bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of distress on the balance between goal-directed and habit networks in obsessive-compulsive disorder
Authors: van der Straten Anouk , van Leeuwen Wieke , Denys Damiaan , van Marle Hein , van Wingen Guido 
Published: February 2020

AbstractThe classical cognitive-behavioral theory of obsessive-compulsive disorder (OCD) holds that compulsions are performed to reduce distress that is evoked by obsessions, whereas a recent neuroscience-inspired theory suggests that compulsivity results from a disbalance between goal-directed and habit-related neural networks. To bridge these theories, we investigated whether the balance between goal-directed and habit networks in patients with OCD was affected during psychological distress. Twenty-three OCD patients and twenty-three healthy controls participated in a controlled stress induction paradigm using the socially evaluated cold-pressor test in a crossover design. Stress responses were evaluated through cortisol levels, blood pressure, and anxiety ratings. Functional connectivity of the caudate nucleus and posterior putamen was assessed using seed region analysis of resting-state functional magnetic resonance imaging data, which are hubs of the goal-directed and habit network, respectively. Stress induction increased blood pressure and psychological stress measures across groups and resulted in blunted cortisol responses in patients. Furthermore, patients showed a blunted reduction in connectivity between the caudate nucleus and precuneus during psychological distress, which was positively correlated with compulsivity but not obsession severity. The posterior putamen showed no significant group differences in distress-induced connectivity. These results suggest that compulsivity in OCD is associated with altered connectivity between the goal-directed and default mode networks during psychological distress.
Contribution of common and rare variants to bipolar disorder susceptibility in extended pedigrees from population isolates
Authors: Sul Jae Hoon , Service Susan K. , Huang Alden Y. , Ramensky Vasily , Hwang Sun-Goo , Teshiba Terri M. , Park YoungJun , Ori Anil P. S. , Zhang Zhongyang , Mullins Niamh , Olde Loohuis Loes M. , Fears Scott C. , Araya Carmen , Araya Xinia , Spesny Mitzi , Bejarano Julio , Ramirez Margarita , Castrillón Gabriel , Gomez-Makhinson Juliana , Lopez Maria C. , Montoya Gabriel , Montoya Claudia P. , Aldana Ileana , Escobar Javier I. , Ospina-Duque Jorge , Kremeyer Barbara , Bedoya Gabriel , Ruiz-Linares Andres , Cantor Rita M. , Molina Julio , Coppola Giovanni , Ophoff Roel A. , Macaya Gabriel , Lopez-Jaramillo Carlos , Reus Victor , Bearden Carrie E. , Sabatti Chiara , Freimer Nelson B. 
Published: February 2020

AbstractCurrent evidence from case/control studies indicates that genetic risk for psychiatric disorders derives primarily from numerous common variants, each with a small phenotypic impact. The literature describing apparent segregation of bipolar disorder (BP) in numerous multigenerational pedigrees suggests that, in such families, large-effect inherited variants might play a greater role. To identify roles of rare and common variants on BP, we conducted genetic analyses in 26 Colombia and Costa Rica pedigrees ascertained for bipolar disorder 1 (BP1), the most severe and heritable form of BP. In these pedigrees, we performed microarray SNP genotyping of 838 individuals and high-coverage whole-genome sequencing of 449 individuals. We compared polygenic risk scores (PRS), estimated using the latest BP1 genome-wide association study (GWAS) summary statistics, between BP1 individuals and related controls. We also evaluated whether BP1 individuals had a higher burden of rare deleterious single-nucleotide variants (SNVs) and rare copy number variants (CNVs) in a set of genes related to BP1. We found that compared with unaffected relatives, BP1 individuals had higher PRS estimated from BP1 GWAS statistics (P = 0.001 ~ 0.007) and displayed modest increase in burdens of rare deleterious SNVs (P = 0.047) and rare CNVs (P = 0.002 ~ 0.033) in genes related to BP1. We did not observe rare variants segregating in the pedigrees. These results suggest that small-to-moderate effect rare and common variants are more likely to contribute to BP1 risk in these extended pedigrees than a few large-effect rare variants.
Suppressing STAT5 signaling affects osteosarcoma growth and stemness
Authors: Subramaniam Dharmalingam , Angulo Pablo , Ponnurangam Sivapriya , Dandawate Prasad , Ramamoorthy Prabhu , Srinivasan Pugazhendhi , Iwakuma Tomoo , Weir Scott J. , Chastain Katherine , Anant Shrikant 
Published: February 2020

AbstractOsteosarcoma (OS) is the most common primary bone tumor that primarily affects children and adolescents. Studies suggested that dysregulation JAK/STAT signaling promotes the development of OS. Cells treated with pimozide, a STAT5 inhibitor suppressed proliferation and colony formation and induced sub G0/G1 cell cycle arrest and apoptosis. There was a reduction in cyclin D1 and CDK2 expression and Rb phosphorylation, and activation of Caspase-3 and PARP cleavage. In addition, pimozide suppressed the formation of 3-dimensional osteospheres and growth of the cells in the Tumor in a Dish lung organoid system. Furthermore, there was a reduction in expression of cancer stem cell marker proteins DCLK1, CD44, CD133, Oct-4, and ABCG2. More importantly, it was the short form of DCLK1 that was upregulated in osteospheres, which was suppressed in response to pimozide. We further confirmed by flow cytometry a reduction in DCLK1+ cells. Moreover, pimozide inhibits the phosphorylation of STAT5, STAT3, and ERK in OS cells. Molecular docking studies suggest that pimozide interacts with STAT5A and STAT5B with binding energies of −8.4 and −6.4 Kcal/mol, respectively. Binding was confirmed by cellular thermal shift assay. To further understand the role of STAT5, we knocked down the two isoforms using specific siRNAs. While knockdown of the proteins did not affect the cells, knockdown of STAT5B reduced pimozide-induced necrosis and further enhanced late apoptosis. To determine the effect of pimozide on tumor growth in vivo, we administered pimozide intraperitoneally at a dose of 10 mg/kg BW every day for 21 days in mice carrying KHOS/NP tumor xenografts. Pimozide treatment significantly suppressed xenograft growth. Western blot and immunohistochemistry analyses also demonstrated significant inhibition of stem cell marker proteins. Together, these data suggest that pimozide treatment suppresses OS growth by targeting both proliferating cells and stem cells at least in part by inhibiting the STAT5 signaling pathway.
Complexity control by gradient descent in deep networks
Authors: Poggio Tomaso , Liao Qianli , Banburski Andrzej 
Published: February 2020

AbstractOverparametrized deep networks predict well, despite the lack of an explicit complexity control during training, such as an explicit regularization term. For exponential-type loss functions, we solve this puzzle by showing an effective regularization effect of gradient descent in terms of the normalized weights that are relevant for classification.
Unveiling the radiative local density of optical states of a plasmonic nanocavity by STM
Authors: Martín-Jiménez Alberto , Fernández-Domínguez Antonio I. , Lauwaet Koen , Granados Daniel , Miranda Rodolfo , García-Vidal Francisco J. , Otero Roberto 
Published: February 2020

AbstractAtomically-sharp tips in close proximity of metal surfaces create plasmonic nanocavities supporting both radiative (bright) and non-radiative (dark) localized surface plasmon modes. Disentangling their respective contributions to the total density of optical states remains a challenge. Electroluminescence due to tunnelling through the tip-substrate gap could allow the identification of the radiative component, but this information is inherently convoluted with that of the electronic structure of the system. In this work, we present a fully experimental procedure to eliminate the electronic-structure factors from the scanning tunnelling microscope luminescence spectra by confronting them with spectroscopic information extracted from elastic current measurements. Comparison against electromagnetic calculations demonstrates that this procedure allows the characterization of the meV shifts experienced by the nanocavity plasmonic modes under atomic-scale gap size changes. Therefore, the method gives access to the frequency-dependent radiative Purcell enhancement that a microscopic light emitter would undergo when placed at such nanocavity.
Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution
Authors: Yang Yongzhi , Sun Pengchuan , Lv Leke , Wang Donglei , Ru Dafu , Li Ying , Ma Tao , Zhang Lei , Shen Xingxing , Meng Fanbo , Jiao Beibei , Shan Lanxing , Liu Man , Wang Qingfeng , Qin Zhiji , Xi Zhenxiang , Wang Xiyin , Davis Charles C. , Liu Jianquan 
Published: February 2020

AbstractAngiosperms represent one of the most spectacular terrestrial radiations on the planet1, but their early diversification and phylogenetic relationships remain uncertain2–5. A key reason for this impasse is the paucity of complete genomes representing early-diverging angiosperms. Here, we present high-quality, chromosomal-level genome assemblies of two aquatic species—prickly waterlily (Euryale ferox; Nymphaeales) and the rigid hornwort (Ceratophyllum demersum; Ceratophyllales)—and expand the genomic representation for key sectors of the angiosperm tree of life. We identify multiple independent polyploidization events in each of the five major clades (that is, Nymphaeales, magnoliids, monocots, Ceratophyllales and eudicots). Furthermore, our phylogenomic analyses, which spanned multiple datasets and diverse methods, confirm that Amborella and Nymphaeales are successively sister to all other angiosperms. Furthermore, these genomes help to elucidate relationships among the major subclades within Mesangiospermae, which contain about 350,000 species. In particular, the species-poor lineage Ceratophyllales is supported as sister to eudicots, and monocots and magnoliids are placed as successively sister to Ceratophyllales and eudicots. Finally, our analyses indicate that incomplete lineage sorting may account for the incongruent phylogenetic placement of magnoliids between nuclear and plastid genomes.
The sequence and de novo assembly of the wild yak genome
Authors: Liu Yanbin , Luo Jiayu , Dou Jiajia , Yan Biyao , Ren Qingmiao , Tang Bolin , Wang Kun , Qiu Qiang 
Published: February 2020

AbstractVulnerable populations of wild yak (Bos mutus), the wild ancestral species of domestic yak, survive in extremely cold, harsh and oxygen-poor regions of the Qinghai-Tibetan Plateau (QTP) and adjacent high-altitude regions. In this study, we sequenced and assembled its genomede novo. In total, six different insert-size libraries were sequenced, and 662 Gb of clean data were generated. The assembled wild yak genome is 2.83 Gb in length, with an N50 contig size of 63.2 kb and a scaffold size of 16.3 Mb. BUSCO assessment indicated that 93.8% of the highly conserved mammal genes were completely present in the genome assembly. Annotation of the wild yak genome assembly identified 1.41 Gb (49.65%) of repetitive sequences and a total of 22,910 protein-coding genes, including 20,660 (90.18%) annotated with functional terms. This first construction of the wild yak genome provides a variable genetic resource that will facilitate further study of the genetic diversity of bovine species and accelerate yak breeding efforts.
Noninvasive imaging of vascular permeability to predict the risk of rupture in abdominal aortic aneurysms using an albumin-binding probe
Authors: Adams Lisa C. , Brangsch Julia , Reimann Carolin , Kaufmann Jan O. , Nowak Kristin , Buchholz Rebecca , Karst Uwe , Botnar Rene M. , Hamm Bernd , Makowski Marcus R. 
Published: February 2020

AbstractAbdominal aortic aneurysm (AAA) remains a fatal disease. Its development encompasses a complex interplay between hemodynamic stimuli on and changes in the arterial wall. Currently available biomarkers fail to predict the risk of AAA rupture independent of aneurysm size. Therefore, novel biomarkers for AAA characterization are needed. In this study, we used a mouse model of AAA to investigate the potential of magnetic resonance imaging (MRI) with an albumin-binding probe to assess changes in vascular permeability at different stages of aneurysm growth. Two imaging studies were performed: a longitudinal study with follow-up and death as endpoint to predict rupture risk and a week-by-week study to characterize AAA development. AAAs, which eventually ruptured, demonstrated a significantly higher in vivo MR signal enhancement from the albumin-binding probe (p = 0.047) and a smaller nonenhancing thrombus area compared to intact AAAs (p = 0.001). The ratio of albumin-binding-probe enhancement of the aneurysm wall to size of nonenhancing-thrombus-area predicted AAA rupture with high sensitivity/specificity (100%/86%). More advanced aneurysms with higher vascular permeability demonstrated an increased uptake of the albumin-binding-probe. These results indicate that MRI with an albumin-binding probe may enable noninvasive assessment of vascular permeability in murine AAAs and prediction of rupture risk.
Task allocation in a cooperative society: specialized castes or age-dependent switching among ant workers
Authors: Iwasa Yoh , Yamaguchi Sachi 
Published: February 2020

AbstractSome ant species have multiple worker castes that differ in body size; workers in one caste remain in the colony and those in the other forage outside the colony (caste polyethism). In other species, all workers engage in both tasks, but the younger workers remain in the colony and the older workers forage (age polyethism). Here, we ask which of these two is the most efficient for colony level performance when foragers suffer a higher daily mortality than workers in the colony and when the optimal worker size differs between two tasks. We studied two models: in the stationary colony model, the colony size and composition remain constant, and the amount of excess resources that can be used for producing reproductive individuals is maximized; in the growing colony model, all of the resources obtained are used for producing new workers, and the rate of the colony growth is maximized. In both models, we observed similar results: caste polyethism is more advantageous than age polyethism if the difference in mortality between the two tasks is small and the difference in the optimal size is large. In the opposite situation, the age polyethism is more advantageous.
Isotopic ratios of uranium and caesium in spherical radioactive caesium-bearing microparticles derived from the Fukushima Dai-ichi Nuclear Power Plant
Authors: Kurihara Yuichi , Takahata Naoto , Yokoyama Takaomi D. , Miura Hikaru , Kon Yoshiaki , Takagi Tetsuichi , Higaki Shogo , Yamaguchi Noriko , Sano Yuji , Takahashi Yoshio 
Published: February 2020

AbstractSpherical radioactive caesium (Cs)-bearing microparticles (CsMPs) were emitted during the Fukushima Dai-ichi Nuclear Power Plant (FDNPP) accident in March, 2011. The emission source (timing) and formation process of these particles remain unclear. In this study, the isotopic ratios of uranium (235U and 238U) and caesium (133Cs, 134Cs, 135Cs, and 137Cs) isotopes in the five spherical CsMPs (ca. 2 μm in size) sampled at 50 km west of the FDNPP were determined using secondary ion mass spectrometry and laser ablation-ICPMS, respectively. Results showed that the 235U/238U ratios of CsMPs were homogeneous (1.93 ± 0.03, N = 4) and close to those estimated for the fuel cores in units 2 and 3, and that the Cs isotopic ratios of CsMP were identical to those of units 2 and 3. These results indicated that U and Cs in the spherical CsMPs originated exclusively from the fuel melt in the reactors. Based on a thorough review of literatures related to the detailed atmospheric releases of radionuclides, the flow of plumes from the FDNPP reactor units during the accident and the U and Cs isotopic ratio results in this study, we hereby suggest that the spherical CsMPs originate only from the fuel in unit 2 on the night of 14 March to the morning of 15 March. The variation range of the analysed 235U/238U isotopic ratios for the four spherical particles was extremely narrow. Thus, U may have been homogenised in the source through the formation of fuel melt, which ultimately evaporating and taken into CsMPs in the reactor and was released from the unit 2.
Interactions between a Polygenic Risk Score and Non-genetic Risk Factors in Young-Onset Breast Cancer
Authors: Shi M. , O’Brien K. M. , Weinberg C. R. 
Published: February 2020

AbstractMost gene-environmental studies have focused on breast cancers generally, the preponderance of which occur after age 50. Young-onset breast cancers (YOBC) tend to be aggressive and may be etiologically different. The goal of this analysis was to assess interactions between an established 77-SNP polygenic risk score (PRS) and non-genetic risk factors for YOBC. We constructed the PRS using a family-based study of 1,291 women diagnosed with breast cancer before age 50 and their parents and unaffected sisters. We used conditional logistic regression to analyze interactions between the PRS and 14 established risk factors. In further analyses we assessed the same interactions, but for invasive cancer, estrogen receptor (ER) positive cancer and with broader inclusion of racial/ethnic groups. Results showed a decreased association between the PRS and YOBC risk for women who had ever used hormonal birth control (odds ratio [OR] = 2.20 versus 3.89) and a stronger association between the PRS and YOBC risk in pre-menopausal women (OR = 2.46 versus 1.23). Restricting the analysis to ER+ cancers or invasive cancers or using samples from all ethnic groups produced similar results. In conclusion, the PRS may interact with hormonal birth control use and with menopausal status on risk of YOBC.
Film-thickness-driven superconductor to insulator transition in cuprate superconductors
Authors: Jang Han-Byul , Lim Ji Soo , Yang Chan-Ho 
Published: February 2020

AbstractThe superconductor-insulator transition induced by film thickness control is investigated for the optimally doped cuprate superconductor La1.85Sr0.15CuO4. Epitaxial thin films are grown on an almost exactly matched substrate LaAlO3 (001). Despite the wide thickness range of 6 nm to 300 nm, all films are grown coherently without significant relaxation of the misfit strain. Electronic transport measurement exhibits systematic suppression of the superconducting phase by reducing the film thickness, thereby inducing a superconductor-insulator transition at a critical thickness of ~10 nm. The emergence of a resistance peak preceding the superconducting transition is discussed based on the weak localization. X-ray photoelectron spectroscopy results show the possibility that oxygen vacancies are present near the interface.
Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation
Authors: Schira-Heinen Jessica , Czapla Agathe , Hendricks Marion , Kloetgen Andreas , Wruck Wasco , Adjaye James , Kögler Gesine , Werner Müller Hans , Stühler Kai , Trompeter Hans-Ingo 
Published: February 2020

AbstractThe contribution of microRNA-mediated posttranscriptional regulation on the final proteome in differentiating cells remains elusive. Here, we evaluated the impact of microRNAs (miRNAs) on the proteome of human umbilical cord blood-derived unrestricted somatic stem cells (USSC) during retinoic acid (RA) differentiation by a systemic approach using next generation sequencing analysing mRNA and miRNA expression and quantitative mass spectrometry-based proteome analyses. Interestingly, regulation of mRNAs and their dedicated proteins highly correlated during RA-incubation. Additionally, RA-induced USSC demonstrated a clear separation from native USSC thereby shifting from a proliferating to a metabolic phenotype. Bioinformatic integration of up- and downregulated miRNAs and proteins initially implied a strong impact of the miRNome on the XXL-USSC proteome. However, quantitative proteome analysis of the miRNA contribution on the final proteome after ectopic overexpression of downregulated miR-27a-5p and miR-221-5p or inhibition of upregulated miR-34a-5p, respectively, followed by RA-induction revealed only minor proportions of differentially abundant proteins. In addition, only small overlaps of these regulated proteins with inversely abundant proteins in non-transfected RA-treated USSC were observed. Hence, mRNA transcription rather than miRNA-mediated regulation is the driving force for protein regulation upon RA-incubation, strongly suggesting that miRNAs are fine-tuning regulators rather than active primary switches during RA-induction of USSC.
Toxicological response of the model fungus Saccharomyces cerevisiae to different concentrations of commercial graphene nanoplatelets
Authors: Suarez-Diez Maria , Porras Santiago , Laguna-Teno Felix , Schaap Peter J. , Tamayo-Ramos Juan A. 
Published: February 2020

AbstractGraphene nanomaterials have attracted a great interest during the last years for different applications, but their possible impact on different biological systems remains unclear. Here, an assessment to understand the toxicity of commercial polycarboxylate functionalized graphene nanoplatelets (GN) on the unicellular fungal model Saccharomyces cerevisiae was performed. While cell proliferation was not negatively affected even in the presence of 800 mg L−1 of the nanomaterial for 24 hours, oxidative stress was induced at a lower concentration (160 mg L−1), after short exposure periods (2 and 4 hours). No DNA damage was observed under a comet assay analysis under the studied conditions. In addition, to pinpoint the molecular mechanisms behind the early oxidative damage induced by GN and to identify possible toxicity pathways, the transcriptome of S. cerevisiae exposed to 160 and 800 mg L−1 of GN was studied. Both GN concentrations induced expression changes in a common group of genes (337), many of them related to the fungal response to reduce the nanoparticles toxicity and to maintain cell homeostasis. Also, a high number of genes were only differentially expressed in the GN800 condition (3254), indicating that high GN concentrations can induce severe changes in the physiological state of the yeast.
Pan-cancer mapping of differential protein-protein interactions
Authors: Gulfidan Gizem , Turanli Beste , Beklen Hande , Sinha Raghu , Arga Kazim Yalcin 
Published: February 2020

AbstractDeciphering the variations in the protein interactome is required to reach a systems-level understanding of tumorigenesis. To accomplish this task, we have considered the clinical and transcriptome data on >6000 samples from The Cancer Genome Atlas for 12 different cancers. Utilizing the gene expression levels as a proxy, we have identified the differential protein-protein interactions in each cancer type and presented a differential view of human protein interactome among the cancers. We clearly demonstrate that a certain fraction of proteins differentially interacts in the cancers, but there was no general protein interactome profile that applied to all cancers. The analysis also provided the characterization of differentially interacting proteins (DIPs) representing significant changes in their interaction patterns during tumorigenesis. In addition, DIP-centered protein modules with high diagnostic and prognostic performances were generated, which might potentially be valuable in not only understanding tumorigenesis, but also developing effective diagnosis, prognosis, and treatment strategies.