Miracle-dz/UniFAR-FTUs huggingface dataset:
Executive Function Training for Deaf Children: Impact of a Music Intervention

Abstract Several studies have reported poor executive function (EF) development in deaf children with subsequent impacts on their social and academic attainment. This paper describes the results of a music-based EF intervention designed for deaf children and carried out in two sets of primary schools. This is the first classroom-based EF training study with deaf children, and it also incorporates a replication phase. The intervention was a within-subject crossover design, with 29 deaf children aged 7–11 years who participated in both an EF and an art class control activity, each lasting 10 hours over 5 weeks. Non-verbal EF skills were assessed at pre-test, the crossover point, and post-test. Findings indicated that the EF intervention led to an improvement in participants’ working memory and inhibitory skills in comparison with their performance on the same tasks after the control activity. The findings were not uniform for all EFs targeted nor for all cognitive ability levels in the sample. We discuss the implications of our findings for deaf children with different ability levels and for how EF interventions can be further improved.
Long non-coding RNA Neat1 triggers renal tubular epithelial cell apoptosis via activating BH3-only protein in membranous nephropathy

Abstract Background and Objective Membranous nephropathy (MN) is an autoimmune disease. The up-regulation of the long non-coding RNA (lncRNA) nuclear paraspeckle assembly transcript 1 (Neat1) has been found in MN but the mechanism is still unclear. Here, we explored the effect and the underlying mechanism of lncRNA Neat1 on the apoptosis of renal tubular epithelial cells in MN. Methods Albumin-stimulated E11 podocytes and proximal tubular epithelial cells in vitro and the cationic-bovine serum albumin-induced MN mouse model in vivo were established. The expression of Neat1 in E11 podocytes, renal tubular epithelial cells, and renal tubules and the mRNA expression of BH3-only (the Bcl-2 homology 3-only) proteins were determined by quantitative reverse transcription-polymerase chain reaction. Levels of Cleaved Caspase 3, 6, 7, and Noxa were examined by western blotting. The number of apoptotic cells was detected by flow cytometry. Cellular proliferation was determined by 5-Ethynyl-2’-deoxyuridine and Cell Counting Kit-8 assay. Interactions between BH3-only protein Noxa and Bcl-2 as well as Bcl-xL were evaluated with co-immunoprecipitation. Results The expression of lncRNA Neat1 was unchanged in albumin-stimulated E11 podocytes, but it was up-regulated in albumin-stimulated renal tubular epithelial cells and MN renal tubule tissues and there was a time-dependent increase in vivo. In the albumin-stimulated proximal tubular epithelial cells, overexpression of Neat1 could increase apoptosis and decrease proliferation. In turn, interference with Neat1 reduced apoptosis and increased proliferation accordingly. The mRNA expression levels of BH3-only proteins (Bad, Bim, Bid, Puma, Noxa) were detected with qRT-PCR, the results indicated that after overexpression of Neat1, mRNA and protein levels of Noxa were significantly increased, and the interference with BH3-only protein Noxa alleviated apoptosis of renal tubular epithelial cells in vitro. Conclusion In our study, we proved that lncRNA Neat1 promoted the development of MN by inducing apoptosis and this effect may be exerted by inhibiting the anti-apoptotic protein activity mediated by Noxa.
Longitudinal Trajectories and Correlates of Post-Caregiving Depressive Symptoms in Former Caregivers of Persons With Alzheimer’s Disease or a Related Dementia

Background: Despite the end of caregiving responsibilities, caregivers’ depressive symptoms continue following the death of the care recipient with Alzheimer’s disease or a related dementia (ADRD). However, long-term patterns of depressive symptoms among ADRD caregivers following the care recipient’s death remain poorly understood. Purpose: To explore longitudinal trajectories and correlates of depressive symptoms in former caregivers of persons with ADRD following the care recipient’s death. Methods: Using the modification of Cooper’s framework presented by Whittemore and Knafl, an integrative review was conducted in 4 stages: problem identification, literature search, data evaluation, and data analysis. The literature search was performed using CINAHL, PubMed, and PsycINFO databases. Articles were included if they were published in English between January 1994 and March 2021, reported in peer-reviewed sources, and described findings of original research related to factors, correlates, or longitudinal patterns of depressive symptoms in former family caregivers following the death of the care recipient with ADRD. Results: Longitudinal trajectories of depressive symptoms were categorized into 3 overarching themes: (1) gradual reduction of depressive symptoms during the first year post-caregiving; (2) failure of depressive symptoms to fully resolve after the first year post-caregiving; and (3) individualized depressive symptom trajectories. Correlates of post-caregiving depressive symptoms were categorized into 3 themes: (1) caregiver personal characteristics; (2) extrinsic factors; and (3) coping resources. Conclusion: These findings indicated that screening for depression and psychosocial support are high priorities during the first year post-caregiving to facilitate early identification of at-risk caregivers and improve mental health outcomes in this population.
Comparative analysis of the MyTH4-FERM myosins reveals insights into the determinants of actin track selection in polarized epithelia

MyTH4-FERM (MF) myosins evolved to play a role in the creation and function of a variety of actin-based membrane protrusions that extend from cells. Here we performed an analysis of the MF myosins, Myo7A, Myo7B, and Myo10, to gain insight into how they select for their preferred actin networks. Using enterocytes that create spatially separated actin tracks in the form of apical microvilli and basal filopodia, we show that actin track selection is principally guided by the mode of oligomerization of the myosin along with the identity of the motor domain, with little influence from the specific composition of the lever arm. Chimeric variants of Myo7A and Myo7B fused to a leucine zipper parallel dimerization sequence in place of their native tails both selected apical microvilli as their tracks, while a truncated Myo10 used its native antiparallel coiled-coil to traffic to the tips of filopodia. Swapping lever arms between the Class 7 and 10 myosins did not change actin track preference. Surprisingly, fusing the motor-neck region of Myo10 to a leucine zipper or oligomerization sequences derived from the Myo7A and Myo7B cargo proteins USH1G and ANKS4B, respectively, re-encoded the actin track usage of Myo10 to apical microvilli with significant efficiency.
Cascading effects of caffeine intake by primary consumers to the upper trophic level

Abstract Secondary metabolites are central to understanding the evolution of plant–animal interactions. Direct effects on phytophagous animals are well-known, but how secondary consumers adjust their behavioural and physiological responses to the herbivore's diet remains more scarcely explored for some metabolites. Caffeine is a neuroactive compound that affects both the behaviour and physiology of several animal species, from humans to insects. It is an alkaloid present in nectar, leaves and even sap of numerous species of plants where it plays a role in chemical defences against herbivores and pathogens. Caffeine effects have been overlooked in generalist herbivores that are not specialized in coffee or tea plants. Using a host–parasitoid system, we show that caffeine intake at a relatively low dose affects longevity and fecundity of the primary consumer, but also indirectly of the secondary one, suggesting that this alkaloid and/or its effects can be transmitted through trophic levels and persist in the food chain. Parasitism success was lowered by ≈16% on hosts fed with caffeine, and parasitoids of the next generation that have developed in hosts fed on caffeine showed a reduced longevity, but no differences in mass and size were found. This study helps at better understanding how plant secondary metabolites, such as caffeine involved in plant–animal interactions, could affect primary consumers, could have knock-on effects on upper trophic levels over generations, and could modify interspecific interactions in multitrophic systems.
Respect the synchrotron beam strength: how to model it, measure it and mitigate it for various scientific fields

Extremely bright synchrotron radiation sources give extremely strong intensities at the sample. Lawrence Bright et al. (2021) [J. Synchrotron Rad. (2021), 28, 1377–1385] dive into the details for materials science. I offer a Commentary including a historical context.
Bacterial survival strategies and responses under heavy metal stress: a comprehensive overview

Abstract Heavy metals bring long-term hazardous consequences and pose a serious threat to all life forms. Being non-biodegradable, they can remain in the food webs for a long period of time. Metal ions are essential for life and indispensable for almost all aspects of metabolism but can be toxic beyond threshold level to all living beings including microbes. Heavy metals are generally present in the environment, but many geogenic and anthropogenic activities has led to excess metal ion accumulation in the environment. To survive in harsh metal contaminated environments, bacteria have certain resistance mechanisms to metabolize and transform heavy metals into less hazardous forms. This also gives rise to different species of heavy metal resistant bacteria. Herein, we have tried to incorporate the different aspects of heavy metal toxicity in bacteria and provide an up-to-date and across-the-board review. The various aspects of heavy metal biology of bacteria encompassed in this review includes the biological notion of heavy metals, toxic effect of heavy metals on bacteria, the factors regulating bacterial heavy metal resistance, the diverse mechanisms governing bacterial heavy metal resistance, bacterial responses to heavy metal stress, and a brief overview of gene regulation under heavy metal stress.
Serum Ferritin and the Risk of Metabolic Syndrome: A Systematic Review and Dose-Response Meta-Analysis of Cross-sectional Studies.

Objective This study aims to assess the dose-response relationship between serum ferritin (SF) and metabolic syndrome (MetS) in the two sexes. Methods We searched for articles on PubMed, the Cochrane Library, EMBASE, and the Web of Science databases that were published from 1950 to 2020. The summary odds ratio ( OR) and 95% confidence interval ( CI) of the association between SF and MetS were estimated using a random-effects model through a meta-analysis. Based on the methods described by Greenland and Longnecker, we explored the dose-response relationship between the two sexes. Results This study included 14 studies and 74,710 samples. The results of the classical meta-analysis showed that SF was positively associated with MetS ( OR = 1.77, 95% CI: 1.59-1.98). Regarding the components of MetS (8 studies included), the results showed that SF was positively associated with abdominal obesity ( OR = 1.42, 95% CI: 1.24-1.62), elevated fasting plasma glucose ( OR = 1.84, 95% CI: 1.50-2.25), elevated blood pressure ( OR = 1.17, 95% CI: 1.08-1.26), elevated triglycerides ( OR= 2.09, 95% CI: 1.72-2.54), and reduced high-density lipoprotein cholesterol ( OR = 1.33, 95% CI: 1.19-1.49). In the linear dose-response meta-analysis, the ORs of males, females, and postmenopausal females were 1.14 (95% CI: 1.13-1.16), 1.32 (95% CI: 1.26-1.39), and 1.34 (95% CI: 1.22-1.47), respectively. Conclusions Our study shows that SF is significantly and positively associated with MetS, and the risk in the male population is higher than that in the female population. This finding also supports the recommendation of using SF as an early warning marker of MetS.
Perceiving the facial trustworthiness: Facial age, emotional expression, and attractiveness

People can make trustworthiness judgements based on facial characteristics. However, the previous findings regarding whether facial age influences interpersonal trust are inconsistent. Using the trust game, the current study investigated the interactions of facial age with attractiveness and emotional expression in regard to trustworthiness judgements. In Experiments 1 and 2, younger participants were asked to invest in either younger or older faces that were shown for 2,000 and 33 ms, respectively. The results showed that people trust the faces of older people more than they do younger people. There was also an interaction between facial age and attractiveness. Participants invested more money in older faces than in younger faces only when they perceived the faces to be less attractive. However, the interaction between facial age and emotional expression was slightly inconsistent in the two experiments. Participants invested more money in older faces that were shown for 2,000 ms when they perceived the happy and sad emotions, but they invested more money in older faces that were shown for 33 ms when they perceived the happy emotion. These results reveal that people make trustworthiness judgements based on multiple facial cues when they view strangers of different ages.
Hepatocellular carcinoma (HCC): the most promising therapeutic targets in the preclinical arena based on tumor biology characteristics

ABSTRACT Introduction : Hepatocellular carcinoma (HCC) is a malignant liver tumor characterized by high molecular heterogeneity, which has hampered the development of effective targeted therapies severely. Recent experimental data have unraveled novel promising targets for HCC treatment. Areas covered : Eligible articles were retrieved from PubMed and Web of Science databases up to July 2021. This review summarizes the established targeted therapies for advanced HCC, focusing on the strategies to overcome drug resistance and the search for combinational treatments. In addition, conventional biomarkers holding the promises for HCC treatments and novel therapeutic targets from the research field are discussed. Expert opinion : HCC is a molecularly complex disease, with several and distinct pathways playing critical roles in different tumor subtypes. Experimental models recapitulating the features of each tumor subset would be highly beneficial to design novel and more effective therapies against this disease. Furthermore, a deeper understanding of combinatorial drug synergism and the role of the tumor microenvironment in HCC will lead to improved therapeutic outcomes.
Reliable Prediction of the Octanol–Air Partition Ratio

The octanol–air equilibrium partition ratio (KOA) is frequently used to describe the volatility of organic chemicals, whereby n‐octanol serves as a substitute for a variety of organic phases ranging from organic matter in atmospheric particles and soils, to biological tissues such as plant foliage, fat, blood, and milk, and to polymeric sorbents. Because measured KOA values exist for just over 500 compounds, most of which are nonpolar halogenated aromatics, there is a need for tools that can reliably predict this parameter for a wide range of organic molecules, ideally at different temperatures. The ability of five techniques, specifically polyparameter linear free energy relationships (ppLFERs) with either experimental or predicted solute descriptors, EPISuite's KOAWIN, COSMOtherm, and OPERA, to predict the KOA of organic substances, either at 25 °C or at any temperature, was assessed by comparison with all KOA values measured to date. In addition, three different ppLFER equations for KOA were evaluated, and a new modified equation is proposed. A technique's performance was quantified with the mean absolute error (MAE), the root mean square error (RMSE), and the estimated uncertainty of future predicted values, that is, the prediction interval. We also considered each model's applicability domain and accessibility. With an RMSE of 0.37 and a MAE of 0.23 for predictions of log KOA at 25 °C and RMSE of 0.32 and MAE of 0.21 for predictions made at any temperature, the ppLFER equation using experimental solute descriptors predicted the KOA the best. Even if solute descriptors must be predicted in the absence of experimental values, ppLFERs are the preferred method, also because they are easy to use and freely available. Environ Toxicol Chem 2021;40:3166–3180. © 2021 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
Machine learning methods, databases and tools for drug combination prediction

Abstract Combination therapy has shown an obvious efficacy on complex diseases and can greatly reduce the development of drug resistance. However, even with high-throughput screens, experimental methods are insufficient to explore novel drug combinations. In order to reduce the search space of drug combinations, there is an urgent need to develop more efficient computational methods to predict novel drug combinations. In recent decades, more and more machine learning (ML) algorithms have been applied to improve the predictive performance. The object of this study is to introduce and discuss the recent applications of ML methods and the widely used databases in drug combination prediction. In this study, we first describe the concept and controversy of synergism between drug combinations. Then, we investigate various publicly available data resources and tools for prediction tasks. Next, ML methods including classic ML and deep learning methods applied in drug combination prediction are introduced. Finally, we summarize the challenges to ML methods in prediction tasks and provide a discussion on future work.
Low lean mass is associated with lower urinary tract symptoms in US men from the 2005–2006 national health and nutrition examination survey dataset

We investigated the relationship between low lean mass (LLM) and lower urinary tract symptoms (LUTS) using the 2005–2006 National Health and Nutrition Examination Survey (NHANES) dataset. We enrolled 959 men with an average age of 52.08 ± 7.91 years and performed weighted multiple regression analysis to determine the independent relationship between exposure variables (LLM, alternate LLM) and outcomes variables (urinary hesitancy, incomplete emptying, urinary frequency, nocturia, daytime LUTS, clinical LUTS) after adjusting for confounding factors. The prevalence of urinary hesitancy (OR = 7.76, P < 0.0001), incomplete emptying (OR = 2.49, P = 0.0070), urinary frequency (OR = 3.28, P < 0.0001), daytime LUTS (OR = 3.88, P < 0.0001) and clinical LUTS (OR = 8.11, P < 0.0001) was significantly higher among men with LLM compared to men without LLM. Moreover, alternate LLM (ALLM) was positively associated with urinary hesitancy (OR = 17.97, P < 0.0001), incomplete emptying (OR = 4.68, P = 0.0003), daytime LUTS (OR = 2.47, P = 0.0136) and clinical LUTS (OR = 12.18, P < 0.0001). These findings demonstrate that both LLM and ALLM were associated with a higher risk of LUTS in men aged ≥ 40 years, which suggested that early management and treatment of lean mass loss may improve or alleviate LUTS.
An updated overview on the regulatory circuits of polyhydroxyalkanoates synthesis

Polyhydroxyalkanoates (PHA) are a promising and sustainable alternative to the petroleum‐based synthetic plastics. Regulation of PHA synthesis is receiving considerable importance as engineering the regulatory factors might help developing strains with improved PHA‐producing abilities. PHA synthesis is dedicatedly regulated by a number of regulatory networks. They tightly control the PHA content, granule size and their distribution in cells. Most PHA‐accumulating microorganisms have multiple regulatory networks that impart a combined effect on PHA metabolism. Among them, several factors ranging from global to specific regulators, have been identified and characterized till now. This review is an attempt to categorically summarize the diverse regulatory circuits that operate in some important PHA‐producing microorganisms. However, in several organisms, the detailed mechanisms involved in the regulation of PHA synthesis is not well‐explored and hence further research is needed. The information presented in this review might help researcher to identify the prevailing research gaps in PHA regulation.
Hepatocytic Activating Transcription Factor 3 Protects Against Steatohepatitis via Hepatocyte Nuclear Factor 4α

Activating transcription factor 3 (ATF3) has been shown to play an important role in HDL metabolism; yet, the role of hepatocytic ATF3 in the development of steatohepatitis remains elusive. Here we show that adenoassociated virus-mediated overexpression of human ATF3 in hepatocytes prevents diet-induced steatohepatitis in C57BL/6 mice and reverses steatohepatitis in db/db mice. Conversely, global or hepatocyte-specific loss of ATF3 aggravates diet-induced steatohepatitis. Mechanistically, hepatocytic ATF3 induces hepatic lipolysis and fatty acid oxidation and inhibits inflammation and apoptosis. We further show that hepatocyte nuclear factor 4α (HNF4α) is required for ATF3 to improve steatohepatitis. Thus, the current study indicates that ATF3 protects against steatohepatitis through, at least in part, hepatic HNF4α. Targeting hepatic ATF3 may be useful for treatment of steatohepatitis.
Heterosis goes underground

This article comments on: Dafna A, Halperin I, Oren E, Isaacson T, Tzuri G, Meir A, Schaffer AA, Burger J, Tadmor Y, Buckler ES, Gur A. 2021. Underground heterosis for yield improvement in melon. Journal of Experimental Botany 72, 6205–6218.
Explaining Evolutionary Agent-Based Models via Principled Simplification

Understanding how evolutionary agents behave in complex environments is a challenging problem. Agents can be faced with complex fitness landscapes derived from multi-stage tasks, interaction with others, and limited environmental feedback. Agents that evolve to overcome these can sometimes access greater fitness, as a result of factors such as cooperation and tool use. However, it is often difficult to explain why evolutionary agents behave in certain ways, and what specific elements of the environment or task may influence the ability of evolution to find goal-achieving behaviours; even seemingly simple environments or tasks may contain features that affect agent evolution in unexpected ways. We explore principled simplification of evolutionary agent-based models, as a possible route to aiding their explainability. Using the River Crossing Task (RCT) as a case study, we draw on analysis in the Minimal River Crossing (RC-) Task testbed, which was designed to simplify the original task while keeping its key features. Using this method, we present new analysis concerning when agents evolve to successfully complete the RCT. We demonstrate that the RC- environment can be used to understand the effect that a cost to movement has on agent evolution, and that these findings can be generalised back to the original RCT. Then, we present new insight into the use of principled simplification in understanding evolutionary agents. We find evidence that behaviour dependent on features that survive simplification, such as problem structure, are amenable to prediction; while predicting behaviour dependent on features that are typically reduced in simplification, such as scale, can be invalid.