Miracle-dz/UniFAR-FTUs huggingface dataset:
Limited Potential for Mineralization of Permafrost Peatland Soil Carbon Following Thermokarst: Evidence From Anoxic Incubation and Priming Experiments

Permafrost thaw in peatlands risks emitting vast stores of soil organic carbon (SOC) as greenhouse gases to the atmosphere, yet anoxic conditions and low peat quality may prevent rapid SOC loss. To assess differences in anaerobic SOC mineralization following thaw and vulnerability of previously‐frozen peat, we incubated peat (5° and 14°C) from 15 depths of ⁓6 m cores from different thaw sites including an intact permafrost peat plateau and thermokarst bogs that thawed ∼30 and ∼200 years ago. Furthermore, a glucose‐addition experiment after >700 days assessed whether labile C inputs occurring following thermokarst could accelerate SOC mineralization (priming). We found a common pattern of SOC mineralization rate decreasing with depth and peat age. However, we found no differences in peat mineralization rates among sites for samples of similar age and of corresponding peatland developmental stage. Priming effects were minor and short‐term, and did not vary among sites or with peat developmental stage. We also found mineralization rates from anoxic incubations more than an order of magnitude higher than rates implied from field observations, suggesting mineralization rates from anaerobic incubations should be used mainly to interpret relative differences. Peat humification and peat nitrogen and phosphorous content explained more than 85% of the variability in mineralization rates. Peat quality did not influence the temperature sensitivity of peat mineralization. Overall, the absence of substantial priming effects and the lack of differences in mineralization rates between permafrost peat and peat thawed 200 years ago suggests that rapid peatland SOC loss following thaw is unlikely.
Solution of the inhomogeneous Rayleigh scattering atmosphere.

The equation of radiative transfer for a Rayleigh scattering atmosphere including polarization is reduced to an azimuth-independent form. The integro-differential equations are then solved by approximating the integrals as sums and the differentials as finite differences. The resultant set of equations is then solved by the Feautrier technique. This method can solve inhomogeneous atmospheres by allowing for arbitrary variations with depth of the single scattering albedo and the source term. As an example, zero-phase geometric albedos and center-to-limb intensities are calculated for a planetary disk with a semi-infinite pressure-induced absorbing atmosphere.
MCP1 Could Mediate FGF23 and Omega 6/Omega 3 Correlation Inversion in CKD

Fibroblast growth factor 23 (FGF23) concentrations rise after the early stages of chronic kidney disease (CKD). FGF23 is involved in inflammatory reactions closely associated with an incremented risk of cardiovascular disease (CVD). There is growing evidence that omega-6 (n-6) and n-3 polyunsaturated fatty acids (PUFA) can modulate inflammation through several mediators producing an opposite effect on cardiovascular (CV) risks. In this study, we explore whether there is any correlation between PUFA, FGF23, and inflammation in CKD patients. We evaluated, cross-sectionally, 56 patients at different stages of CKD. Monocyte chemoattractant protein 1 (MCP1), and intact and c-terminal FGF23 (iFGF23, cFGF23) were quantified by the ELISA, and the fatty acids (FA) profile was analyzed by gas chromatography. Concurrently with an eGFR decrease (p < 0.01) and an MCP1 increase (p = 0.031), we observed an inversion of the correlation between FGF23 and the n-6/n-3 ratio. This last correlation was inversed in CKD stage 3 (r2 (−) 0.502 p = 0.029) and direct in stage 5 (r2 0.657 p = 0.020). The increase in MCP1 seems to trigger events in the inversion of the correlation between FGF23 and the n-6/n-3 PUFA ratio. This result strongly encourages future studies on basal pathways, on possible pharmacological interventions, and on managing kidney transplant patients treated with immunosuppressive therapy.
Problems and Challenges related to Chiang Da Herbal Tea Community Enterprise, Doi Saket District, Chiang Mai Province, Thailand

Purpose: The objective of this qualitative research is to report the problems and challenges related to Chiang Da herbal tea Community Enterprise (CE), Doi Saket District, Chiang Mai Province. Methodology: In-depth interviews (IDI) and Focus groups discussion (FGD) were conducted to obtain genuine comprehension from the CCE leader and members. The data were evaluated using content analysis. Finding: The finding was reported in 4 aspects of problems and challenges: 1) Human resources and membership, 2) marketing, 3) Budget, Finance, and Accounting and 4) Application of modern technology and information technology. The CCE member should develop knowledge and skills related to the issues mentioned above to be able to operate an enterprise group effectively. Practical implications: The government should play a role to promote and support the development of knowledge, skills, and capacity of the group by supporting policy, finance, equipment, and personnel providing advice. Furthermore, it is critical to use a successful community enterprise group as a model for learning and application. Contribution to literature: This study contributes to the existing literature as it is applied to other communities with similar characteristics and contexts, particularly community enterprises in rural areas that produce community products using local resources. The emphasis should be on developing the group members' potential.
Interaction of Depression and Unhealthy Diets on the Risk of Cardiovascular Diseases and All-Cause Mortality in the Chinese Population: A PURE Cohort Substudy

This study aimed to identify the interaction of depression and diets on cardiovascular diseases (CVD) incident and death in China and key subpopulations. We included 40,925 participants from the Prospective Urban Rural Epidemiology (PURE)-China cohort which recruited participants aged 35–70 years from 45 urban and 70 rural communities. Depression was measured by the adapted Short-Form (CIDI-SF). The unhealthy diet was considered when the score of Alternative Healthy Eating Index was below the lowest tertile. The primary outcome was a composite outcome of incident CVD and all-cause mortality. Cox frailty models were used to examine the associations. During a median follow-up of 11.9 years (IQR: 9.6–12.6 years), depression significantly increased the risk of the composite outcome (HR = 2.00; 95% CI, 1.16–3.27), major CVD (HR = 1.82; 95% CI, 1.48–2.23), and all-cause mortality (HR = 2.21; 95% CI, 1.51–3.24) for the unhealthy diet group, but not for the healthy diet group. The interaction between depression and diet for the composite outcome was statistically significant (RERI = 1.19; 95% CI, 0.66–1.72; AP = 0.42, 95% CI, 0.27–0.61; SI = 3.30, 95% CI, 1.42–7.66; multiplicative-scale = 1.74 95% CI, 1.27–2.39), even in the subgroup and sensitivity analyses. In addition, the intake of vegetable and polyunsaturated fatty acids contributed most to the interaction of diets and depression. Depressive participants should focus on healthy diets, especially vegetables and polyunsaturated fatty acids, to avoid premature death and CVD.
ON THE CONSTANCY OF THE SOLAR RADIUS. III.

The Michelson Doppler Imager on board the Solar and Heliospheric Observatory satellite has operated for over a sunspot cycle. This instrument is now relatively well understood and provides a nearly continuous record of the solar radius in combination with previously developed algorithms. Because these data are obtained from above Earth's atmosphere, they are uniquely sensitive to possible long-term changes of the Sun's size. We report here on the first homogeneous, highly precise, and complete solar-cycle measurement of the Sun's radius variability. Our results show that any intrinsic changes in the solar radius that are synchronous with the sunspot cycle must be smaller than 23 mas peak to peak. In addition, we find that the average solar radius must not be changing (on average) by more than 1.2 mas yr−1. If ground- and space-based measurements are both correct, the pervasive difference between the constancy of the solar radius seen from space and the apparent ground-based solar astrometric variability can only be accounted for by long-term changes in the terrestrial atmosphere.
Magnetic damping constant in Co-based full heusler alloy epitaxial films

Co-based full-Heusler alloys, such as Co2MnSi and Co2MnGe, are expected to be used as half-metallic ferromagnetic material, which has complete spin polarization. They are the most promising materials for realizing half-metallicity at room temperature due to their high Curie temperature. The optimization of the magnetic damping constant of ferromagnetic materials is extremely important for achieving high-speed magnetization switching and reducing critical current density for spin torque transfer switching. We have systematically investigated the magnetic damping constant in Co-based full Heusler alloy epitaxial films. We found that the Gilbert damping constant seems to be roughly proportional to the total density of states at the Fermi level (EF) by first principle calculation. A very small magnetic damping constant of 0.003 in the Co2Fe0.4Mn0.6Si epitaxial film was demonstrated. The small magnetic damping constant in Co2FexMn1−xSi films with x < 0.6 can be attributed to the half-metallicity of Heusler alloys. Co-based full Heusler alloys with both half-metallicity and small magnetic damping will be very useful for future applications based on spintronic devices.
Dispersion and wave coupling in inhomogeneous MHD waveguides

The propagation of the fast mode is considered in nonuniform waveguides. We show how the natural dispersion inherent in a waveguide will select waveguide modes with a small wavenumber (ky) along the guide to remain near a localized source region of fast mode energy. It is these modes that are shown to have a coherent periodic time dependence over many cycles that are suitable for driving observable Alfven resonances (magnetic pulsations). We expect the frequencies of Alfven resonances to be very close to the eigenfrequencies of waveguide modes with ky = 0.
Effect of Adjuvant Radiation Dose on Survival in Patients with Esophageal Squamous Cell Carcinoma

Simple Summary For patients with esophageal cancer, postoperative radiotherapy (PORT) improved LRFS. However, concerns about treatment-related toxicity issues limited its application. The authors found that for patients receiving upfront surgical resection, with adjuvant radiation dose (aRTD) escalation, the hazard ratio (HR) of LRFS declined until aRTD exceeded 50 Gy, then remained steady. However, HR of treatment-related mortality was stable until aRTD exceeded 50 Gy, then it increased. There is an adequate aRTD that can afford balanced PORT-related LRFS enhancement and related toxicity. The authors highlighted that clinicians should be aware that PORT has the potential to improve unfavorable LRFS and survival outcomes in ESCC patients treated with upfront surgery. The findings of the current study could serve as evidence for delivering appropriate aRTD and designing additional prospective stratified randomized controlled trials. Abstract Background: For patients with esophageal squamous cell carcinoma (ESCC) treated with surgery alone, the incidence of local-regional recurrence remains unfavorable. Postoperative radiotherapy (PORT) has been associated with increased local-regional recurrence-free survival (LRFS), although its application is limited by concerns of PORT-related toxicities. Methods: Among 3591 patients with ESCC analyzed in this study, 2765 patients with T3-4N0 and T1-4N1-3 lesions and specific local-regional status information were analyzed in a subsequent analysis of adjuvant radiation dose (aRTD) effect. Application of the restricted cubic spline regression model revealed a non-linear relationship between aRTD and survival/radiotoxicity. Linear regression analysis (LRA) was performed to evaluate correlations between LRFS and overall survival (OS)/ disease-free survival (DFS). Results: For patients staged T1–2N0, T1–2N1–3, T3–4N0, and T3–4N1–3, 5-year OS in PORT and non-PORT groups were 77.38% vs. 72.91%, p = 0.919, 52.35% vs. 46.60%, p = 0.032, 73.41% vs. 61.19%, p = 0.005 and 38.30% vs. 25.97%, p < 0.001. With aRTD escalation, hazard ratios (HRs) of OS/DFS declined until aRTD exceeded 50Gy, then increased, whereas that of LRFS declined until aRTD exceeded 50 Gy, then remained steady. HR of treatment-related mortality was stable until aRTD exceeded 50 Gy, then increased. LRA revealed strong correlations between LRFS and OS/DFS (r = 0.984 and r = 0.952, respectively). An absolute 1% advancement in LRFS resulted in 0.32% and 0.34% improvements in OS and DFS. Conclusions: An aRTD of 50Gy was well-tolerated, with favorable survival resulting from PORT-related LRFS improvement in patients staged T3–4N0 or T1-4N1–3. Further stratification analyses based on tumor burden would help determine potential PORT-beneficiaries.
Structural Investigation of DHICA Eumelanin Using Density Functional Theory and Classical Molecular Dynamics Simulations

Eumelanin is an important pigment, for example, in skin, hair, eyes, and the inner ear. It is a highly heterogeneous polymer with 5,6-dihydroxyindole-2-carboxylic acid (DHICA) and 5,6-dihydroxyindole (DHI) building blocks, of which DHICA is reported as the more abundant in natural eumelanin. The DHICA-eumelanin protomolecule consists of three building blocks, indole-2-carboxylic acid-5,6-quinone (ICAQ), DHICA and pyrrole-2,3,5-tricarboxylic acid (PTCA). Here, we focus on the self-assembly of DHICA-eumelanin using multi-microsecond molecular dynamics (MD) simulations at various concentrations in aqueous solutions. The molecule was first parameterized using density functional theory (DFT) calculations. Three types of systems were studied: (1) uncharged DHICA-eumelanin, (2) charged DHICA-eumelanin corresponding to physiological pH, and (3) a binary mixture of both of the above protomolecules. In the case of uncharged DHICA-eumelanin, spontaneous aggregation occurred and water molecules were present inside the aggregates. In the systems corresponding to physiological pH, all the carboxyl groups are negatively charged and the DHICA-eumelanin model has a net charge of −4. The effect of K+ ions as counterions was investigated. The results show high probability of binding to the deprotonated oxygens of the carboxylate anions in the PTCA moiety. Furthermore, the K+ counterions increased the solubility of DHICA-eumelanin in its charged form. A possible explanation is that the charged protomolecules favor binding to the K+ ions rather than aggregating and binding to other protomolecules. The binary mixtures show aggregation of uncharged DHICA-eumelanins; unlike the charged systems with no aggregation, a few charged DHICA-eumelanins are present on the surface of the uncharged aggregation, binding to the K+ ions.
Characterisation, modelling and design of cut-off wavelength of InGaAs/GaAsSb type-II superlattice photodiodes

InGaAs/GaAsSb type-II superlattice (T2SL) photodiodes grown on InP substrates are an alternative detector technology for applications operating in the short wavelength infrared band. Their cut-off wavelengths are heavily influenced by the thickness and material composition of InGaAs and GaAsSb used in the T2SL. We present a single band k.p. model performed using a finite difference approach in nextnano validated against two T2SL photodiode wafers and results from literature. These photodiode wafers cover both lattice matched and strained GaAs1−x Sb x compositions (x = 0.40, wafer A and 0.49, wafer B). The validation data covers temperature dependence of cut-off wavelengths (obtained from phase-sensitive photo response data) from 200 K to room temperature. The cut-off wavelengths were found to reduce at 1.32 nm K−1 for wafer A and 1.07 nm K−1 for wafer B. Good agreement was achieved between the validation data and nextnano simulations, after altering the GaAs1−x Sb x valance band offset (VBO) bowing parameter to −1.06 eV. Using this validated model, we show that the wavefunction overlap drops significantly if the GaAsSb barrier is thicker than the InGaAs well layer, hence defining the upper limit of the barrier layer. This validated model is then used to demonstrate that there is a linear dependence between the maximum achievable wavefunction overlap and cut-off wavelength of a lattice matched InGaAs/GaAsSb T2SL. We also found that the adoption of a 5 nm/3 nm InGaAs/GaAsSb T2SL structure offers an improved wavefunction overlap over the more common 5 nm/5 nm InGaAs/GaAsSb T2SL designs. The data reported in this paper is available from doi: 10.15131/shef.data. 20310591.
Systems Biology in Chronic Heart Failure—Identification of Potential miRNA Regulators

Heart failure (HF) is a complex disease entity with high clinical impact, poorly understood pathophysiology and scantly known miRNA-mediated epigenetic regulation. We have analysed miRNA patterns in patients with chronic HF (cHF) and a sex- and age-matched reference group and pursued an in silico system biology analysis to discern pathways involved in cHF pathophysiology. Twenty-eight miRNAs were identified in cHF that were up-regulated in the reference group, and eight of them were validated by RT-qPCR. In silico analysis of predicted targets by STRING protein-protein interaction networks revealed eight cluster networks (involving seven of the identified miRNAs) enriched in pathways related to cell cycle, Ras, chemokine, PI3K-AKT and TGF-β signaling. By ROC curve analysis, combined probabilities of these seven miRNAs (let-7a-5p, miR-107, miR-125a-5p, miR-139-5p, miR-150-5p, miR-30b-5p and miR-342-3p; clusters 1–4 [C:1–4]), discriminated between HF with preserved ejection fraction (HFpEF) and HF with reduced ejection fraction (HFrEF), and ischaemic and non-ischaemic aetiology. A combination of miR-107, miR-139-5p and miR-150-5p, involved in clusters 5 and 7 (C:5+7), discriminated HFpEF from HFrEF. Pathway enrichment analysis of miRNAs present in C:1–4 (let-7a-5p, miR-125a-5p, miR-30b-5p and miR-342-3p) revealed pathways related to HF pathogenesis. In conclusion, we have identified a differential signature of down-regulated miRNAs in the plasma of HF patients and propose novel cellular mechanisms involved in cHF pathogenesis.
In Vivo Evaluation of the Efficacy of a Nisin–Biogel as a New Approach for Canine Periodontal Disease Control

Periodontal disease (PD) is a common oral disease in dogs. Recent in vitro research revealed that nisin–biogel is a promising compound for canine PD control. In this work, a clinical trial was developed to assess the in vivo efficacy of nisin–biogel in dogs by determining the dental plaque index (DPI), gingivitis index (GI), and periodontal pocket depth (PPD) after dental administration. The biogel’s influence on aerobic bacteria counts was also evaluated, as well as its acceptance/adverse effects in dogs. Twenty animals were allocated to one of two groups: a treatment group (TG) subjected to a dental topical application of nisin–biogel for 90 days and a control group (CG) with no treatment. Besides daily monitoring, on day 1 (T0) and at the end of the assay (T90), animals were subjected to blood analysis, periodontal evaluation, dental plaque sampling, scaling, and polishing. Statistical analysis with mixed models showed a significant reduction in mean PPD (estimate = −0.371, p-value < 0.001) and DPI (estimate = −0.146, p-value < 0.05) in the TG animals at T90. A reduction in the GI (estimate = −0.056, p-value > 0.05) was also observed but with no statistical significance. No influence on total bacterial counts was observed, and no adverse effects were detected. The nisin–biogel was revealed to be a promising compound for canine PD control.
Screening of high-risk deleterious missense variations in the CYP1B1 gene implicated in the pathogenesis of primary congenital glaucoma: A comprehensive in silico approach

Background Primary congenital glaucoma (PCG) is the most common subtype of glaucoma caused by defects in the cytochrome P450 1B1 (CYP1B1) gene. It is developing among infants in more than 80% of cases who exhibit impairments in the anterior chamber angle and the trabecular meshwork. Thus, a comprehensive in silico approach was performed to evaluate the effect of high-risk deleterious missense variations in the CYP1B1 gene. Material and methods All the information for CYP1B1 missense variants was retrieved from the dbSNP database. Seven different tools, namely: SIFT, PolyPhen-2, PROVEAN, SNAP2, PANTHER, PhD-SNP, and Predict-SNP, were used for functional annotation, and two packages, which were I-Mutant 2.0 and MUpro, were used to predict the effect of the variants on protein stability. A phylogenetic conservation analysis using deleterious variants was performed by the ConSurf server. The 3D structures of the wild-type and mutants were generated using the I-TASSER tool, and a 50 ns molecular dynamic simulation (MDS) was executed using the GROMACS webserver to determine the stability of mutants compared to the native protein. Co-expression, protein-protein interaction (PPI), gene ontology (GO), and pathway analyses were additionally performed for the CYP1B1 in-depth study. Results All the retrieved data from the dbSNP database was subjected to functional, structural, and phylogenetic analysis. From the conducted analyses, a total of 19 high-risk variants (P52L, G61E, G90R, P118L, E173K, D291G, Y349D, G365W, G365R, R368H, R368C, D374N, N423Y, D430E, P442A, R444Q, F445L, R469W, and C470Y) were screened out that were considered to be deleterious to the CYP1B1 gene. The phylogenetic analysis revealed that the majority of the variants occurred in highly conserved regions. The MD simulation analysis exhibited that all mutants’ average root mean square deviation (RMSD) values were higher compared to the wild-type protein, which could potentially cause CYP1B1 protein dysfunction, leading to the severity of the disease. Moreover, it has been discovered that CYP1A1, VCAN, HSD17B1, HSD17B2, and AKR1C3 are highly co-expressed and interact with CYP1B1. Besides, the CYP1B1 protein is primarily involved in the metabolism of xenobiotics, chemical carcinogenesis, the retinal metabolic process, and steroid hormone biosynthesis pathways, demonstrating its multifaceted and important roles. Discussion This is the first comprehensive study that adds essential information to the ongoing efforts to understand the crucial role of genetic signatures in the development of PCG and will be useful for more targeted gene-disease association studies.