bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing whether the association between rheumatoid arthritis and schizophrenia is bidirectional: A nationwide population-based cohort study
Authors: Chen Shih-Fen , Wang Ling-Yi , Chiang Jen-Huai , Hsu Chung-Y , Shen Yu-Chih 
Published: March 2019

AbstractSince many studies have shown a reduction in the incidence of rheumatoid arthritis (RA) in patients with schizophrenia (SCZ), little effort has been devoted to studying this link in the Asian population. Moreover, the relationship between these two disorders could be bidirectional, but the influence of RA on the SCZ incidence is unclear. The study aims to determine whether there is a bidirectional association between RA and SCZ in an Asian population. We analyzed a 10-year population- based longitudinal cohort using the National Health Insurance Research Database of Taiwan. In the first analysis, we included a total of 58,847 SCZ patients and 235,382 non-SCZ controls, and in the second analysis, a total of 30,487 RA patients and 121,833 non-RA controls, both matched by gender, age, and index date. Cox regression analyses were performed to examine the risk of RA incidence in the first analysis and the risk of SCZ incidence in the second analysis. The main finding of this study was the discovery of a lower incidence of RA in patients with SCZ (hazard ratio (HR): 0.48, 95% confidence interval (95% CI): 0.31–0.77) after adjustment for baseline demographics and comorbidities. Additionally, the presence of RA predicted a reduced incidence rate for SCZ, but the estimate was not statistically significant (HR: 0.77, 95% CI: 0.44–1.37). The study found a unidirectional association between RA and SCZ. However, RA has an age of onset later than RA, and the protective effect of RA on SCZ incidence would be biased due to the limited number of cases.
A tunable pair electrochemical strategy for the synthesis of new benzenesulfonamide derivatives
Authors: Mokhtari Banafsheh , Nematollahi Davood , Salehzadeh Hamid 
Published: March 2019

AbstractA green, facile and tunable pair electrochemical process was developed for the synthesis of new benzenesulfonamide derivatives by using reductive controlled potential electrolysis of dinitrobenzene (DNB) in the presence of arylsulfinic acids (ASAs). In addition to the usual features associated with paired electrochemical methods, eg high energy efficient, this method has a tunable characteristic, so that, by adjusting the potential, different products can be synthesized. By applying the potential of −0.4 V vs. Ag/AgCl, N-hydroxy-N-(4-nitrophenyl)benzenesulfonamide derivatives are selectively formed, while, by applying the potential of −1.1 V vs. Ag/AgCl, the final products are N-(4-amino-3-(phenylsulfonyl)phenyl) benzenesulfonamide derivatives. This work beautifully shows the potential applications of the electrochemistry as a powerful tool for the synthesis of organic compounds.
Imaging object-scene relations processing in visible and invisible natural scenes
Authors: Faivre Nathan , Dubois Julien , Schwartz Naama , Mudrik Liad 
Published: March 2019

AbstractIntegrating objects with their context is a key step in interpreting complex visual scenes. Here, we used functional Magnetic Resonance Imaging (fMRI) while participants viewed visual scenes depicting a person performing an action with an object that was either congruent or incongruent with the scene. Univariate and multivariate analyses revealed different activity for congruent vs. incongruent scenes in the lateral occipital complex, inferior temporal cortex, parahippocampal cortex, and prefrontal cortex. Importantly, and in contrast to previous studies, these activations could not be explained by task-induced conflict. A secondary goal of this study was to examine whether processing of object-context relations could occur in the absence of awareness. We found no evidence for brain activity differentiating between congruent and incongruent invisible masked scenes, which might reflect a genuine lack of activation, or stem from the limitations of our study. Overall, our results provide novel support for the roles of parahippocampal cortex and frontal areas in conscious processing of object-context relations, which cannot be explained by either low-level differences or task demands. Yet they further suggest that brain activity is decreased by visual masking to the point of becoming undetectable with our fMRI protocol.
Segmentation of Heavily Clustered Nuclei from Histopathological Images
Authors: Abdolhoseini Mahmoud , Kluge Murielle G. , Walker Frederick R. , Johnson Sarah J. 
Published: March 2019

AbstractAutomated cell nucleus segmentation is the key to gain further insight into cell features and functionality which support computer-aided pathology in early diagnosis of diseases such as breast cancer and brain tumour. Despite considerable advances in automated segmentation, it still remains a challenging task to split heavily clustered nuclei due to intensity variations caused by noise and uneven absorption of stains. To address this problem, we propose a novel method applicable to variety of histopathological images stained for different proteins, with high speed, accuracy and level of automation. Our algorithm is initiated by applying a new locally adaptive thresholding method on watershed regions. Followed by a new splitting technique based on multilevel thresholding and the watershed algorithm to separate clustered nuclei. Finalized by a model-based merging step to eliminate oversegmentation and a model-based correction step to improve segmentation results and eliminate small objects. We have applied our method to three image datasets: breast cancer stained for hematoxylin and eosin (H&E), Drosophila Kc167 cells stained for DNA to label nuclei, and mature neurons stained for NeuN. Evaluated results show our method outperforms the state-of-the-art methods in terms of accuracy, precision, F1-measure, and computational time.
Association between Psychosocial Stress and Fecal Microbiota in Pregnant Women
Authors: Hechler C. , Borewicz K. , Beijers R. , Saccenti E. , Riksen-Walraven M. , Smidt H. , de Weerth C. 
Published: March 2019

AbstractMaternal prenatal psychosocial stress is associated with altered child emotional and behavioral development. One potential underlying mechanism is that prenatal psychosocial stress affects child outcomes via the mother’s, and in turn the child’s, intestinal microbiota. This study investigates the first step of this mechanism: the relation between psychosocial stress and fecal microbiota in pregnant mothers. Mothers (N = 70) provided a late pregnancy stool sample and filled in questionnaires on general and pregnancy-specific stress and anxiety. Bacterial DNA was extracted and analysed by Illumina HiSeq sequencing of PCR-amplified 16 S ribosomal RNA gene fragments. Associations between maternal general anxiety and microbial composition were found. No associations between the other measured psychosocial stress variables and the relative abundance of microbial groups were detected. This study shows associations between maternal pregnancy general anxiety and microbial composition, providing first evidence of a mechanism through which psychological symptoms in pregnancy may affect the offspring.
Combined Tissue-Fluid Proteomics to Unravel Phenotypic Variability in Amyotrophic Lateral Sclerosis
Authors: Leoni Emanuela , Bremang Michael , Mitra Vikram , Zubiri Irene , Jung Stephan , Lu Ching-Hua , Adiutori Rocco , Lombardi Vittoria , Russell Claire , Koncarevic Sasa , Ward Malcolm , Pike Ian , Malaspina Andrea 
Published: March 2019

AbstractThe lack of biomarkers for early diagnosis, clinical stratification and to monitor treatment response has hampered the development of new therapies for amyotrophic lateral sclerosis (ALS), a clinically heterogeneous neurodegenerative disorder with a variable site of disease initiation and rate of progression. To identify new biomarkers and therapeutic targets, two separate proteomic workflows were applied to study the immunological response and the plasma/brain proteome in phenotypic variants of ALS. Conventional multiplex (TMT) proteomic analysis of peripheral blood mononuclear cells (PBMCs) was performed alongside a recently introduced method to profile neuronal-derived proteins in plasma using brain tissue-enhanced isobaric tagging (TMTcalibrator). The combined proteomic analysis allowed the detection of regulated proteins linked to ALS pathogenesis (RNA-binding protein FUS, superoxide dismutase Cu-Zn and neurofilaments light polypeptide) alongside newly identified candidate biomarkers (myosin-9, fructose-bisphosphate aldolase and plectin). In line with the proteomic results, orthogonal immunodetection showed changes in neurofilaments and ApoE in bulbar versus limb onset fast progressing ALS. Functional analysis of significantly regulated features showed enrichment of pathways involved in regulation of the immune response, Rho family GTPases, semaphorin and integrin signalling. Our cross-phenotype investigation of PBMCs and plasma/brain proteins provides a more sensitive biomarker exploratory platform than conventional case-control studies in a single matrix. The reported regulated proteins may represent novel biomarker candidates and potentially druggable targets.
Genome-wide Analysis of bZIP Transcription Factors in wheat and Functional Characterization of a TabZIP under Abiotic Stress
Authors: Agarwal Preeti , Baranwal Vinay Kumar , Khurana Paramjit 
Published: March 2019

AbstractThe basic leucine zipper(bZIP) represents one of the largest as well as most diverse transcription factor (TFs) families. They are known to play role in both stress as well as in various plant developmental processes. In the present study, a total of 191 bZIP transcription factors have been identified fromTriticum aestivum. Expression analysis during various stress conditions, developmental stages, different varieties and gene ontology enrichment analysis suggest their possible roles in abiotic stress as well as in developmental responses. In the current analysis, one of the members named asTabZIP(Traes_7AL_25850F96F.1) was selected for detailed analysis to understand its role under different abiotic stress conditions. Gene expression studies revealed differential expression ofTabZIPin various abiotic stress conditions like heat, salinity and dehydration suggesting the possible role of bZIP in various stress mitigation mechanism.Arabidopsistransgenics overexpressingTabZIPshowed enhanced tolerance to salinity, drought, heat and oxidative stress. ThusTabZIP(Traes_7AL_25850F96F.1) can serve as a candidate gene for improving heat as well as other abiotic stress tolerance and can be helpful in enhancing the crop productivity under stress conditions.
Electrocatalytic and Enhanced Photocatalytic Applications of Sodium Niobate Nanoparticles Developed by Citrate Precursor Route
Authors: Farooq Umar , Phul Ruby , Alshehri Saad M. , Ahmed Jahangeer , Ahmad Tokeer 
Published: March 2019

AbstractDevelopment of cost effective and efficient electrocatalysts is crucial to generate H2 as an alternative source of energy. However, expensive noble metal based electrocatalysts show best electrocatalytic performances which acts as main bottle-neck for commercial application. Therefore, non-precious electrocatalysts have become important for hydrogen and oxygen evolution reactions. Herein, we report the synthesis of high surface area (35 m2/g) sodium niobate nanoparticles by citrate precursor method. These nanoparticles were characterized by different techniques like X-ray diffraction, transmission electron microscopy and X-ray photoelectron spectroscopy. Electrocatalytic properties of cost-effective sodium niobate nanoparticles were investigated for HER and OER in 0.5 M KOH electrolyte using Ag/AgCl as reference electrode. The sodium niobate electrode showed significant current density for both OER (≈2.7 mA/cm2) and HER (≈0.7 mA/cm2) with onset potential of 0.9 V for OER and 0.6 V for HER. As-prepared sodium niobate nanoparticles show enhanced photocatalytic property (86% removal) towards the degradation of rose Bengal dye. Dielectric behaviour at different sintering temperatures was explained by Koop’s theory and Maxwell-Wagner mechanism. The dielectric constants of 41 and 38.5 and the dielectric losses of 0.04 and 0.025 were observed for the samples sintered at 500 °C and 700 °C, respectively at 500 kHz. Conductivity of the samples was understood by using power law fit.
Disruption of CUL3-mediated ubiquitination causes proximal tubule injury and kidney fibrosis
Authors: Saritas Turgay , Cuevas Catherina A. , Ferdaus Mohammed Z. , Kuppe Christoph , Kramann Rafael , Moeller Marcus J. , Floege Jürgen , Singer Jeffrey D. , McCormick James A. 
Published: March 2019

AbstractCullin 3 (CUL3) is part of the ubiquitin proteasomal system and controls several cellular processes critical for normal organ function including the cell cycle, and Keap1/Nrf2 signaling. Kidney tubule-specific Cul3 disruption causes tubulointerstitial fibrosis, but little is known about the mechanisms. Therefore, we tested the hypothesis that dysregulation of the cell cycle and Keap1/Nrf2 pathway play a role in initiating the kidney injury upon Cul3 disruption. Cul3 deletion increased expression of cyclin E and p21, associated with uncontrolled proliferation, DNA damage, and apoptosis, all of which preceded proximal tubule injury. The cdk2-cyclin E inhibitor roscovitine did not prevent the effects of Cul3 deletion, but instead exacerbated the kidney injury. Injury occurred despite accumulation and activation of CUL3 substrate Keap1/Nrf2, proposed to be protective in kidney injury. Cul3 disruption led to progressive interstitial inflammation, functionally relevant renal fibrosis and death. Finally, we observed reduced CUL3 expression in several AKI and CKD mouse models and in fibrotic human kidney tissue. These data establish CUL3 knockout mice as a novel genetic CKD model in which dysregulation of the cell cycle may play a primary role in initiating tubule injury, and that CUL3 dysregulation could contribute to acute and fibrotic kidney disease.
Preoperative Prediction of Axillary Lymph Node Metastasis in Breast Cancer Using Mammography-Based Radiomics Method
Authors: Yang Jingbo , Wang Tao , Yang Lifeng , Wang Yubo , Li Hongmei , Zhou Xiaobo , Zhao Weiling , Ren Junchan , Li Xiaoyong , Tian Jie , Huang Liyu 
Published: March 2019

AbstractIt is difficult to accurately assess axillary lymph nodes metastasis and the diagnosis of axillary lymph nodes in patients with breast cancer is invasive and has low-sensitivity preoperatively. This study aims to develop a mammography-based radiomics nomogram for the preoperative prediction of ALN metastasis in patients with breast cancer. This study enrolled 147 patients with clinicopathologically confirmed breast cancer and preoperative mammography. Features were extracted from each patient’s mammography images. The least absolute shrinkage and selection operator regression method was used to select features and build a signature in the primary cohort. The performance of the signature was assessed using support vector machines. We developed a nomogram by incorporating the signature with the clinicopathologic risk factors. The nomogram performance was estimated by its calibration ability in the primary and validation cohorts. The signature was consisted of 10 selected ALN-status-related features. The AUC of the signature from the primary cohort was 0.895 (95% CI, 0.887–0.909) and 0.875 (95% CI, 0.698–0.891) for the validation cohort. The C-Index of the nomogram from the primary cohort was 0.779 (95% CI, 0.752–0.793) and 0.809 (95% CI, 0.794–0.833) for the validation cohort. Our nomogram is a reliable and non-invasive tool for preoperative prediction of ALN status and can be used to optimize current treatment strategy for breast cancer patients.
Convergent Evolution of Copy Number Alterations in Multi-Centric Hepatocellular Carcinoma
Authors: Lackner Carolin , Quagliata Luca , Cross William , Ribi Sebastian , Heinimann Karl , Paradiso Viola , Quintavalle Cristina , Kovacova Monika , Baumhoer Daniel , Piscuoglio Salvatore , Terracciano Luigi , Kovac Michal 
Published: March 2019

AbstractIn the recent years, new molecular methods have been proposed to discriminate multicentric hepatocellular carcinomas (HCC) from intrahepatic metastases. Some of these methods utilize sequencing data to assess similarities between cancer genomes, whilst other achieved the same results with transcriptome and methylome data. Here, we attempt to classify two HCC patients with multi-centric disease using the recall-rates of somatic mutations but find that difficult because their tumors share some chromosome-scale copy-number alterations (CNAs) but little-to-no single-nucleotide variants. To resolve the apparent conundrum, we apply a phasing strategy to test if those shared CNAs are identical by descent. Our findings suggest that the conflicting alterations occur on different homologous chromosomes, which argues for multi-centric origin of respective HCCs.
Happiness is Greater in More Scenic Locations
Authors: Seresinhe Chanuki Illushka , Preis Tobias , MacKerron George , Moat Helen Susannah 
Published: March 2019

AbstractDoes spending time in beautiful settings boost people’s happiness? The answer to this question has long remained elusive due to a paucity of large-scale data on environmental aesthetics and individual happiness. Here, we draw on two novel datasets: first, individual happiness data from the smartphone app, Mappiness, and second, crowdsourced ratings of the “scenicness” of photographs taken across England from the online game Scenic-Or-Not. We find that individuals are happier in more scenic locations, even when we account for a range of factors such as the activity the individual was engaged in at the time, weather conditions and the income of local inhabitants. Crucially, this relationship holds not only in natural environments, but in built-up areas too, even after controlling for the presence of green space. Our results provide evidence that the aesthetics of the environments that policymakers choose to build or demolish may have consequences for our everyday wellbeing.
Genome analysis identifies the mutant genes for common industrial Silverblue and Hedlund white coat colours in American mink
Authors: Manakhov Andrey D. , Andreeva Tatiana V. , Trapezov Oleg V. , Kolchanov Nikolay A. , Rogaev Evgeny I. 
Published: March 2019

AbstractThe fur colour of American mink (Neovison vison) involves over 35 traits, but only three of these have been linked to specific genes. Despite being the most popular, coat colours Silverblue and Hedlund white remain uncharacterized genetically. The former is the first genetic mutant of fur colour identified in minks, while the latter is a commercially valuable phenotype that can be dyed easily. Here, we performed the whole genome sequencing for two American mink breeds with Silverblue and Hedlund white coats. We identified mutations in splice donor sites of genes coding melanophilin (MLPH) and microphthalmia-associated transcription factor (MITF) that regulate melanosome transport and neural-crest-derived melanocyte development, respectively. Both mutations cause mRNA splicing impairments that lead to a shift in open reading frames of MLPH and MITF. We conclude that our data should be useful for tracking economically valuable fur traits in mink breeding programs to contribute to global fur production.
Single cell RNA-seq study of wild type and Hox9,10,11 mutant developing uterus
Authors: Mucenski Michael L. , Mahoney Robert , Adam Mike , Potter Andrew S. , Potter S. Steven 
Published: March 2019

AbstractThe uterus is a remarkable organ that must guard against infections while maintaining the ability to support growth of a fetus without rejection. TheHoxa10andHoxa11genes have previously been shown to play essential roles in uterus development and function. In this report we show that theHoxa9,10,11,Hoxc9,10,11, Hoxd9,10,11genes play a redundant role in the formation of uterine glands. In addition, we use single cell RNA-seq to create a high resolution gene expression atlas of the developing wild type mouse uterus. Cell types and subtypes are defined, for example dividing endothelial cells into arterial, venous, capillary, and lymphatic, while epithelial cells separate into luminal and glandular subtypes. Further, a surprising heterogeneity of stromal and myocyte cell types are identified. Transcription factor codes and ligand/receptor interactions are characterized. We also used single cell RNA-seq to globally define the altered gene expression patterns in all developing uterus cell types for two Hox mutants, with 8 or 9 mutant Hox genes. The mutants show a striking disruption of Wnt signaling as well as the Cxcl12/Cxcr4 ligand/receptor axis.
UHPLC-MS/MS method for analysis of sobuzoxane, its active form ICRF-154 and metabolite EDTA-diamide and its application to bioactivation study
Authors: Reimerová Petra , Jirkovská Anna , Piskáčková Hana Bavlovič , Karabanovich Galina , Roh Jaroslav , Šimůnek Tomáš , Štěrbová-Kovaříková Petra 
Published: March 2019

AbstractSobuzoxane (MST-16) is an approved anticancer agent, a pro-drug of bisdioxopiperazine analog ICRF-154. Due to the structural similarity of ICRF-154 to dexrazoxane (ICRF-187), MST-16 deserves attention as a cardioprotective drug. This study presents for the first time UHPLC-MS/MS assay of MST-16, ICRF-154 and its metabolite (EDTA-diamide) in cell culture medium, buffer, plasma and cardiac cells and provides data on MST-16 bioactivation under conditions relevant to investigation of cardioprotection of this drug. The analysis of these compounds that differ considerably in their lipophilicity was achieved on the Zorbax SB-Aq column using a mixture of aqueous ammonium formate and methanol as a mobile phase. The biological samples were either diluted or precipitated with methanol, which was followed by acidification for the assay of MST-16. The method was validated for determination of all compounds in the biological materials. The application of the method for analysis of samples fromin vitroexperiments provided important findings, namely, that (1) MST-16 is quickly decomposed in biological environments, (2) the cardiac cells actively metabolize MST-16, and (3) MST-16 readily penetrates into the cardiac cells and is converted into ICRF-154 and EDTA-diamide. These data are useful for the in-depth examination of the cardioprotective potential of this drug.
Four millennia of dairy surplus and deposition revealed through compound-specific stable isotope analysis and radiocarbon dating of Irish bog butters
Authors: Smyth Jessica , Berstan Robert , Casanova Emmanuelle , McCormick Finbar , Mulhall Isabella , Sikora Maeve , Synnott Chris , Evershed Richard P. 
Published: March 2019

AbstractBog butters are large white or yellow waxy deposits regularly discovered within the peat bogs of Ireland and Scotland. They represent an extraordinary survival of prehistoric and later agricultural products, comprising the largest deposits of fat found anywhere in nature. Often found in wooden containers or wrapped in animal bladders, they are considered to have been buried intentionally by past farming communities. While previous analysis has determined that Irish bog butters derive from animal fat, their precise characterisation could not be achieved due to diagenetic compositional alterations during burial. Via compound-specific stable isotope analysis, we provide the first conclusive evidence of a dairy fat origin for the Irish bog butter tradition, which differs from bog butter traditions observed elsewhere. Our research also reveals a remarkably long-lived tradition of deposition and possible curation spanning at least 3500 years, from the Early Bronze Age (c. 1700 BC) to the 17th century AD. This is conclusively established via an extensive suite of both bulk and compound-specific radiocarbon dates.