bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parental Involvement and Executive Function in Emerging Adults with Type 1 Diabetes
Authors: Berg Cynthia A , Wiebe Deborah J , Lee Tracy Eunjin , Kelly Caitlin S , Mello Daniel , Turner Sara L , Butner Jonathan E , Munion Ascher K , Mansfield Jessica H , White Perrin C , Murray Mary , Suchy Yana 
Published: April 2019

Abstract

Objective
To examine (a) changes in parental involvement across early emerging adulthood, (b) whether yearly fluctuations in parental involvement were associated with adherence and glycated hemoglobin (HbA1c) over time, and (c) whether higher involvement was more beneficial for those with poorer executive function (EF).

Methods
A total of 228 high school seniors (M age = 17.76) with type 1 diabetes reported on mothers’ and fathers’ acceptance, knowledge of diabetes activities, disclosure to mothers and fathers regarding diabetes, and adherence at four yearly time points. At baseline, participants completed performance-based measures of EF. HbA1c was collected from assay kits.

Results
Growth curve models revealed significant declines in disclosure to fathers and mothers’ and fathers’ knowledge of diabetes activities; no changes were found in mothers’ or fathers’ acceptance nor disclosure to mothers. Multilevel models indicated significant between-person effects for nearly all aspects of parental involvement with more acceptance, knowledge, and disclosure associated with better HbA1c and adherence. Within-person effects for disclosure to fathers, and mothers’ and fathers’ knowledge indicated that in years when emerging adults perceived higher amounts of these types of involvement (compared with their own average), HbA1c was lower. Within-person effects were found for acceptance to mothers, disclosure to mothers and fathers, and mothers’ diabetes knowledge for adherence. Disclosure to fathers and mothers’ knowledge of diabetes activities were especially beneficial for HbA1c for those with poorer EF performance.

Conclusions
Parental involvement in diabetes management remains important during the high-risk time of emerging adulthood, especially for those with poorer EF.
Gravity sensing and signal conversion in plant gravitropism
Authors: Nakamura Moritaka , Nishimura Takeshi , Morita Miyo Terao 
Published: April 2019

AbstractPlant organs control their growth orientation in response to gravity. Within gravity-sensing cells, the input (gravity sensing) and signal conversion (gravity signalling) progress sequentially. The cells contain a number of high-density, starch-accumulating amyloplasts, which sense gravity when they reposition themselves by sedimentation to the bottom of the cell when the plant organ is re-orientated. This triggers the next step of gravity signalling, when the physical signal generated by the sedimentation of the amyloplasts is converted into a biochemical signal, which redirects auxin transport towards the lower flank of the plant organ. This review focuses on recent advances in our knowledge of the regulatory mechanisms that underlie amyloplast sedimentation and the system by which this is perceived, and on recent progress in characterising the factors that play significant roles in gravity signalling by which the sedimentation is linked to the regulation of directional auxin transport. Finally, we discuss the contribution of gravity signalling factors to the mechanisms that control the gravitropic set-point angle.
Plastoglobular protein 18 is involved in chloroplast function and thylakoid formation
Authors: Espinoza-Corral Roberto , Heinz Steffen , Klingl Andreas , Jahns Peter , Lehmann Martin , Meurer Jörg , Nickelsen Jörg , Soll Jürgen , Schwenkert Serena 
Published: April 2019

Abstract
Plastoglobules are lipoprotein particles that are found in different types of plastids. They contain a very specific and specialized set of lipids and proteins. Plastoglobules are highly dynamic in size and shape, and are therefore thought to participate in adaptation processes during either abiotic or biotic stresses or transitions between developmental stages. They are suggested to function in thylakoid biogenesis, isoprenoid metabolism, and chlorophyll degradation. While several plastoglobular proteins contain identifiable domains, others provide no structural clues to their function. In this study, we investigate the role of plastoglobular protein 18 (PG18), which is conserved from cyanobacteria to higher plants. Analysis of a PG18 loss-of-function mutant in Arabidopsis thaliana demonstrated that PG18 plays an important role in thylakoid formation; the loss of PG18 results in impaired accumulation, assembly, and function of thylakoid membrane complexes. Interestingly, the mutant accumulated less chlorophyll and carotenoids, whereas xanthophyll cycle pigments were increased. Accumulation of photosynthetic complexes is similarly affected in both a Synechocystis and an Arabidopsis PG18 mutant. However, the ultrastructure of cyanobacterial thylakoids is not compromised by the lack of PG18, probably due to its less complex architecture.
Learning from Conditionals
Authors: Eva Benjamin , Hartmann Stephan , Rad Soroush Rafiee 
Published: April 2019

AbstractIn this article, we address a major outstanding question of probabilistic Bayesian epistemology: how should a rational Bayesian agent update their beliefs upon learning an indicative conditional? A number of authors have recently contended that this question is fundamentally underdetermined by Bayesian norms, and hence that there is no single update procedure that rational agents are obliged to follow upon learning an indicative conditional. Here we resist this trend and argue that a core set of widely accepted Bayesian norms is sufficient to identify a normatively privileged updating procedure for this kind of learning. Along the way, we justify a privileged formalization of the notion of ‘epistemic conservativity’, offer a new analysis of the Judy Benjamin problem, and emphasize the distinction between interpreting the content of new evidence and updating one’s beliefs on the basis of that content.
Inference of Ancient Whole-Genome Duplications and the Evolution of Gene Duplication and Loss Rates
Authors: Zwaenepoel Arthur , Van de Peer Yves 
Published: April 2019

Abstract
Gene tree–species tree reconciliation methods have been employed for studying ancient whole-genome duplication (WGD) events across the eukaryotic tree of life. Most approaches have relied on using maximum likelihood trees and the maximum parsimony reconciliation thereof to count duplication events on specific branches of interest in a reference species tree. Such approaches do not account for uncertainty in the gene tree and reconciliation, or do so only heuristically. The effects of these simplifications on the inference of ancient WGDs are unclear. In particular, the effects of variation in gene duplication and loss rates across the species tree have not been considered. Here, we developed a full probabilistic approach for phylogenomic reconciliation-based WGD inference, accounting for both gene tree and reconciliation uncertainty using a method based on the principle of amalgamated likelihood estimation. The model and methods are implemented in a maximum likelihood and Bayesian setting and account for variation of duplication and loss rates across the species tree, using methods inspired by phylogenetic divergence time estimation. We applied our newly developed framework to ancient WGDs in land plants and investigated the effects of duplication and loss rate variation on reconciliation and gene count based assessment of these earlier proposed WGDs.
A screening platform to monitor RNA processing and protein-RNA interactions in ribonuclease P uncovers a small molecule inhibitor
Authors: Madrigal-Carrillo Ezequiel-Alejandro , Díaz-Tufinio Carlos-Alejandro , Santamaría-Suárez Hugo-Aníbal , Arciniega Marcelino , Torres-Larios Alfredo 
Published: April 2019

AbstractRibonucleoprotein (RNP) complexes and RNA-processing enzymes are attractive targets for antibiotic development owing to their central roles in microbial physiology. For many of these complexes, comprehensive strategies to identify inhibitors are either lacking or suffer from substantial technical limitations. Here, we describe an activity-binding-structure platform for bacterial ribonuclease P (RNase P), an essential RNP ribozyme involved in 5′ tRNA processing. A novel, real-time fluorescence-based assay was used to monitor RNase P activity and rapidly identify inhibitors using a mini-helix and a pre-tRNA-like bipartite substrate. Using the mini-helix substrate, we screened a library comprising 2560 compounds. Initial hits were then validated using pre-tRNA and the pre-tRNA-like substrate, which ultimately verified four compounds as inhibitors. Biolayer interferometry-based binding assays and molecular dynamics simulations were then used to characterize the interactions between each validated inhibitor and the P protein, P RNA and pre-tRNA. X-ray crystallographic studies subsequently elucidated the structure of the P protein bound to the most promising hit, purpurin, and revealed how this inhibitor adversely affects tRNA 5′ leader binding. This integrated platform affords improved structure-function studies of RNA processing enzymes and facilitates the discovery of novel regulators or inhibitors.
GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure
Authors: Lee Gyu Rie , Won Jonghun , Heo Lim , Seok Chaok 
Published: April 2019

Abstract
The 3D structure of a protein can be predicted from its amino acid sequence with high accuracy for a large fraction of cases because of the availability of large quantities of experimental data and the advance of computational algorithms. Recently, deep learning methods exploiting the coevolution information obtained by comparing related protein sequences have been successfully used to generate highly accurate model structures even in the absence of template structure information. However, structures predicted based on either template structures or related sequences require further improvement in regions for which information is missing. Refining a predicted protein structure with insufficient information on certain regions is critical because these regions may be connected to functional specificity that is not conserved among related proteins. The GalaxyRefine2 web server, freely available via http://galaxy.seoklab.org/refine2, is an upgraded version of the GalaxyRefine protein structure refinement server and reflects recent developments successfully tested through CASP blind prediction experiments. This method adopts an iterative optimization approach involving various structure move sets to refine both local and global structures. The estimation of local error and hybridization of available homolog structures are also employed for effective conformation search.
Structural basis for the function of SuhB as a transcription factor in ribosomal RNA synthesis
Authors: Huang Yong-Heng , Said Nelly , Loll Bernhard , Wahl Markus C 
Published: April 2019

AbstractRibosomal RNA synthesis in Escherichia coli involves a transcription complex, in which RNA polymerase is modified by a signal element on the transcript, Nus factors A, B, E and G, ribosomal protein S4 and inositol mono-phosphatase SuhB. This complex is resistant to ρ-dependent termination and facilitates ribosomal RNA folding, maturation and subunit assembly. The functional contributions of SuhB and their structural bases are presently unclear. We show that SuhB directly binds the RNA signal element and the C-terminal AR2 domain of NusA, and we delineate the atomic basis of the latter interaction by macromolecular crystallography. SuhB recruitment to a ribosomal RNA transcription complex depends on the RNA signal element but not on the NusA AR2 domain. SuhB in turn is required for stable integration of the NusB/E dimer into the complex. In vitro transcription assays revealed that SuhB is crucial for delaying or suppressing ρ-dependent termination, that SuhB also can reduce intrinsic termination, and that SuhB-AR2 contacts contribute to these effects. Together, our results reveal functions of SuhB during ribosomal RNA synthesis and delineate some of the underlying molecular interactions.
Effectiveness of Family Intervention for Preventing Relapse in First-Episode Psychosis Until 24 Months of Follow-up: A Systematic Review With Meta-analysis of Randomized Controlled Trials
Authors: Camacho-Gomez Miguel , Castellvi Pere 
Published: April 2019

Abstract

Background
Relapse risk during the early years of first-episode psychosis (FEP) considerably increases the risk of chronicity. The effectiveness of family intervention for psychosis (FIp) for preventing relapse after FEP remains unknown. We assessed the effectiveness of FIp until 24 months of follow-up for preventing relapse and other relapse-related outcomes in patients following FEP.

Methods
We searched the Cochrane, PubMed, PsycINFO, and ProQuest databases in June 2018. A systematic review with meta-analysis of randomized controlled trials (RCTs), sensitivity analyses, and publication bias were performed, comparing to treatment as usual (TAU) or TAU plus other psychosocial interventions. Outcomes assessed were relapse rates, duration of hospitalization, psychotic symptoms, and functionality. Risk ratios (RRs) and (standardized) mean differences (SMD; MD) were calculated.

Results
Of the 2109 records retrieved, 14 (11 RCTs) were included. Pooled results showed that FIp was effective for preventing relapse (RR = 0.42; 95% CI = 0.29 to 0.61) compared to TAU and/or other psychosocial interventions. It also proved effective when compared to TAU alone (RR = 0.36) and TAU plus other psychosocial interventions (RR = 0.48). FIp showed benefits in reducing duration of hospitalization (TAU, MD = −3.31; other interventions, MD = −4.57) and psychotic symptoms (TAU, SMD = −0.68), and increased functionality (TAU, SMD = 1.36; other interventions, SMD = 1.41).

Conclusions
These findings suggest that FIp is effective for reducing relapse rates, duration of hospitalization, and psychotic symptoms, and for increasing functionality in FEP patients up to 24 months. The study’s main limitations were the inclusion of published research only; authors were not contacted for missing/additional data; and high heterogeneity regarding relapse definition was observed.
Does public outreach impede research performance? Exploring the ‘researcher’s dilemma’ in a sustainability research center
Authors: Kassab Omar 
Published: April 2019

Abstract
Researchers and universities are increasingly urged to communicate their findings to the general public. Despite the broad consensus about the necessity of this task, researchers are still reluctant to engage in public outreach activities. One major reason is that while being somewhat time consuming, engagement in public outreach is not adequately reflected in the metrics that are relevant for career advancement. The study at hand examines to what extent this dilemma is empirically justified. A series of statistical analyses are carried out on the basis of data from a sustainability science research center in Switzerland. The study comes to the conclusion that research performance is overall positively associated to engagement in public outreach activities. This insight has implications for the academic incentive and evaluation system.
Financial Capability and Economic Security among Low-Income Older Asian Immigrants: Lessons from Qualitative Interviews
Authors: Nam Yunju , Sherraden Margaret S , Huang Jin , Lee Eun Jeong , Keovisai Mary 
Published: April 2019

Abstract
This article examines financial capability among low-income older Asian immigrants, using data from in-depth interviews with 13 participants in a subsidized employment program in Los Angeles. Overall, respondents present a portrait of economic insecurity. Qualitative analyses indicate that respondents perceived little need to improve their financial knowledge and management skills because they had “no money to manage.” Most respondents lacked either financial knowledge or financial management skills, which resulted in substantial financial losses among some respondents. Mistrust of financial institutions (“Banks are always vampires”) and other financial barriers (for example, lack of credit history) blocked respondents’ access to formal financial services. In some cases, ethnic financial resources (for example, ethnic banks) reduced the effects of such barriers. There is evidence that respondent financial knowledge and management skills may improve after opening a bank account, suggesting a potential role for financial access in expanding financial capability. Findings demonstrate the importance of financial capability–building interventions for low-income older Asian immigrants. Social workers should be equipped with financial literacy and in-depth understanding of financial needs, perceptions, values, behaviors, and resources of this population.
Biogeographical Network Analysis of Cretaceous Terrestrial Tetrapods: A Phylogeny-Based Approach
Authors: Kubo Tai 
Published: April 2019

Abstract
Network methods are widely used to represent and analyze biogeography. It is difficult, however, to convert occurrence data of fossil vertebrates to a biogeographical network, as most species were known from a single locality. A new method for creating a biogeographical network that can incorporate phylogenetic information is proposed in this study, which increases the number of edges in the network of fossil vertebrates and enables the application of various network methods. Using ancestral state reconstruction via maximum parsimony, the method first estimates the biogeographical regions of all internal nodes of a given phylogeny using biogeographical information on the terminal taxa. Then, each internal node in the phylogenetic tree is converted to an edge in the biogeographical network that connects the region(s), if unambiguously estimated, of its two descendants. The new method was applied to phylogenetic trees generated by a birth–death model. Under all conditions tested, an average of $CDATA[$CDATA[$>$$70% of the internal nodes in phylogenetic trees were converted into edges. Three network indices—link density, average link weight, and endemism index (EI)—were evaluated for their usefulness in comparing different biogeographical networks. The EI reflects the rate of dispersal; the other indices reflect nonbiogeographical parameters, the number of taxa and regions, which highlights the importance of evaluating network indices before applying them to biogeographical studies. Multiple Cretaceous biogeographical networks were constructed from the phylogenies of five tetrapod taxa: terrestrial crocodyliforms, terrestrial turtles, nonavian dinosaurs, avians, and pterosaurs. The networks of avians and pterosaurs showed similar topologies and a strong correlation, and unexpectedly high endemism indices. These similarities were probably a result of shared taphonomic biases (i.e., the Lagerstätten effect) for volant taxa with fragile skeletons. The crocodyliform network was partitioned into the Gondwanan and Laurasian continents. The dinosaur network was partitioned into three groups of continents: 1) North America, Asia, and Australia; 2) Europe and Africa; and 3) India, Madagascar, and South America. When Early and Late Cretaceous dinosaurs were analyzed separately, the dinosaur networks were divided into 1) North America, Asia, and Australia; and 2) Europe, Africa, India, and South America for the Early Cretaceous and 1) North America, Asia, and Europe; and 2) India, Madagascar, and South America for the Late Cretaceous. This partitioning of dinosaur and crocodyliform networks corroborates the results of previous biogeographical studies and indicates that the method introduced here can retrieve biogeographical signals from a source phylogeny when sufficient data are available for most targeted biogeographical regions.
Acetaminophen Responsive miR-19b Modulates SIRT1/Nrf2 Signaling Pathway in Drug-Induced Hepatotoxicity
Authors: Liu Xing , Zhao Hongqian , Luo Chunyan , Du Debin , Huang Jinlong , Ming Quan , Jin Fen , Wang Decheng , Huang Weifeng 
Published: April 2019

AbstractPrevious studies suggest that activation of SIRT1 protects liver from acetaminophen (APAP)-induced injury; however, the detailed mechanism of SIRT1 modulation in this process is still incomplete. Therefore, this study was to investigate the pathophysiological role of SIRT1 in APAP-mediated hepatotoxicity. We found that SIRT1 mRNA and protein were markedly upregulated in human LO2 cells and mouse liver upon APAP exposure. In vitro, the specific knockdown of SIRT1 expression ultimately aggravated APAP-evoked cellular antioxidant defense in LO2 cells. Moreover, lentivirus-mediated knockdown of hepatic SIRT1 expression exacerbated APAP-induced oxidative stress and liver injury, especially reduction of Nrf2 and subsequent downregulation of several antioxidant genes. Intriguingly, 30 mg/kg SRT1720, the specific SIRT1 activator, which greatly enhanced Nrf2 expression and antioxidant defense, and then eventually reversed APAP-induced hepatic liver injury in mice. Furthermore, APAP responsive miR-19b played an important role in regulating SIRT1 expression, whereas overexpression miR-19b largely abolished the induction of SIRT1 by APAP in vitro and in vivo. Specific SIRT1 3′-UTR mutation, which disrupted the interaction of miRNA-3′UTR, and successfully abrogated the modulation by miR-19b. Notably, hepatic miR-19b overexpression worsened the APAP-induced hepatotoxicity. In general, our results support the notion that the strong elevation of SIRT1 by APAP responsive miR-19b may represent a compensatory mechanism to protect liver against the drug-induced damage, at least in part by enhancing Nrf2-mediated antioxidant capacity in the liver.
TSPO PET Using [18F]PBR111 Reveals Persistent Neuroinflammation Following Acute Diisopropylfluorophosphate Intoxication in the Rat
Authors: Hobson Brad A , Rowland Douglas J , Sisó Sílvia , Guignet Michelle A , Harmany Zachary T , Bandara Suren B , Saito Naomi , Harvey Danielle J , Bruun Donald A , Garbow Joel R , Chaudhari Abhijit J , Lein Pamela J 
Published: April 2019

Abstract
Acute intoxication with organophosphates (OPs) can trigger status epilepticus followed by persistent cognitive impairment and/or electroencephalographic abnormalities. Neuroinflammation is widely posited to influence these persistent neurological consequences. However, testing this hypothesis has been challenging, in part because traditional biometrics preclude longitudinal measures of neuroinflammation within the same animal. Therefore, we evaluated the performance of noninvasive positron emission tomography (PET), using the translocator protein (TSPO) radioligand [18F]PBR111 against classic histopathologic measures of neuroinflammation in a preclinical model of acute intoxication with the OP diisopropylfluorophosphate (DFP). Adult male Sprague Dawley rats administered pyridostigmine bromide (0.1 mg/kg, im) 30 min prior to administration of DFP (4 mg/kg, sc), atropine sulfate (2 mg/kg, im) and 2-pralidoxime (25 mg/kg, im) exhibited moderate-to-severe seizure behavior. TSPO PET performed prior to DFP exposure and at 3, 7, 14, 21, and 28 days postexposure revealed distinct lesions, as defined by increased standardized uptake values (SUV). Increased SUV showed high spatial correspondence to immunohistochemical evidence of neuroinflammation, which was corroborated by cytokine gene and protein expression. Regional SUV metrics varied spatiotemporally with days postexposure and correlated with the degree of neuroinflammation detected immunohistochemically. Furthermore, SUV metrics were highly correlated with seizure severity, suggesting that early termination of OP-induced seizures may be critical for attenuating subsequent neuroinflammatory responses. Normalization of SUV values to a cerebellar reference region improved correlations to all outcome measures and seizure severity. Collectively, these results establish TSPO PET using [18F]PBR111 as a robust, noninvasive tool for longitudinal monitoring of neuroinflammation following acute OP intoxication.