Miracle-dz/UniFAR-FTUs huggingface dataset:
Respiration and Carbon Dioxide Accumulation in Soil Microcosms

The thawing of permafrost leads to liberation of soil organic matter and microbial component resulting in significant effect on the carbon cycle. Changes in permafrost soils upon the global climate warming would significantly impact microbial soil activity. Currently, not a great deal is known about what happens to the microbial community after the permafrost thaws. The activity of microbial community was determined in microcosms experiment using respirometry. To assess the CO2 fluctuations during permafrost thawing a titration experiment was performed. Based on calculations using the respirometric equation it was found that CO 2 production increases with temperature, core depth, ion amendments and duration of time.
Type 3 IP3 receptor: Its structure, functions, and related disease implications

ABSTRACT Cell-fate decisions depend on the precise and strict regulation of multiple signaling molecules and transcription factors, especially intracellular Ca2+ homeostasis and dynamics. Type 3 inositol 1,4,5-triphosphate receptor (IP3R3) is an a tetrameric channel that can mediate the release of Ca2+ from the endoplasmic reticulum (ER) in response to extracellular stimuli. The gating of IP3R3 is regulated not only by ligands but also by other interacting proteins. To date, extensive research conducted on the basic structure of IP3R3, as well as its regulation by ligands and interacting proteins, has provided novel perspectives on its biological functions and pathogenic mechanisms. This review aims to discuss recent advancements in the study of IP3R3 and provides a comprehensive overview of the relevant literature pertaining to its structure, biological functions, and pathogenic mechanisms.
Obeticholic acid as a second‐line treatment for low phospholipid‐associated cholelithiasis syndrome

Low phospholipid‐associated cholelithiasis (LPAC) syndrome is a rare genetic cause of hepatolithiasis. A pathogenic variant of the ABCB4 gene is reported in half of all patients. Ursodeoxycholic acid (UDCA) is the only drug approved. However, in some patients, UDCA fails to prevent recurrence of symptoms and complications. Experimental evidence suggests that agonists of the farnesoid‐X receptor (FXR), the main transcription factor regulating ABCB4, may be beneficial in this context.
Controls on the Distribution of Gallium in the Nechalacho REE Deposit, NWT, Canada

Despite the numerous industrial and scientific applications of gallium, its behavior in nature and the processes that concentrate it to potentially economic levels are poorly understood. Although the main supply of this metal is as a by-product of the mining of bauxite, it is also concentrated by magmatic-hydrothermal processes in peralkaline igneous systems. Here we report the results of a study of the distribution of gallium and the controls on this distribution in the Nechalacho rare metal deposit, Northwest Territories, Canada, which has been shown to contain significant reserves of this critical metal. Electron microprobe analyses and X-ray element maps of gallium-bearing minerals were used to determine the mineralogical distribution of gallium in the Nechalacho intrusive suite. Elevated gallium concentrations were identified in albite, biotite, orthoclase, chlorite, and allanite. Of these aluminum-bearing minerals, the most important hosts of gallium are albite, biotite, and orthoclase. Ferric iron-bearing minerals, including magnetite and aegirine, which were considered potential candidates for gallium sequestration, contain relatively low concentrations of the metal. This behavior of gallium, at least from a magmatic perspective, is consistent with its predicted partitioning between phenocrysts and melt. However, there is also evidence that gallium was redistributed by hydrothermal fluids. Chloritization of biotite resulted in the enrichment of gallium in the secondary mineral (chlorite), and the development of secondary albite (albitization) led to a depletion of gallium in primary albite. On the basis of these results, we argue that the overall distribution of gallium within the Nechalacho deposit was controlled by magmatic crystal fractionation, whereas hydrothermal processes led to local remobilization of the metal. During fractional crystallization, gallium was moderately compatible in minerals such as albite and biotite, whereas it bordered between compatibility and incompatibility in minerals such as magnetite and orthoclase, and was incompatible in aegirine. This resulted in a relatively constant bulk gallium concentration in the Nechalacho deposit, although locally, gallium was remobilized hydrothermally, particularly within the most altered parts of the intrusion, notably, the albitite.
Two-Photon Polymerization Printing with High Metal Nanoparticle Loading

Two-photon polymerization (2PP) is an efficient technique to achieve high-resolution, three-dimensional (3D)-printed complex structures. However, it is restricted to photocurable monomer combinations, thus presenting constraints when aiming at attaining functionally active resist formulations and structures. In this context, metal nanoparticle (NP) integration as an additive can enable functionality and pave the way to more dedicated applications. Challenges lay on the maximum NP concentrations that can be incorporated into photocurable resist formulations due to the laser-triggered interactions, which primarily originate from laser scattering and absorption, as well as the limited dispersibility threshold. In this study, we propose an approach to address these two constraints by integrating metallic Rh NPs formed ex situ, purposely designed for this scope. The absence of surface plasmon resonance (SPR) within the visible and near-infrared spectra, coupled with the limited absorption value measured at the laser operating wavelength (780 nm), significantly limits the laser-induced interactions. Moreover, the dispersibility threshold is increased by engineering the NP surface to be compatible with the photocurable resin, permitting us to achieve concentrations of up to 2 wt %, which, to our knowledge, is significantly higher than the previously reported limit (or threshold) for embedded metal NPs. Another distinctive advantage of employing Rh NPs is their role as promising contrast agents for X-ray fluorescence (XRF) bioimaging. We demonstrated the presence of Rh NPs within the whole 2PP-printed structure and emphasized the potential use of NP-loaded 3D-printed nanostructures for medical devices.
Per‐ and polyfluoroalkyl substances and cardiometabolic diseases: A review

Per‐ and polyfluoroalkyl substances (PFAS) are a group of persistent and widespread environmental pollutants that represent a high concern for human health. They have been shown to be associated with several important physiological processes such as lipid metabolism and the immune system. Consequently, PFAS are suspected to play a role in cardiometabolic disease development. However, the evidence regarding associations between PFAS and overt cardiovascular disease and type 2 diabetes remains limited and inconsistent. To address this, we conducted a review of the epidemiological evidence. A deeper understanding of potential underlying molecular mechanisms may help to explain inconsistencies in epidemiological findings. Thus, to gain more mechanistic insight, we also summarized evidence from omics and laboratory studies into an adverse outcome pathway framework. Our observations indicate the potential for associations of PFAS with multiple molecular pathways that could have opposite associations with disease risk, which could be further modified by mixture composition, lifestyle factors or genetic polymorphisms. This identifies the need for exposome studies considering mixture effects, the use of multi‐omics data to gain insight in relevant pathways and the integration of epidemiological and laboratory studies to enhance mechanistic understanding and causal inference. Improved comprehension is essential for environmental health risk assessments.
Measurement of runoff and soil loss from two differently sized plots in a subtropical environment (Brazil)

Studies of soil erosion on small plots present upscaling problems. The results in the literature on the effect of slope length (i.e. scale) on runoff and soil erosion are contradictory. Furthermore, most studies that examine scale effects measured through erosion plots have been conducted in Mediterranean environments. The objective of this study was to assess the effects of plot size on runoff and soil loss in a subtropical environment. Other measurements were taken to appraise the topsoil property changes inside the plots. The soil was ploughed twice, the surface was leveled with a hoe and it was kept bare during the experiment. Data were collected from 10 paired plots, five plots measuring 10 m × 1 m and five plots measuring 1 m × 1 m, installed in the same pedo‐geomorphologic unit. Measurements were carried out from November 2008 to November 2009. During this period, 97 natural storms were registered. The results indicate that the small plots tended to have higher runoff (30% higher) compared to larger plots, especially during periods of greater rainfall volume, duration and intensity. The soil loss was similar in both the 1 m2 plots (6·33 kg/m2) and the 10 m2 plots (6·26 kg/m2). Moreover, the dynamics of the soil loss during the experiment was relatively similar across both plot sizes. The large plots tended to have a greater internal complexity. In these plots, the steps retreat were higher, the overland flow scars were more frequent, and points of rill initiation and protochannels emerged in several parts of the plots. The results of the small plots were comparable to the results obtained on the large plots, especially in relation to soil loss. These plots were useful for short‐term assessments of soil erosion. Copyright © 2011 John Wiley & Sons, Ltd.
Dietary protein recommendations to support healthy muscle ageing in the 21st Century and beyond: considerations and future directions.

1 This review explores the evolution of dietary protein intake requirements and recommendations, with 2 a focus on skeletal muscle remodeling to support healthy ageing based on presentations at the 2023 3 Nutrition Society summer conference. In this review, we describe the role of dietary protein for 4 metabolic health and ageing muscle, explain the origins of protein and amino acid requirements, and 5 discuss current recommendations for dietary protein intake, which currently sits at ~0.8g·kg· -1 day -1 . 6 We also critique existing (e.g., nitrogen balance) and contemporary (e.g., indicator amino acid 7 oxidation) methods to determine protein/amino acid intake requirements and suggest that existing 8 methods may underestimate requirements, with more contemporary assessments indicating protein 9 recommendations may need to be increased to >1.0g·kg· -1 day -1 . One example of evolution in dietary 10 protein guidance is the transition from protein requirements to recommendations. Hence, we discuss 11 the refinement of protein/amino acid requirements for skeletal muscle maintenance with advanced age 12 beyond simply the dose (e.g., source, type, quality, timing, pattern, nutrient co-ingestion) and explore 13 the efficacy and sustainability of alternative protein sources beyond animal-based proteins to facilitate 14 skeletal muscle remodeling in older age. We conclude that, whilst a growing body of research has 15 demonstrated that animal-free protein sources can effectively stimulate support muscle remodeling in 16 a manner that is comparable to animal-based proteins, food systems need to sustainably provide a 17 diversity of both plant and animal source foods, not least for their protein content but other vital 18 nutrients. Finally, we propose some priority research directions for the field of protein nutrition and 19 healthy ageing. 20
Expression of plasma exosomal circLPAR1 in patients with gastric cancer and its clinical application value.

OBJECTIVE To determine plasma exosomal circular RNA LPAR1 (circLPAR1) expression in gastric cancer (GC) and analyze its clinical value in GC diagnosis and prognosis evaluation. METHODS The research subjects were 64 GC patients, 30 chronic gastritis (CG) patients (disease control group) and 30 healthy controls (HCs; healthy control group). RT-PCR quantified circLPAR1 expression in GC tissues and adjacent counterparts of GC patients as well as plasma exosomal circLPAR1 in each group. The correlation of differentially expressed circLPAR1 with clinicopathological indexes was analyzed, and receiver operating characteristics (ROC) and Kaplan-Meier curves were drawn to evaluate the value of plasma exosomal circLPAR1 in GC diagnosis and prognosis assessment. RESULTS GC patients exhibited lower plasma exosomal circLPAR1 levels than CG patients and HCs (P<0.05). Lower circLPAR1 expression was determined in GC tissues than in adjacent counterparts (P<0.05), and a positive connection between GC tissue circLPAR1 and plasma exosomal circLPAR1 was identified in GC patients (P<0.05). Evidently elevated plasma exosomal circLPAR1 was observed in post-surgical GC patients (P<0.05). ROC curves showed that the areas under the curve (AUCs) of plasma exosomal circLPAR1, serum carcinoembryonic antigen (CEA), and serum carbohydrate antigen 19-9 (CA19-9) for the diagnosis of GC were 0.836, 0.767 and 0.746, respectively, and the AUC of their combined diagnosis was 0.914. Low plasma exosomal circLPAR1 was strongly linked to tumor size, differentiation degree, tumor-node-metastasis (TNM) staging, vascular invasion, lymphatic metastasis, and HER2 expression of GC patients (P<0.05). GC patients with high plasma exosomal circLPAR1 expression had significantly longer prognostic survival time than those with low expression (P<0.05). According to univariate and multivariate Cox regression analyses, tissue differentiation degree (HR=1.415), TNM stage (HR=1.637), HER2 expression (HR=1.831), and low plasma exosomal circLPAR1 expression (HR=2.042) were risk factors for adverse prognosis in GC patients. CONCLUSIONS circLPAR1 expression is related to GC progression, and the detection of plasma exosomal circLPAR1 has promising clinical application value in assisting the diagnosis and prognosis evaluation of GC.
A 20-Year Update on the Practice of Thoracic Surgery in Canada: A Survey of the Canadian Association of Thoracic Surgeons

Background This study provides an update to a landmark 2004 report describing demographics, training, and trends in adherence to thoracic surgery practice standards in Canada. Methods An updated questionnaire was administered to all members of the Canadian Association of Thoracic Surgeons via email (n=142, compared to n=68 in 2004). Our report incorporates internal data from Ontario Health and the Canadian Partnership Against Cancer. Results Forty-eight surgeons completed the survey (male, 70.8%; mean±standard deviation age, 50.3±9.3 years). This represents a 33.8% response rate, compared to 64.7% in 2004. Most surgeons (69%) served a patient population of over 1 million per center; 32%–34% reported an on-call ratio of 14–15 days, and the average weekly hours worked was 56.4±11.9. Greater access to dedicated geographic units per center (73% in 2021 vs. 53% in 2004) has improved thoracic-associated services and house staff, notably endoscopy units (100% vs. 91%), with 73% of respondents having access to both endobronchial and endoscopic ultrasound. Access to thoracic radiology has also improved, particularly regarding positron emission tomography scanners per center (76.9% vs. 13%). Annual case volumes for lung (255 vs. 128), esophageal (41 vs. 19), and mediastinal resections (30 vs. 13), along with hiatal hernia repair (45 vs. 20), have increased substantially despite reports of operating room availability and radiology as rate-limiting steps. Conclusion This survey characterizes compliance with current practice standards, addressing the needs of thoracic surgeons across Canada. Over 85% of respondents were aware of the 2004 compliance paper, and 35% had applied for resources and equipment in response.
Guide RNA scaffold variants enabled easy cloning of large gRNA cluster for multiplexed gene editing

Summary Cas9 protein‐mediated gene editing has revolutionized genetic manipulation in most organisms. There are many cases where multiplexed gene editing is needed. Cas9 is capable of multiplex gene editing when expressed with multiple guide RNAs. Conventional cloning methods for multiplexed gene editing vector is not efficient due to repeated use of a single‐guide RNA scaffold and inefficient ligation. In this study, we conducted structure‐guided mutagenesis and random mutagenesis on the original sgRNA scaffold and identified a large number of functional sgRNA scaffold variants. With these scaffold variants and different tRNAs, fusion polymerase chain reaction protocol was developed to rapidly synthesize spacer‐scaffold‐tRNA‐spacer units with up to 9 targets. In conjunction with golden gate cloning, gene editing vectors with up to 24 target sites were efficiently cloned in one‐step cloning. One such gene editing vector targeting 12 genes in tomato were tested in stable transformation and 10 out of the 12 genes were found mutated in a single transgenic line. To facilitate the application of multiplexed gene editing using these scaffold variants and tRNAs from different species, a webserver was created to generate primer sets and provide template sequences for the synthesis of large sgRNA expression units based on the user‐supplied target sequences and species.
Aldehyde Dehydrogenase 2 Preserves Mitochondrial Function in the Ischemic Heart: A Redox-dependent Mechanism for AMPK Activation by Thioredoxin-1

Abstract: Aldehyde dehydrogenase 2 (ALDH2) protects the ischemic heart by activating adenosine 5′-monophosphate-activated protein kinase (AMPK) signaling. However, the molecular mechanisms linking ALDH2 and AMPK signaling are not fully understood. This study aimed to explore the potential mechanisms linking ALDH2 and AMPK in myocardial ischemic injury. An ischemic model was established by ligating the left anterior descending coronary artery in rats. The overexpression or knockdown of ALDH2 in H9c2 cells treated with oxygen–glucose deprivation was obtained through lentivirus infection. Transferase-mediated dUTP nick-end labeling was used to evaluate apoptosis in an ischemic rat model and oxygen–glucose deprivation cells. ALDH2 activity, mitochondrial oxidative stress markers, adenosine triphosphate, respiratory control ratio, and cell viability in H9c2 cells were evaluated using a biological kit and 3-(4,5-dimethylthiazol-2-yl)-2,5 diphenyl tetrazolium bromide. Protein expression of ALDH2, 4-hydroxynonenal, thioredoxin-1 (Trx-1), and AMPK–proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) signaling pathway was detected through Western blotting. ALDH2 activation reduced ischemic-induced myocardial infarct size and apoptosis. ALDH2 protected mitochondrial function by enhancing mitochondrial respiratory control ratio and adenosine triphosphate production, alleviated mitochondrial oxidative stress, and suppressed myocardial apoptosis. Moreover, ALDH2 attenuated ischemia-induced oxidative stress and maintained Trx-1 levels by reducing 4-hydroxynonenal, thereby promoting AMPK–PGC-1α signaling activation. Inhibiting Trx-1 or AMPK abolished the cardioprotective effect of ALDH2 on ischemia. ALDH2 alleviates myocardial injury through increased mitochondrial biogenesis and reduced oxidative stress, and these effects were achieved through Trx1-mediating AMPK–PGC1-α signaling activation.
The role of cardiac resident macrophage in cardiac aging

Advancements in longevity research have provided insights into the impact of cardiac aging on the structural and functional aspects of the heart. Notable changes include the gradual remodeling of the myocardium, the occurrence of left ventricular hypertrophy, and the decline in both systolic and diastolic functions. Macrophages, a type of immune cell, play a pivotal role in innate immunity by serving as vigilant agents against pathogens, facilitating wound healing, and orchestrating the development of targeted acquired immune responses. Distinct subsets of macrophages are present within the cardiac tissue and demonstrate varied functions in response to myocardial injury. The differentiation of cardiac macrophages according to their developmental origin has proven to be a valuable strategy in identifying reparative macrophage populations, which originate from embryonic cells and reside within the tissue, as well as inflammatory macrophages, which are derived from monocytes and recruited to the heart. These subsets of macrophages possess unique characteristics and perform distinct functions. This review aims to summarize the current understanding of the roles and phenotypes of cardiac macrophages in various conditions, including the steady state, aging, and other pathological conditions. Additionally, it will highlight areas that require further investigation to expand our knowledge in this field.
UCHL1-PKM2 axis dysregulation is associated with promoted proliferation and invasiveness of urothelial bladder cancer cells

Background: Bladder cancer is one of the most common type of cancers globally, and the majority of cases belong to urothelial bladder carcinoma (UBC) type. Current researches have demonstrated that multiple genomic abnormalities are related to the sensitivity of cisplatin-based chemotherapy in bladder cancer patients. Previous findings have indicated a controversial role of Ubiquitin Carboxy-Terminal Hydrolase L1 (UCHL1) in malignancy, so we aimed to further explore the role of UCHL1 in UBC. Methods: UBC cell lines and The Cancer Genome Atlas (TCGA) in-silico datasets were utilized to investigate UCHL1 expression pattern and functional as well as prognostic impacts in UBC cancer cell line models and patients. UCHL1 overexpression and silencing vectors and subsequent immunoprecipitation/ubiquitination experiments in combination of cellular functional assays were conducted to explore UCHL1-PKM2 interaction axis and its significance in UBC malignancy. Results: UCHL1 was significantly up-regulated in UBC cancer cells and UCHL1 high-expression was associated with higher pathology/clinical grade and significantly inferior overall prognosis of UBC patients. UCHL1 interacted with PKM2 and enhanced PKM2 protein level through inhibition of PKM2 protein degradation via ubiquitination process. UCHL1-PKM2 interaction significantly promoted UBC cellular proliferation, metastasis and invasion activities. Conclusion: UCHL1-PKM2 interaction played an interesting role in UBC tumor cell proliferation, migration and metastasis. Our study suggests PKM2-targeted treatment might have a potential value in metastatic malignancy therapy development in the future.