Miracle-dz/UniFAR-FTUs huggingface dataset:
Posttranslational Arginylation Enzyme Arginyltransferase1 Shows Genetic Interactions With Specific Cellular Pathways in vivo

Arginyltransferase1 (ATE1) is a conserved enzyme in eukaryotes mediating posttranslational arginylation, the addition of an extra arginine to an existing protein. In mammals, the dysregulations of the ATE1 gene (ate1) is shown to be involved in cardiovascular abnormalities, cancer, and aging-related diseases. Although biochemical evidence suggested that arginylation may be involved in stress response and/or protein degradation, the physiological role of ATE1 in vivo has never been systematically determined. This gap of knowledge leads to difficulties for interpreting the involvements of ATE1 in diseases pathogenesis. Since ate1 is highly conserved between human and the unicellular organism Schizosaccharomyces pombe (S. pombe), we take advantage of the gene-knockout library of S. pombe, to investigate the genetic interactions between ate1 and other genes in a systematic and unbiased manner. By this approach, we found that ate1 has a surprisingly small and focused impact size. Among the 3659 tested genes, which covers nearly 75% of the genome of S. pombe, less than 5% of them displayed significant genetic interactions with ate1. Furthermore, these ate1-interacting partners can be grouped into a few discrete clustered categories based on their functions or their physical interactions. These categories include translation/transcription regulation, biosynthesis/metabolism of biomolecules (including histidine), cell morphology and cellular dynamics, response to oxidative or metabolic stress, ribosomal structure and function, and mitochondrial function. Unexpectedly, inconsistent to popular belief, very few genes in the global ubiquitination or degradation pathways showed interactions with ate1. Our results suggested that ATE1 specifically regulates a handful of cellular processes in vivo, which will provide critical mechanistic leads for studying the involvements of ATE1 in normal physiologies as well as in diseased conditions.
Crystal structure of a putative histidine-containing phosphotransfer protein from Oryza sativa

Os09g0567400 codes for a hypothetical protein from Oryza sativa that is annotated as the “Histidine-containing phosphotransfer (Hpt) protein”. Hpt domain is a protein module with a histidine residue mediating phosphotransfer reaction in the histidine-aspartate phosphorelay system. We report here the crystal structure and analysis of Os09g0567400.
ThePS-IAA4/5-like Family of Early Auxin-inducible mRNAs inArabidopsis thaliana

Abstract The plant hormone auxin transcriptionally activates early genes. We have isolated a 14-member family of DNA sequences complementary to indoleacetic acid (IAA)-inducible transcripts in Arabidopsis thaliana . The corresponding genes, IAA1 and IAA14 , are homologs of PS-1AA4/5 and PS-IAA6 from pea, AUX22 and AUX28 from soybean, ARG3 and ARG4 from mungbean, and AtAux2-11 and AtAux2-27 from Arabidopsis . The members of the family are differentially expressed in mature Arabidopsis plants. Characterization of IAA gene expression in etiolated seedlings demonstrates specificity for auxin inducibility. The response of most family members to IAA is rapid (within 4 to 30 minutes) and insensitive to cyclohexamide. Cyclohexamide alone induces all the early genes. Auxin-induction of two late genes, IAA7 and IAA8 , is inhibited by cyclohexamide, indicating requirement of protein synthesis for their activation. All IAA genes display a biphasic dose response that is optimal at 10 μM IAA. However, individual genes respond differentially between 10 nM and 5μM IAA. Expression of all genes is defective in the Arabidopsis auxin-resistant mutant lines axr1, axr2, and aux1 . The encoded polypeptides share four conserved domains, and seven invariant residues in the intervening regions. The spaces vary considerably in length, rendering the calculated molecular mass of IAA proteins to range from 19 kDa to 36 kDa. Overall sequence identity between members of the family is highly variable (36 to 87%). Their most significant structural features are functional nuclear transport signals, and a putative βαα-fold whose modeled three dimensional structure appears to be compatible with the prokaryotic β-ribbon DNA recognition motif. The data suggest that auxin induces in a differential and hierarchical fashion a large family of early genes that encode a structurally diverse class of nuclear proteins. These proteins are proposed to mediate tissue-specific and cell-type restricted responses to the hormone during plant growth and development.
Soil N dynamics in relation to leaf litter quality and soil fertility in north‐western Patagonian forests

1 We examined the relationships among soil N dynamics, soil chemistry and leaf litter quality in 28 forest stands dominated by conifers, woody broad‐leaf deciduous species or broad‐leaf evergreens. Potential net N mineralization, net nitrification and microbial biomass N were used as indicators of soil N dynamics; pH, organic C, total N, exchangeable cations and extractable P as indicators of soil chemistry and N concentration, lignin concentration, C : N ratio and lignin : N ratio in senescent leaves as indicators of leaf litter quality. N dynamics were assessed in two consecutive years with contrasting precipitation. 2 Net N mineralization was lower in stands of the three conifers and one of three broad‐leaf evergreen species than in stands of the other six broad‐leaf species (40–77 vs. 87–250 mg N kg−1 after 16‐week incubations) and higher in the wetter year. 3 The proportion of N nitrified was high beneath most species regardless of mineralization rates, soil N fertility and leaf litter quality, and was significantly higher for the wetter year. Ammonium was the predominant form of N in three sites affected by seasonal waterlogging and in two sites the predominant form changed from ammonium in the drier year to nitrate during the wetter year, probably due to differences in soil texture affecting soil moisture. 4 Net N mineralization was linearly related to microbial biomass N, implying that the microbial activity per biomass unit was quite similar beneath all species. Constant microbial biomass during the wetter year suggested that as mineralization/nitrification increased, there was a higher potential risk of N losses. 5 Although the litter lignin : N ratio allowed differentiation of soil N dynamics between broad‐leaf species and conifers, its constant value (23–28) in all broad‐leaf species made it a poor predictor of the differences found within this group. Across all sites and between broad‐leaf species, soil N dynamics were best explained by a combination of leaf litter lignin and soil chemistry indicators, particularly soil total N for net N mineralization and net nitrification, and soil organic C for microbial biomass N.
Periphyton-Water Quality Relationships along a Nutrient Gradient in the Northern Florida Everglades

We monitored a 14-km nutrient gradient in the northern Everglades to identify statistical relationships between periphyton and water-quality changes caused by canal discharges into the marsh. Water chemistry measurements were taken at 15 sampling stations every 2 wk over a 20-mo period to quantify changes in major ions along the gradient. Standard algal bioassays were conducted using water from each station to identify trends in nutrient limitation and algal growth potential along the gradient. Patterns of periphyton biomass accumulation and taxonomic composition on artificial substrata were determined in situ during 6 sampling events across seasons. Concentrations of most ions decreased by <25% along the gradient, whereas average total phosphorus (TP) decreased from 150 μg/L at peripheral marsh stations (near canal inflows) to ≤10 μg/L at interior stations (>8 km from inflows). Limiting nutrient assays showed a shift from P limitation at interior stations to possible limitation by other nutrients at peripheral stations. Both algal growth potential and biomass accumulation decreased with increasing distance from the canal, and stepwise regression analysis showed that these changes were best explained by changes in TP along the water-quality gradient. Changes in periphyton taxonomic composition, analyzed using principal components analysis, were also related strongly to distance from canal discharges and to TP. In particular, diatom species indicative of low TP (e.g., Anomoeoneis vitrea, Mastogloia smithii) were consistently replaced by eutrophic indicator species (e.g., Gomphonema parvulum, Nitzschia amphibia) at TP concentrations between 10 and 20 μg/L. The Everglades periphyton assemblage is sensitive to phosphorus enrichment and may provide one of the first reliable indications of eutrophication in the marsh.
A Generalized Alternating Linearization Bundle Method for Structured Convex Optimization with Inexact First-Order Oracles

In this paper, we consider a class of structured optimization problems whose objective function is the summation of two convex functions: f and h, which are not necessarily differentiable. We focus particularly on the case where the function f is general and its exact first-order information (function value and subgradient) may be difficult to obtain, while the function h is relatively simple. We propose a generalized alternating linearization bundle method for solving this class of problems, which can handle inexact first-order information of on-demand accuracy. The inexact information can be very general, which covers various oracles, such as inexact, partially inexact and asymptotically exact oracles, and so forth. At each iteration, the algorithm solves two interrelated subproblems: one aims to find the proximal point of the polyhedron model of f plus the linearization of h; the other aims to find the proximal point of the linearization of f plus h. We establish global convergence of the algorithm under different types of inexactness. Finally, some preliminary numerical results on a set of two-stage stochastic linear programming problems show that our method is very encouraging.
An open source tool to infer epidemiological and immunological dynamics from serological data: serosolver

We present a flexible, open source R package designed to obtain biological and epidemiological insights from serological datasets. Characterising past exposures for multi-strain pathogens poses a specific statistical challenge: observed antibody responses measured in serological assays depend on multiple unobserved prior infections that produce cross-reactive antibody responses. We provide a general modelling framework to jointly infer infection histories and describe immune responses generated by these infections using antibody titres against current and historical strains. We do this by linking latent infection dynamics with a mechanistic model of antibody kinetics that generates expected antibody titres over time. Our aim is to provide a flexible package to identify infection histories that can be applied to a range of pathogens. We present two case studies to illustrate how our model can infer key immunological parameters, such as antibody titre boosting, waning and cross-reaction, as well as latent epidemiological processes such as attack rates and age-stratified infection risk.
Porcine Small Intestinal Submucosa Mesh to Treat Inguinal Hernia in Young Adults Using Laparoscopic Inguinal Hernia Repair: A Retrospective Controlled Study

Background: The authors evaluated the effects and clinical value of small intestinal submucosa (SIS) mesh to treat inguinal hernia in young adults by the laparoscopic method. Methods: The clinical data of 357 cases with inguinal hernia using SIS mesh in our hospital were analyzed retrospectively from June 2014 to June 2018. All cases were divided into 2 groups according to the surgical method. Operation time, hospital stay, cost, postoperative complications, and complications during follow-up were analyzed. Results: Of the 357 patients, 202 (56.6%) underwent Lichtenstein repair and 155 (43.4%) underwent transabdominal preperitoneal (TAPP) repair. Operation time and hospital costs of the Lichtenstein group were significantly lower compared with the TAPP group (P<0.05). The incidence of seroma in the Lichtenstein group was lower than that in the TAPP group at 1 week, 1 month, and 3 months postoperatively with significant differences (P<0.05). Perioperative pain scores in the Lichtenstein group were higher than the TAPP group (P<0.05). No statistical difference was observed for hospital stay between 2 groups (P>0.05). In the Lichtenstein group, 1 case recurred during the follow-up period (0.5%). No intestinal obstruction or intestinal fistula occurred in any patient during the follow-up period. Conclusion: The effect of SIS mesh was positive whether the patient underwent a Lichtenstein or TAPP method. Seroma was more common in the TAPP method that may cause lower postoperative pain. Therefore, we recommend individualized treatment.
Convolutional Neural Network Can Recognize Drug Resistance of Single Cancer Cells

It is known that single or isolated tumor cells enter cancer patients’ circulatory systems. These circulating tumor cells (CTCs) are thought to be an effective tool for diagnosing cancer malignancy. However, handling CTC samples and evaluating CTC sequence analysis results are challenging. Recently, the convolutional neural network (CNN) model, a type of deep learning model, has been increasingly adopted for medical image analyses. However, it is controversial whether cell characteristics can be identified at the single-cell level by using machine learning methods. This study intends to verify whether an AI system could classify the sensitivity of anticancer drugs, based on cell morphology during culture. We constructed a CNN based on the VGG16 model that could predict the efficiency of antitumor drugs at the single-cell level. The machine learning revealed that our model could identify the effects of antitumor drugs with ~0.80 accuracies. Our results show that, in the future, realizing precision medicine to identify effective antitumor drugs for individual patients may be possible by extracting CTCs from blood and performing classification by using an AI system.
Enhancing Drug Delivery for Overcoming Angiogenesis and Improving the Phototherapy Efficacy of Glioblastoma by ICG-Loaded Glycolipid-Like Micelles

Background Phototherapy is a potential new candidate for glioblastoma (GBM) treatment. However inadequate phototherapy due to stability of the photosensitizer and low target specificity induces the proliferation of neovascular endothelial cells for angiogenesis and causes poor prognosis. Methods In this study, we constructed c(RGDfk)-modified glycolipid-like micelles (cRGD-CSOSA) encapsulating indocyanine green (ICG) for dual-targeting neovascular endothelial cells and tumor cells, and cRGD-CSOSA/ICG mediated dual effect of PDT/PTT with NIR irradiation. Results In vitro, cRGD-CSOSA/ICG inhibited cell proliferation and blocked angiogenesis with NIR irradiation. In vivo, cRGD-CSOSA/ICG exhibited increased accumulation in neovascular endothelial cells and tumor cells. Compared with that of CSOSA, the accumulation of cRGD-CSOSA in tumor tissue was further improved after dual-targeted phototherapy pretreatment. With NIR irradiation, the tumor-inhibition rate of cRGD-CSOSA/ICG was 80.00%, significantly higher than that of ICG (9.08%) and CSOSA/ICG (42.42%). Histological evaluation showed that the tumor vessels were reduced and that the apoptosis of tumor cells increased in the cRGD-CSOSA/ICG group with NIR irradiation. Conclusion The cRGD-CSOSA/ICG nanoparticle-mediated dual-targeting phototherapy could enhance drug delivery to neovascular endothelial cells and tumor cells for anti-angiogenesis and improve the phototherapy effect of glioblastoma, providing a new strategy for glioblastoma treatment.
Are we curing one evil with another? A translational approach targeting the role of neoatherosclerosis in late stent failure

Abstract Neoatherosclerosis is defined as foamy macrophage infiltration into the peri-strut or neointimal area after stent implantation, potentially leading to late stent failure through progressive atherosclerotic changes including calcification, fibroatheroma, thin-cap fibroatheroma, and rupture with stent thrombosis (ST) in advanced stages. Human autopsy as well as intravascular imaging studies have led to the understanding of neoatherosclerosis formation as a similar but significantly accelerated pathophysiology as compared to native atherosclerosis. This acceleration is mainly based on disrupted endothelial integrity with insufficient barrier function and augmented transmigration of lipids following vascular injury after coronary intervention and especially after implantation of drug-eluting stents. In this review, we summarize translational insights into disease pathophysiology and discuss therapeutic approaches to tackle this novel disease entity. We introduce a novel animal model of neoatherosclerosis alongside accompanying in vitro experiments, which show impaired endothelial integrity causing increased permeability for low-density lipoprotein cholesterol resulting in foam cell transformation of human monocytes. In addition, we discuss novel intravascular imaging surrogates to improve reliable diagnosis of early stage neoatherosclerosis. Finally, a therapeutic approach to prevent in-stent neoatherosclerosis with magnesium-based bioresorbable scaffolds and systemic statin treatment demonstrated the potential to improve arterial healing and re-endothelialization, leading to significantly mitigated neoatherosclerosis formation in an animal model of neoatherosclerosis.
Influence of Oxygen Diffusion on Thermal Ageing of Cross-Linked Polyethylene Cable Insulation

Thermal ageing of cross-linked polyethylene (XLPE) cable insulation is an important issue threatening the safe operation of power cables. In this paper, thermal ageing of XLPE was carried out at 160 °C in air for 240 h. The influence of oxygen diffusion on thermal ageing of XLPE was investigated by Ultraviolet–visible spectrophotometer (UV–Vis), tensile testing, and Fourier transformed infrared spectroscopy (FTIR). It was observed that the degradation degree not only depended on ageing time but also on sample positions. The thermally aged samples were more oxidized in the surface region, presented a darker color, more carbon atoms appeared in the conjugate cluster, had smaller elongation at break and tensile strength, and a larger carbonyl index. As ageing time increased, the non-uniform oxidation of the XLPE samples became more prominent. The degree of non-uniform oxidation caused by oxygen diffusion was quantitatively studied by first order oxidation kinetic. The calculated results demonstrated that carbonyl index measured by FTIR was more sensitive to non-uniform oxidation with a shape parameter in the range of 1–2. The result shown in this paper is helpful for interpreting and predicting the non-uniform ageing behavior of high voltage XLPE cables.
Addition of pectin-alginate to a carbohydrate beverage does not maintain gastrointestinal barrier function during exercise in hot-humid conditions better than carbohydrate ingestion alone.

PURPOSE To compare the effects of consuming a 16% maltodextrin+fructose+pectin alginate (MAL+FRU+PEC+ALG) drink against a nutrient matched maltodextrin-fructose (MAL+FRU) drink on enterocyte damage and gastrointestinal permeability after cycling in hot and humid conditions. METHODS Fourteen recreational cyclists (7 men) completed three experimental trials in a randomized placebo-controlled design. Participants cycled for 90 min (45% VO2max) and completed a 15 min time-trial in hot (32°C) humid (70% relative humidity) conditions. Every 15-minutes cyclists consumed 143 mL of either (1) water; (2) MAL+FRU+PEC+ALG (90g CHO.hr/16% w/v), (3) - a ratio-matched MAL+FRU drink also (90g CHO.hr/16% w/v). Blood was sampled before and after exercise and gastrointestinal (GI) permeability determined by serum measurements of intestinal fatty acid-binding protein (IFABP) and the percent ratio of lactulose (5g) to rhamnose (2g) recovered in post-exercise urine. RESULTS Compared to WATER, IFABP decreased by 349±67pg.mL-1 with MAL+FRU+PEC+ALG (p=0.007), and by 427±56pg.mL-1 with MAL+FRU (p=0.02). GI permeability was reduced in both the MAL+FRU+PEC+ALG (by 0.019±0.01, p = 0.0003) and MAL+FRU (by 0.014±0.01, p = 0.002) conditions relative to WATER. CONCLUSION Both CHO beverages attenuated GI barrier damage to a similar extent relative to water. No metabolic, cardiovascular, thermoregulatory or performance differences were observed between the CHO beverages. Novelty bullets • Consumption of multiple-transportable CHO, with or without hydrogel properties, preserves GI barrier integrity and reduces enterocyte damage during prolonged cycling in hot-humid conditions.
Monitoring of Processing Conditions of an Ultrasonic Vibration-Assisted Ball-Burnishing Process

Although numerous references present the beneficial effects on surface integrity of ultrasonic vibration-assisted ball burnishing (UVABB), nothing has been reported about the dynamic behavior of the UVABB tool, workpiece, and machine triad during the process. In this paper, a dynamic monitorization through a set of 5 accelerometers is tested to analyze the interactions between the tool–workpiece–machine mechanical assembly. A UVABB tool attached to a milling machine and equipped with a piezoelectric stack that is able to assist the process with a 40-kHz vibration is tested on a milled C45 steel surface. First, the natural frequencies of the mechanical system are obtained through hammer impact tests. Then, the vibratory signals transmitted during the execution of the process are monitored and compared to those: two feed velocities and two burnishing preloads, all with and without vibration-assistance. Results show that the proposed accelerometer set is valid to assess the behavior of a UVABB process. The system’s natural frequencies are not varied by vibration-assistance and are not excited when the piezoelectric is functioning. It is confirmed that UVABB is safe for the machine and the tool, and there is no unexpected excited frequencies due to the piezoelectric excitation.
Efficacy of A Poly(MeOEGMA) Brush on the Prevention of Escherichia coli Biofilm Formation and Susceptibility

Urinary tract infections are one of the most common hospital-acquired infections, and they are often associated with biofilm formation in indwelling medical devices such as catheters and stents. This study aims to investigate the antibiofilm performance of a polymer brush—poly[oligo(ethylene glycol) methyl ether methacrylate], poly(MeOEGMA)—and evaluate its effect on the antimicrobial susceptibility of Escherichia coli biofilms formed on that surface. Biofilms were formed in a parallel plate flow chamber (PPFC) for 24 h under the hydrodynamic conditions prevailing in urinary catheters and stents and challenged with ampicillin. Results obtained with the brush were compared to those obtained with two control surfaces, polydimethylsiloxane (PDMS) and glass. The polymer brush reduced by 57% the surface area covered by E. coli after 24 h, as well as the number of total adhered cells. The antibiotic treatment potentiated cell death and removal, and the total cell number was reduced by 88%. Biofilms adapted their architecture, and cell morphology changed to a more elongated form during that period. This work suggests that the poly(MeOEGMA) brush has potential to prevent bacterial adhesion in urinary tract devices like ureteral stents and catheters, as well as in eradicating biofilms developed in these biomedical devices.