Miracle-dz/UniFAR-FTUs huggingface dataset:
Digital soil mapping using drone images and machine learning at the sloping vegetable fields in cool highland in the Northern Kanto region, Japan

ABSTRACT In the cool highlands agricultural area in the Kanto region in Japan, large-scale vegetable cultivation is taking place in sloping fields where Andosols are distributed. In some steeply sloping fields in the area, soil erosion has resulted in the loss of surface soil and its redeposition, causing heterogeneity of soil productivity. In this study, a high-resolution soil map (1 m resolution) was delineated using drone images and machine learning to understand the status of soil productivity in sloping vegetable fields. A digital elevation model (DEM) and orthoimages were created from the analysis of images taken by a drone. Then, 13 topographic index maps, such as slopes, were created from the DEM. The orthoimages were then converted to black and white images to quantify surface soil color. Based on the black and white images and topographic indices of the field, the distribution map of 1) organic carbon content of surface soil and 2) layer thickness of A horizon in the study area were delineated by the Regression-Kriging method. The Empirical Bayesian Kriging method was used to delineate maps of 3) gravel content in the soil profile (0–60 cm) and 4) depth to the gravel layer. Using the 13 topographic index maps and the maps from 1) to 4) as features, a predicted soil map was delineated using the random forest method with eight soil series groups as the map unit. Nine features were selected by the best-predicted model. High-Humic Cumulic Allophanic Andosols and Skeletal Cumulic Allophanic Andosols were generally covered on gentle slopes with low LS-Factor, which was calculated by slope and specific catchment area. Skeletal Low-humic Allophanic Andosols were mainly distributed on steep slopes with high LS-Factor and susceptible to soil erosion. A high-resolution soil map reflecting soil erosion was able to delineate using drone images and machine learning in Andosol's sloping upland field.
Plant residues do not have an immediate impact on soil bacterial community composition and abundance

Plant residues are often used as soil amendments in laboratory experiments, but they can reportedly release compounds interfering with soil DNA extraction and subsequent molecular biological analyses. Theoretically, for accurate comparison of microbial community composition in soils with and without added plant residues after a period of incubation, no significant difference at the beginning of the experiment is required between the amended and unamended control soils. We mixed plant residue into soil and immediately (within 10 min) commenced DNA extraction, and then performed 16S rRNA gene sequencing and quantitative PCR (qPCR) to determine bacterial community composition and abundance. Soil without plant residue addition served as a control. Five commonly used DNA extraction kits, 16S rRNA gene primer pairs, and soils, and two types (rice straw and alfalfa shoots) and three addition rates (2%, 4%, and 6%; w/w) of plant residue, were tested. In all cases, we found no significant difference in measured bacterial community composition or abundance between the treatments with and without added plant residue.
On A Survey Of the Convergence and Stability of the Finite Difference Solutions of Partial Differential Equations

Finite difference solution of partial differential equations must satisfy the requirement of convergence and stability if th ey are to be reasonably accurate . In this paper, we examined convergence and stability criterion of finite difference scheme for solving a partial differential equation. A case which is possible when the cumulative effect of all rounding errors is negligible. Consequently, we investigated the prop agation of these errors as increases by applying the Fourier series method.
Study on the effect of hydro‐chemical dissolution on shear properties of rock fractures using the improved discontinuous deformation analysis

Hydro‐chemical erosion has critical effects on the short‐ and long‐term stability of fractured rock masses in subsurface engineering. Attempts have been made to study this water‐rock interaction process using numerical approaches. However, the majority of the existing approaches quantify the degradation based on the homogeneity hypothesis, which leads to unrealistic results in the case of rock mass with discontinuities. In this study, the hydro‐chemical degradation is represented through geometrical variation of a single crack and reflected in the modified bilinear constitutive model by introducing the hydro‐chemical damage factor. Then, discontinuous deformation analysis (DDA) method embedded in such improvements is chosen to implement the direct shearing process of the rock fracture after hydro‐chemical erosion. The results reveal that the peak shear strength decrease with the increase in the acidity solutions, and a logarithmic relation is found between the decreasing percentage of shear properties and soaking time, which are consistent with the laboratory results. Besides, based on the proposed method, the change in peak shear strength presents synchronism with the variation in the mineral ion and H+${H}^ + $ concentration, shown to be in good agreement with the basic understanding of the dissolution process. In addition, the failure patterns of the sheared samples under different normal stress are studied. This research provides an effective tool to quantify the hydro‐chemical damage from the microscale and will be a significant complement to the coupled numerical analysis of the water‐rock interaction process.
Behavioral Aspects of Healthy Longevity

The Policy Research Working Paper Series disseminates the findings of work in progress to encourage the exchange of ideas about development issues. An objective of the series is to get the findings out quickly, even if the presentations are less than fully polished. The papers carry the names of the authors and should be cited accordingly. The findings, interpretations, and conclusions expressed in this paper are entirely those of the authors. They do not necessarily represent the views of the International Bank for Reconstruction and Development/World Bank and its affiliated organizations, or those of the Executive Directors of the World Bank or the governments they represent.
External Validation of the Augmented Renal Clearance Predictor in Critically Ill COVID-19 Patients

The ARC predictor is a prediction model for augmented renal clearance (ARC) on the next intensive care unit (ICU) day that showed good performance in a general ICU setting. In this study, we performed a retrospective external validation of the ARC predictor in critically ill coronavirus disease 19 (COVID-19) patients admitted to the ICU of the University Hospitals Leuven from February 2020 to January 2021. All patient-days that had serum creatinine levels available and measured creatinine clearance on the next ICU day were enrolled. The performance of the ARC predictor was evaluated using discrimination, calibration, and decision curves. A total of 120 patients (1064 patient-days) were included, and ARC was found in 57 (47.5%) patients, corresponding to 246 (23.1%) patient-days. The ARC predictor demonstrated good discrimination and calibration (AUROC of 0.86, calibration slope of 1.18, and calibration-in-the-large of 0.14) and a wide clinical-usefulness range. At the default classification threshold of 20% in the original study, the sensitivity and specificity were 72% and 81%, respectively. The ARC predictor is able to accurately predict ARC in critically ill COVID-19 patients. These results support the potential of the ARC predictor to optimize renally cleared drug dosages in this specific ICU population. Investigation of dosing regimen improvement was not included in this study and remains a challenge for future studies.
Targeting Toxoplasma gondii ME49 TgAPN2: A Bioinformatics Approach for Antiparasitic Drug Discovery

As fewer therapeutic options are available for treating toxoplasmosis, newer antiparasitic drugs that can block TgAPN2 M1 aminopeptidase are of significant value. Herein, we employed several computer-aided drug-design approaches with the objective of identifying drug molecules from the Asinex library with stable conformation and binding energy scores. By a structure-based virtual screening process, three molecules—LAS_52160953, LAS_51177972, and LAS_52506311—were identified as promising candidates, with binding affinity scores of −8.6 kcal/mol, −8.5 kcal/mol, and −8.3 kcal/mol, respectively. The compounds produced balanced interacting networks of hydrophilic and hydrophobic interactions, vital for holding the compounds at the docked cavity and stable binding conformation. The docked compound complexes with TgAPN2 were further subjected to molecular dynamic simulations that revealed mean RMSD for the LAS_52160953 complex of 1.45 Å), LAS_51177972 complex 1.02 Å, and LAS_52506311 complex 1.087 Å. Another round of binding free energy validation by MM-GBSA/MM-PBSA was done to confirm docking and simulation findings. The analysis predicted average MM-GBSA value of <−36 kcal/mol and <−35 kcal/mol by MM-PBSA. The compounds were further classified as appropriate candidates to be used as drug-like molecules and showed favorable pharmacokinetics. The shortlisted compounds showed promising biological potency against the TgAPN2 enzyme and may be used in experimental validation. They may also serve as parent structures to design novel derivatives with enhanced biological potency.
Treatment Selection and Survival in Patients with Gray Zone Lymphoma: A Comprehensive Population-Based Analysis.

BACKGROUND AND OBJECTIVES There are no treatment guidelines for gray-zone lymphoma (GZL), given the disease's rarity and being a relatively new entity. Our objective was to assess factors affecting treatment selection in GZL and its effect on survival, focusing on combined modality treatment (CMT) versus chemotherapy alone. PATIENTS AND METHODS We identified 1047 patients with GZL treated with CMT or chemotherapy alone between 2004 and 2016 from the National Cancer Database (NCDB). We excluded patients without histologic confirmation of the diagnosis, those who did not receive chemotherapy, and those who started chemotherapy >120 days or radiation >365 days from diagnosis to account for immortal time bias. Factors affecting treatment selection were investigated using a logistic regression model. A propensity score-matched methodology was used to compare survival outcomes. RESULTS Only 164 patients (15.7%) received CMT, while 883 (84.3%) received chemotherapy alone. Treatment selection was affected by clinical factors (age, odds ratio [OR] 0.99, 95% confidence interval [CI] 0.98-0.997, p-value 0.01 and advanced stage, OR for stage 4: 0.21, 95% CI 0.13-0.34, p-value < 0.001) but not socioeconomic factors. Higher median income was associated with better survival, while increased age, higher comorbidity score, and B symptoms were associated with worse survival. The use of CMT had a survival advantage over chemotherapy alone (hazard ratio [HR] 0.54, 95% CI 0.351-0.833, p-value 0.005). CONCLUSION CMT is associated with survival advantage in our analysis. Careful selection of patients is essential to achieve the best outcomes with minimal toxicity. Socioeconomic factors affect treatment selection in patients with GZL that can alter outcomes. Future work should focus on strategies that access disparities without compromising survival.
Comparative genomics of Viola selkirkii and V. ulleungdoensis (Violaceae)

Chloroplast genomes of two morphologically similar species, Viola selkirkii and V. ulleungdoensis, were compared. For this comparison, three individuals of V. selkirkiii from Ulleung-do Island (UE), Jeju-do Island (JJ), and Hwacheon-gun (HC) and one of V. ulleungdoensis from UE were collected. According to chloroplast genome sequencing of V. selkirkiii and V. ulleungdoensis, their genomes were found to contain 156,774–157,454 and 157,575 bp, respectively, and a total of 111 genes. In the comparison of the three V. selkirkiii individuals, V. selkirkiii obtained in UE was distinguished from those of the other regions of HC and JJ, and in the comparison of the three V. selkirkiii individuals and one V. ulleungdoensis individual, V. selkirkiii obtained from UE and V. ulleungdoensis were distinguished from the species in the other regions. In addition, a phylogenetic analysis revealed that 32 taxa of Viola formed a monophyletic group (bootstrap support [BS] = 100). The four Viola individuals used in this study (three V. selkirkiii and one V. ulleungdoensis) formed a monophyletic group (BS = 100), which was further divided into two subclades. One subclade comprised V. selkirkiii found in UE and V. ulleungdoensis, whereas the other subclade comprised V. selkirkiii found in HC and JJ. These results support the view of prior studies that V. selkirkiii growing in UE and V. ulleungdoensis are the same species.
Salivary Biomarkers Analysis and Neurobehavioral Assessment in Nurses Working Rotation Shifts: A Pilot Study

Currently, about one in five workers is employed in night shift work in Europe. Shift work including nighttime hours is essential in several activities, especially the healthcare sector. Importantly, night working may be associated with the occurrence of sleep disorders or work-related stress, both potentially augmenting the risk of errors and accidents at work. This study aims to examine the presence of neurobehavioral alterations that can be a consequence of shift working and concurrent misalignment of the sleep times and circadian rhythms. Nurses (n = 102) employed at a University Hospital located in North-Eastern Sicily, Italy, voluntarily participated in this pilot study. During medical surveillance, morning and evening salivary samples were collected, and seven psychodiagnostics questionnaires were administered to all the subjects. On one hand, the salivary levels of stress-related biomarkers (cortisol and alpha-amylase) and a circadian biomarker (melatonin) were evaluated. On the other hand, several neurobehavioral features were assessed, including depression, anxiety, work-related, and sleep issues. Interestingly, a positive relationship between salivary morning cortisol and depression scale, as well as a negative relationship between salivary morning alpha-amylase and work ability scale, were observed. Based on these results, the integration of subjective questionnaire outcomes and objective salivary biomarker quantification can help to identify workers with increased susceptibility to developing neurobehavioral alterations. This approach may contribute to ameliorating preventive strategies towards sensitive categories, such as nurses working rotation shifts.
The Origin and Invasion Pathway of Brown Rats Rattus norvegicus on Dok-Do Island Revealed by Genome-Wide Markers from 3-RADseq Approach

Simple Summary Biological invasion on islands poses ecological threats, and understanding invasion pathways can aid in preventing invasive species. Recently, brown rats (Rattus norvegicus) arrived on Dok-do, a remote, small island in the East Sea of Korea. Due to strict regulation on human disturbances, including trapping, we adopted 3-RADseq to compensate for our small sample size and determine the origin of the invading rats. Our genomic analysis will aid in controlling and managing invasive species on this protected island. Abstract Biological invasions are known to cause local extinctions on islands. Dok-do, a small, remote volcanic island in the East Sea of Korea in the western Pacific, has recently been invaded by rats, posing ecological problems. To infer their origin and invasion pathway, we collected rats from Dok-do and from the potential introduction source locations, Ulleung-do in the Pacific Ocean, and four east coastal ports. First, we identified that the brown rat (Rattus norvegicus) was the only rat species occurring at collecting sites based on the key morphological characteristics. To determine the population-level genetic diversity pattern, we applied the 3-RADseq approach. After a series of filtrations (minor allele frequency < 0.05, Hardy–Weinberg equilibrium p < 1 × 10−7), 4042 SNPs were retained for the final dataset from the 25,439 SNPs initially isolated. The spatial structure and genetic diversity pattern of brown rats suggested that the rat population on Dok-do was likely introduced from Ulleung-do. Our work provides practical information that will assist in the management of invasive brown rats in vulnerable island ecosystems.
Teleoperation of Soft Robots with Real‐Time Fingertip Haptic Feedback Using Small Batteries

Soft robots are promising candidates for robust grasping and manipulation of different types of objects; however, their development has been a scientific challenge because of the lack of compact, yet precise, controllable soft actuators. In this work, innovative haptic interactive systems based on sensor‐integrated actuators powered by small batteries are reported. A liquid‐metal strain sensor with a versatile form factor and robust sensing performance is incorporated into a fast‐switching high‐force ionic polymer actuator. The structure of the sensor‐integrated actuator is rationally designed through encapsulation technology to achieve the best sensitivity and actuation while maintaining compactness, allowing for accurate, real‐time estimation and tracking of the actuation process. In a closed loop between the user and sensor‐integrated actuator, the motion and manipulation dynamics of a soft gripper made of sensor‐integrated actuators can be controlled by hand motions during a task. By combining with a thimble‐type haptic feedback device, the states of the gripper can be transmitted back to the user in real‐time via the proprioception of the integrated sensor. The approach opens a prospective avenue for the development of future robotic technologies without requiring camera‐based sensors for versatile, wearable, and scalable haptic systems.
Antibacterial and Antibiofilm Efficacy of Copper-Doped Phosphate Glass on Pathogenic Bacteria

This study aimed to investigate the antibacterial [minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC)] and antibiofilm activity [log10 colony forming unit/mL (CFU/mL) and biofilm disruption] of copper-doped phosphate glass (CDPG) against Streptococcus oralis, Enterococcus faecalis, Lactobacillus casei, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. Methods: the antibacterial activity was determined using microbroth dilution and time-kill assay. The antibiofilm activity was investigated using crystal violet and confocal laser scanning microscopy. Bacteria growing in absence of CDPG were used as controls. Results: the MIC was ≥125 mg of CPDG/mL; the log10 CFU/mL reduction ranged from 2.66–3.14 to 6.23–9.65 after 4 and 24 h respectively. Generally, no growth was observed after 24 h of treatment with CDPG; the MBC was 250 mg/mL for L. casei and S. oralis while 500 mg/mL for the rest of the bacteria. The highest and lowest antibiofilm activity was observed against S. oralis and E. coli respectively. Three patterns of complete biofilm disruption were seen: (i) large areas with E. fecalis and S. oralis, (ii) medium-size pockets with S. aureus and P. aeruginosa, or (iii) small areas with E. coli and L. casei. Conclusion: CDPG can be potentially used as an antibacterial and an antibiofilm agent against oral biofilm-forming bacteria.
Mixed reality navigation system for oral implant surgery based on TopoTag

As the number of patients with missing teeth increases year by year, oral health is becoming more and more important to people. Dental implants are the preferred restoration option for missing teeth. Dynamic navigation systems are essential for dental implant surgery. However, the existing dynamic navigation system has problems such as a small navigation range, inconvenient operation, and unintuitive effects. A mixed-reality navigation system for oral implant surgery based on TopoTag is proposed in this study. The corresponding experimental results demonstrate that the presented system realizes real-time, accurate, clear, and three-dimensional surgical navigation, addressing the shortcomings of existing navigation systems.
Volatile Organic Compounds of Bacillus velezensis GJ-7 against Meloidogyne hapla through Multiple Prevention and Control Modes

The Bacillus velezensis GJ-7 strain isolated from the rhizosphere soil of Panax notoginseng showed high nematicidal activity and therefore has been considered a biological control agent that could act against the root-knot nematode Meloidogyne hapla. However, little was known about whether the GJ-7 strain could produce volatile organic compounds (VOCs) that were effective in biocontrol against M. hapla. In this study, we evaluated the nematicidal activity of VOCs produced by the fermentation of GJ-7 in three-compartment Petri dishes. The results revealed that the mortality rates of M. hapla J2s were 85% at 24 h and 97.1% at 48 h after treatment with the VOCs produced during GJ-7 fermentation. Subsequently, the VOCs produced by the GJ-7 strain were identified through solid-phase micro-extraction gas chromatography mass spectrometry (SPME-GC/MS). Six characteristic VOCs from the GJ-7 strain fermentation broth were identified, including 3-methyl-1-butanol, 3-methyl-2-pentanone, 5-methyl-2-hexanone, 2-heptanone, 2,5-dimethylpyrazine, and 6-methyl-2-heptanone. The in vitro experimental results from 24-well culture plates showed that the six volatiles had direct-contact nematicidal activity against M. hapla J2s and inhibition activity against egg hatching. In addition, 3-methyl-1-butanol and 2-heptanone showed significant fumigation effects on M. hapla J2s and eggs. Furthermore, all six of the VOCs repelled M. hapla J2 juveniles in 2% water agar Petri plates. The above data suggested that the VOCs of B. velezensis GJ-7 acted against M. hapla through multiple prevention and control modes (including direct-contact nematicidal activity, fumigant activity, and repellent activity), and therefore could be considered as potential biocontrol agents against root-knot nematodes.