Miracle-dz/UniFAR-FTUs huggingface dataset:
Feedback inhibition derived from the posterior parietal cortex regulates the neural properties of the mouse visual cortex

Feedback regulation from the higher association areas is thought to control the primary sensory cortex, contribute to the cortical processing of sensory information, and work for higher cognitive functions such as multimodal integration and attentional control. However, little is known about the underlying neural mechanisms. Here, we show that the posterior parietal cortex (PPC) persistently inhibits the activity of the primary visual cortex (V1) in mice. Activation of the PPC causes the suppression of visual responses in V1 and induces the short‐term depression, which is specific to visual stimuli. In contrast, pharmacological inactivation of the PPC or disconnection of cortical pathways from the PPC to V1 results in an effect of transient enhancement of visual responses in V1. Two‐photon calcium imaging demonstrated that the cortical disconnection caused V1 excitatory neurons an enhancement of visual responses and a reduction of orientation selectivity index (OSI). These results show that the PPC regulates the response properties of V1 excitatory neurons. Our findings reveal one of the functions of the PPC, which may contribute to higher brain functions in mice.
A simple method to estimate noise levels in the workplace based on self-reported speech communication effort in noise

Abstract Objective: To validate a method using self-reported speech communication effort in noise to estimate occupational noise levels by comparing with measured noise levels. Design: A comparative observational study. Reported vocal effort to communicate with a person at a distance of 1.2 m during workplace-related tasks was used to provide an estimate of noise levels in the workplace. These estimated noise levels were compared against noise level measurements obtained using personal noise dosimetry badges for corresponding tasks undertaken by participants. Study sample: Participants (n = 168) aged 16–25 years were recruited from companies where workplace noise levels were at least 85 dB(A). Results: Estimated noise levels using speech communication ability were evenly distributed above and below the measured noise levels (n = 134), indicating a lack of systematic bias in the method. For 91% of participants, estimates of noise levels using speech communication were within ±6 dB of the measured levels, whilst 56% were within ±3 dB. Conclusions: Report of speech communication effort required in noise by employees is an effective method of estimating noise levels within the workplace. This can be used for retrospective noise level assessment where there are no recorded noise level measurements, such as for retrospective research studies or in medicolegal work.
Functional assessment of hydrophilic domains of late embryogenesis abundant proteins from distant organisms

Late embryogenesis abundant (LEA) proteins play a protective role during desiccation and oxidation stresses. LEA3 proteins are a major group characterized by a hydrophilic domain (HD) with a highly conserved repeating 11‐amino acid motif. We compared four different HD orthologs from distant organisms: (i) DrHD from the extremophilic bacterium Deinococcus radiodurans; (ii) CeHD from the nematode Caenorhabditis elegans; (iii) YlHD from the yeast Yarrowia lipolytica; and (iv) BnHD from the plant Brassica napus. Circular dichroism spectroscopy showed that all four HDs were intrinsically disordered in phosphate buffer and then folded into α‐helical structures with the addition of glycerol or trifluoroethanol. Heterologous HD expression conferred enhanced desiccation and oxidation tolerance to Escherichia coli. These four HDs protected the enzymatic activities of lactate dehydrogenase (LDH) by preventing its aggregation under desiccation stress. The HDs also interacted with LDH, which was intensified by the addition of hydrogen peroxide (H2O2), suggesting a protective role in a chaperone‐like manner. Based on these results, the HDs of LEA3 proteins show promise as protectants for desiccation and oxidation stresses, especially DrHD, which is a potential ideal stress‐response element that can be applied in synthetic biology due to its extraordinary protection and stress resistance ability.
MicroRNA-deficient mouse embryonic stem cells acquire a functional interferon response

When mammalian cells detect a viral infection, they initiate a type I interferon (IFNs) response as part of their innate immune system. This antiviral mechanism is conserved in virtually all cell types, except for embryonic stem cells (ESCs) and oocytes which are intrinsically incapable of producing IFNs. Despite the importance of the IFN response to fight viral infections, the mechanisms regulating this pathway during pluripotency are still unknown. Here we show that, in the absence of miRNAs, ESCs acquire an active IFN response. Proteomic analysis identified MAVS, a central component of the IFN pathway, to be actively silenced by miRNAs and responsible for suppressing IFN expression in ESCs. Furthermore, we show that knocking out a single miRNA, miR-673, restores the antiviral response in ESCs through MAVS regulation. Our findings suggest that the interaction between miR-673 and MAVS acts as a switch to suppress the antiviral IFN during pluripotency and present genetic approaches to enhance their antiviral immunity.
MicroRNA-31 Negatively Regulates Interleukin-34 Expression In Vitro

ABSTRACT Interleukin-34 (IL-34) is a recently discovered cytokine that promotes tissue macrophage maturation and differentiation. We previously found that 1α,25-Dihydroxyvitamin D3 up-regulated IL-34 expression in SH-SY5Y neural cells. However, whether microRNA regulates IL-34 expression is not completely clear. By using on-line TargetScan and MiRanda software, we found that there was only one conserved microRNA-31 (miR-31) binding site in the 3ʹ untranslated region (3ʹUTR) of IL-34 mRNA. Intriguingly, using qPCR we demonstrated that miR-31 levels were negatively correlated to IL-34 mRNA levels in different cell lines. By examining the effect of miR-31 on IL-34 3ʹ UTR reporter luciferase activity and on IL-34 mRNA and argonaute RISC catalytic component 2 (AGO2) binding, it was found that miR-31 bound directly to IL-34 3ʹUTR and regulated the post-transcriptional expression of IL-34 in MGC-803 cells. Moreover, a miR-31 mimic significantly reduced IL-34 expression levels while a miR-31 inhibitor up-regulated IL-34 expression in KYSE-45 and HT-29 cells. Taken together, these results show that miR-31 negatively regulates IL-34 expression by directly binding to the IL-34 3ʹ UTR in vitro.
Stochastic Primal-Dual Algorithms with Faster Convergence than O(1/√T) for Problems without Bilinear Structure

Previous studies on stochastic primal-dual algorithms for solving min-max problems with faster convergence heavily rely on the bilinear structure of the problem, which restricts their applicability to a narrowed range of problems. The main contribution of this paper is the design and analysis of new stochastic primal-dual algorithms that use a mixture of stochastic gradient updates and a logarithmic number of deterministic dual updates for solving a family of convex-concave problems with no bilinear structure assumed. Faster convergence rates than $O(1/\sqrt{T})$ with $T$ being the number of stochastic gradient updates are established under some mild conditions of involved functions on the primal and the dual variable. For example, for a family of problems that enjoy a weak strong convexity in terms of the primal variable and has a strongly concave function of the dual variable, the convergence rate of the proposed algorithm is $O(1/T)$. We also investigate the effectiveness of the proposed algorithms for learning robust models and empirical AUC maximization.
A murine model of the effects of inhaled CuO nanoparticles on cells of innate and adaptive immunity – a kinetic study of a continuous three-month exposure

Abstract The inhalation or application of nanoparticles (NPs) has serious impacts on immunological reactivity. However, the effects of NPs on the immune system are influenced by numerous factors, which cause a high variability in the results. Here, mice were exposed to a three month continuous inhalation of copper oxide (CuO) NPs, and at different time intervals (3, 14, 42 and 93 days), the composition of cell populations of innate and adaptive immunity was evaluated in the spleen by flow cytometry. The ability of spleen cells from exposed and control mice to respond to stimulation with T- or B-cell mitogens by proliferation and by production of cytokines IL-2, IL-6, IL-10, IL-17 and IFN-γ was characterized. The results showed that the inhalation of CuO NPs predominantly affects the cells of innate immunity (changes in the proportion of eosinophils, neutrophils, macrophages and antigen-presenting cells) with a minimal effect on the percentage of T and B lymphocytes. However, the proliferative and secretory activity of T cells was already significantly enhanced after 3 days from the start of inhalation, decreased on day 14 and normalized at the later time intervals. There was no correlation between the impacts of NPs on the cells of innate and adaptive immunity. The results have shown that the inhalation of CuO NPs significantly alters the composition of cell populations of innate immunity and modulates the proliferation and production of cytokines by cells of the adaptive immune system. However, the immunomodulatory effects of inhaled NPs strongly depend on the time of inhalation.
The Potential of Game-Based Digital Biomarkers for Modeling Mental Health

Background Assessment for mental health is performed by experts using interview techniques, questionnaires, and test batteries and following standardized manuals; however, there would be myriad benefits if behavioral correlates could predict mental health and be used for population screening or prevalence estimations. A variety of digital sources of data (eg, online search data and social media posts) have been previously proposed as candidates for digital biomarkers in the context of mental health. Playing games on computers, gaming consoles, or mobile devices (ie, digital gaming) has become a leading leisure activity of choice and yields rich data from a variety of sources. Objective In this paper, we argue that game-based data from commercial off-the-shelf games have the potential to be used as a digital biomarker to assess and model mental health and health decline. Although there is great potential in games developed specifically for mental health assessment (eg, Sea Hero Quest), we focus on data gathered “in-the-wild” from playing commercial off-the-shelf games designed primarily for entertainment. Methods We argue that the activity traces left behind by natural interactions with digital games can be modeled using computational approaches for big data. To support our argument, we present an investigation of existing data sources, a categorization of observable traits from game data, and examples of potentially useful game-based digital biomarkers derived from activity traces. Results Our investigation reveals different types of data that are generated from play and the sources from which these data can be accessed. Based on these insights, we describe five categories of digital biomarkers that can be derived from game-based data, including behavior, cognitive performance, motor performance, social behavior, and affect. For each type of biomarker, we describe the data type, the game-based sources from which it can be derived, its importance for mental health modeling, and any existing statistical associations with mental health that have been demonstrated in prior work. We end with a discussion on the limitations and potential of data from commercial off-the-shelf games for use as a digital biomarker of mental health. Conclusions When people play commercial digital games, they produce significant volumes of high-resolution data that are not only related to play frequency, but also include performance data reflecting low-level cognitive and motor processing; text-based data that are indicative of the affective state; social data that reveal networks of relationships; content choice data that imply preferred genres; and contextual data that divulge where, when, and with whom the players are playing. These data provide a source for digital biomarkers that may indicate mental health. Produced by engaged human behavior, game data have the potential to be leveraged for population screening or prevalence estimations, leading to at-scale, nonintrusive assessment of mental health.
Sleep disturbances in ankylosing spondylitis: a systematic review and meta-analysis

ABSTRACT The aim of this meta-analysis was to compare sleep outcomes of AS patients and controls. Six electronic databases were searched: PubMed, Embase, IndMed, Cochrane Library, CNKI and Web of Science. Statistical analyses were executed using Revman 5.3 software. Nine studies and a total of 3169 participants were included in the meta-analysis. When sleep was assessed using PSQI, significant differences were observed in subjective sleep quality, sleep latency, sleep efficiency, sleep disorders, sleep medication use and total PSQI between patients with AS and controls, and subjective sleep quality was most severely aﬀected. In PSG, eight variables of sleep quality (stage I sleep, stage II sleep, slow wave sleep, rapid eye movement, arousal index, periodic leg movement index, sleep latency, sleep efficiency) were lower in AS patients than in controls. Three variables of sleep quality assessed by USI (estimated sleep time, sleep sufficiency index, number of awakenings per night) and two variables of sleep quality assessed by MOS sleep scale (sleep disturbance scale, sleep problem index II) were lower in AS patients than in controls. It indicated that AS patients experience more serious sleep disorders. Early recognition and appropriate interventions are essential to improve patients’ sleep quality.
Non-overlapping and Inverse Associations Between the Sexes in Structural Brain-Trait Associations

Personality reflects the set of psychological traits and mechanisms characteristic for an individual. The brain-trait association between personality and gray matter volume (GMv) has been well studied. However, a recent study has shown that brain structure-personality relationships are highly dependent on sex. In addition, the present study investigates the role of sex on the association between temperaments and regional GMv. Sixty-six participants (33 male) completed the Temperament and Character Inventory (TCI) and underwent structural magnetic resonance brain imaging. Mann-Whitney U tests showed a significant higher score on Novelty Seeking (NS) and Reward Dependence (RD) for females, but no significant group effects were found for Harm Avoidance (HA) and Persistence (P) score. Full factor model analyses were performed to investigate sex-temperament interaction effects on GMv. This revealed increased GMv for females in the superior temporal gyrus when linked to NS, middle temporal gyrus for HA, and the insula for RD. Males displayed increased GMv compared to females relating to P in the posterior cingulate gyrus, the medial superior frontal gyrus, and the middle cingulate gyrus, compared to females. Multiple regression analysis showed clear differences between the brain regions that correlate with female subjects and the brain correlates that correlate with male subjects. No overlap was observed between sex-specific brain-trait associations. These results increase the knowledge of the role of sex on the structural neurobiology of personality and indicate that sex differences reflect structural differences observed in the normal brain. Furthermore, sex hormones seem an important underlying factor for the found sex differences in brain-trait associations. The present study indicates an important role for sex in these brain structure-personality relationships, and implies that sex should not just be added as a covariate of no interest.
A Novel Homozygous Non-sense Mutation in the Catalytic Domain of MTHFR Causes Severe 5,10-Methylenetetrahydrofolate Reductase Deficiency

Background: Severe 5,10-methylenetetrahydrofolate reductase (MTHFR) deficiency is a heterogeneous metabolic disorder inherited in an autosomal recessive manner. Pathogenic mutations in MTHFR gene have been associated with severe MTHFR deficiency. The clinical presentation of MTHFR deficiency is highly variable and associated with several neurological anomalies. Methods: Direct whole-exome sequencing (WES) was performed in all the five available individuals from the family, including the affected individual (III-7) using standard procedures. Results: We observed a proband (III-7) with an abnormality in the cerebral white matter, apnoea, and microcephaly. WES analysis identified a novel homozygous non-sense mutation (c.154C>T; p.Arg52*) in MTHFR gene that segregated with the disease phenotype within the family. Conclusion: We identified a novel non-sense mutation in MTHFR gene in a single Egyptian family with severe MTHFR deficiency. The present investigation is clinically important, as it adds to the growing list of MTHFR mutations, which might help in genetic counseling of families of affected children and proper genotype-phenotype correlation.
Optimizing Search API Queries for Twitter Topic Classifiers Using a Maximum Set Coverage Approach

Twitter has grown to become an important platform to access immediate information about major events and dynamic topics. As one example, recent work has shown that classifiers trained to detect topical content on Twitter can generalize well beyond the training data. Since access to Twitter data is hidden behind a limited search API, it is impossible (for most users) to apply these classifiers directly to the Twitter unfiltered data streams ("firehose"). Rather, applications must first decide what content to retrieve through the search API before filtering that content with topical classifiers. Thus, it is critically important to query the Twitter API relative to the intended topical classifier in a way that minimizes the amount of negatively classified data retrieved. In this paper, we propose a sequence of query optimization methods that generalize notions of the maximum coverage problem to find the subset of query terms within the API limits that cover most of the topically relevant tweets without sacrificing precision. We evaluate the proposed methods on a large dataset of Twitter data collected during 2013 and 2014 labeled using manually curated hashtags for eight topics. Among many insights, our analysis shows that the best of the proposed methods can significantly outperform the firehose on precision and F1-score while achieving high recall within strict API limitations.
Exposure to Insecticides Reduces Populations of Rhynchophorus palmarum in Oil Palm Plantations with Bud Rot Disease

The South American palm weevil (SAPW), Rhynchophorus palmarum Linnaeus (Coleoptera: Curculionidae) is the main pest of Elaeis guineensis and damages palm trees with bud rot disease in the Americas. The effects of six neurotoxic insecticides (abamectin, carbaryl, deltamethrin, fipronil, imidacloprid and spinosad) were evaluated against SAPW for toxicity, survival, reproduction, and mortality. Abamectin (LC50 = 0.33 mg mL−1), Carbaryl (LC50 = 0.24 mg mL−1), deltamethrin (LC50 = 0.17 mg mL−1), and fipronil (LC50 = 0.42 mg mL−1) were the most toxic to SAPW. Adult survival was 95% without exposure to insecticides, decreasing to 78–65% in insects treated with the LC25 and 49–35% in insects exposed to LC50. Sublethal doses of carbaryl, fipronil and imidacloprid showed significant effect on the reproduction of this insect. Mortality of SAPW populations caused by insecticides had similar effects in the laboratory and field conditions. The results suggest that carbaryl, deltamethrin, fipronil, and imidacloprid caused significantly higher mortality as compared to the control in SAPW and may be used to control its populations in oil palm trees where bud rot appears as the key disease for SAPW attraction and infestation.
Effect of Electrospun Fiber Mat Thickness and Support Method on Cell Morphology

Electrospun fiber mats (EFMs) are highly versatile biomaterials used in a myriad of biomedical applications. Whereas some facets of EFMs are well studied and can be highly tuned (e.g., pore size, fiber diameter, etc.), other features are under characterized. For example, although substrate mechanics have been explored by several groups, most studies rely on Young’s modulus alone as a characterization variable. The influence of fiber mat thickness and the effect of supports are variables that are often not considered when evaluating cell-mechanical response. To assay the role of these features in EFM scaffold design and to improve understanding of scaffold mechanical properties, we designed EFM scaffolds with varying thickness (50–200 µm) and supporting methodologies. EFM scaffolds were comprised of polycaprolactone and were either electrospun directly onto a support, suspended across an annulus (3 or 10 mm inner diameter), or “tension-released” and then suspended across an annulus. Then, single cell spreading (i.e., Feret diameter) was measured in the presence of these different features. Cells were sensitive to EFM thickness and suspended gap diameter. Overall, cell spreading was greatest for 50 µm thick EFMs suspended over a 3 mm gap, which was the smallest thickness and gap investigated. These results are counterintuitive to conventional understanding in mechanobiology, which suggests that stiffer materials, such as thicker, supported EFMs, should elicit greater cell polarization. Additional experiments with 50 µm thick EFMs on polystyrene and polydimethylsiloxane (PDMS) supports demonstrated that cells can “feel” the support underlying the EFM if it is rigid, similar to previous results in hydrogels. These results also suggest that EFM curvature may play a role in cell response, separate from Young’s modulus, possibly because of internal tension generated. These parameters are not often considered in EFM design and could improve scaffold performance and ultimately patient outcomes.