bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell RNA sequencing of a European and an African lymphoblastoid cell line
Authors: Osorio Daniel , Yu Xue , Yu Peng , Serpedin Erchin , Cai James J. 
Published: July 2019

AbstractIn biomedical research, lymphoblastoid cell lines (LCLs), often established by in vitro infection of resting B cells with Epstein-Barr virus, are commonly used as surrogates for peripheral blood lymphocytes. Genomic and transcriptomic information on LCLs has been used to study the impact of genetic variation on gene expression in humans. Here we present single-cell RNA sequencing (scRNA-seq) data on GM12878 and GM18502—two LCLs derived from the blood of female donors of European and African ancestry, respectively. Cells from three samples (the two LCLs and a 1:1 mixture of the two) were prepared separately using a 10x Genomics Chromium Controller and deeply sequenced. The final dataset contained 7,045 cells from GM12878, 5,189 from GM18502, and 5,820 from the mixture, offering valuable information on single-cell gene expression in highly homogenous cell populations. This dataset is a suitable reference for population differentiation in gene expression at the single-cell level. Data from the mixture provide additional valuable information facilitating the development of statistical methods for data normalization and batch effect correction.
Contrapositive logic suggests space radiation not having a strong impact on mortality of US astronauts and Soviet and Russian cosmonauts
Authors: Reynolds Robert J. , Bukhtiyarov Igor V. , Tikhonova Galina I. , Day Steven M. , Ushakov Igor B. , Gorchakova Tatyana Y. U. 
Published: July 2019

AbstractSpace travelers are exposed to unique forms of ionizing radiation that pose potentially serious health hazards. Prior analyses have attempted to quantify excess mortality risk for astronauts exposed to space radiation, but low statistical power has frustrated inferences. If exposure to deep space radiation were causally linked to deaths due to two particular causes, e.g., cancer and cardiovascular disease, then those cause-specific deaths would not be statistically independent. In this case, a Kaplan-Meier survival curve for a specific cause that treats deaths due to competing causes as uninformative censored events would result in biased estimates of survival probabilities. Here we look for evidence of a deleterious effect of historical exposure to space radiation by assessing whether or not there is evidence for such bias in Kaplan-Meier estimates of survival probabilities for cardiovascular disease and cancer. Evidence of such bias may implicate space radiation as a common causal link to these two disease processes. An absence of such evidence would be evidence that no such common causal link to radiation exposure during space travel exists. We found that survival estimates from the Kaplan-Meier curves were largely congruent with those of competing risk methods, suggesting that if ionizing radiation is impacting the risk of death due to cancer and cardiovascular disease, the effect is not dramatic.
Semen cryopreservation for the Mediterranean brown trout of the Biferno River (Molise-Italy): comparative study on the effects of basic extenders and cryoprotectants
Authors: Di Iorio Michele , Esposito Stefano , Rusco Giusy , Roncarati Alessandra , Miranda Marsia , Gibertoni Pier Paolo , Cerolini Silvia , Iaffaldano Nicolaia 
Published: July 2019

AbstractThis study was designed to optimize the semen freezing protocol of the native Mediterranean brown trout inhabiting the Molise rivers through two experiments: an in vitro analysis of the effects of two basic extenders combined with three cryoprotectants on post-thaw semen quality; and an in vivo test to assess the fertilization and hatching rate. Semen was diluted at a ratio of 1:3 in a freezing medium composed of a glucose extender (A) or mineral extender (B). Each basic component contained 10% dimethylsulfoxide, dimethylacetamide or methanol. The post-semen quality was evaluated considering motility, duration of motility, viability and DNA integrity. The basic extender and cryoprotectant were shown to have significant effects on these variables, and the best results were obtained using extender A or B combined with dimethylsulfoxide (P < 0.05). These freezing protocols were selected for fertilization trials in vivo. Fertilization and hatching rates were significantly higher in fresh semen. No significant differences were observed in frozen semen using extender A or B, although higher percentages of eyed eggs and hatching rates were recorded using extender A. According to our in vitro and in vivo results, the glucose-based extender and dimethylsulfoxide emerged as the best combination for an effective cryopreservation protocol for semen of this trout.
A Characterization of the DNA Data Storage Channel
Authors: Heckel Reinhard , Mikutis Gediminas , Grass Robert N. 
Published: July 2019

AbstractOwing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many short DNA molecules that are stored in an unordered way, and can only be read by sampling from this DNA pool. Moreover, imperfections in writing (synthesis), reading (sequencing), storage, and handling of the DNA, in particular amplification via PCR, lead to a loss of DNA molecules and induce errors within the molecules. In order to design DNA storage systems, a qualitative and quantitative understanding of the errors and the loss of molecules is crucial. In this paper, we characterize those error probabilities by analyzing data from our own experiments as well as from experiments of two different groups. We find that errors within molecules are mainly due to synthesis and sequencing, while imperfections in handling and storage lead to a significant loss of sequences. The aim of our study is to help guide the design of future DNA data storage systems by providing a quantitative and qualitative understanding of the DNA data storage channel.
A Rapid Fenton treatment of bio-treated dyeing and finishing wastewater at second-scale intervals: kinetics by stopped-flow technique and application in a full-scale plant
Authors: Chen Yunlu , Cheng Yunqin , Guan Xiaohong , Liu Yan , Nie Jianxin , Li Chenxi 
Published: July 2019

AbstractA rapid Fenton treatment at second-scale intervals was investigated for further removal of organic compounds in the effluent of bio-treated dyeing and finishing wastewater (BDFW). The decolorization kinetics was studied using a stopped-flow spectrophotometer (SFS) at second-scale intervals. A combined first-order model was found to fit well for the decrease of both methylene blue and rhodamine B in SFS as well as SCOD (soluble chemical oxygen demand) and DOC (dissolved organic carbon) in real BDFW in batch test during Fenton oxidation. A full-scale plant with treatment capacity of 400,000 m3·d−1 was designed and has been run continuously based on the results of the stopped-flow study to treat the effluent of BDFW using Fenton oxidation in 16 pipeline reactors, each with a volume of 6.9 m3 and 24 s of reaction time since 2014. The COD, SCOD and DOC decreased from 140, 110 and 35 mg·L−1 to 77, 71 and 26 mg·L−1 respectively, which can meet the latest strict discharge limitations. The natural fluorescent substances detected in the BDFW were completely removed. The main organic pollutants in the BDFW can be significantly reduced using both gas chromatography-mass spectrometry and ultrahigh-performance liquid chromatography-hybrid quadrupole time-of-flight mass spectrometry. The rapid Fenton reaction applied in pipeline reactors at second intervals has several advantages over the conventional Fenton’s process such as much shorter reaction time at second scale intervals, no need to build extra pH adjustment or reaction tanks, simple operation, low capital cost, etc.
Scanning tunneling microscopy on cleaved Mn3Sn(0001) surface
Authors: Yang Hung-Hsiang , Lee Chi-Cheng , Yoshida Yasuo , Ikhlas Muhammad , Tomita Takahiro , Nugroho Agustinus , Ozaki Taisuke , Nakatsuji Satoru , Hasegawa Yukio 
Published: July 2019

AbstractWe have studied in-situ cleaved (0001) surfaces of the magnetic Weyl semimetal Mn3Sn by low-temperature scanning tunneling microscopy and spectroscopy (STM/S). It was found that freshly cleaved Mn3Sn surfaces are covered with unknown clusters, and the application of voltage pulses in the tunneling condition was needed to achieve atomically flat surfaces. STM topographs taken on the flat terrace show a bulk-terminated 1 × 1 honeycomb lattice with the Sn site brightest. First-principles calculations reveal that the brightest contrast at the Sn site originates from the surrounding surface Mn d orbitals. Tunneling spectroscopy performed on the as-cleaved and voltage-pulsed surfaces show a prominent semimetal valley near the Fermi energy.
Analysis of Minerals as Electrode Materials for Ca-based Rechargeable Batteries
Authors: Torres A. , Luque F. J. , Tortajada J. , Arroyo-de Dompablo M. E. 
Published: July 2019

AbstractRechargeable lithium-ion batteries dominate the consumer electronics and electric vehicle markets. However, concerns on Li availability have prompted the development of alternative high energy density electrochemical energy storage systems. Rechargeable batteries based on a Ca metal anode can exhibit advantages in terms of energy density, safety and cost. The development of rechargeable Ca metal batteries requires the identification of suitable high specific energy cathode materials. This work focuses on Ca-bearing minerals because they represent stable and abundant compounds. Suitable minerals should contain a transition metal able of being reversibly reduced and oxidized, which points to several major classes of silicates and carbonates: olivine (CaFeSiO4; kirschsteinite), pyroxene (CaFe/MnSi2O6; hedenbergite and johannsenite, respectively), garnet (Ca3Fe/Cr2Si3O12; andradite and uvarovite, respectively), amphibole (Ca2Fe5Si8O22(OH)2; ferroactinolite) and double carbonates (CaMn(CO3)2; kutnahorite and CaFe(CO3)2; ankerite). This work discusses their electrode characteristics based on crystal chemistry analysis and density functional theory (DFT) calculations. The results indicate that upon Ca deintercalation, compounds such as pyroxene, garnet and double carbonate minerals could display high theoretical energy densities (ranging from 780 to 1500 Wh/kg) with moderate structural modifications. As a downside, DFT calculations indicate a hampered Ca mobility in their crystal structures. The overall analysis then disregards olivine, garnet, pyroxene, amphibole and double carbonates as structural types for future Ca-cathode materials design.
Characterization of bacterial communities in wastewater with enhanced taxonomic resolution by full-length 16S rRNA sequencing
Authors: Numberger Daniela , Ganzert Lars , Zoccarato Luca , Mühldorfer Kristin , Sauer Sascha , Grossart Hans-Peter , Greenwood Alex D. 
Published: July 2019

AbstractWastewater treatment is crucial to environmental hygiene in urban environments. However, wastewater treatment plants (WWTPs) collect chemicals, organic matter, and microorganisms including pathogens and multi-resistant bacteria from various sources which may be potentially released into the environment via WWTP effluent. To better understand microbial dynamics in WWTPs, we characterized and compared the bacterial community of the inflow and effluent of a WWTP in Berlin, Germany using full-length 16S rRNA gene sequences, which allowed for species level determination in many cases and generally resolved bacterial taxa. Significantly distinct bacterial communities were identified in the wastewater inflow and effluent samples. Dominant operational taxonomic units (OTUs) varied both temporally and spatially. Disease associated bacterial groups were efficiently reduced in their relative abundance from the effluent by the WWTP treatment process, except for Legionella and Leptospira species which demonstrated an increase in relative proportion from inflow to effluent. This indicates that WWTPs, while effective against enteric bacteria, may enrich and release other potentially pathogenic bacteria into the environment. The taxonomic resolution of full-length 16S rRNA genes allows for improved characterization of potential pathogenic taxa and other harmful bacteria which is required to reliably assess health risk.
Orographic lift shapes flight routes of gulls in virtually flat landscapes
Authors: Sage Elspeth , Bouten Willem , Hoekstra Bart , Camphuysen Kees C. J. , Shamoun-Baranes Judy 
Published: July 2019

AbstractInteractions between landscape and atmosphere result in a dynamic flight habitat which birds may use opportunistically to save energy during flight. However, their ability to utilise these dynamic landscapes and its influence on shaping movement paths is not well understood. We investigate the degree to which gulls utilise fine scale orographic lift created by wind deflected upwards over landscape features in a virtually flat landscape. Using accelerometer measurements and GPS tracking, soaring flight is identified and analysed with respect to orographic lift, modelled using high-resolution digital elevation models and wind measurements. The relationship between orographic lift and flight routes suggests gulls have advanced knowledge of their aerial surroundings and the benefits to be gained from them, even regarding small features such as tree lines. We show that in a landscape constantly influenced by anthropogenic change, the structure of our landscape has an aerial impact on flight route connectivity and costs.
The Homeobox gene,
HOXB13, Regulates a Mitotic Protein-Kinase Interaction Network in Metastatic Prostate Cancers
Authors: Yao Jiqiang , Chen Yunyun , Nguyen Duy T. , Thompson Zachary J. , Eroshkin Alexey M. , Nerlakanti Niveditha , Patel Ami K. , Agarwal Neha , Teer Jamie K. , Dhillon Jasreman , Coppola Domenico , Zhang Jingsong , Perera Ranjan , Kim Youngchul , Mahajan Kiran 
Published: July 2019

AbstractHOXB13, a homeodomain transcription factor, is linked to recurrence following radical prostatectomy. While HOXB13 regulates Androgen Receptor (AR) functions in a context dependent manner, its critical effectors in prostate cancer (PC) metastasis remain largely unknown. To identify HOXB13 transcriptional targets in metastatic PCs, we performed integrative bioinformatics analysis of differentially expressed genes (DEGs) in the proximity of the human prostate tumor-specific AR binding sites. Unsupervised Principal Component Analysis (PCA) led to a focused core HOXB13 target gene-set referred to as HOTPAM9 (HOXB13 Targets separating Primary And Metastatic PCs). HOTPAM9 comprised 7 mitotic kinase genes overexpressed in metastatic PCs, TRPM8, and the heat shock protein HSPB8, whose levels were significantly lower in metastatic PCs compared to the primary disease. The expression of a two-gene set, CIT and HSPB8 with an overall balanced accuracy of 98.8% and a threshold value of 0.2347, was sufficient to classify metastasis. HSPB8 mRNA expression was significantly increased following HOXB13 depletion in multiple metastatic CRPC models. Increased expression of HSPB8 by the microtubule inhibitor Colchicine or by exogenous means suppressed migration of mCRPC cells. Collectively, our results indicate that HOXB13 promotes metastasis of PCs by coordinated regulation of mitotic kinases and blockade of a putative tumor suppressor gene.
Prognostic implications of post-percutaneous coronary intervention neutrophil-to-lymphocyte ratio on infarct size and clinical outcomes in patients with acute myocardial infarction
Authors: Hong David , Choi Ki Hong , Song Young Bin , Lee Joo Myung , Park Taek Kyu , Yang Jeong Hoon , Hahn Joo-Yong , Choi Jin-Ho , Choi Seung-Hyuk , Kim Sung Mok , Choe Yeonhyeon , Kim Eun Kyoung , Chang Sung A. , Lee Sang-Chol , Oh Jae K. , Gwon Hyeon-Cheol 
Published: July 2019

AbstractThis study evaluated the prognostic implications of post-percutaneous coronary intervention (PCI) neutrophil-to-lymphocyte ratio (NLR) in patients with acute myocardial infarction (AMI). A total of 309 patients with AMI who underwent cardiac magnetic resonance imaging (CMR) and a complete blood cell count within 24 hours before and after PCI were enrolled. Primary outcome was infarct size. Patients were assigned to high (n = 118) or low (n = 191) NLR groups according to the best cut-off value of 3.88. Infarct size (% of total left ventricular mass) was significantly higher in the high NLR group than in the low NLR group (24.1 ± 11.0 vs. 16.7 ± 9.1, p < 0.001). Post-PCI NLR ≥ 3.88 was associated with risk of a large-sized infarction (≥20%) (OR 2.91, 95% CI 1.73–4.88, p < 0.001). The risk of MACE was also significantly higher in the high NLR group than in the low NLR group (15.8% vs. 7.4%, HR 2.60, 95% CI 1.21–5.60, p = 0.015). Among patients with AMI who underwent PCI, high post-PCI NLR value was associated with higher risk of large-sized infarction as measured by CMR, as well as adverse clinical outcomes. Our findings suggest that post-PCI NLR is a useful tool for risk assessment in patients with AMI who undergo PCI.
Modafinil treatment modulates functional connectivity in stroke survivors with severe fatigue
Authors: Visser Milanka M. , Goodin Peter , Parsons Mark W. , Lillicrap Thomas , Spratt Neil J. , Levi Christopher R. , Bivard Andrew 
Published: July 2019

AbstractPost-stroke fatigue has a significant impact on stroke survivors’ mental and physical well-being. Our recent clinical trial showed significant reduction of post-stroke fatigue with modafinil treatment, however functional connectivity changes in response to modafinil have not yet been explored in stroke survivors with post-stroke fatigue. Twenty-eight participants (multidimensional fatigue inventory-20 ≥ 60) had MRI scans at baseline, and during modafinil and placebo treatment. Resting-state functional MRI data were obtained, and independent component analysis was used to extract functional networks. Resting-state functional connectivity (rsFC) was examined between baseline, modafinil and placebo treatment using permutation testing with threshold-free cluster enhancement. Overall twenty-eight participants (mean age: 62 ± 14.3, mean baseline MFI-20: 72.3 ± 9.24) were included. During modafinil treatment, increased rsFC was observed in the right hippocampus (p = 0.004, 11 voxels) compared to placebo. This coincided with lower rsFC in the left frontoparietal (inferior parietal lobule, p = 0.023, 13 voxels), somatosensory (primary somatosensory cortex; p = 0.009, 32 voxels) and mesolimbic network (temporal pole, p = 0.016, 35 voxels). In conclusion, modafinil treatment induces significant changes in rsFC in post-stroke fatigue. This modulation of rsFC may relate to a reduction of post-stroke fatigue; however, the relationship between sensory processing, neurotransmitter expression and fatigue requires further exploration.
BRCA1 regulates the cancer stem cell fate of breast cancer cells in the context of hypoxia and histone deacetylase inhibitors
Authors: Kim Hoon , Lin Qun , Yun Zhong 
Published: July 2019

AbstractCancer cell stemness is essential for enabling malignant progression and clonal evolution. Cancer cell fate is likely determined by complex mechanisms involving both cell-intrinsic pathways and stress signals from tumor microenvironment. In this study, we examined the role of the tumor suppressor BRCA1 and hypoxia in the regulation of cancer cell stemness using genetically matched breast cancer cell lines. We have found that BRCA1, a multifunctional protein involved in DNA repair and epigenetic regulation, plays a critical role in the regulation of cancer stem cell (CSC)-like characteristics. Reconstitution of BRCA1 resulted in significant decrease of the CSC-like populations in breast cancer cells whereas down-regulation of BRCA1 resulted in significant increase of the CSC-like populations. Furthermore, the BRCA1-reconstituted tumor cells are more sensitive to the histone deacetylase (HDAC) inhibitor-induced loss of stemness than the BRCA1-deficient cells are. Surprisingly, hypoxia preferentially blocks HDAC inhibitor-induced differentiation of the BRCA1-reconstituted breast cancer cells. In light of the increasing numbers of clinical trials involving HDAC inhibitors in human cancers, our observations strongly suggest that the BRCA1 status and tumor hypoxia should be considered as potentially important clinical parameters that may affect the therapeutic efficacy of HDAC inhibitors.
Reproduction of molecular subtypes of gastric adenocarcinoma by transcriptome sequencing of archival tissue
Authors: Heo You Jeong , Park Charny , Yu Doyeong , Lee Jeeyun , Kim Kyoung-Mee 
Published: July 2019

AbstractGastric cancer (GC) is a heterogeneous disease, so molecular classification is important for selecting the most appropriate treatment strategies for GC patients. To be applicable in the clinic, there is an urgent need for a platform that will allow screening real-life archival tissue specimens. For this purpose, we performed RNA sequencing of 50 samples from our Asian Cancer Research Group (ACRG) GC cohort to reproduce the molecular subtypes of GC using archival tissues with different platforms. We filtered out genes from the epithelial-to-mesenchymal transition (EMT) and microsatellite instability-high (MSI) signatures (coefficient ≤ 0.4) followed by the ACRG molecular subtype strategy. Overall accuracy of reproduction of ACRG subtype was 66% (33/50). Given the importance of EMT subtype in future clinical trials, we further developed the minimum number of genes (10 genes) for EMT signatures correlating highly with the original EMT signatures (correlation ≥ 0.65). Using our 10-gene model, we could classify EMT subtypes with high sensitivity (0.9576) and specificity (0.811). In conclusion, we reproduced ACRG GC subtypes using different platforms and could predict EMT subtypes with 10 genes and are now planning to use them in our prospective clinical study of precision oncology in GC.