Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison and evaluation of updates to WRF-Chem (v3.9) biogenic emissions using MEGAN

Abstract. Natural gases produced by the Earth’s ecosystem include a wide range of volatile compounds such as isoprene, monoterpene, nitric oxide, carbon monoxide, and other non-methane volatile organic compounds: the so-called biogenic volatile organic compounds (BVOCs). BVOCs are highly reactive and thus can impact air quality and aerosol radiative forcing. BVOC emission fluxes have been consistently included in global and regional chemical transport models (e.g., Model of Emissions of Gases and Aerosols from Nature, MEGAN). However, present climate models still have large uncertainties in estimating biogenic trace gases. These uncertainties result from several factors, including uncertainties in emission activity factors that are controlled by environmental conditions, specification of vegetation type, and plant emission factors. This work concerns the evaluation and test of a set of updates made to MEGAN, a model for estimating fluxes of biogenic compounds between terrestrial ecosystem and the atmosphere, which is embedded into the Weather Research and Forecasting model coupled with chemistry (WRF-Chem version 3.9). Two different test cases are presented, the first covering Europe, and the second for a domain in the Southeast United States. Our study considers four simulations for each update made to MEGAN, (i) a control run with no changes to MEGAN; (ii) a simulation with the emission activity factors modified following MEGAN version 2.10; (iii) a simulation considering the changes to the plant functional type emission factor; (iv) a simulation with the isoprene emission factor calculated within the MEGAN module (the emission factor of isoprene is obtained from the input database directly in WRF-Chem). For the Europe domain region, a sensitivity study on BVOC emissions was performed for a high-ozone episode in August 2015. The updated MEGAN model led to significant increases, by factors of 2 or more, of the estimated BVOC emissions. The comparison of WRF-Chem results for the European domain with experimental data from the Airbase web-portal (European air quality database) showed that the temporal and spatial distribution of ozone are well represented. However, comparing the updated MEGAN simulations with the control run, ozone concentration bias increased substantially. Results from the U.S. domain are compared with the Nitrogen, Oxidants, Mercury and Aerosol Distributions, Sources and Sinks (NOMADSS) field campaign data (June 2013), which allows for direct comparison of isoprene mixing ratios with observations. The comparison between the modeled data and aircraft observations shows that isoprene mixing ratios agree well with measured isoprene for the M2.04 simulation but are overpredicted considerably by the M2.10 simulation.
Conformational change in the monomeric alpha-synuclein imparts fibril polymorphs

α-Synuclein inclusions are a pathological hallmark of several neurodegenerative diseases. Although it has been demonstrated a relationship between fibril polymorphism and different pathologies, the molecular origins of polymorphism are not understood. Employing biophysical approaches, we revealed that the conformational state of the monomeric αSyn is responsible for fibril polymorphism: αSyn adopts specific conformations at high NaCl that produce rod fibrils, and different conformations at low NaCl that generate twisted fibrils. Using NMR, we found that the high NaCl conformations establish a polar interaction between the initial part of the NAC region and a wide section of the C-terminus domain. These high NaCl conformations can be commonly promoted by changes in the chemical environment, like NaCl, the presence of Ca2+ or cellular components, like endotoxins, that alter the interaction NAC/C-terminus domain. Our results provide mechanistic insights that explain how the behavior of the C-terminus domain imparts polymorphism during the fibril formation. Significance Statement The accumulation of the protein α-Synuclein into amyloid aggregates in the brain is a key characteristic of neurodegenerative disorders like Parkinson’s disease and multiple system atrophy. Intensive research has demonstrated that structurally different amyloid fibrils are related to the development of different diseases; however, the molecular mechanisms that originate such fibril diversity from the same protein remain unknown. In this work, we discovered that the conformational state of the monomeric αSyn, regulated by an intramolecular polar interaction NAC region/C-terminus domain, is crucial for the generation of different fibrils. Our results represent the monomeric molecular events behind the diversity of fibrils and open the conformational state of αSyn as a target to understand how the fibrils get formed in the brain.
Overexpression of CAPG Is Associated with Poor Prognosis and Immunosuppressive Cell Infiltration in Ovarian Cancer

Historically, immunotherapies have only resulted in a partial response from patients with advanced ovarian cancer, resulting in poor clinical efficacy. A full understanding of immune-related gene expression and immunocyte infiltration in ovarian cancer would be instrumental for the improved implementation of immunotherapy. The Capping Actin Protein, Gelsolin-Like (CAPG) gene encodes an actin-regulatory protein, which plays important roles in tumor progression and immune regulation. This study is aimed at identifying the potential therapeutic and prognostic roles of CAPG in ovarian cancer. CAPG expression and clinical information were investigated in the data collected from TCGA, Oncomine, GEPIA, UALCAN, and Kaplan-Meier plotter. CAPG coexpression networks were evaluated by LinkedOmics, GeneMANIA, and NetworkAnalyst. The correlation of CAPG with immune infiltrates was analyzed via TIMER, ImmuCellAI, and GEPIA. Our result showed that patients with high tumoral CAPG expression had significantly shorter 5-year overall survival. Functional enrichment analysis indicated that CAPG-related phenotypes were largely involved in inflammatory response, chemokine and cytokine signaling, cell adhesion, and Toll-like receptor signaling pathways. CAPG expression was positively correlated with infiltrating levels of regulatory T cells (Tregs), tumor-associated macrophages (TAMs), and exhausted T cells (Texs) while being negatively correlated with infiltrating levels of natural killer T cells (NKTs) and neutrophils in ovarian cancer. Moreover, the expression of FOXP3, CD25, CD127, CCR8, and TGFβ in respect to Tregs; CCL2 and CD68 in respect to TAM; CD163, VSIG4, and MS4A4A in respect to M2 macrophages; CD33 and CD11b in respect to myeloid-derived suppressor cells (MDSCs); and PD1, CTLA4, LAG3, TIM3, GZMB, 2B4, and TIGIT in respect to Texs was significantly correlated with CAPG expression in ovarian cancer. These findings suggest that CAPG may contribute to the immunosuppressive tumor microenvironment in ovarian cancer, leading to an exhausted T cell phenotype and tumor progression. Therefore, CAPG can be used as a potential biomarker for determining prognosis and immunotherapy effectiveness in ovarian cancer.
Efficacy of Chitosan Nanoparticle Loaded-Salicylic Acid and -Silver on Management of Cassava Leaf Spot Disease

Leaf spot is one of the most important cassava diseases. Nanotechnology can be applied to control diseases and improve plant growth. This study was performed to prepare chitosan (CS) nanoparticle (NP)-loaded salicylic acid (SA) or silver (Ag) by the ionic gelation method, and to evaluate their effectiveness on reducing leaf spot disease and enhancing the growth of cassava plants. The CS (0.4 or 0.5%) and Pentasodium triphosphate (0.2 or 0.5%) were mixed with SA varying at 0.05, 0.1, or 0.2% or silver nitrate varying at 1, 2, or 3 mM to prepare three formulations of CS-NP-loaded SA named N1, N2, and N3 or CS-NP-loaded Ag named N4, N5, and N6. The results showed that the six formulations were not toxic to cassava leaves up to 800 ppm. The CS-NP-loaded SA (N3) and CS-NP-loaded Ag (N6) were more effective than the remaining formulations in reducing the disease severity and the disease index of leaf spot. Furthermore, N3 at 400 ppm and N6 at 200, 400, and 800 ppm could reduce disease severity (68.9–73.6% or 37.0–37.7%, depending on the time of treatment and the pathogen density) and enhance plant growth more than or equal to commercial fungicide or nano-fungicide products under net-house conditions. The study indicates the potential to use CS-NP-loaded SA or Ag as elicitors to manage cassava leaf spot disease.
Pre-Exposure to Stress-Inducing Agents Increase the Anticancer Efficacy of Focused Ultrasound against Aggressive Prostate Cancer Cells

Despite the initial success in treatment of localized prostate cancer (PCa) using surgery, radiation or hormonal therapy, recurrence of aggressive tumors dictates morbidity and mortality. Focused ultrasound (FUS) is being tested as a targeted, noninvasive approach to eliminate the localized PCa foci, and strategies to enhance the anticancer potential of FUS have a high translational value. Since aggressive cancer cells utilize oxidative stress (Ox-stress) and endoplasmic reticulum stress (ER-stress) pathways for their survival and recurrence, we hypothesized that pre-treatment with drugs that disrupt stress-signaling pathways in tumor cells may increase FUS efficacy. Using four different PCa cell lines, i.e., LNCaP, C4-2B, 22Rv1 and DU145, we tested the in vitro effects of FUS, alone and in combination with two clinically tested drugs that increase Ox-stress (i.e., CDDO-me) or ER-stress (i.e., nelfinavir). As compared to standalone FUS, significant (p < 0.05) suppressions in both survival and recurrence of PCa cells were observed following pre-sensitization with low-dose CDDO-me (100 nM) and/or nelfinavir (2 µM). In drug pre-sensitized cells, significant anticancer effects were evident at a FUS intensity of as low as 0.7 kW/cm2. This combined mechanochemical disruption (MCD) approach decreased cell proliferation, migration and clonogenic ability and increased apoptosis/necrosis and reactive oxygen species (ROS) production. Furthermore, although activated in cells that survived standalone FUS, pre-sensitization with CDDO-me and/or nelfinavir suppressed both total and activated (phosphorylated) NF-κB and Akt protein levels. Thus, a combined MCD therapy may be a safe and effective approach towards the targeted elimination of aggressive PCa cells.
Optimization of Gate-All-Around Device to Achieve High Performance and Low Power with Low Substrate Leakage

In this study on multi-nanosheet field-effect transistor (mNS-FET)—one of the gate-all-around FETs (GAAFET) in the 3 nm technology node dimension—3D TCAD (technology computer-aided design) was used to attain optimally reduced substrate leakage from options including a punch-through-stopper (PTS) doping scheme and a bottom oxide (BO) scheme for bottom isolation, with the performance improvement being shown in the circuit-level dynamic operation using the mNS-FET. The PTS doping concentration requires a high value of >5 × 1018 cm−3 to reduce gate induced drain leakage (GIDL), regardless of the presence or absence of the bottom isolation layer. When the bottom isolation is applied together with the PTS doping scheme, the capacitance reduction is larger than the on-state current reduction, as compared to when only the PTS doping concentration is applied. The effects of such transistor characteristics on the performance and capabilities of various circuit types—such as an inverter ring oscillator (RO), a full adder (FA) circuit, and a static random-access memory (SRAM)—were assessed. For the RO, applying BO along with the PTS doping allows the operating speed to be increased by 11.3% at the same power, or alternatively enables 26.4% less power consumption at the same speed. For the FA, power can be reduced by 6.45%, energy delay product (EDP) by 21.4%, and delay by 16.8% at the same standby power when BO and PTS are both applied. Finally, for the SRAM, read current (IREAD) increased by 18.7% and bit-line write margin (BWRM) increased by 12.5% at the same standby power. Through the circuit simulations, the Case 5 model (PTS doping concentration: 5.1 × 1018 cm−3, with BO) is the optimum condition for the best device and circuit performance. These observations confirm that PTS and bottom isolation applications in mNS-FETs can be utilized to enable the superior characteristics of such transistors to translate into high performance integrated circuits.
Mapping Seismic Hazard in the Central and Eastern United States

INTRODUCTION The U.S. Geological Survey (USGS) has been publishing probabilistic seismic hazard maps for the United States since 1976 (e.g., Algermissen and Perkins, 1976; Algermissen et al., 1990). We are preparing new national maps for the 1997 edition of the NEHRP Recommended Provisions for the Development of Seismic Regulations for New Buildings , published by the Building Seismic Safety Council (NEHRP stands for National Earthquake Hazards Reduction Program). The USGS hazard maps are to be the basis for design value maps for buildings to be included in the Provisions . We are conducting a series of regional workshops to discuss the methodology and input to the maps. As of this writing, workshops have been held in the Pacific Northwest, the northeastern U.S., and northern California. We intend to make maps showing ground motions with 10% probability of exceedance (PE) in 50, 100, and 250 years. These correspond to return times of 475,.
Principles for Responsible Management Education: An Axiological Approach

In this article, we rely on the development of a Massive Open Online Course (MOOC) to show the relevance of a values-based approach to responsible management. To clarify the notion of values, we draw on Heinich’s axiological sociology, which presents values as principles of judgment and action. Building on this approach, we interviewed 35 management scholars to understand the values they attribute to responsible management. Our analysis led to the identification of seven actionable values that can be used to circumscribe responsible management. We also show how three interrelated levels of analysis—namely, individual (micro), organizational (meso), and societal (macro)—allowed us to further organize the interview data to produce rich content for the MOOC. Our contribution is twofold: first, our values-based approach helps overcome the axiological ambiguity of the Principles for Responsible Management Education (PRME), which invoke the importance of incorporating “the values of global social responsibility” (Principle 2), but fail to define and operationalize these values. Second, we provide a rationale and guidance for implementing values-based responsible management education in Business Schools.
On Eddy Making Component of Roll Damping Force on Naked Hull

From the results of the forced roll tests of two-dimensional cylinders having various cross sections, it is found that the eddy making component of roll damping force is proportional to the square of the frequency and the amplitude of roll motion. In other words, the damping coefficient CR of this component for ship-like sections can be regarded to be independent of the period parameter for practical use.An empirical formula for the eddy making component of the roll damping force for two-dimensional sections is deduced from the theoretical considerations on the basis of these experimental results. For three-dimensional ship forms without bilge keels at zero Froude number, the estimated results of the roll damping force which consist of the eddy making, the wave making and the frictional component, are in fairly good agreement with experimental results of ship models.
An evaluation of RNA-seq differential analysis methods

RNA-seq is a high-throughput sequencing technology widely used for gene transcript discovery and quantification under different biological or biomedical conditions. A fundamental research question in most RNA-seq experiments is the identification of differentially expressed genes among experimental conditions or sample groups. Numerous statistical methods for RNA-seq differential analysis have been proposed since the emergence of the RNA-seq assay. To evaluate popular differential analysis methods used in the open source R and Bioconductor packages, we conducted multiple simulation studies to compare the performance of eight RNA-seq differential analysis methods used in RNA-seq data analysis (edgeR, DESeq, DESeq2, baySeq, EBSeq, NOISeq, SAMSeq, Voom). The comparisons were across different scenarios with either equal or unequal library sizes, different distribution assumptions and sample sizes. We measured performance using false discovery rate (FDR) control, power, and stability. No significant differences were observed for FDR control, power, or stability across methods, whether with equal or unequal library sizes. For RNA-seq count data with negative binomial distribution, when sample size is 3 in each group, EBSeq performed better than the other methods as indicated by FDR control, power, and stability. When sample sizes increase to 6 or 12 in each group, DESeq2 performed slightly better than other methods. All methods have improved performance when sample size increases to 12 in each group except DESeq. For RNA-seq count data with log-normal distribution, both DESeq and DESeq2 methods performed better than other methods in terms of FDR control, power, and stability across all sample sizes. Real RNA-seq experimental data were also used to compare the total number of discoveries and stability of discoveries for each method. For RNA-seq data analysis, the EBSeq method is recommended for studies with sample size as small as 3 in each group, and the DESeq2 method is recommended for sample size of 6 or higher in each group when the data follow the negative binomial distribution. Both DESeq and DESeq2 methods are recommended when the data follow the log-normal distribution.
Utilization of MOOCs Using Kahoot and Student Engagement in Digital Learning During Covid-19 Pandemics

New technology advancements have frequently been credited as holding the potential to cause significant contributions to education. This study contributes to high-quality learning by putting students in real-world e-learning situations while still allowing them to use scientific techniques to complete their project assignments. The subjects of this study were 80 first-year undergraduate students enrolled in the Bahasa Inggris course. The snowball method questionnaire was obtained, and questionnaires were distributed to the students’ WhatsApp groups by performing snowball operational. The Lectures combined virtual face-to-face video conferencing applications on e-learning. Kahoot is an add-on application used. In general, online learning has a positive effect on students’ learning success. However, there are still learning obstacles in academic performance in online learning. On the other hand, learning obstacles occur because of students' limitations in developing themselves or their mental readiness to learn. As a result, digital learning may blend real issues with theoretical concepts in the classroom without neglecting the learning objectives that have been set for student engagement.
Study of Objective Quality Evaluation for the Speech Systems

Using the LPC CD,Bark SD and Mel CD distortion measures,we experimentally study the Objective Quality Eva luation of a large number of the speech systems.The result shows that each of these measures gives better correlation between objective and subjective measurement when they are used independently to those systems.Combining their results through a weighted and average way,higher correlation coefficient can be given,we can conclude that these measures have certain validity and utility to appraise the quality of speech systems.
Over 30 Years of Pediatric Liver Transplantation at the Charité—Universitätsmedizin Berlin

Background: Pediatric liver transplantation (LT) is the treatment of choice for children with end-stage liver disease and in certain cases of hepatic malignancies. Due to low case numbers, a technically demanding procedure, the need for highly specialized perioperative intensive care, and immunological, as well as infectious, challenges, the highest level of interdisciplinary cooperation is required. The aim of our study was to analyze short- and long-term outcomes of pediatric LT in our center. Methods: We conducted a retrospective single-center analysis of all liver transplantations in pediatric patients (≤16 years) performed at the Department of Surgery, Charité – Universitätsmedizin Berlin between 1991 and 2021. Three historic cohorts (1991–2004, 2005–2014 and 2015–2021) were defined. Graft- and patient survival, as well as perioperative parameters were analyzed. The study was approved by the institutional ethics board. Results: Over the course of the 30-year study period, 212 pediatric LTs were performed at our center. The median patient age was 2 years (IQR 11 years). Gender was equally distributed (52% female patients). The main indications for liver transplantation were biliary atresia (34%), acute hepatic necrosis (27%) and metabolic diseases (13%). The rate of living donor LT was 25%. The median cold ischemia time for donation after brain death (DBD) LT was 9 h and 33 min (IQR 3 h and 46 min). The overall donor age was 15 years for DBD donors and 32 years for living donors. Overall, respective 1, 5, 10 and 30-year patient and graft survivals were 86%, 82%, 78% and 65%, and 78%, 74%, 69% and 55%. One-year patient survival was 85%, 84% and 93% in the first, second and third cohort, respectively (p = 0.14). The overall re-transplantation rate was 12% (n = 26), with 5 patients (2%) requiring re-transplantation within the first 30 days. Conclusion: The excellent long-term survival over 30 years showcases the effectiveness of liver transplantation in pediatric patients. Despite a decrease in DBD organ donation, patient survival improved, attributed, besides refinements in surgical technique, mainly to improved interdisciplinary collaboration and management of perioperative complications.
Successful Mechanical Thrombectomy for Acute Middle Cerebral Artery Occlusion in a Centenarian

Clinical trials have proven the efficacy and beneficial therapeutic outcomes of endovascular therapy in patients with major arterial occlusion. However, its efficacy for very elderly patients, such as nonagenarians or centenarians, is not well established. In this case report, we describe the successful use of mechanical thrombectomy for the management of stroke in a centenarian. The 100-year-old woman with severe right-sided paralysis and total aphasia was admitted to our hospital approximately 30 min from the onset of symptoms. The National Institutes of Health Stroke Scale score was 24 at admission, and three-dimensional computed tomography angiography revealed occlusion in the M1 segment of left middle cerebral artery. She had persistent atrial fibrillation and was diagnosed with colon cancer one month prior to the admission. The modified Rankin Scale score before the stroke was 1, and she was generally independent. The patient successfully underwent mechanical thrombectomy, and recanalization with thrombolysis in cerebral infarction grade 3 was accomplished 129 minutes after the onset. The patient made a remarkable recovery with a National Institutes of Health Stroke Scale score of 4 at 48 h and was discharged home with a modified Rankin Scale score of 2 on day 8. Thus, mechanical thrombectomy can be performed with a good outcome even in centenarians.