bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic and environmental sources of familial coaggregation of obsessive−compulsive disorder and suicidal behavior: a population-based birth cohort and family study
Authors: Sidorchuk Anna , Kuja-Halkola Ralf , Runeson Bo , Lichtenstein Paul , Larsson Henrik , Rück Christian , D’Onofrio Brian M , Mataix-Cols David , Fernández de la Cruz Lorena 
Published: April 2019

AbstractObsessive−compulsive disorder (OCD) is associated with high risk of suicide. It is yet unknown whether OCD and suicidal behaviors coaggregate in families and, if so, what are the mechanisms underlying this coaggregation. In a population-based birth cohort and family study, we linked individuals born in Sweden in 1967–2003 (n = 3,594,181) to their parents, siblings, and cousins, and collected register-based diagnoses of OCD, suicide attempts, and deaths by suicide and followed them until December 31, 2013. We also applied quantitative genetic modeling to estimate the contribution of genetic and environmental factors to the familial coaggregation of OCD and suicidal behavior. An elevated risk of suicide attempts was observed across all relatives of individuals with OCD, increasing proportionally to the degree of genetic relatedness, with odds ratios (OR) ranging from 1.56 (95% confidence interval (CI) 1.49–1.63) in parents to 1.11 (95% CI 1.07–1.16) in cousins. The risk of death by suicide also increased alongside narrowing genetic distance, but was only significant in parents (OR 1.55; 95% CI 1.40–1.72) and full siblings (OR 1.80; 95% CI 1.43–2.26) of individuals with OCD. Familial coaggregation of OCD and suicide attempts was explained by additive genetic factors (60.7%) and non-shared environment (40.4%), with negligible contribution of shared environment. Similarly, familial coaggregation with death by suicide was attributed to additive genetics (65.8%) and nonshared environment (34.2%). Collectively, these observations indicate that OCD and suicidal behaviors coaggregate in families largely due to genetic factors. The contribution of unique environment is also considerable, providing opportunities to target high-risk groups for prevention and treatment.
Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics
Authors: Tan Sha , Liu Jun , Fang Yun , Hedlund Brian P , Lian Zheng-Han , Huang Li-Ying , Li Jin-Tian , Huang Li-Nan , Li Wen-Jun , Jiang Hong-Chen , Dong Hai-Liang , Shu Wen-Sheng 
Published: April 2019

Abstract
Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.
Quantitative optical assessment of photonic and electronic properties in halide perovskite
Authors: Bercegol Adrien , Ory Daniel , Suchet Daniel , Cacovich Stefania , Fournier Olivier , Rousset Jean , Lombez Laurent 
Published: April 2019

AbstractThe development of high efficiency solar cells relies on the management of electronic and optical properties that need to be accurately measured. As the conversion efficiencies increase, there is a concomitant electronic and photonic contribution that affects the overall performances. Here we show an optical method to quantify several transport properties of semiconducting materials and the use of multidimensional imaging techniques allows decoupling and quantifying the electronic and photonic contributions. Example of application is shown on halide perovskite thin film for which a large range of transport properties is given in the literature. We therefore optically measure pure carrier diffusion properties and evidence the contribution of optical effects such as the photon recycling as well as the photon propagation where emitted light is laterally transported without being reabsorbed. This latter effect has to be considered to avoid overestimated transport properties such as carrier mobility, diffusion length or diffusion coefficient.
Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency
Authors: Gisler Santiago , Gonçalves Joana P. , Akhtar Waseem , de Jong Johann , Pindyurin Alexey V. , Wessels Lodewyk F. A. , van Lohuizen Maarten 
Published: April 2019

AbstractUnderstanding the impact of guide RNA (gRNA) and genomic locus on CRISPR-Cas9 activity is crucial to design effective gene editing assays. However, it is challenging to profile Cas9 activity in the endogenous cellular environment. Here we leverage our TRIP technology to integrate ~ 1k barcoded reporter genes in the genomes of mouse embryonic stem cells. We target the integrated reporters (IRs) using RNA-guided Cas9 and characterize induced mutations by sequencing. We report that gRNA-sequence and IR locus explain most variation in mutation efficiency. Predominant insertions of a gRNA-specific nucleotide are consistent with template-dependent repair of staggered DNA ends with 1-bp 5′ overhangs. We confirm that such staggered ends are induced by Cas9 in mouse pre-B cells. To explain observed insertions, we propose a model generating primarily blunt and occasionally staggered DNA ends. Mutation patterns indicate that gRNA-sequence controls the fraction of staggered ends, which could be used to optimize Cas9-based insertion efficiency.
Investigating underlying mechanism in spectral narrowing phenomenon induced by microcavity in organic light emitting diodes
Authors: Wang Miaosheng , Lin Jie , Hsiao Yu-Che , Liu Xingyuan , Hu Bin 
Published: April 2019

AbstractThis paper reports our experimental studies on the underlying mechanism responsible for electroluminescence spectral narrowing phenomenon in the cavity-based organic light-emitting diodes. It is found that the microcavity generates an emerging phenomenon: a magneto-photoluminescence signal in Poly(9,9-dioctylfluorene-alt-benzothiadiazole) polymer under photoexcitation, which is completely absent when microcavity is not used. This provides an evidence that microcavity leads to the formation of spatially extended states, functioning as the intermediate states prior to the formation of Frenkel excitons in organic materials. This is confirmed by the magneto-electroluminescence solely observed from the cavity-based light-emitting diodes under electrical injection. Furthermore, the narrowed electroluminescence output shows a linear polarization, concurrently occurred with magneto-electroluminescence. This indicates that the spatially extended sates become aligned towards forming coherent light-emitting excitons within the microcavity through optical resonance. Clearly, the spatially extended states present the necessary condition to realize electroluminescence spectral narrowing phenomenon towards lasing actions in cavity-based organic light-emitting diodes.
Large-scale proteomic analysis of human brain identifies proteins associated with cognitive trajectory in advanced age
Authors: Wingo Aliza P. , Dammer Eric B. , Breen Michael S. , Logsdon Benjamin A. , Duong Duc M. , Troncosco Juan C. , Thambisetty Madhav , Beach Thomas G. , Serrano Geidy E. , Reiman Eric M. , Caselli Richard J. , Lah James J. , Seyfried Nicholas T. , Levey Allan I. , Wingo Thomas S. 
Published: April 2019

AbstractIn advanced age, some individuals maintain a stable cognitive trajectory while others experience a rapid decline. Such variation in cognitive trajectory is only partially explained by traditional neurodegenerative pathologies. Hence, to identify new processes underlying variation in cognitive trajectory, we perform an unbiased proteome-wide association study of cognitive trajectory in a discovery (n = 104) and replication cohort (n = 39) of initially cognitively unimpaired, longitudinally assessed older-adult brain donors. We find 579 proteins associated with cognitive trajectory after meta-analysis. Notably, we present evidence for increased neuronal mitochondrial activities in cognitive stability regardless of the burden of traditional neuropathologies. Furthermore, we provide additional evidence for increased synaptic abundance and decreased inflammation and apoptosis in cognitive stability. Importantly, we nominate proteins associated with cognitive trajectory, particularly the 38 proteins that act independently of neuropathologies and are also hub proteins of protein co-expression networks, as promising targets for future mechanistic studies of cognitive trajectory.
Distinguishing the sources of silica nanoparticles by dual isotopic fingerprinting and machine learning
Authors: Yang Xuezhi , Liu Xian , Zhang Aiqian , Lu Dawei , Li Gang , Zhang Qinghua , Liu Qian , Jiang Guibin 
Published: April 2019

AbstractOne of the key shortcomings in the field of nanotechnology risk assessment is the lack of techniques capable of source tracing of nanoparticles (NPs). Silica is the most-produced engineered nanomaterial and also widely present in the natural environment in diverse forms. Here we show that inherent isotopic fingerprints offer a feasible approach to distinguish the sources of silica nanoparticles (SiO2 NPs). We find that engineered SiO2 NPs have distinct Si–O two-dimensional (2D) isotopic fingerprints from naturally occurring SiO2 NPs, due probably to the Si and O isotope fractionation and use of isotopically different materials during the manufacturing process of engineered SiO2 NPs. A machine learning model is developed to classify the engineered and natural SiO2 NPs with a discrimination accuracy of 93.3%. Furthermore, the Si–O isotopic fingerprints are even able to partly identify the synthetic methods and manufacturers of engineered SiO2 NPs.
A metabolomic study of the effect of Candida albicans glutamate dehydrogenase deletion on growth and morphogenesis
Authors: Han Ting-Li , Cannon Richard D. , Gallo Sandra M. , Villas-Bôas Silas G. 
Published: April 2019

AbstractThere are two glutamate dehydrogenases in the pathogenic fungusCandida albicans. One is an NAD+-dependent glutamate dehydrogenase (GDH2) and the other is an NADPH-dependent glutamate dehydrogenase (GDH3). These two enzymes are part of the nitrogen and nicotinate/nicotinamide metabolic pathways, which have been identified in our previous studies as potentially playing an important role inC. albicansmorphogenesis. In this study, we created single gene knockout mutants of both dehydrogenases in order to investigate whether or not they affect the morphogenesis ofC. albicans. TheGDHgenes were deleted and the phenotypes of the knockout mutants were studied by growth characterisation, metabolomics, isotope labelling experiments, and by quantifying cofactors under various hyphae-inducing conditions. We found that thegdh2/gdh2mutant was unable to grow on either arginine or proline as a sole carbon and nitrogen source. While thegdh3/gdh3mutant could grow on these carbon and nitrogen sources, the strain was locked in the yeast morphology in proline-containing medium. We detected different concentrations of ATP, NAD+, NADH, NAPD+, NADPH, as well as 62 other metabolites, and 19 isotopically labelled metabolites between the mutant and the wild-type strains. These differences were associated with 44 known metabolic pathways. It appears that the disequilibrium of cofactors in thegdh3/gdh3mutant leads to characteristic proline degradation in the central carbon metabolism. The analysis of thegdh2/gdh2and thegdh3/gdh3mutants confirmed our hypothesis that redox potential and nitrogen metabolism are related to filament formation and identified these metabolic pathways as potential drug targets to inhibit morphogenesis.
Retreating marsh shoreline creates hotspots of high-marsh plant diversity
Authors: Elsey-Quirk Tracy , Mariotti Giulio , Valentine Kendall , Raper Kirk 
Published: April 2019

AbstractMarsh edge retreat by wave erosion, an ubiquitous process along estuaries, could affect vegetation dynamics in ways that differ from well-established elevation-driven interactions. Along the marshes of Delaware Bay (USA) we show that species composition from marsh edge to interior is driven by gradients in wave stress, bed elevation, and sediment deposition. At the marsh edge, large wave stress allows only short-statured species. Approximately 17m landward, decreasing wave stress and increasing deposition cause the formation of a ridge. There, high marsh fugitive and shrub species prevails. Both the marsh edge and the ridge retreat synchronously by several meters per year causing wave energy and deposition to change rapidly. Yet, the whole ecogeomorphologic profile translates landward in a dynamic equilibrium, where the low marsh replaces the high marsh ridge community and the high marsh ridge community replaces the mid-marsh grasses on the marsh plain. A plant competition model shows that the disturbances associated with sediment deposition are necessary for the high marsh species to outcompete the mid-marsh grasses during rapid transgression. Marsh retreat creates a moving framework of physical gradients and disturbances that promote the co-existence of over ten different species adjacent to the marsh edge in an otherwise species-poor landscape.
Significance of the Tks4 scaffold protein in bone tissue homeostasis
Authors: Vas Virag , Kovács Tamás , Körmendi Szandra , Bródy Andrea , Kudlik Gyöngyi , Szeder Bálint , Mező Diána , Kállai Dóra , Koprivanacz Kitti , Merő Balázs L. , Dülk Metta , Tóvári József , Vajdovich Péter , Şenel Ş. Neslihan , Özcan Ilknur , Helyes Zsuzsanna , Dobó-Nagy Csaba , Buday László 
Published: April 2019

AbstractThe main driver of osteoporosis is an imbalance between bone resorption and formation. The pathogenesis of osteoporosis has also been connected to genetic alterations in key osteogenic factors and dysfunction of bone marrow mesenchymal stem/stromal cells (BM-MSCs). Tks4 (encoded by the Sh3pxd2b gene) is a scaffold protein involved in podosome organization. Homozygous mutational inactivation of Sh3pxd2b causes Frank-ter Haar syndrome (FTHS), a genetic disease that affects bone tissue as well as eye, ear, and heart functions. To date, the role of Tks4 in adult bone homeostasis has not been investigated. Therefore, the aim of this study was to analyze the facial and femoral bone phenotypes of Sh3pxd2b knock-out (KO) mice using micro-CT methods. In addition to the analysis of the Sh3pxd2b-KO mice, the bone microstructure of an FTHS patient was also examined. Macro-examination of skulls from Tks4-deficient mice revealed craniofacial malformations that were very similar to symptoms of the FTHS patient. The femurs of the Sh3pxd2b-KO mice had alterations in the trabecular system and showed signs of osteoporosis, and, similarly, the FTHS patient also showed increased trabecular separation/porosity. The expression levels of the Runx2 and osteocalcin bone formation markers were reduced in the bone and bone marrow of the Sh3pxd2b-KO femurs, respectively. Our recent study demonstrated that Sh3pxd2b-KO BM-MSCs have a reduced ability to differentiate into osteoblast lineage cells; therefore, we concluded that the Tks4 scaffold protein is important for osteoblast formation, and that it likely plays a role in bone cell homeostasis.
Direct and indirect associations between dietary magnesium intake and breast cancer risk
Authors: Huang Wu-Qing , Long Wei-Qing , Mo Xiong-Fei , Zhang Nai-Qi , Luo Hong , Lin Fang-Yu , Huang Jing , Zhang Cai-Xia 
Published: April 2019

AbstractThis study aimed to explore the effect of dietary magnesium intake on breast cancer risk both directly and indirectly via its effect on inflammatory markers C-reactive protein (CRP) and interleukin-6 (IL-6). This case-control study recruited 1050 case patients and 1229 control subjects. Inflammatory marker levels of 322 cases and 322 controls, randomly selected, were measured using ELISA, and data on dietary magnesium intake were collected using a food frequency questionnaire. Multivariable logistic regression was used to estimate the odds ratio (OR) and 95% confidence interval (CI), and path analysis was used to investigate the mediating effect. A higher magnesium intake was associated with a lower breast cancer risk (adjusted OR = 0.80, 95% CI = 0.65, 0.99). A positive association was found between the CRP level and breast cancer risk (adjusted OR = 1.43, 95% CI = 1.02–2.01). However, IL-6 was not found to be associated with breast cancer risk. Path analysis revealed that dietary magnesium affected breast cancer risk both directly and indirectly by influencing the CRP level. The results indicate that a direct negative association and an indirect association through influencing the CRP level were observed between dietary magnesium intake and breast cancer risk.
Direct quantification of surface barriers for mass transfer in nanoporous crystalline materials
Authors: Gao Mingbin , Li Hua , Yang Miao , Gao Shushu , Wu Pengfei , Tian Peng , Xu Shutao , Ye Mao , Liu Zhongmin 
Published: April 2019

AbstractMass transfer of guest molecules in nanoporous crystalline materials has gained attention in catalysis, separation, electrochemistry, and other fields. Two mechanisms, surface barriers and intracrystalline diffusion, dominate the mass transport process. Lack of methods to separately quantify these two mechanisms restricts further understanding and thus rational design and efficient application of nanoporous materials. Here we derive an approximate expression of uptake rate relying solely on surface permeability, offering an approach to directly quantify surface barriers and intracrystalline diffusion. By use of this approach, we study the diffusion in zeolitic materials, and find that the intracrystalline diffusivity is intrinsic to the topological structure of host materials at low molecular loading for the given guest molecules, while the surface permeability is sensitive to the non-ideality of a crystalline surface owing to the physical and chemical properties of the crystalline surface, host–guest interaction at the surface, and change of the environment.
Light-exposure at night impairs mouse ovary development via cell apoptosis and DNA damage
Authors: Li Yapeng , Cheng Shunfeng , Li Lan , Zhao Yong , Shen Wei , Sun Xiaofeng 
Published: April 2019

AbstractThe alternation of light and dark rhythm causes a series of physiological, biochemical and metabolic changes in animals, which also alters the growth and development of animals, and feeding, migration, reproduction and other behavioral activities. In recent years, many studies have reported the effects of long-term (more than 6 weeks) illumination on ovarian growth and development. In the present study, we observed the damage, repair and apoptosis of ovarian DNA in a short period of illumination. The results showed that, in short time (less than 2 weeks) illumination conditions, the 24-h light treatment caused the reduction of total ovarian follicle number and down-regulation of circadian clock related genes. Furthermore, the changed levels of serum sex hormones were also detected after 24-h light exposure, of which the concentrations of LH (luteinizing hormone), FSH (follicle-stimulating hormone) and E2 (estradiol) were increased, but the concentration of PROG (progesterone) was decreased. Moreover, 24-h light exposure increased the expression of DNA damage and repair related genes, the number of TUNEL and RAD51 positive cells. These results indicated that 24-h light exposure for 4, 8 and 12 days increased DNA damage and cell apoptosis, thereby affecting the development of ovary.
Clinical significance of high expression of stanniocalcin-2 in hepatocellular carcinoma
Authors: Wang Yuan , Wu Jian , Xu Jiangyan , Lin Shengyou 
Published: April 2019

Abstract
To investigate the significance of stanniocalcin-2 (STC2) expression in hepatocellular carcinoma (HCC) tissues and adjacent tissues. Levels of STC2 in HCC tissue were detected in 200 HCC patients tissues and adjacent tissues as controls by immunohistochemistry technique (IHC) and reverse transcriptase-PCR (RT-PCR). Single factor analysis was used to study the relationship between expression of STC2 mRNA and protein and clinicopathological features of HCC. Multifactor Cox survival analysis was used to relationship between the expression of STC2 and overall survival of postoperative patients with HCC. IHC staining showed that the expression of STC2 protein rate was 81.00% (163/200). And the positive rate of adjacent tissues was 29.00% (58/200). Western blot showed that the expression of STC2 protein in HCC was significantly higher than that in the adjacent tissues (P<0.05). RT-PCR showed that the positive rates of STC2 mRNA expression in HCC were 75.50% (151/200), which was significantly higher than that in adjacent tissues 14.50% (29/200) (P<0.05). Both STC2 mRNA and protein expression are related to tumor diameter, stage, tumor metastasis, carcinoma emboli in the portal vein and the degree of tumor differentiation in HCC. The HCC patients with higher expression of STC2 had shorter median survival time. STC2 expression, tumor diameter, carcinoma emboli in the portal vein, tumor differentiation degree, and tumor stage were independent factors affecting the overall survival of postoperative patients. The high expression of STC2 mRNA and protein expression in HCC may be associated with the occurrence, development, and prognosis of HCC. STC2 may also be possible to help developing new therapeutic strategies for HCC.
The role of APOE4 in Alzheimer’s disease: strategies for future therapeutic interventions
Authors: Hunsberger Holly C. , Pinky Priyanka D. , Smith Warren , Suppiramaniam Vishnu , Reed Miranda N. 
Published: April 2019

Abstract
Alzheimer’s disease (AD) is the leading cause of dementia affecting almost 50 million people worldwide. The ε4 allele of Apolipoprotein E (APOE) is the strongest known genetic risk factor for late-onset AD cases, with homozygous APOE4 carriers being approximately 15-times more likely to develop the disease. With 25% of the population being APOE4 carriers, understanding the role of this allele in AD pathogenesis and pathophysiology is crucial. Though the exact mechanism by which ε4 allele increases the risk for AD is unknown, the processes mediated by APOE, including cholesterol transport, synapse formation, modulation of neurite outgrowth, synaptic plasticity, destabilization of microtubules, and β-amyloid clearance, suggest potential therapeutic targets. This review will summarize the impact of APOE on neurons and neuronal signaling, the interactions between APOE and AD pathology, and the association with memory decline. We will then describe current treatments targeting APOE4, complications associated with the current therapies, and suggestions for future areas of research and treatment.