Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of conformational equilibrium by phosphorylation underlies the activation of deubiquitinase A

Deubiquitinases deconjugate ubiquitin modifications from target proteins and are involved in many cellular processes in eukaryotes. The functions of deubiquitinases are regulated by post-translational modifications, mainly phosphorylation and ubiquitination. Post-translational modifications can result in subtle changes in structural and dynamic properties, which are difficult to identify but functionally important. In this work, we used NMR spectroscopy to characterize the conformational properties of the human deubiquitinase A (DUBA), a negative regulator of type I interferon. DUBA activity is regulated by phosphorylation at a single serine residue, Ser-177. We found that the catalytic rate constant of DUBA is enhanced by phosphorylation. By comparing NMR and enzyme kinetics data among different forms of DUBA with low and high activities, we concluded that a two-state equilibrium that was present only in phosphorylated DUBA is important for DUBA activity. Our results highlight the importance of defining conformational dynamics in understanding the mechanism of DUBA activation.
Spatial mapping of tissue properties in vivo reveals a 3D stiffness gradient in the mouse limb bud

Significance Many biological processes are inherently physical in nature. Increasingly, biologists are proposing that the mechanical properties of tissues are critical for processes such as embryonic development and the progression of diseases including cancer and chronic inflammation. However, currently available methods are insufficient to quantitatively test hypotheses that concern the physical properties of living tissues. We introduce a method of three-dimensionally mapping the absolute stiffness and viscosity of tissue in a nontoxic fashion using a multipole magnetic device. By applying our method to the embryonic mouse limb bud, we show how a previously unrecognized distribution of physical properties leads to an important hypothesis, namely that cells move up a stiffness gradient to shape tissue during embryonic development. Numerous hypotheses invoke tissue stiffness as a key parameter that regulates morphogenesis and disease progression. However, current methods are insufficient to test hypotheses that concern physical properties deep in living tissues. Here we introduce, validate, and apply a magnetic device that generates a uniform magnetic field gradient within a space that is sufficient to accommodate an organ-stage mouse embryo under live conditions. The method allows rapid, nontoxic measurement of the three-dimensional (3D) spatial distribution of viscoelastic properties within mesenchyme and epithelia. Using the device, we identify an anteriorly biased mesodermal stiffness gradient along which cells move to shape the early limb bud. The stiffness gradient corresponds to a Wnt5a-dependent domain of fibronectin expression, raising the possibility that durotaxis underlies cell movements. Three-dimensional stiffness mapping enables the generation of hypotheses and potentially the rigorous testing of mechanisms of development and disease.
The grief and communication family support intervention: Intervention fidelity, participant experiences, and potential outcomes

Abstract This study aimed to evaluate intervention fidelity and explore participants’ experiences and potential outcomes after participating in the intervention. Using a pretest post-test pilot study, 10 parentally bereaved families completed the three-session manual-based intervention with a family therapist. Sessions were audio-recorded. Therapists completed an adherence checklist to assess fidelity. Assessments via questionnaires and interviews occurred at one month post-intervention and via questionnaires at baseline and six months post-intervention. This study showed a high level of fidelity. The study shows preliminary evidence of the intervention’s capacity to improve communication and relationships in parentally bereaved families.
Noninvasive muscle activity imaging using magnetography

Significance Historically, the activity of muscle groups has been evaluated indirectly, through strength and range of movement measurements. While direct evaluation of muscle activity has been achieved using surface or invasive electrodes, the latter methodologies are limited to individual muscles. By contrast, magnetic recording of muscle activity, as illustrated here, offers a noninvasive approach to evaluate the activity of large muscle groups. This includes deep structures such as the heart and intraabdominal musculature such as the iliacus muscle. An unexpected finding was the ability to image activity associated with muscle pain. Thus, this method offers a noninvasive biomarker for muscular pain and, significantly, of neck and back pain, which now relies mainly on the patient’s report of signs and symptoms. A spectroscopic paradigm has been developed that allows the magnetic field emissions generated by the electrical activity in the human body to be imaged in real time. The growing significance of imaging modalities in biology is evident by the almost exponential increase of their use in research, from the molecular to the ecological level. The method of analysis described here allows totally noninvasive imaging of muscular activity (heart, somatic musculature). Such imaging can be obtained without additional methodological steps such as the use of contrast media.
Effects of Normobaric Hypoxia on Oxygen Saturation Variability.

Background: The study is the first to evaluate the effects of graded normobaric hypoxia on SpO2 variability in healthy individuals. Materials and Methods: Twelve healthy males (mean [standard deviation] age 22 [4] years) were exposed to four simulated environments (fraction of inspired oxygen [FIO2]: 0.12, 0.145, 0.17, and 0.21) for 45 minutes, in a balanced crossover design. Results: Sample entropy, a tool that quantifies the irregularity of pulse oximetry fluctuations, was used as a measure of SpO2 variability. SpO2 entropy increased as the FIO2 decreased, and there was a strong significant negative correlation between mean SpO2 and its entropy during hypoxic exposure (r = -0.841 to -0.896, p < 0.001). In addition, SpO2 sample entropy, but not mean SpO2, was correlated (r = 0.630-0.760, p < 0.05) with dyspnea in FIO2 0.17, 0.145, and 0.12 and importantly, SpO2 sample entropy at FIO2 0.17 was correlated with dyspnea at FIO2 0.145 (r = 0.811, p < 0.01). Conclusions: These findings suggest that SpO2 variability analysis may have the potential to be used in a clinical setting as a noninvasive measure to identify the negative sequelae of hypoxemia.
The iron–sulfur helicase DDX11 promotes the generation of single-stranded DNA for CHK1 activation

The iron–sulfur cluster helicase DDX11 promotes the generation of ssDNA and the phosphorylation of CHK1 at serine-345, possibly by unwinding replication-dependent DNA secondary structures. The iron–sulfur (FeS) cluster helicase DDX11 is associated with a human disorder termed Warsaw Breakage Syndrome. Interestingly, one disease-associated mutation affects the highly conserved arginine-263 in the FeS cluster-binding motif. Here, we demonstrate that the FeS cluster in DDX11 is required for DNA binding, ATP hydrolysis, and DNA helicase activity, and that arginine-263 affects FeS cluster binding, most likely because of its positive charge. We further show that DDX11 interacts with the replication factors DNA polymerase delta and WDHD1. In vitro, DDX11 can remove DNA obstacles ahead of Pol δ in an ATPase- and FeS domain-dependent manner, and hence generate single-stranded DNA. Accordingly, depletion of DDX11 causes reduced levels of single-stranded DNA, a reduction of chromatin-bound replication protein A, and impaired CHK1 phosphorylation at serine-345. Taken together, we propose that DDX11 plays a role in dismantling secondary structures during DNA replication, thereby promoting CHK1 activation.
Older lesbian and gay men’s perceptions on lesbian and gay youth in Australia

Abstract Older lesbian and gay people are increasingly open about their sexuality but have also experienced a lifetime of discrimination. These groups have experienced a long history of changes to lesbian and gay rights, and many were also at the forefront of activist movements during the latter half of the 20th century. A deeper knowledge is needed of the life experiences of these groups, including how they view their lives in relation to younger lesbian and gay people. This would assist agencies working with older lesbian and gay people, such as health and support services, to provide more informed engagement, support, understanding, and culturally safe services. Drawing on 33 qualitative interviews with older (60+ years) lesbian and gay people, we explored their experiences during their younger years and their perspectives on how these experiences compare with those of younger lesbian and gay people today. Our findings note that older lesbian and gay people feel life is, in some ways, easier, and in others, still challenging for young lesbian and gay people, and they articulate a need for mutual respect across age groups.
Prevalence and Selected Sociodemographic of Movement Behaviors in Schoolchildren from Low- and Middle-Income Families in Nanjing, China: A Cross-Sectional Questionnaire Survey

Background: To investigate the prevalence of meeting the 24-h movement guidelines and its sociodemographic correlates in youth from low- and middle-income families (LMIFs) in Nanjing, China. Methods: Cross-sectional data on moderate to vigorous physical activity (MVPA), screen time (ST), and sleep (SLP) were collected using the Chinese version of Health Behavior School-Aged Children questionnaire among grade schoolchildren of 4th–12th (mean age 13.6 years). The prevalence of meeting the 24-h movement guidelines was in line with the recommendations of the Canadian 24-h movement guidelines. Generalized linear models were used to explore the relationships of correlates with the prevalence of meeting the movement guidelines. Results: The prevalence of meeting the MVPA, ST, and SLP guidelines and their combination was 9.9%, 65.2%, 37.2%, and 2.9%, respectively. As for the prevalence of meeting the MVPA guidelines, boys, younger schoolchildren, and those living in urban areas had a higher chance of meeting them. With regards to the prevalence of meeting the ST guidelines, girls, urban schoolchildren, and the oldest participants were more likely to meet the guidelines. Residential areas and grades were two correlates of meeting the SLP guidelines as well as 24-h movement guidelines. Conclusions: The majority of schoolchildren from LMIFs in Nanjing, China had unhealthy movement behaviors. This concerning situation was mainly predicted by schoolchildren’s grades, indicating older schoolchildren exhibited lower levels of movement behavior. Improved studies are encouraged to identify the correlates of movement behaviors in schoolchildren, which in turn designs and implements effective interventions.
Reduced White Matter Integrity and Deficits in Neuropsychological Functioning in Adults With Autism Spectrum Disorder

Autism spectrum disorder (ASD) is currently viewed as a disorder of cortical systems connectivity, with a heavy emphasis being on the structural integrity of white matter tracts. However, the majority of the literature to date has focused on children with ASD. Understanding the integrity of white matter tracts in adults may help reveal the nature of ASD pathology in adulthood and the potential contributors to cognitive impairment. This study examined white matter water diffusion using diffusion tensor imaging in relation to neuropsychological measures of cognition in a sample of 45 adults with ASD compared to 20 age, gender, and full‐scale‐IQ‐matched healthy volunteers. Tract‐based spatial statistics were used to assess differences in diffusion along white matter tracts between groups using permutation testing. The following neuropsychological measures of cognition were assessed: processing speed, attention vigilance, working memory, verbal learning, visual learning, reasoning and problem solving, and social cognition. Results indicated that fractional anisotropy (FA) was significantly reduced in adults with ASD in the anterior thalamic radiation (P = 0.022) and the right cingulum (P = 0.008). All neuropsychological measures were worse in the ASD group, but none of the measures significantly correlated with reduced FA in either tract in the adults with ASD or in the healthy volunteers. Together, this indicates that the tracts that are the most impacted in autism may not be (at least directly) responsible for the behavioral deficits in ASD. Autism Res 2020, 13: 702–714. © 2020 International Society for Autism Research, Wiley Periodicals, Inc.
miR-1272 Exerts Tumor-Suppressive Functions in Prostate Cancer via HIP1 Suppression

The development of novel therapies or the improvement of currently used approaches to treat prostate cancer (PCa), the most frequently diagnosed male tumor in developed countries, is an urgent need. In this regard, the functional characterization of microRNAs, molecules shown to regulate a number of cancer-related pathways, is instrumental to their possible clinical exploitation. Here, we demonstrate the tumor-suppressive role of the so far uncharacterized miR-1272, which we found to be significantly down-modulated in PCa clinical specimens compared to normal tissues. Through a gain-of-function approach using miRNA mimics, we showed that miR-1272 supplementation in two PCa cell models (DU145 and 22Rv1) reverted the mesenchymal phenotype by affecting migratory and invasive properties, and reduced cell growth in vitro and in vivo in SCID mice. Additionally, by targeting HIP1 encoding the endocytic protein HIP1, miR-1272 balanced EGFR membrane turnover, thus affecting the downstream AKT/ERK pathways, and, ultimately, increasing PCa cell response to ionizing radiation. Overall, our results show that miR-1272 reconstitution can affect several tumor traits, thus suggesting this approach as a potential novel therapeutic strategy to be pursued for PCa, with the multiple aim of reducing tumor growth, enhancing response to radiotherapy and limiting metastatic dissemination.
What Do Theory-of-Mind Tasks Actually Measure? Theory and Practice

In recent decades, the ability to represent others’ mental states (i.e., theory of mind) has gained particular attention in various disciplines ranging from ethology to cognitive neuroscience. Despite the exponentially growing interest, the functional architecture of social cognition is still unclear. In the present review, we argue that not only the vocabulary but also most of the classic measures for theory of mind lack specificity. We examined classic tests used to assess theory of mind and noted that the majority of them do not require the participant to represent another’s mental state or, sometimes, any mental state at all. Our review reveals that numerous classic tests measure lower-level processes that do not directly test for theory of mind. We propose that more attention should be paid to methods used in this field of social cognition to improve the understanding of underlying concepts.
Role of Arginine 214 in the Substrate Specificity of OXA-48

Increasing numbers of variants of the carbapenem-hydrolyzing class D β-lactamase OXA-48 are identified in Enterobacterales worldwide. Among them, OXA-181 and OXA-232 are of particular interest, as they differ from each other by a single amino acid substitution at position 214 (R in OXA-181 and S in OXA-232) that results in reduced carbapenem-hydrolyzing activity for OXA-232. To investigate the role of amino acid position 214 (AA214), the X-ray structure of OXA-232 was determined and AA214 of OXA-48 and of OXA-232 was replaced by G, L, D, E, S, R, and K using site-directed mutagenesis. ABSTRACT Increasing numbers of variants of the carbapenem-hydrolyzing class D β-lactamase OXA-48 are identified in Enterobacterales worldwide. Among them, OXA-181 and OXA-232 are of particular interest, as they differ from each other by a single amino acid substitution at position 214 (R in OXA-181 and S in OXA-232) that results in reduced carbapenem-hydrolyzing activity for OXA-232. To investigate the role of amino acid position 214 (AA214), the X-ray structure of OXA-232 was determined and AA214 of OXA-48 and of OXA-232 was replaced by G, L, D, E, S, R, and K using site-directed mutagenesis. These mutants were phenotypically characterized, and three mutants of OXA-232 were purified to study their steady-state kinetic properties. The X-ray structure of OXA-232 along with molecular modeling studies showed that the interaction via a salt bridge between R214 and D159 in OXA-48 is not possible with the G214 or S214 mutation. In contrast, with K214, which is also positively charged, the interaction with D159 is maintained. With the E214 mutant, an alternative binding conformation of imipenem that is not compatible with a nucleophilic attack by S70 was evidenced. Thus, imipenem has a very poor apparent affinity for the E214 mutant because of its nonproductive binding mode. Similarly, we could explain the lack of temocillin hydrolysis by the OXA-232-S214E mutant, which is due to the unfavorable interaction between the negatively charged R1 substituent of temocillin with the E214 residue. Overall, we demonstrate that AA214 in OXA-48-like β-lactamases is critical for the carbapenemase activity.
MicroRNA 122 Reflects Liver Injury in Children with Intestinal Failure-Associated Liver Disease Treated with Intravenous Fish Oil.

BACKGROUND There is evidence that microRNA (MIR) 122 is a biomarker for various liver diseases in adults and children. To date, MIR122 has not been explored in children with intestinal failure-associated liver disease (IFALD, or hyperbilirubinemia associated with prolonged parenteral nutrition). OBJECTIVES This study's purpose was to investigate changes in plasma miR-122, correlate miR-122 with serum liver function tests and enzymes, and investigate changes in whole blood transcripts including miR-122 targets in a group of children with IFALD who received pure intravenous fish oil (FO) as a treatment for cholestasis. METHODS This was a prospective, observational study that enrolled children with IFALD who received intravenous FO (1 g/kg/d) and whose cholestasis resolved with FO. Plasma miR-122 was measured using reverse transcription-quantitative real-time PCR, and whole blood miR-122 targets were quantified using RNA sequencing. RESULTS Fourteen subjects with median age 6 mo (IQR: 3-65 mo) were enrolled. RNA sequence data were available for 4 subjects. When compared with the start of FO, median miR-122 concentrations at 6 mo of FO therapy decreased [1.0 (IQR: 1.0-1.0) compared with 0.04 (IQR: 0.01-0.6), P = 0.009]. At the start of FO, miR-122 correlated with conjugated bilirubin (r = 0.56; P = 0.038). At ∼3 mo of FO, miR-122 correlated with conjugated bilirubin (r = 0.56; P = 0.045). Reactive oxygen species, heme metabolism, coagulation, adipogenesis, IL-6-Janus kinase-signal transducer and activator of transcription (JAK-STAT) 3, IL-2-STAT5, transforming growth factor-β, TNF-α, inflammatory response, mammalian target of rapamycin gene families (normalized enrichment scores < -1.4), and miR-122 target genes were significantly downregulated with FO. CONCLUSIONS In this small cohort of young children with IFALD, miR-122 decreased with FO therapy and correlated with conjugated bilirubin. Key pathways involving oxidation, inflammation, cellular differentiation, and nutrient regulation were downregulated. Data from this study provide information about IFALD and FO. This trial was registered at www.clinicaltrials. gov as NCT00969332.
ONE-HELIX PROTEIN1 and 2 Form Heterodimers to Bind Chlorophyll in Photosystem II Biogenesis1[OPEN]

Chlorophyll binding to the ONE-HELIX PROTEINS1/2 depends on heterodimer formation, mediated by conserved amino acids in their chlorophyll-binding motifs, and is essential for PSII biogenesis. Members of the light-harvesting complex protein family participate in multiple processes connected with light sensing, light absorption, and pigment binding within the thylakoid membrane. Amino acid residues of the light-harvesting chlorophyll a/b-binding proteins involved in pigment binding have been precisely identified through x-ray crystallography experiments. In vitro pigment-binding studies have been performed with LIGHT-HARVESTING-LIKE3 proteins, and the pigment-binding ability of cyanobacterial high-light-inducible proteins has been studied in detail. However, analysis of pigment binding by plant high-light-inducible protein homologs, called ONE-HELIX PROTEINS (OHPs), is lacking. Here, we report on successful in vitro reconstitution of Arabidopsis (Arabidopsis thaliana) OHPs with chlorophylls and carotenoids and show that pigment binding depends on the formation of OHP1/OHP2 heterodimers. Pigment-binding capacity was completely lost in each of the OHPs when residues of the light-harvesting complex chlorophyll-binding motif required for chlorophyll binding were mutated. Moreover, the mutated OHP variants failed to rescue the respective knockout (T-DNA insertion) mutants, indicating that pigment-binding ability is essential for OHP function in vivo. The scaffold protein HIGH CHLOROPHYLL FLUORESCENCE244 (HCF244) is tethered to the thylakoid membrane by the OHP heterodimer. We show that HCF244 stability depends on OHP heterodimer formation and introduce the concept of a functional unit consisting of OHP1, OHP2, and HCF244, in which each protein requires the others. Because of their pigment-binding capacity, we suggest that OHPs function in the delivery of pigments to the D1 subunit of PSII.
Contribution to ellipsoidal and zonotopic set-membership state estimation. (Contribution à l'estimation d'état par méthodes ensemblistes ellipsoidales et zonotopiques)

Dans le contexte des systemes dynamiques, cette these developpe des techniques d'estimation d'etat ensemblistes pour differentes classes de systemes. On considere pour cela le cas d'un systeme standard lineaire invariant dans le temps soumis a des perturbations, des bruits de mesure et des incertitudes inconnus, mais bornes. Dans une premiere etape, une technique d'estimation d'etat ellipsoidale est etendue, puis appliquee sur un modele d'octorotor utilise dans un contexte radar. Une extension de cette approche ellipsoidale d'estimation d'etat est proposee pour des systemes descripteurs. Dans la deuxieme partie, nous proposons une methode fondee sur la minimisation du P-rayon d'un zonotope, appliquee a un modele d'octorotor. Cette methode est ensuite etendue pour traiter les systemes affines par morceaux. Dans la continuite des approches precedentes, un nouveau filtre de Kalman sous contraintes zonotopiques est propose dans la derniere partie de cette these. En utilisant la forme duale d'un probleme d'optimisation, l'algorithme projette l'etat sur un zonotope qui forme l'enveloppe de l'ensemble des contraintes auxquelles l'etat est soumis. La complexite de l'algorithme est ensuite amelioree en remplacant le zonotope initial par une forme reduite en limitant son nombre de generateurs.