bluuebunny/crossref_metadata_2025_split huggingface dataset:
The non-coding RNA landscape of human hematopoiesis and leukemia
Authors: Schwarzer Adrian , Emmrich Stephan , Schmidt Franziska , Beck Dominik , Ng Michelle , Reimer Christina , Adams Felix Ferdinand , Grasedieck Sarah , Witte Damian , Käbler Sebastian , Wong Jason W. H. , Shah Anushi , Huang Yizhou , Jammal Razan , Maroz Aliaksandra , Jongen-Lavrencic Mojca , Schambach Axel , Kuchenbauer Florian , Pimanda John E. , Reinhardt Dirk , Heckl Dirk , Klusmann Jan-Henning 
Published: August 2017

AbstractNon-coding RNAs have emerged as crucial regulators of gene expression and cell fate decisions. However, their expression patterns and regulatory functions during normal and malignant human hematopoiesis are incompletely understood. Here we present a comprehensive resource defining the non-coding RNA landscape of the human hematopoietic system. Based on highly specific non-coding RNA expression portraits per blood cell population, we identify unique fingerprint non-coding RNAs—such as LINC00173 in granulocytes—and assign these to critical regulatory circuits involved in blood homeostasis. Following the incorporation of acute myeloid leukemia samples into the landscape, we further uncover prognostically relevant non-coding RNA stem cell signatures shared between acute myeloid leukemia blasts and healthy hematopoietic stem cells. Our findings highlight the importance of the non-coding transcriptome in the formation and maintenance of the human blood hierarchy.
Single-cell analyses identify bioengineered niches for enhanced maintenance of hematopoietic stem cells
Authors: Roch Aline , Giger Sonja , Girotra Mukul , Campos Vasco , Vannini Nicola , Naveiras Olaia , Gobaa Samy , Lutolf Matthias P. 
Published: August 2017

AbstractThe in vitro expansion of long-term hematopoietic stem cells (HSCs) remains a substantial challenge, largely because of our limited understanding of the mechanisms that control HSC fate choices. Using single-cell multigene expression analysis and time-lapse microscopy, here we define gene expression signatures and cell cycle hallmarks of murine HSCs and the earliest multipotent progenitors (MPPs), and analyze systematically single HSC fate choices in culture. Our analysis revealed twelve differentially expressed genes marking the quiescent HSC state, including four genes encoding cell–cell interaction signals in the niche. Under basal culture conditions, most HSCs rapidly commit to become early MPPs. In contrast, when we present ligands of the identified niche components such as JamC or Esam within artificial niches, HSC cycling is reduced and long-term multipotency in vivo is maintained. Our approach to bioengineer artificial niches should be useful in other stem cell systems.
Fourteen sequence variants that associate with multiple sclerosis discovered by meta-analysis informed by genetic correlations
Authors: Olafsson Sigurgeir , Stridh Pernilla , Bos Steffan Daniël , Ingason Andres , Euesden Jack , Sulem Patrick , Thorleifsson Gudmar , Gustafsson Omar , Johannesson Ari , Geirsson Arni J. , Thorsson Arni V. , Sigurgeirsson Bardur , Ludviksson Bjorn Runar , Olafsson Elias , Kristjansdottir Helga , Jonasson Jon G. , Olafsson Jon Hjaltalin , Orvar Kjartan B. , Benediktsson Rafn , Bjarnason Ragnar , Kristjansdottir Sjofn , Gislason Thorarinn , Valdimarsson Trausti , Mikaelsdottir Evgenia , Sigurdsson Snaevar , Jonsson Stefan , Rafnar Thorunn , Aarsland Dag , Djurovic Srdjan , Fladby Tormod , Knudsen Gun Peggy , Celius Elisabeth G. , Myhr Kjell-Morten , Grondal Gerdur , Steinsson Kristjan , Valdimarsson Helgi , Bjornsson Sigurdur , Bjornsdottir Unnur S. , Bjornsson Einar S , Nilsson Bjorn , Andreassen Ole A. , Alfredsson Lars , Hillert Jan , Kockum Ingrid Skelton , Masson Gisli , Thorsteinsdottir Unnur , Gudbjartsson Daniel F. , Stefansson Hreinn , Hjaltason Haukur , Harbo Hanne F. , Olsson Tomas , Jonsdottir Ingileif , Stefansson Kari 
Published: August 2017

AbstractA meta-analysis of publicly available summary statistics on multiple sclerosis combined with three Nordic multiple sclerosis cohorts (21,079 cases, 371,198 controls) revealed seven sequence variants associating with multiple sclerosis, not reported previously. Using polygenic risk scores based on public summary statistics of variants outside the major histocompatibility complex region we quantified genetic overlap between common autoimmune diseases in Icelanders and identified disease clusters characterized by autoantibody presence/absence. As multiple sclerosis-polygenic risk scores captures the risk of primary biliary cirrhosis and vice versa (P = 1.6 × 10−7, 4.3 × 10−9) we used primary biliary cirrhosis as a proxy-phenotype for multiple sclerosis, the idea being that variants conferring risk of primary biliary cirrhosis have a prior probability of conferring risk of multiple sclerosis. We tested 255 variants forming the primary biliary cirrhosis-polygenic risk score and found seven multiple sclerosis-associating variants not correlated with any previously established multiple sclerosis variants. Most of the variants discovered are close to or within immune-related genes. One is a low-frequency missense variant in TYK2, another is a missense variant in MTHFR that reduces the function of the encoded enzyme affecting methionine metabolism, reported to be dysregulated in multiple sclerosis brain.
Interface strength and degradation of adhesively bonded porous aluminum oxides
Authors: Abrahami Shoshan T. , de Kok John M. M. , Gudla Visweswara C. , Ambat Rajan , Terryn Herman , Mol Johannes M. C. 
Published: August 2017

AbstractFor more than six decades, chromic acid anodizing has been the main step in the surface treatment of aluminum for adhesively bonded aircraft structures. Soon this process, known for producing a readily adherent oxide with an excellent corrosion resistance, will be banned by strict international environmental and health regulations. Replacing this traditional process in a high-demanding and high-risk industry such as aircraft construction requires an in-depth understanding of the underlying adhesion and degradation mechanisms at the oxide/resin interface resulting from alternative processes. The relationship between the anodizing conditions in sulfuric and mixtures of sulfuric and phosphoric acid electrolytes and the formation and durability of bonding under various environmental conditions was investigated. Scanning electron microscopy was used to characterize the oxide features. Selected specimens were studied with transmission electron microscopy coupled with energy-dispersive X-ray spectroscopy to measure resin concentration within structurally different porous anodic oxide layers as a function of depth. Results show that there are two critical morphological aspects for strong and durable bonding. First, a minimum pore size is pivotal for the formation of a stable interface, as reflected by the initial peel strengths. Second, the increased surface roughness of the oxide/resin interface caused by extended chemical dissolution at higher temperature and higher phosphoric acid concentration is crucial to assure bond durability under water ingress. There is, however, an upper limit to the beneficial amount of anodic dissolution above which bonds are prone for corrosive degradation. Morphology is, however, not the only prerequisite for good bonding and bond performance also depends on the oxides’ chemical composition.
Prognostic value from integrative analysis of transcription factors c-Jun and Fra-1 in oral squamous cell carcinoma: a multicenter cohort study
Authors: Xu Hao , Jin Xin , Yuan Yao , Deng Peng , Jiang Lu , Zeng Xin , Li Xiao-Song , Wang Zhi-Yong , Chen Qian-Ming 
Published: August 2017

AbstractTranscription factors c-Jun and Fra-1 have been reported to play a role during the initiation and progression in oral squamous cell carcinoma (OSCC). However, cohort studies are rarely reported. Here is an integrative analysis of their prognostic value in OSCC through a multicenter cohort study.313 OSCC patients were included in this study and received regular follow-up. The survival rate and hazard ratios(HR) were generated by survival analysis. The concordance probability and receiver operating characteristic curve area were chosen to measure the model discrimination. High expressions of c-Jun or Fra-1 were associated with poor prognosis, meanwhile the high expression of Fra-1 meant worse prognosis of patients than the high expression of c-Jun. Besides, the interaction effect of c-Jun and Fra-1 was antagonism, when the expression of c-Jun and Fra-1 was both high, the HR was lower than the hazard ratio when only the Fra-1 was at high expression. c-Jun and Fra-1 were both proved to be high risky predictors of death in OSCC, the antagonistic effect suggested that these biomarkers’ activities could be influenced by each other. It may provide a new sight for the studies of OSCC prognosis and treatment.
Effects of prey of different nutrient quality on elemental nutrient budgets in Noctiluca scintillans
Authors: Zhang Shuwen , Liu Hongbin , Glibert Patricia M. , Guo Cui , Ke Ying 
Published: August 2017

AbstractNoctiluca scintillans (Noctiluca) is a cosmopolitan red tide forming heterotrophic dinoflagellate. In this study, we investigated its ingestion, elemental growth yield and excretion when supplied with different quality food (nutrient-balanced, N-limited and P-limited). Total cellular elemental ratios of Noctiluca were nearly homeostatic, but the ratio of its intracellular NH4+ and PO43− was weakly regulated. Noctiluca thus seems able to differentially allocate N and P to organic and inorganic pools to maintain overall homeostasis, and it regulated its internal N more strongly and efficiently than P. The latter was substantiated by its comparatively stable C:N ratio and compensatory feeding on N-limited prey. Using both starvation experiments and mass balance models, it was found that excretion of C, N, and P by Noctiluca is highly affected by prey nutritional quality. However, based on modeling results, nutrients seem efficiently retained in actively feeding Noctiluca for reproduction rather than directly released as was shown experimentally in starved cells. Moreover, actively feeding Noctiluca tend to retain P and preferentially release N, highlighting its susceptible to P-limitation. Recycling of N and P by Noctiluca may supply substantial nutrients for phytoplankton growth, especially following bloom senescence.
Transcriptome profiling of mouse brains with qkI-deficient oligodendrocytes reveals major alternative splicing defects including self-splicing
Authors: Darbelli Lama , Choquet Karine , Richard Stéphane , Kleinman Claudia L. 
Published: August 2017

AbstractThe qkI gene encodes a family of RNA binding proteins alternatively spliced at its 3′ end, giving rise to three major spliced isoforms: QKI-5, QKI-6 and QKI-7. Their expression is tightly regulated during brain development with nuclear QKI-5 being the most abundant during embryogenesis followed by QKI-6 and QKI-7 that peak during myelination. Previously, we generated a mouse conditional qkI allele where exon 2 is excised using Olig2-Cre resulting in QKI-deficient oligodendrocytes (OLs). These mice have dysmyelination and die at the third post-natal week. Herein, we performed a transcriptomic analysis of P14 mouse brains of QKI-proficient (QKI
FL/FL;-
) and QKI-deficient (QKI
FL/FL;Olig2-Cre
) OLs. QKI deficiency results in major global changes of gene expression and RNA processing with >1,800 differentially expressed genes with the top categories being axon ensheathment and myelination. Specific downregulated genes included major myelin proteins, suggesting that the QKI proteins are key regulators of RNA metabolism in OLs. We also identify 810 alternatively spliced genes including known QKI targets, MBP and Nfasc. Interestingly, we observe in QKI
FL/FL;Olig2-Cre
a switch in exon 2-deficient qkI mRNAs favoring the expression of the qkI-5 rather than the qkI-6 and qkI-7. These findings define QKI as regulators of alternative splicing in OLs including self-splicing.
Lithium Titanate/Carbon Nanotubes Composites Processed by Ultrasound Irradiation as Anodes for Lithium Ion Batteries
Authors: Coelho João , Pokle Anuj , Park Sang-Hoon , McEvoy Niall , Berner Nina C. , Duesberg Georg S. , Nicolosi Valeria 
Published: August 2017

AbstractIn this work, lithium titanate nanoparticles (nLTO)/single wall carbon nanotubes (SWCNT) composite electrodes are prepared by the combination of an ultrasound irradiation and ultrasonic spray deposition methods. It was found that a mass fraction of 15% carbon nanotubes optimizes the electrochemical performance of nLTO electrodes. These present capacities as high as 173, 130, 110 and 70 mAh.g−1at 0.1C, 1C, 10C and 100C, respectively. Moreover, after 1000 cycles at 1C, the nLTO/SWCNT composites present a capacity loss of just 9% and a Coulombic efficiency of 99.8%. Therefore, the presented methodology might be extended to other suitable active materials in order to manufacture binder free electrodes with optimal energy storage capabilities.
Differential impact in young and older individuals of blue-enriched white light on circadian physiology and alertness during sustained wakefulness
Authors: Gabel Virginie , Reichert Carolin F. , Maire Micheline , Schmidt Christina , Schlangen Luc J. M. , Kolodyazhniy Vitaliy , Garbazza Corrado , Cajochen Christian , Viola Antoine U. 
Published: August 2017

AbstractWe tested the effect of different lights as a countermeasure against sleep-loss decrements in alertness, melatonin and cortisol profile, skin temperature and wrist motor activity in healthy young and older volunteers under extendend wakefulness. 26 young [mean (SE): 25.0 (0.6) y)] and 12 older participants [(mean (SE): 63.6 (1.3) y)] underwent 40-h of sustained wakefulness during 3 balanced crossover segments, once under dim light (DL: 8 lx), and once under either white light (WL: 250 lx, 2,800 K) or blue-enriched white light (BL: 250 lx, 9,000 K) exposure. Subjective sleepiness, melatonin and cortisol were assessed hourly. Skin temperature and wrist motor activity were continuously recorded. WL and BL induced an alerting response in both the older (p = 0.005) and the young participants (p = 0.021). The evening rise in melatonin was attentuated under both WL and BL only in the young. Cortisol levels were increased and activity levels decreased in the older compared to the young only under BL (p = 0.0003). Compared to the young, both proximal and distal skin temperatures were lower in older participants under all lighting conditions. Thus the color temperature of normal intensity lighting may have differential effects on circadian physiology in young and older individuals.
3D printed personalized titanium plates improve clinical outcome in microwave ablation of bone tumors around the knee
Authors: Ma Limin , Zhou Ye , Zhu Ye , Lin Zefeng , Chen Lingling , Zhang Yu , Xia Hong , Mao Chuanbin 
Published: August 2017

AbstractMicrowave ablation has been widely accepted in treating bone tumor. However, its procedure is time-consuming and usually results in postoperative fractures. To solve this problem, we designed and fabricated titanium plates customized to the patients’ bone structures. The personalized titanium plates were then used for fixation after the removal of tumorous tissue. Specifically, 3D models of tumor-bearing bone segments were constructed by using computed tomography (CT) and magnetic resonance imaging (MRI). The 3D models were used to design the personalized titanium plates. The plate model was transferred into a numerical control machine for manufacturing the personalized titanium plates by 3D printing. The plates were then surgically implanted for reconstruction assistance following microwave-induced hyperthermia to remove the bone tumor. Implementation parameters and knee functions were then evaluated. No postoperative fractures, implant failures or loosening problems occurred; mean Musculoskeletal Tumor Society score was 27.17 from the latest follow-up. Mean maximum flexion of affected knees was 114.08°. The results of knee gait analysis were comparable with normal population data. Our work suggests that personalized titanium plates can significantly improve the clinical outcomes in the surgical removal of bone tumor. This study represents the first-time effort in using personalized titanium plates for such surgery.
Novel animal model defines genetic contributions for neuron-to-neuron transfer of α-synuclein
Authors: Tyson Trevor , Senchuk Megan , Cooper Jason F. , George Sonia , Van Raamsdonk Jeremy M. , Brundin Patrik 
Published: August 2017

AbstractCell-to-cell spreading of misfolded α-synuclein (α-syn) is suggested to contribute to the progression of neuropathology in Parkinson’s disease (PD). Compelling evidence supports the hypothesis that misfolded α-syn transmits from neuron-to-neuron and seeds aggregation of the protein in the recipient cells. Furthermore, α-syn frequently appears to propagate in the brains of PD patients following a stereotypic pattern consistent with progressive spreading along anatomical pathways. We have generated a C. elegans model that mirrors this progression and allows us to monitor α-syn neuron-to-neuron transmission in a live animal over its lifespan. We found that modulation of autophagy or exo/endocytosis, affects α-syn transfer. Furthermore, we demonstrate that silencing C. elegans orthologs of PD-related genes also increases the accumulation of α-syn. This novel worm model is ideal for screening molecules and genes to identify those that modulate prion-like spreading of α-syn in order to target novel strategies for disease modification in PD and other synucleinopathies.
CODA: Integrating multi-level context-oriented directed associations for analysis of drug effects
Authors: Yu Hasun , Jung Jinmyung , Yoon Seyeol , Kwon Mijin , Bae Sunghwa , Yim Soorin , Lee Jaehyun , Kim Seunghyun , Kang Yeeok , Lee Doheon 
Published: August 2017

AbstractIn silico network-based methods have shown promising results in the field of drug development. Yet, most of networks used in the previous research have not included context information even though biological associations actually do appear in the specific contexts. Here, we reconstruct an anatomical context-specific network by assigning contexts to biological associations using protein expression data and scientific literature. Furthermore, we employ the context-specific network for the analysis of drug effects with a proximity measure between drug targets and diseases. Distinct from previous context-specific networks, intercellular associations and phenomic level entities such as biological processes are included in our network to represent the human body. It is observed that performances in inferring drug-disease associations are increased by adding context information and phenomic level entities. In particular, hypertension, a disease related to multiple organs and associated with several phenomic level entities, is analyzed in detail to investigate how our network facilitates the inference of drug-disease associations. Our results indicate that the inclusion of context information, intercellular associations, and phenomic level entities can contribute towards a better prediction of drug-disease associations and provide detailed insight into understanding of how drugs affect diseases in the human body.
N-representability of the Jastrow wave function pair density of the lowest-order
Authors: Higuchi Katsuhiko , Higuchi Masahiko 
Published: August 2017

AbstractConditions for the N-representability of the pair density (PD) are needed for the development of the PD functional theory. We derive sufficient conditions for the N-representability of the PD that is calculated from the Jastrow wave function within the lowest order. These conditions are used as the constraints on the correlation function of the Jastrow wave function. A concrete procedure to search the suitable correlation function is also presented.
Effect of extra cysteine residue of new mutant 1Ax1 subunit on the functional properties of common wheat
Authors: Li Miao , Wang Yaqiong , Ma Fengyun , Zeng Jian , Chang Junli , Chen Mingjie , Li Kexiu , Yang Guangxiao , Wang Yuesheng , He Guangyuan 
Published: August 2017

AbstractSubunit pair 1Dx5 + 1Dy10 was recognized as superior subunit combination in wheat and contained an extra repetitive-domain cysteine residue in 1Dx5 that was important for understanding the formation of dough viscoelasticity. In this research, one specific serine codon of the 1Ax1 gene corresponding to the extra cysteine residue of 1Dx5 was substituted by a cysteine codon through site-directed mutagenesis. Four homozygous transgenic lines (T4) expressing the mutant 1Ax1 gene (mut1Ax1) were produced. Their greater dough strength and stability were confirmed by mixograph and were associated with highly increased gluten index, larger amounts of gluten macropolymers, larger size distribution for glutenin macropolymer particles and varied sodium-dodecyl-sulfate sedimentation volumes, compared with those of the one line expressing wild 1Ax1 that had similar expression level of transgene. The contents of β-sheets in dough and disulfide groups in gluten of the mut1Ax1 transgenic lines were significantly increased. The microstructure of dough mixed to peak showed a more continuous gluten matrix in the mutant transgenic lines than the one line mentioned-above. It was concluded that the extra cysteine residue of mutant 1Ax1 subunit plays a positive role in contributing to dough strength and stability of wheat by cross-linking into gluten aggregates through inter-chain disulfide bonds.
Involvement of Insulin Signaling Disturbances in Bisphenol A-Induced Alzheimer’s Disease-like Neurotoxicity
Authors: Wang Tingwei , Xie Cuiwei , Yu Pengfei , Fang Fangfang , Zhu Jingying , Cheng Jie , Gu Aihua , Wang Jun , Xiao Hang 
Published: August 2017

AbstractBisphenol A (BPA), a member of the environmental endocrine disruptors (EDCs), has recently received increased attention because of its effects on brain insulin resistance. Available data have indicated that brain insulin resistance may contribute to neurodegenerative diseases. However, the associated mechanisms that underlie BPA-induced brain-related outcomes remain largely unknown. In the present study, we identified significant insulin signaling disturbances in the SH-SY5Y cell line that were mediated by BPA, including the inhibition of physiological p-IR Tyr1355 tyrosine, p-IRS1 tyrosine 896, p-AKT serine 473 and p-GSK3α/β serine 21/9 phosphorylation, as well as the enhancement of IRS1 Ser307 phosphorylation; these effects were clearly attenuated by insulin and rosiglitazone. Intriguingly, Alzheimer’s disease (AD)-associated pathological proteins, such as BACE-1, APP, β-CTF, α-CTF, Aβ 1–42 and phosphorylated tau proteins (S199, S396, T205, S214 and S404), were substantially increased after BPA exposure, and these effects were abrogated by insulin and rosiglitazone treatment; these findings underscore the specific roles of insulin signaling in BPA-mediated AD-like neurotoxicity. Thus, an understanding of the regulation of insulin signaling may provide novel insights into potential therapeutic targets for BPA-mediated AD-like neurotoxicity.