Miracle-dz/UniFAR-FTUs huggingface dataset:
Critical review of non‐histone human substrates of metal‐dependent lysine deacetylases

Lysine acetylation is a posttranslational modification that occurs on thousands of human proteins, most of which are cytoplasmic. Acetylated proteins are involved in numerous cellular processes and human diseases. Therefore, how the acetylation/deacetylation cycle is regulated is an important question. Eleven metal‐dependent lysine deacetylases (KDACs) have been identified in human cells. These enzymes, along with the sirtuins, are collectively responsible for reversing lysine acetylation. Despite several large‐scale studies which have characterized the acetylome, relatively few of the specific acetylated residues have been matched to a proposed KDAC for deacetylation. To understand the function of lysine acetylation, and its association with diseases, specific KDAC‐substrate pairs must be identified. Identifying specific substrates of a KDAC is complicated both by the complexity of assaying relevant activity and by the non‐catalytic interactions of KDACs with cellular proteins. Here, we discuss in vitro and cell‐based experimental strategies used to identify KDAC‐substrate pairs and evaluate each for the purpose of directly identifying non‐histone substrates of metal‐dependent KDACs. We propose criteria for a combination of reproducible experimental approaches that are necessary to establish a direct enzymatic relationship. This critical analysis of the literature identifies 108 proposed non‐histone substrate‐KDAC pairs for which direct experimental evidence has been reported. Of these, five pairs can be considered well‐established, while another thirteen pairs have both cell‐based and in vitro evidence but lack independent replication and/or sufficient cell‐based evidence. We present a path forward for evaluating the remaining substrate leads and reliably identifying novel KDAC substrates.
Mathematical models for estimating the parameters of ruminal degradation kinetics of protein concentrates

This studied aimed to evaluate the parameters of ruminal degradation kinetics of protein concentrates, soybean meal (SM) and cotton cake (CC). To estimate the in situ degradation parameters of DM and CP from coproducts were fitted 5different non-linear mathematical models: Exponencial, Van Milgen, Logistico, Gompertz and Richards. For in situ evaluation were used two cattle cannulated in the rumen. The samples were incubate dat 0, 2, 4, 6, 12, 16, 24, 36, 48 and 72 hours and in the incubation residues were determined DM and CP and their degradability. The DM degradability of SM were 86.35, 74.23, 65.50% and to CC were 53.44, 41.70 and 35.21% in passage rates of 0.02; 0.05 and 0.08. h-1, respectively. The SM and CC showed values for the CP soluble fraction of the 18.15, 34.77% and 79.76, 55.10% to insoluble potentially degradable fraction, respectively. According to the Akaike weights (Wi) the model of Richards has 95.45 and 49.64% of chance to be the most suitable model to characterize the in situ DM degradation of SM and CC. However, the Gompertz model has 63.86 and 66.49% chance to be the most suitable model to characterize the CP in situ degradation of SM and CC.
Expanding the concept of sustainable seafood using Life Cycle Assessment

Fisheries management and sustainability assessment of fisheries more generally have recently expanded their scope from single-species stock assessment to ecosystem-based approaches, aiming to incorporate economic, social and local environmental impacts, while still excluding global-scale environmental impacts. In parallel, Life Cycle Assessment (LCA) has emerged as a widely used and recommended framework to assess environmental impacts of products, including global scale impacts. For over a decade, LCA has been applied to seafood supply chains, leading to new insights into the environmental impact of seafood products. We present insights from seafood LCA research with particular focus on evaluating fisheries management, which strongly influences the environmental impact of seafood products. Further, we suggest tangible ways in which LCA could be taken up in management. By identifying trade-offs, LCA can be a useful decision support tool and avoids problem shifting from one concern (or activity) to another. The integrated, product-based and quantitative perspective brought by LCA could complement existing tools. One example is to follow up fuel use of fishing, as the production and combustion of fuel used dominates overall results for various types of environmental impacts of seafood products, and is also often linked to biological impacts of fishing. Reducing the fuel use of fisheries is therefore effective to reduce overall impacts. Allocating fishing rights based on environmental performance could likewise facilitate the transition to low-impact fisheries. Taking these steps in an open dialogue between fishers, managers, industry, NGOs and consumers would enable more targeted progress towards sustainable fisheries.
Standardized aqueous stem bark extract of Gmelina arborea roxb. possesses nephroprotection against adriamycin-induced nephrotoxicity in Wistar rats

Abstract Nephrotoxicity is a major limitation of adriamycin (ADR) chemotherapy. We hypothesized that administration of standardized aqueous bark extract of Gmelina arborea Roxb. (GA) (Family; Verbenaceae), a traditional therapeutic agent, may reduce the nephrotoxicity caused by ADR in Wistar rats. The dose-dependent nephroprotective activity of the standardized GA extract was investigated in ADR-induced (20 mg/kg, ip) nephrotoxicity in male Wistar rats (n = 6/group). The lyophilized powder of the aqueous refluxed (4 h) GA extract was administered at 100, 300 and 500 mg/kg doses orally for three consecutive days. Fosinopril sodium (0.09 mg/kg) was used as the positive control. Assessment of biochemical parameters on serum, urine and histopathology on H and E stained kidney sections were done at the end of the intervention. The treatment with GA and fosinopril decreased the elevation of serum creatinine, blood urea nitrogen, cystatin C, β2-microglobulin and loss of total protein in urine in nephrotoxic rats in a dose-dependent manner (p < 0.05). In contrast, serum concentrations of albumin and total protein were increased significantly (p < 0.05). H and E stained kidney sections showed an attenuation of renal parenchymal injury following the treatment. The aqueous extract of GA demonstrated antioxidant potential in vitro. Present findings conclude that the standardized aqueous extract of GA stem bark exerted a dose-dependent protection against ADR-induced nephrotoxicity in vivo and may be a promising adjunct in ADR chemotherapy.
Catching a glimpse of the bacterial gut community of companion animals: a canine and feline perspective

Dogs and cats have gained a special position in human society by becoming our principal companion animals. In this context, efforts to ensure their health and welfare have increased exponentially, with in recent times a growing interest in assessing the impact of the gut microbiota on canine and feline health. Recent technological advances have generated new tools to not only examine the intestinal microbial composition of dogs and cats, but also to scrutinize the genetic repertoire and associated metabolic functions of this microbial community. The application of high‐throughput sequencing techniques to canine and feline faecal samples revealed similarities in their bacterial composition, with Fusobacteria, Firmicutes and Bacteroidetes as the most prevalent and abundant phyla, followed by Proteobacteria and Actinobacteria. Although key bacterial members were consistently present in their gut microbiota, the taxonomic composition and the metabolic repertoire of the intestinal microbial population may be influenced by several factors, including diet, age and anthropogenic aspects, as well as intestinal dysbiosis. The current review aims to provide a comprehensive overview of the multitude of factors which play a role in the modulation of the canine and feline gut microbiota and that of their human owners with whom they share the same environment.
Diagnosis, prevalence, and clinical impact of sarcopenia in COPD: a systematic review and meta‐analysis

Sarcopenia prevalence and its clinical impact are reportedly variable in chronic obstructive pulmonary disease (COPD) due partly to definition criteria. This review aimed to identify the criteria used to diagnose sarcopenia and the prevalence and impact of sarcopenia on health outcomes in people with COPD. This review was registered in PROSPERO (CRD42018092576). Five electronic databases were searched to August 2018 to identify studies related to sarcopenia and COPD. Study quality was assessed using validated instruments matched to study designs. Sarcopenia prevalence was determined using authors' definitions. Comparisons were made between people who did and did not have sarcopenia for pulmonary function, exercise capacity, quality of life, muscle strength, gait speed, physical activity levels, inflammation/oxidative stress, and mortality. Twenty‐three studies (70% cross‐sectional) from Europe (10), Asia (9), and North and South America (4) involving 9637 participants aged ≥40 years were included (69.5% men). Sarcopenia criteria were typically concordant with recommendations of hEuropean and Asian consensus bodies. Overall sarcopenia prevalence varied from 15.5% [95% confidence interval (CI) 11.8–19.1; combined muscle mass, strength, and/or physical performance criteria] to 34% (95%CI 20.6–47.3; muscle mass criteria alone) (P = 0.009 between subgroups) and was greater in people with more severe [37.6% (95%CI 24.8–50.4)] versus less severe [19.1% (95%CI 10.2–28.0)] lung disease (P = 0.020), but similar between men [41.0% (95%CI 26.2–55.9%)] and women [31.9% (95%CI 7.0–56.8%)] (P = 0.538). People with sarcopenia had lower predicted forced expiratory volume in the first second (mean difference −7.1%; 95%CI −9.0 to −5.1%) and poorer exercise tolerance (standardized mean difference −0.8; 95%CI −1.4 to −0.2) and quality of life (standardized mean difference 0.26; 95%CI 0.2–0.4) compared with those who did not (P < 0.001 for all). No clear relationship was observed between sarcopenia and inflammatory or oxidative stress biomarkers. Incident mortality was unreported in the literature. Sarcopenia is prevalent in a significant proportion of people with COPD and negatively impacts upon important clinical outcomes. Opportunities exist to optimize its early detection and management and to evaluate its impact on mortality in this patient group.
Plantamajoside inhibits hypoxia-induced migration and invasion of human cervical cancer cells through the NF-κB and PI3K/akt pathways

Abstract Plantamajoside (PMS) is a major compound of Plantago asiatica and possesses anti-tumor property in several types of cancers. However, the effect of PMS on cervical cancer has not been investigated. This study aimed to investigate the effect of PMS on the migration and invasion of cervical cancer cell lines under hypoxic condition. Our results demonstrated that PMS significantly inhibited hypoxia-caused increases in cell migration and invasion of cervical cancer cells. The hypoxia-induced epithelial-mesenchymal transition (EMT) process was prevented by PMS with increased E-cadherin expression, and decreased expression levels of N-cadherin and vimentin in cervical cancer cells. Besides, the expression levels of transcription factors slug and snail were suppressed by PMS in hypoxia-induced cervical cancer cells. The increased mRNA and protein levels of hypoxia-inducible factor 1alpha (HIF-1α) in hypoxia-induced cervical cancer cells were prevented by PMS. Furthermore, PMS blocked the hypoxia-induced activation of NF-κB and PI3K/Akt pathway in cervical cancer cells. Taken together, these findings suggest that PMS exerted an anti-tumor activity in cervical cancer through preventing the hypoxia-induced EMT. Thus, PMS might serve as a therapeutic agent for the treatment of cervical cancer.
Physiological and histopathological alterations in male Swiss mice after exposure to titanium dioxide (anatase) and zinc oxide nanoparticles and their binary mixture

Abstract Existing studies have shown the systemic damage of titanium dioxide (TiO2) or zinc oxide (ZnO) nanoparticles (NPs), but there is little or no existing knowledge on the potential adverse toxic effects of the mixture of the two. In order to investigate the in vivo toxic effect of the mixture of TiO2 NPs and ZnO NPs, the acute toxicities of TiO2 NPs, ZnO NPs by themselves, and their mixture (1:1) were determined. The systemic toxicities of the individual NPs and mixture were evaluated in mice using hematological indices, hepatic, renal, and lipid profile parameters, and histopathology as endpoints. NPs were intraperitoneally administered at doses of 9.38, 18.75, 37.50, 75.00, and 150.00 mg/kg bw each. Individual NPs and their mixture were administered daily for 5 and 10 d, respectively. The LD50 of ZnO NPs was 299.9 mg/kg while TiO2 NPs by themselves or TiO2 NPs + ZnO NPs were indeterminate due to the absence of mortality of the male mice treated. TiO2 NPs, ZnO NPs by themselves and TiO2 NPs + ZnO NPs induced significant alterations in the hematological and biochemical parameters, with higher toxicity at 10 d. Histopathological lesions were observed in the liver, kidneys, spleen, heart, and brain of mice treated with the individual NPs and their mixture. TiO2 NPs + ZnO NPs were able to induce a higher systemic toxicity than TiO2 NPs or ZnO NPs individually. Our data suggest that more comprehensive risk assessments should be carried out on the mixture of NPs before utilization in consumer products.
IN SILICO MODELING OF THE REDOX METABOLISM IN HUMAN ERYTHROCYTES

There was elaborated the mathematical model of erythrocytes metabolism, including glycolysis (Embden-Meyerhof pathway), pentose phosphate pathway, metHb restoration pathway, Н 2 О 2 metabolism reaction. The final model includes 50 reactions and 60 metabolites. Within the model was studied the change of activity of some enzymes and concentrations of metabolites in stationary state, that take part in the processes of utilization of oxygen active forms and restoration of metgemoglobin, depending on amount of exogenous and endogenous Н 2 О 2 . There was demonstrated the threshold character of changes of the many studied parameters, that testifies that the cells can be practically in physiological state at the change of external conditions for rather long time. There was carried out an assessment of redox-state of erythrocytes at oxidizing load: was demonstrated the change of E GSSG/2GSH , E NADP + /NADPH and E NAD + /NADH from the concentration of endogenous Н 2 О 2 . There was established that in the studied diapason of concentrations of endogenous Н 2 О 2 was observed the high slope of the change of E GSSG/2GSH , that was not observed for E NADP + /NADPH and the other redox-pairs. The results of modeling coincide with existing views on the functioning of enzymes of antioxidant protection in human erythrocytes and testify to the possibility of practical use of the model
Efficacy of metformin in the treatment of estrogen-dependent endometrial carcinoma complicated with type 2 diabetes mellitus and analysis of its prognosis.

PURPOSE To explore the efficacy of metformin in the treatment of estrogen-dependent endometrial carcinoma (EC) complicated with type 2 diabetes mellitus (T2DM), and the influencing factors for the prognosis of such patients. METHODS The clinical data of 68 patients histopathologically diagnosed with estrogen-dependent EC complicated with T2DM in our hospital from April 2013 to March 2016, and 132 estrogen-dependent EC patients with normal blood glucose during the same period were retrospectively analyzed. The clinical and pathological features were compared between diabetic patients and non-diabetic patients. The diabetic patients were divided into the metformin group and the non-metformin group according to whether metformin was taken. The survival curves were plotted and analyzed using the Kaplan-Meier method, and the overall survival (OS) and progression-free survival (PFS) were compared among the three groups. Moreover, the multivariate analysis was performed using the COX regression model, so as to analyze the influencing factors for the prognosis of patients with estrogen-dependent EC complicated with T2DM. RESULTS Compared with non-diabetic patients, diabetic patients had higher age of onset, a higher BMI, higher proneness to hypertension, more advanced tumor stage, a higher histological grade, deeper myometrial invasion and a higher risk of lymph node metastasis. Both OS and PFS of T2DM patients who took metformin were significantly prolonged compared with those of T2DM patients who did not take metformin (p=0.021, p=0.011). There were no statistically significant differences in the PFS and OS between diabetic patients who took metformin and non-diabetic patients (p>0.05). According to the results of Cox multivariate analysis, OS was obviously shortened in case of high age of onset, complicated T2DM, late pathological stage of tumor advanced tumor stage, high histological grade, deep myometrial invasion and positive lymph node metastasis, while PFS could was obviously shortened in case of complicated T2DM, late pathological stage of tumor advanced tumor stage, high histological grade, deep myometrial invasion and positive lymph node metastasis. Metformin evidently improved OS and PFS. CONCLUSION Complicated T2DM, high age of onset, advanced tumor stage, high histological grade, deep myometrial invasion and positive lymph node metastasis are factors for the poor prognosis of patients with estrogen-dependent EC, and metformin can significantly ameliorate both OS and PFS in these patients, thereby improving their prognosis.
Correlative evidence for the involvement of phenolic compounds and peroxidase in resistance against Phytophthoracolocasiaeleaf blight in Colocasiaesculenta(taro)

Summary Peroxidases (PODs) are involved in many plant disease defence responses. Twenty-eight varieties of Colocasia esculenta (taro), with varying degrees of resistance to leaf blight disease caused by Phytophthora colocasiae, were used to assess the possible role of phenolic compounds in resistance to the disease.Total soluble phenolic compound (TSPC) concentrations were negatively correlated with mean lesion diameter (MLD); however, ester-bound phenolic compound (EBPC) concentrations were positively correlated with MLD. Degenerate primers were designed to amplify partial genomic sequences of POD genes, and high-tail PCR was used to clone the flanking sequences from a taro variety that was immune to P. colocasiae with the highest TSPC concentration, in order to obtain a full-length sequence of a taro POD gene. The cloned gene contained the complete open reading frame as well as 5'-upstream and 3'-downstream sequences. It contained four exons, as well as the predicted transcription start site and the poly(A) tail signal. Expression of the taro POD gene (GenBank Accession No. KJ591051) increased more rapidly in an incompatible interaction than in a compatible interaction with P. colocasiae based on real-time quantitative RT-PCR (RT-qPCR).
Dual Trajectories of Social Isolation and Dementia in Older Adults: A Population-Based Longitudinal Study

Objectives: To identify the interrelations between the trajectories of social isolation and dementia in older adults. Methods: Data came from the National Health and Aging Trends Study 2011–2018 surveys. Group-based dual trajectory modeling was used to examine trajectories and their interrelations. Results: Four trajectories of social isolation—rarely isolated (62.2%), steady increase (13.5%), steady decrease (7.4%), and persistently isolated (16.9%) and dementia risk—persistently low risk (80.4%), increasing with early onset (3.9%), increasing with late onset (4.5%), and persistently high risk (11.2%) emerged. Two-thirds of the low-risk dementia group were in the rarely isolated group. The high-risk dementia group had the most overlap with the decreasing social isolation group (47%), followed by the persistently isolated group (28%). Conclusions: Social isolation and dementia mostly evolved in the same direction. However, the pattern of associations between these trajectories is intricate and may be reversed among long-term dementia survivors.
Minimally Invasive Removal of Extra- and Intradural Spinal Tumors Using Full Endoscopic Visualization

Study Design: Retrospective cohort study. Objective: To evaluate the clinical efficacy of minimally invasive endoscopic surgery in patients with spinal extradural and intradural-extramedullary tumors. Methods: This was a study of 15 consecutive patients with spinal extradural or intradural-extramedullary tumors up to 2 levels treated by minimal invasive surgery using a full endoscopic visualization and Caspar’s retraction system (for cervical, thoracic, and lumbar tumors) over a 4-year period between January 2015 to April 2019 at a tertiary center. Results: A gross total remove was achieved in all patients (100%), determined by postoperative contrast computed tomography scans and magnetic resonance imaging. There was no postoperative spinal instability. All patients had equal or better neurologic functions after surgery at follow-up. The average preoperative Nurick’s grade mean was 1.9 and the postoperative was 1.1. The average preoperative McCormick’s grade mean was 2.9 versus 1.3 in the postoperative period. Conclusions: Selective extradural or intradural-extramedullary tumors well localized and up to 2 levels can be safely and effectively treated by minimally invasive surgery using a full endoscopic visualization and the Caspar’s retractor. However, there is insufficient evidence to recommend this approach over the classical or other microsurgical approach described.
Genome resources of four distinct pathogenic races within Fusarium oxysporum f. sp. vasinfectum that cause vascular wilt disease of cotton.

Whole Genome Sequence (WGS) based identifications are being increasingly used by regulatory and public health agencies to facilitate the detection, investigation, and control of pathogens and pests. Fusarium oxysporum f. sp. vasinfectum (FOV) is a significant vascular wilt pathogen of cultivated cotton, and consists of several pathogenic races that are not each other's closest phylogenetic relatives. We have developed WGS assemblies for isolates of race 1 (FOV1), race 4 (FOV4), race 5 (FOV5), and race 8 (FOV8) using a combination of Nanopore (MinION) and Illumina sequencing technology (Mi-Seq). This resulted in assembled contigs with more than 100X coverage for each of the FOV races and estimated genome sizes of FOV1 52 Mb, FOV4 68 Mb, FOV5 68 Mb and FOV8 55 Mb. The AUGUSTUS gene prediction program predicted 16,263 genes in FOV1, 20,259 genes in FOV4, 20,375 genes in FOV5 and 16,615 genes in FOV8. We were able to identify 525 genes unique to FOV1, 570 unique to FOV4, 1242 unique to FOV5 and 383 unique to FOV8. We expect that these findings will help in comparative genomics, and in the identification of unique genes as candidate targets for diagnostic marker and methods development to permit rapid differentiation of FOV subgroups.