Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-term combined organic manure and chemical fertilizer application enhances aggregate-associated C and N storage in an agricultural Udalfs soil

Little information is known on whether carbon (C) and nitrogen (N) immobilization is synchronized in different sizes of aggregates under different agricultural management practices. Carbon and N concentrations and the C/N ratios in different sizes of aggregates down to 40 cm depth were determined after long-term application of chemical fertilizers combined with manure or without manure in a wheat-rice cropping system. Manure application usually produced significantly (P < 0.05) higher C and N concentrations and lower C/N ratios in bulk soil and in different sizes of aggregates down to 20 cm depth than the other treatments, and the 1.5 MNPK treatment at 0–10 cm depth had the highest SOC concentration of 26.3 g/kg. The C and N concentrations in bulk soil and all aggregate fractions decreased markedly with increasing soil depth. Among water stable aggregates in all soil depths, the highest C (48.2–66.4%) and N (47.8–68.3%) concentrations as a percentage of SOC were found in the small macroaggregates (2000–250 μm, SM). Manure application significantly (P < 0.05) increased the mass and C and N concentrations of SM and SM fractions down to 20 depth. The mean C/N ratios of silt-clay within large and small macroaggregates (inter-SC) were 1.57 and 1.46 units lower than those of silt-clay particles, respectively, indicating that inter-SC had relative high N availability. Moreover, the C and N content of SM down to 40 cm depth tended to saturation with increasing C input rate. Overall, manure application effectively improved soil structure, SM were the dominant particles involved in soil C and N storage, and inter-SC were the main particles responsible for N availability.
The influences of AlGaN barrier epitaxy in multiple quantum wells on the optoelectrical properties of AlGaN-based deep ultra-violet light-emitting diodes

The growth conditions of the AlGaN barrier in AlGaN/AlGaN deep ultra-violet (DUV) multiple quantum wells (MQWs) have crucial influences on the light output power of DUV light-emitting diodes (LEDs). The reduction of the AlGaN barrier growth rate improved the qualities of AlGaN/AlGaN MQWs, such as surface roughness and defects. The light output power enhancement could reach 83% when the AlGaN barrier growth rate was reduced from 900 nm h−1 to 200 nm h−1. In addition to the light output power enhancement, lowering the AlGaN barrier growth rate altered the far-field emission patterns of the DUV LEDs and increased the degree of polarization in the DUV LEDs. The enhanced transverse electric polarized emission indicates that the strain in AlGaN/AlGaN MQWs was modified by lowering the AlGaN barrier growth rate.
CD8/PD-L1 immunohistochemical reactivity and gene alterations in cutaneous squamous cell carcinoma

In recent years, several immune checkpoint inhibitors targeting programmed death-ligand 1 (PD-L1) or PD-1 have been developed for cancer therapy. The genetic background of tumors and factors that influence PD-L1 expression in tumor tissues are not yet elucidated in cutaneous squamous cell carcinoma (cSCC). CD8-positive tumor-infiltrating lymphocytes (TILs) are known to be related to tumor immunity. Here, we aimed to study the relationship between CD8/PD-L1 immunohistochemical reactivity and gene alterations in cSCC. Tumorigenic genes were examined to identify gene alterations using next-generation sequencing (NGS). We collected 27 cSCC tissue samples (from 13 metastatic and 14 non-metastatic patients at primary diagnosis). We performed immunohistochemical staining for CD8 and PD-L1, and NGS using a commercially available sequencing panel (Illumina Cancer Hotspot Panel V2) that targets 50 cancer-associated genes. Immunohistochemically, CD8-positive TILs showed a high positive score in cSCC without metastasis; in these cases, cSCC occurred predominantly in sun-exposed areas, the tumor size was smaller, and the total gene variation numbers were notably low. The tumor depth, PD-L1 positivity, and gene variation number with or without tumor metastasis were not related, but the gene variation number tended to be higher in cSCCs arising in non-sun-exposed areas. Tumor metastasis was more common in cSCC arising in non-sun-exposed areas, which decreased the number of TILs or CD8-positive cells. From a genetic perspective, the total gene alterations were higher in cSCC with metastasis. Among them, ERBB4 and NPM1 are presumably involved in cSCC tumorigenesis; in addition, GNAQ, GNAS, JAK2, NRAS, IDH2, and CTNNB1 may be related to tumor metastasis. These results provide information on potential genes that can be targeted for cSCC therapy and on immune checkpoint inhibitors that may be used for cSCC therapy.
Impact of blood factors on endothelial cell metabolism and function in two diverse heart failure models

Role of blood-based factors in development and progression of heart failure (HF) is poorly characterized. Blood contains factors released during pathophysiological states that may impact cellular function and provide mechanistic insights to HF management. We tested effects of blood from two distinct HF models on cardiac metabolism and identified possible cellular targets of the effects. Blood plasma was obtained from daunorubicin- and myocardial infarction-induced HF rabbits (Dauno-HF and MI-HF) and their controls (Dauno-Control and MI-Control). Effects of plasma on bioenergetics of myocardial tissue from healthy mice and cellular cardiac components were assessed using high-resolution respirometry and Seahorse flux analyzer. Since endothelial cell respiration was profoundly affected by HF plasma, effects of plasma on endothelial cell barrier function and death were further evaluated. Western-blotting and electron microscopy were performed to evaluate mitochondrial proteins and morphology. Brief exposure to HF plasma decreased cardiac tissue respiration. Endothelial cell respiration was most impacted by exposure to HF plasma. Endothelial cell monolayer integrity was decreased by incubation with Dauno-HF plasma. Apoptosis and necrosis were increased in cells incubated with Dauno-HF plasma for 24 h. Down-regulation of voltage-dependent anion-selective channel (VDAC)-1, translocase of outer membrane 20 (Tom20), and mitochondrial fission factor (MFF) in cells exposed to Dauno-HF plasma and mitochondrial signal transducer and activator of transcription 3 (Stat3) and MFF in cells exposed to MI-HF plasma were observed. Mitochondrial structure was disrupted in cells exposed to HF plasma. These findings indicate that endothelial cells and mitochondrial structure and function may be primary target where HF pathology manifests and accelerates. High-throughput blood-based screening of HF may provide innovative ways to advance disease diagnosis and management.
Pharyngeal pumping rate does not reflect lifespan extension in C. elegans transgenerational longevity mutants

Epigenetic modifications must be reprogrammed with each new generation. In Caenorhabditis elegans , defects in histone methylation reprogramming allow for the transgenerational acquisition of longevity. For example, mutations in the putative H3K9 demethylase JHDM-1 extend lifespan after six to ten generations. We noticed that long-lived jhdm-1 mutants appear healthier than wild-type animals from the same generation. To quantify health, we compared the common metric of pharyngeal pumping rate at specific adult ages between early-gen populations with normal lifespans and late-gen populations with long lifespans. Longevity did not affect pumping rate, but long-lived mutants stop pumping at a younger age, suggesting a possible conservation of energy to extend lifespan.
Frobenius and monodromy operators in rigid analysis, and Drinfel'd's symmetric space

We define Frobenius and monodromy operators on the de Rham cohomology of $K$-dagger spaces (rigid spaces with overconvergent structure sheaves) with strictly semistable reduction $Y$, over a complete discrete valuation ring $K$ of mixed characteristic. For this we introduce log rigid cohomology and generalize the so called Hyodo-Kato isomorphism to versions for non-proper $Y$, for non-perfect residue fields, for non-integrally defined coefficients, and for the various strata of $Y$. We apply this to define and investigate crystalline structure elements on the de Rham cohomology of Drinfel'd's symmetric space $X$ and its quotients. Our results are used in a critical way in the recent proof of the monodromy-weight conjecture for quotients of $X$ given by de Shalit.
ELECTROMAGNETIC WAVE INTERACTION WITH STRATIFIED NEGATIVE ISOTROPIC MEDIA

In this paper we provide a general formulation for the electromagnetic wave interaction with stratified media and then specialize to slabs of negative isotropic media. The field solutions are obtained in all regions of the stratified medium. The characteristic waves in negative isotropic media are backward waves. We derive the field solutions and show that a Gaussian beam is laterally shifted by a negative isotropic slab. The amount of beam center shift is calculated for both cases of transmission and reflection. Guided waves in stratified media are studied. Placing a linear antenna and all types of Hertzian dipole antennas in a stratified medium, we obtained solutions in all regions. We demonstrate and locate the positions of the perfect images of the antenna sources in the presence of negative isotropic slabs.
Thermodynamic Stability of Modified Konishi-Kaneko System

The Konishi-Kaneko system is modified to a continuous time system. The system has clustered equilibrium states as well as uniform equilibrium states for 1/T > 4π/kM, where k is a coupling constant and M is the total mass of the particles. The clustered equilibrium states are thermodynamically stable and the uniform states are unstable for 1/T > 4π/kM
Visualizing increased uptake of [18F]FDG and [18F]FTHA in kidneys from obese high-fat diet fed C57BL/6J mice using PET/CT ex vivo

It is known that high-fat diet (HFD) and/or diabetes may influence substrate preferences and energy demands in the heart preceding diabetic cardiomyopathy. They may also induce structural glomerular changes causing diabetic nephropathy. PET/CT has been utilized to examine uptake of energy substrates, and to study metabolic changes or shifts before onset of metabolic disorders. However, conventional PET/CT scanning of organs with relatively low uptake, such as the kidney, in small animals in vivo may render technical difficulties. To address this issue, we developed a PET/CT ex vivo protocol with radiolabeled glucose and fatty acid analouges, [18F]FDG and [18F]FTHA,to study substrate uptake in mouse kidneys. We also aimed to detect a possible energy substrate shift before onset of diabetic nephropathy. The ex vivo protocol reduced interfering background as well as interindividual variances. We found increased uptake of [18F]FDG and [18F]FTHA in kidneys after HFD, compared to kidneys from young mice on standard chow. Levels of kidney triglycerides also increased on HFD. Lipoprotein lipase (LPL) activity, the enzyme responsible for release of fatty acids from circulating lipoproteins, is normally increased in postprandial mice kidneys. After long-term HFD, we found that LPL activity was suppressed, and could therefore not explain the increased levels of stored triglycerides. Suppressed LPL activity was associated with increased expression of angiopoietin-like protein4, an inhibitor of LPL. HFD did not alter the transcriptional control of some common glucose and fatty acid transporters that may mediate uptake of [18F]FDG and [18F]FTHA. Performing PET/CT ex vivo reduced interfering background and interindividual variances. Obesity and insulin resistance induced by HFD increased the uptake of [18F]FDG and [18F]FTHA and triglyceride accumulation in mouse kidneys. Increased levels of [18F]FDG and [18F]FTHA in obese insulin resistant mice could be used clinically as an indicator of poor metabolic control, and a complementary test for incipient diabetic nephropathy.
Modeling the three-dimensional connectivity of in vitro cortical ensembles coupled to Micro-Electrode Arrays

Nowadays, in vitro three-dimensional (3D) neuronal networks are becoming a consolidated experimental model to overcome most of the intrinsic limitations of bi-dimensional (2D) assemblies. In the 3D environment, experimental evidence revealed a wider repertoire of activity patterns, characterized by a modulation of the bursting features, than the one observed in 2D cultures. However, it is not totally clear and understood what pushes the neuronal networks towards different dynamical regimes. One possible explanation could be the underlying connectivity, which could involve a larger number of neurons in a 3D rather than a 2D space and could organize following well-defined topological schemes. Driven by experimental findings, achieved by recording 3D cortical networks organized in multi-layered structures coupled to Micro-Electrode Arrays (MEAs), in the present work we developed a large-scale computational network model made up of leaky integrate-and-fire (LIF) neurons to investigate possible structural configurations able to sustain the emerging patterns of electrophysiological activity. In particular, we investigated the role of the number of layers defining a 3D assembly and the spatial distribution of the connections within and among the layers. These configurations give rise to different patterns of activity that could be compared to the ones emerging from real in vitro 3D neuronal populations. Our results suggest that the introduction of three-dimensionality induced a global reduction in both firing and bursting rates with respect to 2D models. In addition, we found that there is a minimum number of layers necessary to obtain a change in the dynamics of the network. However, the effects produced by a 3D organization of the cells is somewhat mitigated if a scale-free connectivity is implemented in either one or all the layers of the network. Finally, the best matching of the experimental data is achieved supposing a 3D connectivity organized in structured bundles of links located in different areas of the 2D network.
Bias‐reduced estimators of conditional odds ratios in matched case‐control studies with unmatched confounding

We study bias‐reduced estimators of exponentially transformed parameters in general linear models (GLMs) and show how they can be used to obtain bias‐reduced conditional (or unconditional) odds ratios in matched case‐control studies. Two options are considered and compared: the explicit approach and the implicit approach. The implicit approach is based on the modified score function where bias‐reduced estimates are obtained by using iterative procedures to solve the modified score equations. The explicit approach is shown to be a one‐step approximation of this iterative procedure. To apply these approaches for the conditional analysis of matched case‐control studies, with potentially unmatched confounding and with several exposures, we utilize the relation between the conditional likelihood and the likelihood of the unconditional logit binomial GLM for matched pairs and Cox partial likelihood for matched sets with appropriately setup data. The properties of the estimators are evaluated by using a large Monte Carlo simulation study and an illustration of a real dataset is shown. Researchers reporting the results on the exponentiated scale should use bias‐reduced estimators since otherwise the effects can be under or overestimated, where the magnitude of the bias is especially large in studies with smaller sample sizes.
Asynchronous measurments and control : a case study on motor synchronisation

In this paper the synchronisation between two or more electrical motors (a master and one or more slaves) is studied. To reduce the costs of the master-slaves combination, the slave motors are mounted with a very low resolution encoder (one or several pulses per revolution). The low resolution of the slave encoders has severe consequences on the control algorithm. Two methods are proposed to deal with the low resolution encoders: the hybrid and the asynchronous control scheme. In the hybrid scheme the measurement is updated at the time that slave position information is available, the control is updated at a fixed time rate. In the asynchronous scheme, both the measurement and the control value are updated only at the time the slave position becomes available. Since the sample times are now determined by state-events (a system variable crossing certain values), standard control and analysis techniques are not applicable. For the asynchronous controller a new design technique is proposed. The presented controllers are tested successfully on a real industrial master-multi-slave system as is used in mailing machines.
Identification of candidate genes for nicotine withdrawal in C57BL/6J × DBA/2J recombinant inbred mice

Nicotine is the reinforcing ingredient in tobacco. Following chronic exposure, sudden cessation of nicotine use produces negative symptoms of withdrawal that contribute to dependence. The molecular mechanisms underlying nicotine withdrawal behaviors, however, are poorly understood. Using recombinant inbred mice, chronic nicotine was delivered by minipump and withdrawal induced using mecamylamine. Somatic signs of withdrawal, and anxiety‐like behavior using elevated plus maze, were then assessed. Interval mapping was used to identify associations between genetic variation and withdrawal behaviors, and with basal gene expression. Differential gene expression following nicotine exposure and withdrawal was also assessed in progenitor mice using microarrays. Quantitative trait loci mapping identified chromosome intervals with significant genetic associations to somatic signs of withdrawal or withdrawal‐induced anxiety‐like behavior. Using bioinformatics, and association with basal gene expression in nucleus accumbens, we implicated Rb1, Bnip3l, Pnma2, Itm2b, and Kif13b as candidate genes for somatic signs of withdrawal, and Galr1, which showed trans‐regulation from a region of chromosome 14 that was associated with somatic signs of withdrawal. Candidate genes within the chromosome 9 region associated with anxiety‐like withdrawal behavior included Dixdc1, Ncam1, and Sorl1. Bioinformatics identified six genes that were also significantly associated with nicotine or alcohol traits in recent human genome‐wide association studies. Withdrawal‐associated somatic signs and anxiety‐like behavior had strong non‐overlapping genetic associations, respectively, with regions of chromosome 14 and chromosome 9. Genetic, behavioral and gene expression correlations, and bioinformatics analysis identified several candidate genes that may represent novel molecular targets for modulating nicotine withdrawal symptoms.
A Retro-Aldol Reaction Prompted the Evolvability of a Phosphotransferase System for the Utilization of a Rare Sugar

Microorganisms generate energy through glycolysis, which might have preceded a rapid burst of evolution, including the evolution of cellular respiration in the primordial biosphere. However, little is known about the evolvability of cellular sugar preferences. ABSTRACT The evolution of the bacterial phosphotransferase system (PTS) linked to glycolysis is dependent on the availability of naturally occurring sugars. Although bacteria exhibit sugar specificities based on carbon catabolite repression, the acquisition and evolvability of the cellular sugar preference under conditions that are suboptimal for growth (e.g., environments rich in a rare sugar) are poorly understood. Here, we generated Escherichia coli mutants via a retro-aldol reaction to obtain progeny that can utilize the rare sugar d-tagatose. We detected a minimal set of adaptive mutations in the d-fructose-specific PTS to render E. coli capable of d-tagatose utilization. These E. coli mutant strains lost the tight regulation of both the d-fructose and N-acetyl-galactosamine PTS following deletions in the binding site of the catabolite repressor/activator protein (Cra) upstream from the fruBKA operon and in the agaR gene, encoding the N-acetylgalactosamine (GalNAc) repressor, respectively. Acquired d-tagatose catabolic pathways then underwent fine-tuned adaptation via an additional mutation in 1-phosphofructose kinase to adjust metabolic fluxes. We determined the evolutionary trajectory at the molecular level, providing insights into the mechanism by which enteric bacteria evolved a substrate preference for the rare sugar d-tagatose. Furthermore, the engineered E. coli mutant strain could serve as an in vivo high-throughput screening platform for engineering non-phosphosugar isomerases to produce rare sugars. IMPORTANCE Microorganisms generate energy through glycolysis, which might have preceded a rapid burst of evolution, including the evolution of cellular respiration in the primordial biosphere. However, little is known about the evolvability of cellular sugar preferences. Here, we generated Escherichia coli mutants via a retro-aldol reaction to obtain progeny that can utilize the rare sugar d-tagatose. Consequently, we identified mutational hot spots and determined the evolutionary trajectory at the molecular level. This provided insights into the mechanism by which enteric bacteria evolved substrate preferences for various sugars, accounting for the widespread occurrence of these taxa. Furthermore, the adaptive laboratory evolution-induced cellular chassis could serve as an in vivo high-throughput screening platform for engineering tailor-made non-phosphorylated sugar isomerases to produce low-calorigenic rare sugars showing antidiabetic, antihyperglycemic, and antitumor activities.
Cinnamaldehyde Induces the Expression of MicroRNA-1285-5p and MicroRNA-140-5p in Chondrocytes to Ameliorate the Apoptosis and Inflammatory Response

Objective Cinnamaldehyde (CA) is an active ingredient of Wenyang Tongluo capsule. This study was performed to investigate the function of CA on human chondrocytes. Design Different doses of CA were used to treat C28/I2 cells, which were stimulated by interleukin-1β (IL-1β), and then the viability and apoptosis of the cells were examined by cell counting kit-8 and flow cytometry. Interleukin-6 (IL-6), interleukin-20 (IL-20), and tumor necrosis factor-α (TNF-α) were measured by enzyme-linked immunosorbent assay. Quantitative real-time reverse transcriptase polymerase chain reaction was performed to measure miR-1285-5p, miR-140-5p, IL-20, and high-mobility group box 1 (HMGB1) messenger RNA (mRNA) expression. Western blot assay was performed to detect IL-20, HMGB1, IKBα, phospho-IKBα, IKKα/β, and phospho-IKKα/β expression. Moreover, the relationships between miR-1285-5p and IL-20, as well as miR-140-5p and HMGB1, were validated by dual-luciferase reporter assay. Results CA promoted the viability and inhibited the apoptosis of C28/I2 cells stimulated by IL-1β and repressed IL-6, IL-20, and TNF-α levels. CA increased miR-1285-5p and miR-140-5p expression levels. MiR-1285-5p and miR-140-5p promoted the viability and inhibited the apoptosis and inflammation of C28/I2 cells. IL-20 was a target gene of miR-1285-5p, and HMGB1 was a target gene of miR-140-5p. Overexpression of IL-20 or HMGB1 could reverse the effect of CA on C28/I2 cells treated with IL-1β. In addition, HMGB1 increased phospho-IKBα and phospho-IKKα/β expression in IL-1β- and CA-treated C28/I2 cells. Conclusions CA protects chondrocytes via regulating miR-1285-5p/IL-20 axis and miR-140-5p/HMGB1/nuclear factor kappa B pathway.