Miracle-dz/UniFAR-FTUs huggingface dataset:
Homocysteine and Folic Acid: Risk Factors for Alzheimer's Disease—An Updated Meta-Analysis

Background: Recent studies have reported that homocysteine (Hcy) may play a vital role in the pathogenesis of vascular dementia (VaD) and Alzheimer's disease (AD). Our study explored the relationship between the plasma Hcy and folate levels and the risk of dementia. Methods: We searched Embase, PubMed, and Web of Science for published literature, including case-control studies and prospective cohort studies, and performed a systematic analysis. Results: The results of our meta-analysis, consisting of case-control studies, showed higher levels of Hcy and lower levels of folate in dementia, AD, and VaD patients than those in non-demented controls (for dementia: SMD = 0.812, 95% CI [0.689, 0.936], p = 0.000 for Hcy; SMD = −0.677, 95% CI [−0.828, −0.525], p = 0.000 for folate). AD patients showed significantly lower plasma Hcy levels compared to VaD patients (SMD = −0.278, 95% CI [−0.466, −0.09], p = 0.000). Subgroup analysis revealed that ethnicity, average age, and dementia type had no significant effect on this association. Furthermore, from the analysis of prospective cohort studies, we identified that elevated plasma Hcy levels were associated with an increased risk of dementia, AD, and VaD (RRdementia = 1.22, 95% CI [1.08, 1.36]; RRAD = 1.07, 95% CI [1.04, 1.11]; RRVaD = 1.13, 95% CI [1.04, 1.23]). In addition, every 5 μmol/L increase in the plasma Hcy level was associated with a 9% increased risk of dementia and a 12% increased risk of AD. Conclusion: Hcy and folic acid are potential predictors of the occurrence and development of AD. A better understanding of their function in dementia could provide evidence for clinicians to rationalize clinical intervention strategies.
Liver Transplantation Versus Liver Resection for Stage I and II Hepatocellular Carcinoma: Results of an Instrumental Variable Analysis

Background This study aimed to compare the long-term outcomes of liver transplantation (LT) and liver resection (LR) among patients with stage I and II hepatocellular carcinoma (HCC). Methods SEER 18 registry from 2004 to 2015 was retrieved for this study. We included 1,765 and 1,746 cases with stage I–II (AJCC, 7th) HCC in the multivariable analyses and instrumental variable (IV) analyses, respectively. Propensity score matching (PSM) was further carried out to ensure comparability. Propensity score to receive LT was adjusted by stabilized inverse probability of treatment weighting (IPTW) and standardized mortality ratio weighting (SMRW) methods. In addition, IV analysis was performed to adjust both measured and unmeasured confounding factors. Results We identified 1,000 (56.7%) and 765 (43.3%) patients treated with LR and LT, respectively. In the multivariable adjusted cohort, after adjusting potential confounders, patients undergoing LT offered significant prognostic advantages over LR in overall survival (OS, P < 0.001) and disease-free survival (DSS, P < 0.001). The instrument variable in this study is LT rates in various Health Service Areas (HSAs). Results from the IV analysis showed that cases treated with LT had significantly longer OS (P = 0.001) and DSS (P < 0.001). In IV analysis stratified by clinicopathologic variables, the treatment effect of LT vs. LR in OS was consistent across all subgroups. Regarding DSS in IV analyses, the subgroup analyses observed that LT had better DSS across all subgroups, except for similar results in the older patients (interaction P value = 0.039) and the non-White patients (interaction P value = 0.041). In the propensity-matched cohort, patients with LT still had better OS (P < 0.001) and DSS (P < 0.001) in comparison to cases who underwent LR. In both IPTW and SMRW cohorts, patients who underwent LT had better OS (both P values < 0.001) and DSS (both P values < 0.001). Conclusions LT provided a survival benefit for cases with stage I–II HCC. These results indicated that if LT rate was to increase in the future, average long-term survival may also increase. However, for some special populations such as the elderly patients, owing to the similar outcomes between LT and LR, the selection of LT should be cautious.
Nitric Oxide Alters the Pattern of Auxin Maxima and PIN-FORMED1 During Shoot Development

Hormone patterns tailor cell fate decisions during plant organ formation. Among them, auxins and cytokinins are critical phytohormones during early development. Nitric oxide (NO) modulates root architecture by the control of auxin spatial patterns. However, NO involvement during the coordination of shoot organogenesis remains unclear. Here, we explore the effect of NO during shoot development by using a phenotypic, cellular, and genetic analysis in Arabidopsis thaliana and get new insights into the characterization of NO-mediated leaf-related phenotypes. NO homeostasis mutants are impaired in several shoot architectural parameters, including phyllotactic patterns, inflorescence stem elongation, silique production, leaf number, and margin. Auxin distribution is a key feature for tissue differentiation and need to be controlled at different levels (i.e., synthesis, transport, and degradation mechanisms). The phenotypes resulting from the introduction of the cue1 mutation in the axr1 auxin resistant and pin1 backgrounds exacerbate the relationship between NO and auxins. Using the auxin reporter DR5:GUS, we observed an increase in auxin maxima under NO-deficient mutant backgrounds and NO scavenging, pointing to NO-ASSOCIATED 1 (NOA1) as the main player related to NO production in this process. Furthermore, polar auxin transport is mainly regulated by PIN-FORMED 1 (PIN1), which controls the flow along leaf margin and venations. Analysis of PIN1 protein levels shows that NO controls its accumulation during leaf development, impacting the auxin mediated mechanism of leaf building. With these findings, we also provide evidence for the NO opposite effects to determine root and shoot architecture, in terms of PIN1 accumulation under NO overproduction.
Exploring the Pathogenesis of Psoriasis Complicated With Atherosclerosis via Microarray Data Analysis

Background Although more and more evidence has supported psoriasis is prone to atherosclerosis, the common mechanism of its occurrence is still not fully elucidated. The purpose of this study is to further explore the molecular mechanism of the occurrence of this complication. Methods The gene expression profiles of psoriasis (GSE30999) and atherosclerosis (GSE28829) were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the common differentially expressed genes (DEGs) of psoriasis and atherosclerosis, three kinds of analyses were performed, namely functional annotation, protein‐protein interaction (PPI) network and module construction, and hub gene identification and co-expression analysis. Results A total of 94 common DEGs (24 downregulated genes and 70 upregulated genes) was selected for subsequent analyses. Functional analysis emphasizes the important role of chemokines and cytokines in these two diseases. In addition, lipopolysaccharide-mediated signaling pathway is closely related to both. Finally, 16 important hub genes were identified using cytoHubba, including LYN, CSF2RB, IL1RN, RAC2, CCL5, IRF8, C1QB, MMP9, PLEK, PTPRC, FYB, BCL2A1, LCP2, CD53, NCF2 and TLR2. Conclusions Our study reveals the common pathogenesis of psoriasis and atherosclerosis. These common pathways and hub genes may provide new ideas for further mechanism research.
Salt Balance Studies in Saline Water Irrigated Soils

Salt balance studies of the soils irrigated with saline water (EC 2.7 to 12 mmhos/cm) in four different crop sequences have shown seasonal cyclic changes in salinity, exchangeable sodium and ionic composition. Salt concentration increased during irrigation cycle, whereas, monsoon rain preverted salt accumulation in the surface layers. High salinity of the irrigation water lowered the evapo transpiration (ET) but increased the leaching fraction (LF) of irrigation water and modified the ionic composition. Irrigation depth, salt concentration and leaching fraction governed the salt accumulation in soil. Only 23–27% of the added salts of sodium and chloride accumulated in the soil and the rest got leached down during crop season itself. Frequent irrigations with saline water were conducive for higher values of ET and LF and to lower the salinity and ESP levels of the soil, thereby resulting in higher yields of different crops.
Examining the Relationship of Clinical and Laboratory Parameters With Infectiousness to Phlebotomus perniciosus and Its Potential Infectivity in Dogs With Overt Clinical Leishmaniasis

Infected dogs are considered the main domestic animal reservoirs for Leishmania infantum parasite. Infectiousness to competent phlebotomine vectors has been associated with many factors, the main being the severity of the disease exhibited by infected dogs. This study examines the relationship between different clinical parameters and the infectiousness to colonized Phlebotomus perniciosus sand flies having a blood meal on dogs. Data obtained in the present study come from an untreated group of Leishmania sick dogs submitted to xenodiagnosis for the evaluation of a spot on insecticide solution. Seventeen dogs were diagnosed as affected by leishmaniasis through clinical examination, immunofluorescence antibody test (IFAT) serology, and loop-mediated isothermal amplification (LAMP). The disease severity (clinical score) was staged by using a numeric value derived from eight clinical and parasitological parameters. Xenodiagnosis was performed on caged dogs exposed for 1.5 h to sand-fly bites. The following parameters related to sand flies were examined: blood feeding (% of blood engorged females), promastigote detection (% of promastigote-positive sand flies), promastigote burden, and the promastigote stage maturation (potential transmissibility rate). Statistical relationship between the clinical score and entomological parameters was investigated, as well as the possible correlation between each clinical and laboratory parameters and sand fly infection/infectivity. The severity of clinical score may influence the blood feeding by, and the probability of promastigote detection in, sand flies; skin lesions seem to be the main factor that influences the rate of blood feeding. Promastigote burden is related to IFAT titer, skin lesions, and clinical score. All entomological parameters are strongly related among them. This study confirms that both P. perniciosus infection and infectivity are influenced by a dog's clinical condition.
Advantages of polycarboxylic over dicarboxylic anhydrides in the melt modification of PPC

We present an alternative polymer modification of poly (propylene carbonate) (PPC). A conventional practice for PPC melt processing is the melt - modification with maleic anhydride (MAH) - a di-carboxylic anhydride -. In our work, PPC is melt-modified with pyromellitic di-anhydride (PDAH) - a tetra-carboxylic dianhydride -. Using MAH modified PPC as reference, the polymer degradation and the thermal and viscoelastic properties of the materials are studied. Both anhydrides after their melt compounding have similar efficiency in the conservation of the molecular weight. Strikingly, the use of PDAH is advantageous over MAH considering the improvement of the thermal stability, the decrease of the complex melt viscosity and higher storage modulus (stiffness) of the modified PPC. It is speculated that the changes in the material performance arise from the occurrence of long chain branching and non-covalent interactions from the PDAH modifier.
Unveiling Operator Growth Using Spin Correlation Functions

In this paper, we study non-equilibrium dynamics induced by a sudden quench of strongly correlated Hamiltonians with all-to-all interactions. By relying on a Sachdev-Ye-Kitaev (SYK)-based quench protocol, we show that the time evolution of simple spin-spin correlation functions is highly sensitive to the degree of k-locality of the corresponding operators, once an appropriate set of fundamental fields is identified. By tracking the time-evolution of specific spin-spin correlation functions and their decay, we argue that it is possible to distinguish between operator-hopping and operator growth dynamics; the latter being a hallmark of quantum chaos in many-body quantum systems. Such an observation, in turn, could constitute a promising tool to probe the emergence of chaotic behavior, rather accessible in state-of-the-art quench setups.
A Two-Stage Hybrid Default Discriminant Model Based on Deep Forest

Background: the credit scoring model is an effective tool for banks and other financial institutions to distinguish potential default borrowers. The credit scoring model represented by machine learning methods such as deep learning performs well in terms of the accuracy of default discrimination, but the model itself also has many shortcomings such as many hyperparameters and large dependence on big data. There is still a lot of room to improve its interpretability and robustness. Methods: the deep forest or multi-Grained Cascade Forest (gcForest) is a decision tree depth model based on the random forest algorithm. Using multidimensional scanning and cascading processing, gcForest can effectively identify and process high-dimensional feature information. At the same time, gcForest has fewer hyperparameters and has strong robustness. So, this paper constructs a two-stage hybrid default discrimination model based on multiple feature selection methods and gcForest algorithm, and at the same time, it optimizes the parameters for the lowest type II error as the first principle, and the highest AUC and accuracy as the second and third principles. GcForest can not only reflect the advantages of traditional statistical models in terms of interpretability and robustness but also take into account the advantages of deep learning models in terms of accuracy. Results: the validity of the hybrid default discrimination model is verified by three real open credit data sets of Australian, Japanese, and German in the UCI database. Conclusions: the performance of the gcForest is better than the current popular single classifiers such as ANN, and the common ensemble classifiers such as LightGBM, and CNNs in type II error, AUC, and accuracy. Besides, in comparison with other similar research results, the robustness and effectiveness of this model are further verified.
Cancer Niches and Their Kikuchi Free Energy

Biological forms depend on a progressive specialization of pluripotent stem cells. The differentiation of these cells in their spatial and functional environment defines the organism itself; however, cellular mutations may disrupt the mutual balance between a cell and its niche, where cell proliferation and specialization are released from their autopoietic homeostasis. This induces the construction of cancer niches and maintains their survival. In this paper, we characterise cancer niche construction as a direct consequence of interactions between clusters of cancer and healthy cells. Explicitly, we evaluate these higher-order interactions between niches of cancer and healthy cells using Kikuchi approximations to the free energy. Kikuchi’s free energy is measured in terms of changes to the sum of energies of baseline clusters of cells (or nodes) minus the energies of overcounted cluster intersections (and interactions of interactions, etc.). We posit that these changes in energy node clusters correspond to a long-term reduction in the complexity of the system conducive to cancer niche survival. We validate this formulation through numerical simulations of apoptosis, local cancer growth, and metastasis, and highlight its implications for a computational understanding of the etiopathology of cancer.
Biases and Variability from Costly Bayesian Inference

When humans infer underlying probabilities from stochastic observations, they exhibit biases and variability that cannot be explained on the basis of sound, Bayesian manipulations of probability. This is especially salient when beliefs are updated as a function of sequential observations. We introduce a theoretical framework in which biases and variability emerge from a trade-off between Bayesian inference and the cognitive cost of carrying out probabilistic computations. We consider two forms of the cost: a precision cost and an unpredictability cost; these penalize beliefs that are less entropic and less deterministic, respectively. We apply our framework to the case of a Bernoulli variable: the bias of a coin is inferred from a sequence of coin flips. Theoretical predictions are qualitatively different depending on the form of the cost. A precision cost induces overestimation of small probabilities, on average, and a limited memory of past observations, and, consequently, a fluctuating bias. An unpredictability cost induces underestimation of small probabilities and a fixed bias that remains appreciable even for nearly unbiased observations. The case of a fair (equiprobable) coin, however, is singular, with non-trivial and slow fluctuations in the inferred bias. The proposed framework of costly Bayesian inference illustrates the richness of a ‘resource-rational’ (or ‘bounded-rational’) picture of seemingly irrational human cognition.
Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan

Thermoflexus hugenholtzii JAD2T, the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2T and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing “Candidatus Thermoflexus japonica,” “Candidatus Thermoflexus tengchongensis,” and “Candidatus Thermoflexus sinensis. ” Genomics was integrated with targeted exometabolomics and 13C metabolic probing of T. hugenholtzii. The Thermoflexus genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The T. hugenholtzii JAD2T exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms in situ. Metabolic probing of T. hugenholtzii JAD2T using 13C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific 13C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of Thermoflexus in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms in situ.
PHYSICS OF NUCLEI AND ELEMENTARY PARTICLES Monte Carlo Simulation of a 18 MV Medical Linac Photon Beam Using GATE/GEANT4

In radiotherapy applications, Monte Carlo (MC) simulation for dose calculations is well acknowledged for its accuracy in predicting dose deposition in the patient. The full modeling of a highenergy photon beam from Varian Clinac 2100C 18 MV medical linear accelerator is presented here by using the GATE/GEANT4 Monte Carlo codes. To evaluate dose distributions associated with the simulated linac head model, dosimetric quantities including the Percentage Depth Dose (PDD), transverse dose profiles, and a set of beam-quality indicators were measured and calculated in a water phantom for square field sizes of 4× 4 cm and 10× 10 cm. Simulations accuracy was validated through Gamma Index analysis using different acceptance criteria within 2%/2 mm, 3%/2 mm, 2%/3 mm, and 3%/3 mm. In terms of Gamma Index comparison, good agreements were found between the calculated and measured dose distributions for all field sizes. The differences between simulation and measurement of beam quality indicators were smaller than 2%.
A mobile, scanning eye-safe lidar for the study of atmospheric aerosol particles and transport processes in the lower troposphere

A high-power eye-safe scanning aerosol lidar system in the ultraviolet wavelength region is introduced for the study of the optical properties of aerosol particles and transport processes in the atmosphere, especially in the atmospheric boundary layer (ABL). This system operates with an average power of 9 W in combination with a 40-cm scanner with a speed of up to 10° s-1. A modified version of the lidar inversion algorithm is developed for the retrieval of optical properties of aerosols from scanning lidar measurements. The lidar data can be analyzed with previously unachieved temporal and spatial resolution of 0.03 s and 3 m, respectively. Zur Untersuchung optischer Eigenschaften von Aerosolpartikeln und Transportprozessen in der Atmosphare, speziell in der atmospharischen Grenzschicht (atmospheric boundary layer, ABL), wird ein augensicheres Hochleistungs-Scanning-Lidarsystem im ultravioletten Wellenlangenbereich vorgestellt. Das System arbeitet mit einer durchschittlichen Leistung von 9 W in Kombination mit einem 40 cm Scanner mit einer Geschwindigkeit bis zu 10° s-1. Eine modifizierte Version des Lidar-Inversionsalgorithmus zur Rekonstruktion der optischen Eigenschaften von Aerosolpartikeln aus den Scanning-Lidar-Messungen wird entwickelt. Die Lidar-Daten konnen mit einer bisher nicht erreichten zeitlichen und raumlichen Auflosung von 0,03 s bzw. 3 m analysiert werden.