bluuebunny/crossref_metadata_2025_split huggingface dataset:
A three-dimensional thalamocortical dataset for characterizing brain heterogeneity
Authors: Prasad Judy A. , Balwani Aishwarya H. , Johnson Erik C. , Miano Joseph D. , Sampathkumar Vandana , De Andrade Vincent , Fezzaa Kamel , Du Ming , Vescovi Rafael , Jacobsen Chris , Kording Konrad P. , Gürsoy Doga , Gray Roncal William , Kasthuri Narayanan , Dyer Eva L. 
Published: October 2020

AbstractNeural microarchitecture is heterogeneous, varying both across and within brain regions. The consistent identification of regions of interest is one of the most critical aspects in examining neurocircuitry, as these structures serve as the vital landmarks with which to map brain pathways. Access to continuous, three-dimensional volumes that span multiple brain areas not only provides richer context for identifying such landmarks, but also enables a deeper probing of the microstructures within. Here, we describe a three-dimensional X-ray microtomography imaging dataset of a well-known and validated thalamocortical sample, encompassing a range of cortical and subcortical structures from the mouse brain . In doing so, we provide the field with access to a micron-scale anatomical imaging dataset ideal for studying heterogeneity of neural structure.
A contemporary baseline record of the world’s coral reefs
Authors: Rodriguez-Ramirez Alberto , González-Rivero Manuel , Beijbom Oscar , Bailhache Christophe , Bongaerts Pim , Brown Kristen T. , Bryant Dominic E. P. , Dalton Peter , Dove Sophie , Ganase Anjani , Kennedy Emma V. , Kim Catherine J. S. , Lopez-Marcano Sebastian , Neal Benjamin P. , Radice Veronica Z. , Vercelloni Julie , Beyer Hawthorne L. , Hoegh-Guldberg Ove 
Published: October 2020

AbstractAddressing the global decline of coral reefs requires effective actions from managers, policymakers and society as a whole. Coral reef scientists are therefore challenged with the task of providing prompt and relevant inputs for science-based decision-making. Here, we provide a baseline dataset, covering 1300 km of tropical coral reef habitats globally, and comprised of over one million geo-referenced, high-resolution photo-quadrats analysed using artificial intelligence to automatically estimate the proportional cover of benthic components. The dataset contains information on five major reef regions, and spans 2012–2018, including surveys before and after the 2016 global bleaching event. The taxonomic resolution attained by image analysis, as well as the spatially explicit nature of the images, allow for multi-scale spatial analyses, temporal assessments (decline and recovery), and serve for supporting image recognition developments. This standardised dataset across broad geographies offers a significant contribution towards a sound baseline for advancing our understanding of coral reef ecology and thereby taking collective and informed actions to mitigate catastrophic losses in coral reefs worldwide.
Machine learning-based prediction of microsatellite instability and high tumor mutation burden from contrast-enhanced computed tomography in endometrial cancers
Authors: Veeraraghavan Harini , Friedman Claire F. , DeLair Deborah F. , Ninčević Josip , Himoto Yuki , Bruni Silvio G. , Cappello Giovanni , Petkovska Iva , Nougaret Stephanie , Nikolovski Ines , Zehir Ahmet , Abu-Rustum Nadeem R. , Aghajanian Carol , Zamarin Dmitriy , Cadoo Karen A. , Diaz Luis A. , Leitao Mario M. , Makker Vicky , Soslow Robert A. , Mueller Jennifer J. , Weigelt Britta , Lakhman Yulia 
Published: October 2020

AbstractTo evaluate whether radiomic features from contrast-enhanced computed tomography (CE-CT) can identify DNA mismatch repair deficient (MMR-D) and/or tumor mutational burden-high (TMB-H) endometrial cancers (ECs). Patients who underwent targeted massively parallel sequencing of primary ECs between 2014 and 2018 and preoperative CE-CT were included (n = 150). Molecular subtypes of EC were assigned using DNA polymerase epsilon (POLE) hotspot mutations and immunohistochemistry-based p53 and MMR protein expression. TMB was derived from sequencing, with > 15.5 mutations-per-megabase as a cut-point to define TMB-H tumors. After radiomic feature extraction and selection, radiomic features and clinical variables were processed with the recursive feature elimination random forest classifier. Classification models constructed using the training dataset (n = 105) were then validated on the holdout test dataset (n = 45). Integrated radiomic-clinical classification distinguished MMR-D from copy number (CN)-low-like and CN-high-like ECs with an area under the receiver operating characteristic curve (AUROC) of 0.78 (95% CI 0.58–0.91). The model further differentiated TMB-H from TMB-low (TMB-L) tumors with an AUROC of 0.87 (95% CI 0.73–0.95). Peritumoral-rim radiomic features were most relevant to both classifications (p ≤ 0.044). Radiomic analysis achieved moderate accuracy in identifying MMR-D and TMB-H ECs directly from CE-CT. Radiomics may provide an adjunct tool to molecular profiling, especially given its potential advantage in the setting of intratumor heterogeneity.
MicroRNA dynamics during hibernation of the Australian central bearded dragon (Pogona vitticeps)
Authors: Capraro Alexander , O‘Meally Denis , Waters Shafagh A. , Patel Hardip R. , Georges Arthur , Waters Paul D. 
Published: October 2020

AbstractHibernation is a physiological state employed by many animals that are exposed to limited food and adverse winter conditions. Controlling tissue-specific and organism wide changes in metabolism and cellular function requires precise regulation of gene expression, including by microRNAs (miRNAs). Here we profile miRNA expression in the central bearded dragon (Pogona vitticeps) using small RNA sequencing of brain, heart, and skeletal muscle from individuals in late hibernation and four days post-arousal. A total of 1295 miRNAs were identified in the central bearded dragon genome; 664 of which were novel to central bearded dragon. We identified differentially expressed miRNAs (DEmiRs) in all tissues and correlated mRNA expression with known and predicted target mRNAs. Functional analysis of DEmiR targets revealed an enrichment of differentially expressed mRNA targets involved in metabolic processes. However, we failed to reveal biologically relevant tissue-specific processes subjected to miRNA-mediated regulation in heart and skeletal muscle. In brain, neuroprotective pathways were identified as potential targets regulated by miRNAs. Our data suggests that miRNAs are necessary for modulating the shift in cellular metabolism during hibernation and regulating neuroprotection in the brain. This study is the first of its kind in a hibernating reptile and provides key insight into this ephemeral phenotype.
A possible link between coral reef success, crustose coralline algae and the evolution of herbivory
Authors: Teichert Sebastian , Steinbauer Manuel , Kiessling Wolfgang 
Published: October 2020

AbstractCrustose coralline red algae (CCA) play a key role in the consolidation of many modern tropical coral reefs. It is unclear, however, if their function as reef consolidators was equally pronounced in the geological past. Using a comprehensive database on ancient reefs, we show a strong correlation between the presence of CCA and the formation of true coral reefs throughout the last 150 Ma. We investigated if repeated breakdowns in the potential capacity of CCA to spur reef development were associated with sea level, ocean temperature, CO2concentration, CCA species diversity, and/or the evolution of major herbivore groups. Model results show that the correlation between the occurrence of CCA and the development of true coral reefs increased with CCA diversity and cooler ocean temperatures while the diversification of herbivores had a transient negative effect. The evolution of novel herbivore groups compromised the interaction between CCA and true reef growth at least three times in the investigated time interval. These crises have been overcome by morphological adaptations of CCA.
Association between serum CCL-18 and IL-23 concentrations and disease progression of chronic obstructive pulmonary disease
Authors: Rong Biaoxue , Fu Tian , Rong Congxue , Liu Wen , Li Kai , Liu Hua 
Published: October 2020

AbstractThis study aimed to investigate the association between serum concentrations of chemokine (C–C Motif) ligand 18 (CCL-18) and interleukin 23 (IL-23) and clinical parameters of chronic obstructive pulmonary disease (COPD). The serum concentrations of CCL-18 and IL-23 were tested by enzyme linked immunosorbent assay (ELISA). The association between their concentrations and clinical parameters of COPD patients were analyzed by linear regression, logistic regression and ROC curve. The results showed that the serum concentrations of CCL-18 and IL-23 in COPD patients were increased compared with healthy people (P < 0.001) and that patients with acute exacerbation of COPD (AECOPD) had higher serum CCL-18 and IL-23 concentrations than stable patients (P < 0.001). Synergistic increase of CCL-18 and IL-23 in COPD patients was positively correlated with COPD patients' higher GOLD grade (P < 0.001), higher mMRC score (P < 0.001) and longer medical history (P < 0.001), but negatively correlated with the forced expiratory volume in one second (FEV1)/forced vital capacity (FVC) (P < 0.001) and FEV1% predicted (P < 0.001). The serum concentrations of CCL-18 and IL-23 were most related to the GOLD grade (OR = 2.764 for CCL-18 and OR = 4.215 for IL-23) and detection of both showed considerable sensitivity (72.57% for CCL-18 and 76.92% for IL-23) and specificity (92.50% for CCL-18 and 77.5% for IL-23) in identifying COPD. Increased serum concentrations of CCL-18 and IL-23 correlated with the disease progression of COPD and they could be used as biomarkers for disease evaluation of COPD.
Deletion of CD38 and supplementation of NAD+ attenuate axon degeneration in a mouse facial nerve axotomy model
Authors: Takaso Yuji , Noda Masao , Hattori Tsuyoshi , Roboon Jureepon , Hatano Miyako , Sugimoto Hisashi , Brenner Charles , Yamamoto Yasuhiko , Okamoto Hiroshi , Higashida Haruhiro , Ito Makoto , Yoshizaki Tomokazu , Hori Osamu 
Published: October 2020

AbstractFollowing facial nerve axotomy, nerve function is not fully restored even after reconstruction. This may be attributed to axon degeneration/neuronal death and sustained neuroinflammation. CD38 is an enzyme that catalyses the hydrolysis of nicotinamide adenine dinucleotide (NAD+) and is a candidate molecule for regulating neurodegeneration and neuroinflammation. In this study, we analyzed the effect of CD38 deletion and NAD+supplementation on neuronal death and glial activation in the facial nucleus in the brain stem, and on axon degeneration and immune cell infiltration in the distal portion of the facial nerve after axotomy in mice. Compared with wild-type mice, CD38 knockout (KO) mice showed reduced microglial activation in the facial nucleus, whereas the levels of neuronal death were not significantly different. In contrast, the axon degeneration and demyelination were delayed, and macrophage accumulation was reduced in the facial nerve of CD38 KO mice after axotomy. Supplementation of NAD+with nicotinamide riboside slowed the axon degeneration and demyelination, although it did not alter the level of macrophage infiltration after axotomy. These results suggest that CD38 deletion and supplementation of NAD+may protect transected axon cell-autonomously after facial nerve axotomy.
Occurrence of multiclass endocrine disrupting compounds in a drinking water supply system and associated risks
Authors: Wee Sze Yee , Aris Ahmad Zaharin , Yusoff Fatimah Md. , Praveena Sarva Mangala 
Published: October 2020

AbstractContamination by endocrine disrupting compounds (EDCs) concerns the security and sustainability of a drinking water supply system and human exposure via water consumption. This study analyzed the selected EDCs in source (river water, n = 10) and supply (tap water, n = 155) points and the associated risks. A total of 14 multiclass EDCs was detected in the drinking water supply system in Malaysia. Triclosan (an antimicrobial agent) and 4-octylphenol (a plasticizer) were only detected in the tap water (up to 9.74 and 0.44 ng/L, respectively). Meanwhile, chloramphenicol and 4-nonylphenol in the system were below the method detection limits. Bisphenol A was observed to be highest in tap water at 66.40 ng/L (detection: 100%; median concentration: 0.28 ng/L). There was a significant difference in triclosan contamination between the river and tap water (p < 0.001). Overall, the life groups were estimated at no possible risk of EDCs (risk quotient < 1). Nonetheless, the results concern the transport and impact of EDCs on the drinking water supply system regarding treatment sustainability and water security. Further exploration of smart monitoring and management using Big Data and Internet of Things and the need to invent rapid, robust, sensitive, and efficient sensors is warranted.
The relationship between axial length, age and intraocular pressure in children with primary congenital glaucoma
Authors: Al-Obaida Ibrahim , Al Owaifeer Adi Mohammed , Ahmad Khabir , Malik Rizwan 
Published: October 2020

AbstractWhilst axial length (AxL) from ultrasound examination is a useful clinical parameter for monitoring progression in younger children with glaucoma, distinguishing AxL changes due to raised intraocular pressure (IOP) from age is often challenging. Existing normograms have included a limited number of children with glaucoma. The aim of this study was to evaluate the relationship between AxL with age and IOP in children with primary congenital glaucoma (PCG) and develop a model for expected AxL increase with age. All children (n = 208; 397 eyes) with PCG who attended our tertiary eye care facility from June 2014 and July 2018 and had AxL and IOP measurements were included. The relationship of AxL with age and IOP was studied by applying a LOWESS fit and then mixed effects models. In the final model, age was the most significant factor influencing the growth of AxL (coefficient age 3.14[95% CI 2.91–3.35, p < 0.001], coefficient age2 − 0.53[95% CI, − 0.59 to − 0.47, p < 0.001]), and this association was influenced by the interaction of IOP with sex (p = 0.098 for girls relative to boys), the number of antiglaucoma medications (AGM [p < 0.001 for ≥ 3 AGM]) and glaucoma surgery (p = 0.015). This model enabled us to derive predicted values for clinical use in children with PCG to predict those with progressive glaucoma.
Prevalence of Malassezia species on the skin of HIV-seropositive patients
Authors: Krzyściak Paweł , Bakuła Zofia , Gniadek Agnieszka , Garlicki Aleksander , Tarnowski Mikołaj , Wichowski Michał , Jagielski Tomasz 
Published: October 2020

AbstractMalassezia is a genus of lipophilic yeasts residing on the skin of warm-blooded animals. The correlation between specific species and their involvement in skin diseases has been well researched. However, only very few studies have investigated the distribution of Malassezia spp. on the healthy skin of patients infected with human immunodeficiency virus (HIV). The purpose of this work was to analyze whether the composition of Malassezia spp. isolated from the skin of the HIV-infected patients differs from that of healthy individuals. The study included a total of 96 subjects, who were divided into two equally sized groups: HIV-seropositive and HIV-seronegative. The specimens were collected from the subjects by swabbing four anatomical sites (face, chest, back, and scalp). Species were identified using phenotype-based methods, and the identification of strains isolated from the HIV-seropositive patients was confirmed by PCR sequencing of the rDNA cluster. Malassezia spp. were isolated from 33 (69%) HIV-seropositive patients and 38 (79%) healthy volunteers. It was found that men were much more likely to have their heads colonized with Malassezia spp. than women. The most prevalent species on the skin of both HIV-seropositive and HIV-seronegative individuals were Malassezia sympodialis, M. globosa, and M. furfur, albeit at different proportions in the two populations. The diversity of Malassezia spp. was the highest on the face of the HIV-seropositive patients (Shannon–Weiner Index H = 1.35) and lowest on the back of the healthy volunteers (H = 0.16). The phenotype- and molecular-based identification methods were congruent at 94.9%. It was observed a tendency that the HIV-seropositive patients had higher CD4+ cell counts, indicating higher colonization with Malassezia spp.
Validation of galectin-1 as potential diagnostic biomarker of early rheumatoid arthritis
Authors: Triguero-Martínez Ana , de la Fuente Hortensia , Montes Nuria , Ortiz Ana María , Roy-Vallejo Emilia , Castañeda Santos , González-Alvaro Isidoro , Lamana Amalia 
Published: October 2020

AbstractGalectin 1 (Gal1) is a lectin with a wide cellular expression that functions as a negative regulator of the immune system in several animal models of autoimmune diseases. Identification of patients with rheumatoid arthritis (RA) has improved during the last decade, although there is still a need for biomarkers allowing an early diagnosis. In this regard, it has been recently proposed that Gal1 serum levels are increased in patients with RA compared to the general population. However, this topic is controversial in the literature. In this work, we provide additional information about the potential usefulness of Gal1 serum levels as a biomarker for RA diagnosis. We studied Gal1 serum and synovial fluid levels and clinical parameters in samples from 62 patients with early arthritis belonging to the PEARL study. In addition, 24 healthy donors were studied. We found that both patients fulfilling RA criteria and patients with undifferentiated arthritis showed higher Gal1 levels than healthy donors. Similar findings were observed in synovial fluid, which showed even higher levels than serum. However, we did not find correlation between Gal1 levels and disease activity or disability. Therefore, our results suggest that Gal1 could be a diagnostic but not a severity biomarker.
The cardioprotective effects of the new crystal form of puerarin in isoproterenol-induced myocardial ischemia rats based on metabolomics
Authors: Zhou Yuzhi , Li Mengru , Song Jia , Shi Yongqiang , Qin Xuemei , Gao Zhaolin , Lv Yang , Du Guanhua 
Published: October 2020

AbstractPuerarin has shown unique pharmacological effects on myocardial ischemia (MI). Changing the crystal form is an effective approach to improve the cardioprotective effects of puerarin. However, the mechanisms of the new crystal form of puerarin are unclear. In this study, an electrocardiogram, echocardiography, cardiac marker enzymatic activity, oxidative stress indices, and myocardial histology analysis of cardiac tissues were performed to evaluate the cardioprotective effects of the new crystal form of puerarin. Moreover, serum and cardiac tissue metabolomics based on nuclear magnetic resonance (NMR) were used to investigate the potential mechanism of the new crystal form. The results indicated that the new crystal form of puerarin (30 mg/kg) could improve oxidative stress indices, and these improvements were similar to those of the original crystal form of puerarin (120 mg/kg). The new crystal form of puerarin (30 mg/kg) could effectively improve the activities of cardiac marker enzymes, and the improvement effects were better than those of the original crystal form (120 mg/kg). Moreover, metabolomics analysis showed that amino acid metabolism, oxidative stress and energy metabolism were disturbed after MI and could be improved by puerarin. These results demonstrated that the new crystal form of puerarin was effective in treating MI.
Comparative physiological and transcriptomic analyses of photosynthesis in Sphagneticola calendulacea (L.) Pruski and Sphagneticola trilobata (L.) Pruski
Authors: Cai Min-Ling , Zhang Qi-Lei , Zhang Jun-Jie , Ding Wen-Qiao , Huang Hong-Ying , Peng Chang-Lian 
Published: October 2020

AbstractSphagneticola trilobata (L.) Pruski is one of the fast-growing malignant weeds in South China. It has severely influenced local biodiversity and native plant habitat. Photosynthesis is the material basis of plant growth and development. However, there are few reports on the photosynthetic transcriptome of S. trilobata. In this study, S. trilobata had a relatively large leaf area and biomass. The gas exchange parameters per unit area of leaves, including net photosynthetic capacity (Pn), intercellular CO2 (Ci), stomatal conductance (Gs), transpiration rate (Tr), water use efficiency (WUE), photosynthetic pigment and Rubisco protein content were higher than those of the native plant Sphagneticola calendulacea (L.) Pruski. On this basis, the differences in photosynthesis pathways between the two Sphagneticola species were analyzed by using the Illumina HiSeq platform. The sequencing results for S. trilobata and S. calendulacea revealed 159,366 and 177,069 unigenes, respectively. Functional annotation revealed 119,350 and 150,846 non-redundant protein database annotations (Nr), 96,637 and 115,711 Swiss-Prot annotations, 49,159 and 60,116 Kyoto Encyclopedia of Genes and Genomes annotations (KEGG), and 83,712 and 97,957 Gene Ontology annotations (GO) in S. trilobata and S. calendulacea, respectively. Additionally, our analysis showed that the expression of key protease genes involved in the photosynthesis pathway, particularly CP43, CP47, PsbA and PetC, had high expression levels in leaves of S. trilobata in comparison to native species. Physiological and transcriptomic analyses suggest the high expression of photosynthetic genes ensures the high photosynthetic capacity of leaves, which is one of the inherent advantages underlying the successful invasion by S. trilobata.
B-box transcription factor 28 regulates flowering by interacting with constans
Authors: Liu Yin , Lin Guang , Yin Chunmei , Fang Yuda 
Published: October 2020

AbstractB-box transcription factors (BBXs) are important regulators of flowering, photomorphogenesis, shade-avoidance, abiotic and biotic stresses and plant hormonal pathways. In Arabidopsis, 32 BBX proteins have been identified and classified into five groups based on their structural domains. Little is known about the fifth group members (BBX26–BBX32) and the detailed molecular mechanisms relevant to their functions. Here we identified B-box transcription factor 28 (BBX28) that interacts with Constans (CO), a transcriptional activator of Flowering Locus T (FT). Overexpressing BBX28 leads to late flowering with dramatically decreased FT transcription, and bbx28 deficient mutant displays a weak early flowering phenotype under long days (LD), indicating that BBX28 plays a negative and redundant role in flowering under LD. Additionally, the interaction between BBX28 and CO decreases the recruitment of CO to FT locus without affecting the transcriptional activation activity of CO. Moreover, the N-terminal cysteines, especially those within the B-box domain, are indispensable for the heterodimerization between BBX28 and CO and activation of CO on FT transcription. Genetic evidences show that the later flowering caused by BBX28 overexpression is compromised by CO ectopic expression. Collectively, these results supported that BBX28 functions with CO and FT to negatively regulate Arabidopsis flowering, in which the N-terminal conserved cysteines of BBX28 might play a central role.