Miracle-dz/UniFAR-FTUs huggingface dataset:
Postoperative Acute Kidney Injury

Postoperative AKI is a common complication of major surgery and is associated with significant morbidity and mortality. The Kidney Disease Improving Global Outcomes AKI definition allows consensus classification and identification of postoperative AKI through changes in serum creatinine and/or urine output. However, such conventional diagnostic criteria may be inaccurate in the postoperative period, suggesting a potential to refine diagnosis by application of novel diagnostic biomarkers. Risk factors for the development of postoperative AKI can be thought of in terms of preoperative, intraoperative, and postoperative factors and, as such, represent areas that may be targeted perioperatively to minimize the risk of AKI. The treatment of postoperative AKI remains predominantly supportive, although application of management bundles may translate into improved outcomes.
Use of DNA image cytometry in conducting oral cancer screening in rural India

Oral cancer screening can assist in the early detection of oral potentially malignant lesions (OPMLs) and prevention of oral cancers. It can be challenging for clinicians to differentiate OPMLs from benign conditions. Adjunct screening tools such as fluorescence visualisation (FV) and DNA image cytometry (DNA‐ICM) have shown success in identifying OPMLs in high‐risk clinics. For the first time we aimed to assess these technologies in Indian rural settings and evaluate if these tools helped clinicians identify high‐risk lesions during screening.
Yeast phospholipase D, Spo14, is not required for macroautophagy

Autophagy‐related gene (Atg) proteins are key players in autophagy. Some proteins that function in vesicle trafficking and lipid metabolism are also involved in autophagy. The SPO14 in yeast, which encodes phospholipase D (PLD), is involved in membrane trafficking and plays a vital role in sporulation during meiosis. Crosstalk has been identified between autophagy and sporulation. Although the PLD is required for macroautophagy in mammals, its role in yeast macroautophagy remains unclear. We observed that Spo14 is not required for macroautophagy in yeast and that it is dispensable for Atg8 lipidation, which plays an important role in phagophore extension. Our results also revealed that green fluorescent protein (GFP)‐Atg8 degradation is not completely blocked in atg1Δ/atg1Δ cells under sporulation condition. Therefore, Spo14 is not required for macroautophagy in yeast.
Optimization of Offshore Direct Drive Wind Turbine Generators With Consideration of Permanent Magnet Grade and Temperature

In this paper, the main objective is to optimize permanent magnet synchronous generators for offshore direct drive wind turbine, examining the best choice of magnet grades, BHmax, and working temperature. A surface-mounted Nd–Fe–B generator is designed electromagnetically and structurally and optimized for different rated powers of 6, 8, and 10 MW. The results show that the cost of energy decreases as the wind turbine's rated power increases. Further optimizations were carried out using different neodymium magnet grades, and it was found that the higher magnet grades produce a lower cost of energy. In addition, steps were taken to estimate the effect of magnet temperature. A detailed thermal model is used to calculate the cooling airflow requirements to bring the magnet operating temperature from 120 to 80 °C. Allowing the use of cheaper temperature grades of magnets, the additional cooling reduces winding losses and improves the effective BHmax of the magnets.
Food and gut originated bacteriocins involved in gut microbe-host interactions

Abstract The gut microbes interact with each other as well as host, influencing human health and some diseases. Many gut commensals and food originated bacteria produce bacteriocins which can inhibit pathogens and modulate gut microbiota. Bacteriocins have comparable narrow antimicrobial spectrum and are attractive potentials for precision therapy of gut disorders. In this review, the bacteriocins from food and gut microbiomes and their involvement in the interaction between producers and gut ecosystem, along with their characteristics, types, biosynthesis, and functions are described and discussed. Bacteriocins are produced by many intestinal commensals and food microbes among which lactic acid bacteria (many are probiotics) has been paid more attention. Bacteriocin production has been generally regarded as a probiotic trait. They give a competitive advantage to bacteria, enabling their colonization in human gut, and mediating the interaction between the producers and host ecosystem. They fight against unwanted bacteria and pathogens without significant impact on the composition of commensal microbiota. Bacteriocins assist the producers to survive and colonize in the gut microbial populations. There is a great need to evaluate and utilize the potential of bacteriocins for improved therapeutic implications for intestinal health.
Breaking Sitting Time with Physical Activity Increases Energy Expenditure but Does Not Alter Postprandial Metabolism in Girls

ABSTRACT Purpose Young people spend a substantial proportion of their time at school sedentary; therefore, this setting represents an important target for interventions aimed at displacing sedentary time with physical activity. This study aimed to examine the postprandial metabolic effects of breaking sedentary time by accumulating walking and repeated bouts of nonambulatory standing during simulated school days in inactive adolescent girls. Methods Seventeen girls (mean ± SD = 12.8 ± 0.4 yr) completed two 3-d experimental conditions. On days 1 and 2 of the standing + walking (STD-WLK) experimental trial, participants interrupted sedentary time by completing 4 × 10 min bouts of self-paced walking and accumulated 18 × 5 min standing bouts during each simulated school day. On day 3 of STD-WLK, participants attended school as normal with no additional physical activity or standing prescribed. On all 3 d of the control condition (CON), participants attended school as normal with no physical activity intervention. On days 2 and 3 of both STD-WLK and CON, a baseline capillary blood sample was provided to determine fasting [TAG] and [glucose]. Participants then consumed a standardized breakfast (0 h) and lunch (4.7 h), and blood samples were provided postprandially at 2.7, 5.3, and 7.3 h for [TAG] and [glucose]. Results Energy expenditure was 28% (95% confidence interval = 8% to 52%) higher during school hours on day 1 and day 2 during STD-WLK compared with CON (2171 vs 1693 kJ; effect size = 0.89, P = 0.008). However, no reduction of fasting or postprandial [TAG] or [glucose] was observed on day 2 or day 3 (P ≥ 0.245). Conclusions Two consecutive days of breaking prolonged sitting with self-paced walking and intermittent standing had no meaningful effect on postprandial metabolism in adolescent girls.
Understanding enemy’s weapons to an effective prevention: common virulence effects across microbial phytopathogens kingdoms

Abstract Plant–pathogens interaction is an ongoing confrontation leading to the emergence of new diseases. The majority of the invading microorganisms inject effector proteins into the host cell, to bypass the sophisticated defense system of the host. However, the effectors could also have other specialized functions, which can disrupt various biological pathways of the host cell. Pathogens can enrich their effectors arsenal to increase infection success or expand their host range. This usually is accomplished by the horizontal gene transfer. Nowadays, the development of specialized software that can predict proteins structure, has changed the experimental designing in effectors’ function research. Different effectors of distinct plant pathogens tend to fold alike and have the same function and focussed structural studies on microbial effectors can help to uncover their catalytic/functional activities, while the structural similarity can enable cataloguing the great number of pathogens’ effectors. In this review, we collectively present phytopathogens' effectors with known enzymatic functions and proteins structure, originated from all the kingdoms of microbial plant pathogens. Presentation of their common domains and motifs is also included. We believe that the in-depth understanding of the enemy’s weapons will help the development of new strategies to prevent newly emerging or re-emerging plant pathogens.
Expressive flexibility and health-related quality of life: The predictive role of enhancement and suppression abilities and relationships with trait emotional intelligence.

This study aims to examine the ability to flexibly enhance and suppress emotional expression, known as expressive flexibility, in relation to physical and psychological health, as well as trait emotional intelligence (EI). A sample of 503 Italian (Mage = 28.65 ± 9.26 years, 85.1% females) participants completed the Italian version of Flexible Regulation of Emotional Expression (FREE) Scale, the TEIQue-SF, and the Short Form-12 Health Survey. Confirmatory factor analysis indicated that the Italian version of FREE showed adequate psychometric properties. In both genders, results of correlational analyses indicated that enhancement ability was associated with well-being, emotionality, and sociability, whereas suppression ability was associated with self-control. Regression analyses, controlling for age and gender, indicated that suppression and inversely enhancement abilities, predicted the perceived psychological but not physical health. Well-being, self-control, and sociability also contributed to explaining variance in the model. The interaction effect of enhancement and suppression was not significantly associated with either physical or psychological health. Overall, these results suggest that enhancement and suppression abilities differentially contribute to psychological health when trait EI is accounted for. Clinical implications and future directions for research on expressive flexibility are discussed.
Two Distinct Immune Cell Signatures Predict the Clinical Outcomes in Patients With Amyopathic Dermatomyositis With Interstitial Lung Disease

Amyopathic dermatomyositis (ADM) is a heterogeneous and life‐threatening autoimmune disease with a high mortality rate. In particular, anti–melanoma differentiation–associated protein 5 antibody–positive patients are at a high risk of developing rapidly progressive interstitial lung disease (RPILD). This study was undertaken to identify immunologic signatures among patients who have ADM with ILD (ADM‐ILD) and to discover the biomarkers predicting prognosis.
A Hypoxia-Sensitive Drug Delivery System Constructed by Nitroimidazole and its Application in the Treatment of Hepatocellular Carcinoma

Hypoxia is an important pathological phenomenon, and it can induce many tumor microenvironment changes, such as accumulations of intracellular lactic acid, decrease of tumor microenvironment pH value, and regulate a series of physiological and pathological processes such as adhesion, metastasis, and immune escape. Hypoxic tumor cells act as a key target for treating tumor. In this research, we designed and prepared PEG-nitroimidazole grafts, PEG-NI, and FA-PEG-NI. We first explored their physical and chemical properties to serve as a drug carrier. Then, the hypoxia-sensitive properties such as particle size changes and drug release were investigated. Finally, the tumor targeting ability was studied in vitro and in vivo, and anti-tumor capacity was determined. Both grafts showed excellent property as a nanodrug carrier and showed favorable drug encapsulation ability of sorafenib with the help of the hydrophobic chain of 6-(BOC-amino) hexyl bromide. The micelles responded to the hypoxic tumor environment with chemical and spatial structure changes leading to sensitive and fast drug release. With the modification of folic acid, FA-PEG-NI gained tumor targeting ability in vivo. FA-PEG-NI graft proved a potential targeting drug delivery system in the treatment of hypoxic hepatocellular carcinoma.
Torsion‐dependent spectral response of long‐period fiber grating based on electric arc technique with axial rotation of the fiber

We present a novel technique for manufacturing a long‐period fiber grating (LPFG) with enhanced torsion sensitivity based on electric arc technique. The proposed method rotates the fiber around its axis of rotation at each electric arc discharge. We experimentally investigated the torsion‐dependent spectral response of the produced grating and the results showed that an enhanced linear torsion sensitivity up to 0.197 nm/(rad/m) was achieved, which is higher than that of the conventional arc‐induced LPFGs.
Direct tracking of reverse-transcriptase speed and template sensitivity: implications for sequencing and analysis of long RNA molecules

Abstract Although reverse-transcriptase (RT) enzymes are critical reagents for research and biotechnology, their mechanical properties are not well understood. In particular, we know little about their relative speed and response to structural obstacles in the template. Commercial retroviral RTs stop at many positions along mixed sequence templates, resulting in truncated cDNA products that complicate downstream analysis. By contrast, group II intron-encoded RTs appear to copy long RNAs with high processivity and minimal stops. However, their speed, consistency and pausing behavior have not been explored. Here, we analyze RT velocity as the enzyme moves through heterogeneous sequences and structures that are embedded within a long noncoding RNA transcript. We observe that heterogeneities in the template are highly disruptive to primer extension by retroviral RTs. However, sequence composition and template structure have negligible effects on behavior of group II intron RTs, such as MarathonRT (MRT). Indeed, MRT copies long RNAs in a single pass, and displays synchronized primer extension at a constant speed of 25 nt/sec. In addition, it passes through stable RNA structural motifs without perturbation of velocity. Taken together, the results demonstrate that consistent, robust translocative behavior is a hallmark of group II intron-encoded RTs, some of which operate at high velocity.
The effect of a fruit-rich diet on liver biomarkers, insulin resistance, and lipid profile in patients with non-alcoholic fatty liver disease: a randomized clinical trial

Abstract Background Despite confirmed dietary approaches to improve the Non-Alcoholic Fatty Liver Disease (NAFLD), the effect of fruits on NAFLD is not clear. The present study aimed to investigate the effect of a fruit rich diet (FRD) on liver steatosis, liver enzymes, Insulin resistance, and lipid profile in patients with NAFLD. Methods Eighty adults with NAFLD participated in this randomized controlled trial. The participants were randomly assigned to the FRD group with consumption of at least 4 servings of fruits daily or the control group with fruits consumption of less than 2 servings/day. The grade of steatosis, serum levels of liver enzymes including alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), and gamma-glutamyl transferase (GGT), total cholesterol (TC), triglyceride (TG), low-density lipoprotein (LDL), high-density lipoprotein (HDL), glucose, and homeostatic model assessment for insulin resistance (HOMA-IR) were measured at the baseline and at the end of the study. Results After 6 months of intervention, the FRD group had significantly higher BMI (31.40 ± 2.61 vs. 25.68 ± 2.54, p < .001), WC (113.5 ± 10.7 vs. 100.5 ± 7.5, p < .001), the grade of steatosis, ALT (89.1 ± 92.9 vs. 32.0 ± 19.2, p < .001), AST (74.5 ± 107.8 vs. 24.0 ± 8.5, p < .001), ALP (273.4 ± 128.5 vs. 155.0 ± 43.9, p < .001), GGT (92.7 ± 16.2 vs. 21.2 ± 7.7, p < .001), TC (206.1 ± 40.5 vs. 172.7 ± 42.4, p < .01), LDL (126.9 ± 32.3 vs. 99.8 ± 29.8, p < .001), glucose (115.5 ± 30.0 vs. 97.7 ± 19.0, p < .01), and insulin resistance (7.36 ± 4.37 vs. 2.66 ± 1.27, p < .001), and lower HDL (41.4 ± 8.9 vs. 53.8 ± 15.1, p < .001) compared to the control group. Adjusting for BMI and calorie intake did not change the results. Conclusion The results of the present study indicated that consumption of fruits more than 4 servings/day exacerbates steatosis, dyslipidemia, and glycemic control in NAFLD patients. Further studies are needed to identify the underlying mechanisms of the effects of fruits on NAFLD. Clinical trial registration This trial was registered at Iranian randomized clinical trial website with IRCT registration no. IRCT20201010048982N1on October 15, 2020.
A syntax–lexicon trade-off in language production

Significance This work evaluates the long-debated relationship between word selection and syntax selection during language production in a sample of 231 individuals (79 patients with primary progressive aphasia [PPA] and 152 healthy speakers). We first provide a characterization of syntactic complexity based on the frequency of the syntactic rules, which allows for the direct comparison of syntactic and lexical complexities. We then provide converging evidence for a syntax–lexicon complexity trade-off in utterance planning in picture description which might reflect a basic property of language production.
Towards ‘end-to-end’ analysis and understanding of biological timecourse data

Petabytes of increasingly complex and multidimensional live cell and tissue imaging data are generated every year. These videos hold large promise for understanding biology at a deep and fundamental level, as they capture single-cell and multicellular events occurring over time and space. However, the current modalities for analysis and mining of these data are scattered and user-specific, preventing more unified analyses from being performed over different datasets and obscuring possible scientific insights. Here, we propose a unified pipeline for storage, segmentation, analysis, and statistical parametrization of live cell imaging datasets.
An optimality theory account of the non-concatenative morphology of the nominal system of Libyan Arabic, with special reference to the broken plural

This work presents a full and unified investigation of the phenomenon of non-concatenative nominal morphology in Libyan Arabic (LA), with special reference to the formation of the broken plural (BP). The analysis provides a morphophonological account of morphologically derived words in LA. It is based on two main ideas: the first is specifying the input for the derivational morphological process which represents the underlying structure of the derived word; the second is to account for the phonological constraints which interact with each other on the underlying structure in order to determine the optimal output for the derived word. In contrast to previous studies which fail to recognize derivational morphological processes and consequently cannot identify the nature of the input of the derived word, this thesis identifies the input as the starting point to justify the resulting derived output. This thesis argues that the nature of the input in non-concatenative morphology must be accounted for first. The morphological process starts when elements of the input which are carried over to the output are identified, and the specified derivational morphemes are supplied. These together form the underlying structure of any derived word. The underlying structure of the derived word in this thesis is considered to be the string of root consonants and any morphological component associated with the input, plus the derivational morphemes of the intended morphological process. As a consequence of identifying the nature of the input, the template which has been associated with Arabic language, is revealed in this thesis that it is not a primitive but rather it is an artefact of the phonology operating on morphological products. Thus, phonology has no role in the underlying structure, but comes into play to repair any ill-formed surfaced structure. The types of constraints which operate on the outputs are phonological constraints concerning markedness and faithfulness constraints. The function of markedness constraints is to maintain the well-formedness of the output, while the function of faithfulness constraints is to preserve the morphological identity of the components of the underlying structure.
Cre/lox regulated conditional rescue and inactivation with zebrafish UFlip alleles generated by CRISPR-Cas9 targeted integration

The ability to regulate gene activity spatially and temporally is essential to investigate cell-type-specific gene function during development and in postembryonic processes and disease models. The Cre/lox system has been widely used for performing cell and tissue-specific conditional analysis of gene function in zebrafish. However, simple and efficient methods for isolation of stable, Cre/lox regulated zebrafish alleles are lacking. Here, we applied our GeneWeld CRISPR-Cas9 targeted integration strategy to generate floxed alleles that provide robust conditional inactivation and rescue. A universal targeting vector, UFlip, with sites for cloning short homology arms flanking a floxed 2A-mRFP gene trap, was integrated into an intron in rbbp4 and rb1. rbbp4off and rb1off integration alleles resulted in strong mRFP expression,>99% reduction of endogenous gene expression, and recapitulated known indel loss-of-function phenotypes. Introduction of Cre led to stable inversion of the floxed cassette, loss of mRFP expression, and phenotypic rescue. rbbp4on and rb1on integration alleles did not cause phenotypes in combination with a loss-of-function mutation. Addition of Cre led to conditional inactivation by stable inversion of the cassette, gene trapping and mRFP expression, and the expected mutant phenotype. Neural progenitor Cre drivers were used for conditional inactivation and phenotypic rescue to showcase how this approach can be used in specific cell populations. Together these results validate a simplified approach for efficient isolation of Cre/lox-responsive conditional alleles in zebrafish. Our strategy provides a new toolkit for generating genetic mosaics and represents a significant advance in zebrafish genetics.
Estimation of Time-Averaged Shear Wave Velocity (SWV) to 30 m considering Site SWV Structural Characteristic

The time-averaged shear wave velocity (SWV) to 30 m (VS30) is a site condition parameter that has been widely used to specify the site class in building codes. However, the penetration depth of some building sites is less than 30 m, and thus, VS30 cannot be determined based on the velocity profiles. To estimate the site parameter VS30 accurately, we examined the effect of the velocity structural characteristic parameter of site profiles, βH, on VS30 by performing a residual analysis. Further, a method to estimate VS30 was established considering the effect of βH, and the validity of the proposed model was assessed based on site data pertaining to Japan and California (USA). The results show that the time-averaged shear wave velocity to the depth H (H < 30 m), VSH, is weakly correlated with the parameter βH. However, βH has a significant effect on VS30; for the same site VSH, VS30 tended to increase with βH. Compared with the extrapolation method, the proposed model can significantly reduce the standard deviation for the estimation of VS30, while increasing the correlation between the estimated and measured values of VS30. Thus, the estimation accuracy can be significantly improved by considering the effect of βH.