patients with ARD admitted to the ICU from 2012 to 2018. Patient data included demographic and clinical characteristics, ICU admission diagnoses, length of stay, complications, and immunosuppressive regimen. Short-term and long-term outcomes were assessed. Results A total of 80 ARD patients were identified with the mean age of 48.8, 67% were female, and 56% were Hispanic. The most common disease associated with ICU admission was systemic lupus erythematosus (42%), followed by rheumatoid arthritis (26%), and 12% of patients had systemic vasculitis. Sepsis was the leading cause of ICU admission, accounting for 31%, followed by respiratory failure due to pneumonia (10%) and congestive heart failure (10%). Twenty percent of patients died in the ICU, 5% died 30 days after ICU admission, and 7.5% died within 1 year after the ICU stay, resulting in overall mortality of 33% by the end of 1 year. Nonsurvivors were more likely to need mechanical ventilation (p = 0.001), vasopressor support (p < 0.001), had renal (p = 0.041) or cardiovascular (p < 0.001) involvement on admission, APACHE II score higher than 19 (p = 0.001), and 4 days or longer stay in the ICU (p = 0.001). Conclusions Our findings indicated that systemic lupus erythematosus is the most common ARD associated with ICU admission, and sepsis was the most frequent cause. Predictors associated with higher mortality were the requirement for mechanical ventilation, vasopressor support, increase length of ICU stay, and renal and cardiovascular involvement on admission.
Performance Analysis of Direct GPS Spoofing Detection Method with AHRS/Accelerometer

The global positioning system (GPS) is an essential technology that provides positioning capabilities and is used in various applications such as navigation, surveying, mapping, robot simultaneous localization and mapping (SLAM), location-based service (LBS), etc. However, the GPS is known to be vulnerable to intentional attacks such as spoofing because of its simple signal structure. In this study, a direct method is proposed for GPS spoofing detection, using Attitude and Heading Reference System (AHRS) accelerometer and analyzing the detection performance with corresponding probability density functions (PDFs). The difference in the acceleration between the GPS receiver and the accelerometer is used to detect spoofing. The magnitude of the acceleration error may be used as a decision variable. Additionally, using the magnitude of the north (or east) component of the acceleration error as another decision variable is proposed, which shows better performance in some conditions. The performance of the two decision variables is compared by calculating the probability of spoofing detection and the detectable minimum spoofing acceleration (DMSA), given a pre-defined false alarm probability and a pre-defined detection probability. It turns out that both decision variables need to be used together to obtain the best spoofing detection performance.
Ring finger protein 5 activates sterol regulatory element–binding protein 2 (SREBP2) to promote cholesterol biosynthesis via inducing polyubiquitination of SREBP chaperone SCAP

Sterol regulatory element–binding protein 2 (SREBP2) is the master transcription factor that regulates cholesterol metabolism. SREBP2 activation is regulated by SREBP chaperone SCAP. Here we show that ring finger protein 5 (RNF5), an endoplasmic reticulum-anchored E3 ubiquitin ligase, mediates the Lys-29–linked polyubiquitination of SCAP and thereby activates SREBP2. RNF5 knockdown inhibited SREBP2 activation and reduced cholesterol biosynthesis in human hepatoma cells, and RNF5 overexpression activated SREBP2. Mechanistic studies revealed that RNF5 binds to the transmembrane domain of SCAP and ubiquitinates the Lys-305 located in cytosolic loop 2 of SCAP. Moreover, the RNF5-mediated ubiquitination enhanced an interaction between SCAP luminal loop 1 and loop 7, a crucial event for SREBP2 activation. Notably, an overexpressed K305R SCAP variant failed to restore the SREBP2 pathway in SCAP-deficient cell lines. These findings define a new mechanism by which an ubiquitination-induced SCAP conformational change regulates cholesterol biosynthesis.
Folic acid-modified celastrol nanoparticles: synthesis, characterization, anticancer activity in 2D and 3D breast cancer models

Celastrol is used in traditional Chinese medicine for treating cancers. However, its low water solubility and poor tumour selection represent major pitfalls for clinical application. In the present study, gold nanoparticle (AuNP) firstly was conjugated with PVP-co-2-dimethylaminoethyl methacrylate (Polymer) and celastrol then modified by folic acid. The as-prepared folate receptor-targeted celastrol AuNP (FCA) was characterized using attenuated total reflection Fourier transform infrared spectroscopy, UV-Vis spectrometry, transmission electron microscope, and inductively coupled plasma mass spectrometry. The physical properties of FCA were also determined in solubility, drug encapsulation and in vitro drug release. Its anticancer activities were assessed in the 2D and 3D breast cancer models. The results showed that FCA was synthesized successfully with good solubility, high encapsulation efficiency and loading content. FCA showed the optimal cumulative release at pH 5.0 and high cellular uptake and exhibited significant inhibition on breast cancer cells. FCA also induced more significant apoptosis either in 2D and 3D breast cancer model than the celastrol AuNP and celastrol alone. These findings demonstrate that FCA improves water solubility of celastrol and enhances its anticancer activities against breast cancer. FCA might be a potential candidate of anticancer drug for breast cancer in the future if further development.
Physicochemical properties and energy content of yellow dent corn from different climatic origins in growing pigs

Objective The objective of this study was to determine the digestible energy (DE) and metabolizable energy (ME) of yellow dent corn sourced from different meteorological origins fed to growing pigs and develop equations to predict the DE and ME of yellow dent corn from southwestern China. Methods Sixty crossbred barrows were allotted to 20 treatments in a triplicate 20×2 incomplete Latin square design with 3 replicated pigs per dietary treatment during 2 consecutive periods. Each period lasted for 12 days, and total feces and urine during the last 5 days of each period were collected to calculate the energy contents. Results On dry matter (DM) basis, the DE and ME in 20 corn grain samples ranged from 15.38 to 16.78 MJ/kg and from 14.93 to 16.16 MJ/kg, respectively. Selected best-fit prediction equations for DE and ME (MJ/kg DM basis) for yellow dent corn (n = 16) sourced from southwestern China were as follows: DE = 28.58–(0.12×% hemicellulose)+(0.35×% ether extract)–(0.83×MJ/kg gross energy)+(0.20×% crude protein)+(0.49×% ash); ME = 30.42–(0.11×% hemicellulose)+(0.31×% ether extract)–(0.81×MJ/kg gross energy). Conclusion Our results indicated that the chemical compositions, but not the meteorological conditions or physical characteristics could explain the variation of energy contents in yellow dent corn sourced from southwestern China fed to growing pigs.
Intake of a Mixture of Sake Cake and Rice Malt Increases Mucin Levels and Changes in Intestinal Microbiota in Mice

Amazake is a traditional Japanese beverage. Its main ingredients are sake cake and rice malt. In this study, we examined the effect of sake cake and rice malt on the intestinal barrier function and gut microbiota. BALB/c mice were fed a control diet or a diet containing a mixture of sake cake and rice malt powder (SRP) for four weeks. Fecal IgA values did not change between groups, but the fecal mucin level was significantly greater in the SRP-fed group. Gene expression analysis in the ileum by real-time PCR demonstrated Muc2 expression did not change, while the Muc3 expression was upregulated in the SRP-fed group. Furthermore, microbiota analysis demonstrated a change by SRP intake at the family level, and the proportion of Lactobacillaceae significantly increased in the SRP-fed group. At the genus level, the proportion of Lactobacillus also significantly increased in the SRP-fed group. These results suggest that the intake of a mixture of sake cake and rice malt improves intestinal barrier function by increasing mucin levels and inducing changes in intestinal microbiota.
Hierarchical Organization of Functional Brain Networks Revealed by Hybrid Spatiotemporal Deep Learning

OBJECTIVE Hierarchical organization of brain function has been an established concept in the neuroscience field for a long time, however, it has been rarely demonstrated how such hierarchical macroscale functional networks are actually organized in the human brain. In this study, to answer this question, we propose a novel methodology to provide an evidence of evidence on hierarchical organization of functional brain networks. METHOD This paper introduces the Hybrid Spatiotemporal Deep Learning (HSDL), by jointly using Deep Belief Networks (DBN) and Deep LASSO to reveal the temporal hierarchical features and spatial hierarchical maps of brain networks based on the Human Connectome Project (HCP) 900 fMRI datasets. Briefly, the key idea of HSDL is to extract the weights between two adjacent layers of DBN, which are then treated as the hierarchical dictionaries for Deep LASSO to identify the corresponding hierarchical spatial maps. CONCLUSION Our results demonstrate that both spatial and temporal aspects of dozens of functional networks exhibit multiscale properties that can be well characterized and interpreted based on existing computational tools and neuroscience knowledge. SIGNIFICANCE Our proposed novel hybrid deep model is employed to provide the first insightful opportunity to reveal the potential hierarchical organization of time series and functional brain networks, using task-based fMRI signals of human brain.
Chemical promenades: Exploring potential‐energy surfaces with immersive virtual reality

The virtual‐reality framework AVATAR (Advanced Virtual Approach to Topological Analysis of Reactivity) for the immersive exploration of potential‐energy landscapes is presented. AVATAR is based on modern consumer‐grade virtual‐reality technology and builds on two key concepts: (a) the reduction of the dimensionality of the potential‐energy surface to two process‐tailored, physically meaningful generalized coordinates, and (b) the analogy between the evolution of a chemical process and a pathway through valleys (potential wells) and mountain passes (saddle points) of the associated potential energy landscape. Examples including the discovery of competitive reaction paths in simple A + BC collisional systems and the interconversion between conformers in ring‐puckering motions of flexible rings highlight the innovation potential that augmented and virtual reality convey for teaching, training, and supporting research in chemistry.
Rapid Evaluation and Optimization of Medium Components Governing Tryptophan Production by Pediococcus acidilactici TP-6 Isolated from Malaysian Food via Statistical Approaches

Tryptophan is one of the most extensively used amino acids in livestock industry owing to its effectiveness in enhancing the growth performance of animals. Conventionally, the production of tryptophan relies heavily on genetically modified Escherichia coli but its pathogenicity is a great concern. Our recent study demonstrated that a lactic acid bacterium (LAB), Pediococcus acidilactici TP-6 that isolated from Malaysian food was a promising tryptophan producer. However, the tryptophan production must enhance further for viable industrial application. Hence, the current study evaluated the effects of medium components and optimized the medium composition for tryptophan production by P. acidilactici TP-6 statistically using Plackett-Burman Design, and Central Composite Design. The optimized medium containing molasses (14.06 g/L), meat extract (23.68 g/L), urea (5.56 g/L) and FeSO4 (0.024 g/L) significantly enhanced the tryptophan production by 150% as compared to the control de Man, Rogosa and Sharpe medium. The findings obtained in this study revealed that rapid evaluation and effective optimization of medium composition governing tryptophan production by P. acidilactici TP-6 were feasible via statistical approaches. Additionally, the current findings reveal the potential of utilizing LAB as a safer alternative tryptophan producer and provides insight for future exploitation of various amino acid productions by LAB.
Dietary Patterns, Ultra-processed Food, and the Risk of Inflammatory Bowel Diseases in the NutriNet-Santé Cohort.

BACKGROUND The incidence of inflammatory bowel diseases (IBDs) tended to increase for several decades. Diet is suspected to be a major determinant of the occurrence of these diseases. This prospective study aimed to assess the associations among occurrence of IBD, dietary patterns, and ultra-processed food in the French NutriNet-Santé cohort. METHODS Participants of the NutriNet-Santé cohort who completed at least three 24-hour dietary records were included. Incident IBD cases were identified from 3 questionnaires and confirmed by phone or email interview. Major dietary patterns (DPs) were computed using a principal component analysis (PCA) based on 29 food groups' consumption, whereas proportions of ultra-processed foods (UPFs) were obtained using the NOVA classification. Multivariable Poisson models were performed to evaluate associations among DP quintiles, UPF proportion (UPFp) in the diet, and incident IBD. RESULTS A total of 105,832 participants were included, contributing 238,924 person-years in a mean follow-up of 2.3 ± 2.2 years. Among them, 75 participants reported an incident IBD. Three major DPs were retained: "healthy," "traditional," and "western. " No significant association was found for DPs and UPFp after adjustments for covariates. CONCLUSIONS In this study, neither DPs nor UPF proportion in the diet were significantly associated with the risk of incident IBD after adjustments for covariates. Further studies are needed to investigate the long-term association between diet and IBD.
Evaluation of Toxic Amyloid β42 Oligomers in Rat Primary Cerebral Cortex Cells and Human iPS-derived Neurons Treated with 10-Me-Aplog-1, a New PKC Activator

Amyloid β42 (Aβ42), a causative agent of Alzheimer’s disease (AD), is derived extracellularly from Aβ precursor protein (APP) following the latter’s cleavage by β-secretase, but not α-secretase. Protein kinase Cα (PKCα) activation is known to increase α-secretase activity, thereby suppressing Aβ production. Since Aβ42 oligomer formation causes potent neurotoxicity, APP modulation by PKC ligands is a promising strategy for AD treatment. Although bryostatin-1 (bryo-1) is a leading compound for this strategy, its limited natural availability and the difficulty of its total synthesis impedes further research. To address this limitation, Irie and colleagues have developed a new PKC activator with few side effects, 10-Me-Aplog-1, (1), which decreased Aβ42 in the conditioned medium of rat primary cerebral cortex cells. These results are associated with increased α-secretase but not PKCε-dependent Aβ-degrading enzyme. The amount of neuronal embryonic lethal abnormal vision (nELAV), a known β-secretase stabilizer, was reduced by treatment with 1. Notably, 1 prevented the formation of intracellular toxic oligomers. Furthermore, 1 suppressed toxic oligomerization within human iPS-derived neurons such as bryo-1. Given that 1 was not neurotoxic toward either cell line, these findings suggest that 1 is a potential drug lead for AD therapy.
Current Status of “Watch-and-Wait” Rectal Cancer Treatment in Asia-Pacific Countries

Purpose Current acceptance of the watch-and-wait (W&W) approach by surgeons in Asia-Pacific countries is unknown. An international survey was performed to determine status of the W&W approach on behalf of the Asia-Pacific Federation of Coloproctology (APFCP). Methods Surgeons in the APFCP completed an Institutional Review Board-approved anonymous e-survey and/or printed letters (for China) containing 19 questions regarding nonsurgical close observation in patients who achieved clinical complete response (cCR) to neoadjuvant chemoradiotherapy (nCRT). Results Of the 417 responses, 80.8% (n = 337) supported the W&W approach and 65.5% (n = 273) treated patients who achieved cCR after nCRT. Importantly, 78% of participants (n = 326) preferred a selective W&W approach in patients with old age and medical comorbidities who achieved cCR. In regard to restaging methods after nCRT, the majority of respondents based their decision to use W&W on a combination of magnetic resonance imaging results (94.5%, n = 394) with other test results. For interval between nCRT completion and tumor response assessment, most participants used 8 weeks (n = 154, 36.9%), followed by 6 weeks (n = 127, 30.5%) and 4 weeks (n = 102, 24.5%). In response to the question of how often responders followed-up after W&W, the predominant period was every 3 months (209 participants, 50.1%) followed by every 2 months (75 participants, 18.0%). If local regrowth was found during follow-up, most participants (79.9%, n = 333) recommended radical surgery as an initial management. Conclusion The W&W approach is supported by 80% of Asia-Pacific surgeons and is practiced at 65%, although heterogeneous hospital or society protocols are also observed. These results inform oncologists of future clinical study participation.
Use of diuretics in shock: Temporal trends and clinical impacts in a propensity-matched cohort study

Objective Fluid overload is common among critically ill patients and is associated with worse outcomes. We aimed to assess the effect of diuretics on urine output, vasopressor dose, acute kidney injury (AKI) incidence, and need for renal replacement therapies (RRT) among patients who receive vasopressors. Patients and methods This is a single-center retrospective study of all adult patients admitted to the intensive care unit between January 2006 and December 2016 and received >6 hours of vasopressor therapy and at least one concomitant dose of diuretic. We excluded patients from cardiac care units. Hourly urine output and vasopressor dose for 6 hours before and after the first dose of diuretic therapy was compared. Rates of AKI development and RRT initiation were assessed with a propensity-matched cohort of patients who received vasopressors but did not receive diuretics. Results There was an increasing trend of prescribing diuretics in patients receiving vasopressors over the course of the study. We included 939 patients with median (IQR) age of 68(57, 78) years old and 400 (43%) female. The average hourly urine output during the first six hours following time zero in comparison with average hourly urine output during the six hours prior to time zero was significantly higher in diuretic group in comparison with patients who did not receive diuretics [81 (95% CI 73–89) ml/h vs. 42 (95% CI 39–45) ml/h, respectively; p<0.001]. After propensity matching, the rate of AKI within 7 days of exposure and the need for RRT were similar between the study and matched control patients (66 (15.6%) vs. 83 (19.6%), p = 0.11, and 34 (8.0%) vs. 37 (8.7%), p = 0.69, respectively). Mortality, however, was higher in the group that received diuretics. Ninety-day mortality was 191 (45.2%) in the exposed group VS 156 (36.9%) p = . 009. Conclusions While the use of diuretic therapy in critically ill patients receiving vasopressor infusions augmented urine output, it was not associated with higher vasopressor requirements, AKI incidence, and need for renal replacement therapy.
An improved strategy for CRISPR/Cas9 gene knockout and subsequent wildtype and mutant gene rescue

A fluorescence marker mOrange was inserted to the popular pLentiCrispr-V2 to create pLentiCrispr-V2-mOrange (V2mO) that contained both a puromycin selection and a fluorescent marker, making viral production and target transduction visible. Lentiviruses packaged with this plasmid and appropriate guide RNAs (gRNAs) successfully knocked out the genes RhoA, Gli1, and Gal3 in human gastric cancer cell lines. Cas9-gRNA editing efficiency could be estimated directly from Sanger electropherograms of short polymerase chain reaction products around the gRNA regions in Cas9-gRNA transduced cells. Single cloning of transduced target cell pools must be performed to establish stable knockout clones. Rescue of wildtype (RhoA and Gal3) and mutant (RhoA.Y42C) genes into knockout cells was successful only when cDNAs, where gRNAs bind, were modified by three nucleotides while the amino acid sequences remained unchanged. Stringent on-target CRISPR/Cas9 editing was observed in Gal3 gene, but not in RhoA gene since RhoA.Y42C already presented a nucleotide change in gRNA5 binding site. In summary, our improved strategy added these advantages: adding visual marker to the popular lentiviral system, monitoring lentiviral production and transduction efficiencies, cell-sorting Cas9+ cells in target cells by fluorescence-activated cell sorting, direct estimation of gene editing efficiency of target cell pools by short PCR electropherograms around gRNA binding sites, and successful rescue of wildtype and mutant genes in knockout cells, overcoming Cas9 editing by modifying cDNAs.