bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial respiratory dysfunction disturbs neuronal and cardiac lineage commitment of human iPSCs
Authors: Yokota Mutsumi , Hatakeyama Hideyuki , Ono Yasuha , Kanazawa Miyuki , Goto Yu-ichi 
Published: January 2017

AbstractMitochondrial diseases are genetically heterogeneous and present a broad clinical spectrum among patients; in most cases, genetic determinants of mitochondrial diseases are heteroplasmic mitochondrial DNA (mtDNA) mutations. However, it is uncertain whether and how heteroplasmic mtDNA mutations affect particular cellular fate-determination processes, which are closely associated with the cell-type-specific pathophysiology of mitochondrial diseases. In this study, we established two isogenic induced pluripotent stem cell (iPSC) lines each carrying different proportions of a heteroplasmic m.3243A>G mutation from the same patient; one exhibited apparently normal and the other showed most likely impaired mitochondrial respiratory function. Low proportions of m.3243A>G exhibited no apparent molecular pathogenic influence on directed differentiation into neurons and cardiomyocytes, whereas high proportions of m.3243A>G showed both induced neuronal cell death and inhibited cardiac lineage commitment. Such neuronal and cardiac maturation defects were also confirmed using another patient-derived iPSC line carrying quite high proportion of m.3243A>G. In conclusion, mitochondrial respiratory dysfunction strongly inhibits maturation and survival of iPSC-derived neurons and cardiomyocytes; our presenting data also suggest that appropriate mitochondrial maturation actually contributes to cellular fate-determination processes during development.
A hitchhiker’s guide to an ISS experiment in under 9 months
Authors: Nadir Andrei James 
Published: January 2017

AbstractThe International Space Station National Laboratory gives students a platform to conduct space-flight science experiments. To successfully take advantage of this opportunity, students and their mentors must have an understanding of how to develop and then conduct a science project on international space station within a school year. Many factors influence the speed in which a project progresses. The first step is to develop a science plan, including defining a hypothesis, developing science objectives, and defining a concept of operation for conducting the flight experiment. The next step is to translate the plan into well-defined requirements for payload development. The last step is a rapid development process. Included in this step is identifying problems early and negotiating appropriate trade-offs between science and implementation complexity. Organizing the team and keeping players motivated is an equally important task, as is employing the right mentors. The project team must understand the flight experiment infrastructure, which includes the international space station environment, payload resource requirements and available components, fail-safe operations, system logs, and payload data. Without this understanding, project development can be impacted, resulting in schedule delays, added costs, undiagnosed problems, and data misinterpretation. The information and processes for conducting low-cost, rapidly developed student-based international space station experiments are presented, including insight into the system operations, the development environment, effective team organization, and data analysis. The details are based on the Valley Christian Schools (VCS, San Jose, CA) fluidic density experiment and penicillin experiment, which were developed by 13- and 14-year-old students and flown on ISS.
Designing new ferroelectrics with a general strategy
Authors: Xu Ke , Lu Xue-Zeng , Xiang Hongjun 
Published: January 2017

AbstractThe presence of a switchable spontaneous electric polarization makes ferroelectrics ideal candidates for the use in many applications such as memory and sensors devices. Since known ferroelectrics are rather limited, finding new ferroelectric materials has become a flourishing field. One promising route is to design the improper ferroelectrics. However, previous approach based on the Landau theory is not easily adopted for systems that are unrelated to the Pbnm perovskite structure. To this end, we develop a general design rule that is applicable to any system. By combining this rule with the density functional theory calculations, we identify previously unrecognized classes of ferroelectric materials. It is shown that the $$R\bar{3}c$$
R

3

̄

c
perovskite structure can become ferroelectric by substituting half of the B-site cations. Compound ZnSrO2 with a non-perovskite layered structure can also be ferroelectric through the anion substitution. Moreover, our approach can be used to design new multiferroics as illustrated in the case of fluorine substituted LaMnO3.
Functional MRI of the Reserpine-Induced Putative Rat Model of Fibromyalgia Reveals Discriminatory Patterns of Functional Augmentation to Acute Nociceptive Stimuli
Authors: Wells Jack A. , Shibata Sayaka , Fujikawa Akihiko , Takahashi Masayasu , Saga Tsuneo , Aoki Ichio 
Published: January 2017

AbstractFunctional neuroimaging, applied to pre-clinical models of chronic pain, offers unique advantages in the drive to discover new treatments for this prevalent and oppressive condition. The high spatial and temporal resolution of fMRI affords detailed mapping of regional pharmacodynamics that underlie mechanisms of pain suppression by new analgesics. Despite evidence supporting the translational relevance of this approach, relatively few studies have investigated fMRI abnormalities in rodent models of chronic pain. In this study, we used fMRI to map the BOLD response in a recently developed putative rat model of fibromyalgia to innocuous and acute nociceptive stimuli by applying a step-wise graded electrical forepaw stimulation paradigm, with comparison to healthy controls. We observed discriminatory functional signatures (p < 0.001) to 2 mA electrical forepaw stimulation, found to be innocuous in the control group. As such, this translational approach provides sensitive and quantitative neural correlates of the underlying chronic disease. The regional patterns of functional augmentation were found to be concordant with previous studies of nociception in the anaesthetised rat brain, supporting the specificity of this approach in the study of altered central pain processing in reserpine induced myalgia. The methodology introduced in this work represents a novel platform for emerging treatment evaluation in highly experimentally controlled conditions.
Improving the Concentrations of the Active Components in the Herbal Tea Ingredient, Uraria crinita: The Effect of Post-harvest Oven-drying Processing
Authors: Chao Jung , Dai Yuntao , Cheng Hao-Yuan , Lam Wing , Cheng Yung-Chi , Li Ke , Peng Wen-Huang , Pao Li-Heng , Hsieh Ming-Tsuen , Qin Xue-Mei , Lee Meng-Shiou 
Published: January 2017

AbstractUraria crinita is widely used as a popular folk drink; however, little is known about how the post-harvest operations affect the chemical composition and bioactivity of UC. We assessed three drying methods (Oven-drying, Air-drying, Sun-drying), as well as the Oven-drying temperature using metabolomics approaches and bioactivity assays. The samples processed at 40 degree show a greater effect on the levels of estrogen receptor-alpha activity and nuclear factor erythroid 2–related factor 2 activity, anti-oxidative activity, and cyclooxygenase-2 inhibition compared with the other samples. A multivariate analysis showed a clear separation between the 40 degree Oven-dried samples and the other samples, which is consistent with the results of bioactivity assay. These results are ascribed to at least two-fold increase in the concentrations of flavonoids, spatholosineside A and triterpenoids in the oven-dried samples compared with the other groups. The proposed Oven-drying method at 40 degree results in an improved quality of UC.
Discovering potential serological biomarker for chronic Hepatitis B Virus-related hepatocellular carcinoma in Chinese population by MAL-associated serum glycoproteomics analysis
Authors: Liu Tianhua , Liu Denghe , Liu Riqiang , Jiang Hucong , Yan Guoquan , Li Wei , Sun Lu , Zhang Shu , Liu Yinkun , Guo Kun 
Published: January 2017

AbstractThe accuracy of current biomarkers for the diagnosis of hepatocellular carcinoma (HCC), especially chronic Hepatitis B Virus (HBV)-related HCC, is limited. Recent progress in glycoproteomics has provided a novel platform for screening novel serological biomarkers of HCC. In this study, lectin affinity chromatography by Maackia amurensis lectin (MAL) and iTRAQ combined with mass spectrometric analysis were performed to enrich and identify the glycoprotein fractions in serum samples from HBV-related HCC patients and from healthy controls. Seventeen differential MAL-associated glycoproteins were identified. Among them, Galectin 3 binding protein (Gal-3BP) was selected for further evaluated by ELISA analysis and showed a high diagnostic potential of HBV-related HCC, with the AUC of 0.898 and a sensitivity, specificity and accuracy of 80.00%, 93.75% and 86.88%, respectively. Moreover, we constructed a predictive model through the combined use of serum Gal-3BP and Alpha Fetoprotein (AFP), which improved the sensitivity (from 87.5% to 95%), specificity (from 93.75% to 95%) and accuracy (from 90.63% to 95%) of diagnosing early HCC. These data suggested serum Gal-3BP level is a promising biomarker to identify HBV-related HCC and the combined use of serum Gal-3BP and AFP improves the diagnostic potential of HBV-HCC compared with AFP alone in current clinical practice.
A kind of universal quantum secret sharing protocol
Authors: Chen Xiu-Bo , Dou Zhao , Xu Gang , He Xiao-Yu , Yang Yi-Xian 
Published: January 2017

AbstractUniversality is an important feature, but less researched in quantum communication protocols. In this paper, a kind of universal quantum secret sharing protocol is investigated. Firstly, we design a quantum secret sharing protocol based on the Borras-Plastino-Batle (BPB) state. Departing from previous research, our protocol has a salient feature in that participants in our protocol only need projective measurement instead of any unitary operations. It makes our protocol more flexible. Secondly, universality of quantum communication protocols is studied for the first time. More specifically, module division of quantum communication protocols and coupling between different modules are discussed. Our aforementioned protocol is analyzed as an example. On one hand, plenty of quantum states (the BPB-class states and the BPB-like-class states, which are proposed in this paper) could be used as carrier to perform our protocol. On the other hand, our protocol also could be regarded as a quantum private comparison protocol with a little revision. These features are rare for quantum communication protocols, and make our protocol more robust. Thirdly, entanglements of the BPB-class states are calculated in the Appendix.
New experimental evidence to support roaming in the reaction Cl + isobutene (i-C4H8)
Authors: Chen Li-Wei , Hung Ching-Ming , Matsui Hiroyuki , Lee Yuan-Pern 
Published: January 2017

AbstractThe reaction Cl + isobutene (i-C4H8) was reported by Suits et al. to proceed via, in addition to abstraction, an addition-elimination path following a roaming excursion of Cl; a near-zero translational energy release and an isotropic angular distribution observed at a small collision energy characterized this mechanism. We employed a new experimental method to further characterize this roaming mechanism through observation of the internal distribution of HCl (v, J) and their temporal behavior upon irradiation of a mixture of Cl2C2O2 and i-C4H8 in He or Ar buffer gas. With 1–3 Torr buffer gas added to approach the condition of small collision energy, the intensities of emission of HCl (v = 1, 2) and the HCl production rates increased significantly; Ar shows a more significant effect than He because Ar quenches Cl more efficiently to reduce the collisional energy and facilitate the roaming path. According to kinetic modeling, the rate of addition-elimination (roaming) increased from kE ≈ 2 × 105 s−1 when little buffer gas was present to ~1.9 × 106 s−1 when 2–3 Torr of Ar was added, and the branching ratio for formation of [HCl (v = 2)]/[HCl (v = 1)] increased from 0.02 ± 0.01 for abstraction to 0.06 ± 0.01 for roaming.
Transcriptome and network analyses in Saccharomyces cerevisiae reveal that amphotericin B and lactoferrin synergy disrupt metal homeostasis and stress response
Authors: Pang Chi Nam Ignatius , Lai Yu-Wen , Campbell Leona T. , Chen Sharon C.-A. , Carter Dee A. , Wilkins Marc R. 
Published: January 2017

AbstractInvasive fungal infections are difficult to treat. The few available antifungal drugs have problems with toxicity or efficacy, and resistance is increasing. To overcome these challenges, existing therapies may be enhanced by synergistic combination with another agent. Previously, we found amphotericin B (AMB) and the iron chelator, lactoferrin (LF), were synergistic against a range of different fungal pathogens. This study investigates the mechanism of AMB-LF synergy, using RNA-seq and network analyses. AMB treatment resulted in increased expression of genes involved in iron homeostasis and ATP synthesis. Unexpectedly, AMB-LF treatment did not lead to increased expression of iron and zinc homeostasis genes. However, genes involved in adaptive response to zinc deficiency and oxidative stress had decreased expression. The clustering of co-expressed genes and network analysis revealed that many iron and zinc homeostasis genes are targets of transcription factors Aft1p and Zap1p. The aft1Δ and zap1Δ mutants were hypersensitive to AMB and H2O2, suggesting they are key regulators of the drug response. Mechanistically, AMB-LF synergy could involve AMB affecting the integrity of the cell wall and membrane, permitting LF to disrupt intracellular processes. We suggest that Zap1p- and Aft1p-binding molecules could be combined with existing antifungals to serve as synergistic treatments.
Interleukin-32 Gamma Stimulates Bone Formation by Increasing miR-29a in Osteoblastic Cells and Prevents the Development of Osteoporosis
Authors: Lee Eun-Jin , Kim Sang-Min , Choi Bongkun , Kim Eun-Young , Chung Yeon-Ho , Lee Eun-Ju , Yoo Bin , Lee Chang-Keun , Hong Seokchan , Kim Beom-Jun , Koh Jung-Min , Kim Soo-Hyun , Kim Yong-Gil , Chang Eun-Ju 
Published: January 2017

AbstractInterleukin-32 gamma (IL-32γ) is a recently discovered cytokine that is elevated in inflamed tissues and contributes to pathogenic features of bone in human inflammatory rheumatic diseases. Nevertheless, the role of IL-32γ and its direct involvement in bone metabolism is unclear. We investigated the molecular mechanism of IL-32γ in bone remodeling and the hypothetical correlation between IL-32γ and disease activity in osteoporosis patients. Transgenic (TG) mice overexpressing human IL-32γ showed reduced bone loss with advancing age, increased bone formation, and high osteogenic capacity of osteoblast compared to wild-type (WT) mice through the upregulation of miR-29a, which caused a reduction of Dickkopf-1 (DKK1) expression. IL-32γ TG mice were protected against ovariectomy (OVX)induced osteoporosis compared with WT mice. Decreased plasma IL-32γ levels were associated with bone mineral density (BMD) in human patients linked to increased DKK1 levels. These results indicate that IL-32γ plays a protective role for bone loss, providing clinical evidence of a negative correlation between IL-32γ and DKK1 as bone metabolic markers.
Critical role for CaFEN1 and CaFEN12 of Candida albicans in cell wall integrity and biofilm formation
Authors: Alfatah Md. , Bari Vinay K. , Nahar Anubhav S. , Bijlani Swati , Ganesan K. 
Published: January 2017

AbstractSphingolipids are involved in several cellular functions, including maintenance of cell wall integrity. To gain insight into the role of individual genes of sphingolipid biosynthetic pathway, we have screened Saccharomyces cerevisiae strains deleted in these genes for sensitivity to cell wall perturbing agents calcofluor white and congo red. Only deletants of FEN1 and SUR4 genes were found to be sensitive to both these agents. Candida albicans strains deleted in their orthologs, CaFEN1 and CaFEN12, respectively, also showed comparable phenotypes, and a strain deleted for both these genes was extremely sensitive to cell wall perturbing agents. Deletion of these genes was reported earlier to sensitise cells to amphotericin B (AmB), which is a polyene drug that kills the cells mainly by binding and sequestering ergosterol from the plasma membrane. Here we show that their AmB sensitivity is likely due to their cell wall defect. Further, we show that double deletant of C. albicans is defective in hyphae formation as well as biofilm development. Together this study reveals that deletion of FEN1 and SUR4 orthologs of C. albicans leads to impaired cell wall integrity and biofilm formation, which in turn sensitise cells to AmB.
CircRNA_000203 enhances the expression of fibrosis-associated genes by derepressing targets of miR-26b-5p, Col1a2 and CTGF, in cardiac fibroblasts
Authors: Tang Chun-Mei , Zhang Ming , Huang Lei , Hu Zhi-qin , Zhu Jie-Ning , Xiao Zhen , Zhang Zhuo , Lin Qiu-xiong , Zheng Xi-Long , -Yang Min , Wu Shu-Lin , Cheng Jian-Ding , Shan Zhi-Xin 
Published: January 2017

AbstractCircular RNAs (circRNAs) participate in regulating gene expression in diverse biological and pathological processes. The present study aimed to investigate the mechanism underlying the modulation of circRNA_000203 on expressions of fibrosis-associated genes in cardiac fibroblasts. CircRNA_000203 was shown upregulated in the diabetic mouse myocardium and in Ang-II-induced mouse cardiac fibroblasts. Enforced-expression of circRNA_000203 could increase expressions of Col1a2, Col3a1 and α-SMA in mouse cardiac fibroblasts. RNA pull-down and RT-qPCR assay indicated that circRNA_000203 could specifically sponge miR-26b-5p. Dual luciferase reporter assay revealed that miR-26b-5p interacted with 3′UTRs of Col1a2 and CTGF, and circ_000203 could block the interactions of miR-26b-5p and 3′UTRs of Col1a2 and CTGF. Transfection of miR-26b-5p could post-transcriptionaly inhibit expressions of Col1a2 and CTGF, accompanied with the suppressions of Col3a1 and α-SMA in cardiac fibroblasts. Additionally, over-expression of circRNA_000203 could eliminate the anti-fibrosis effect of miR-26b-5p in cardiac fibroblasts. Together, our results reveal that suppressing the function of miR-26b-5p contributes to the pro-fibrosis effect of circRNA_000203 in cardiac fibroblasts.
Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD)
Authors: Fernandes Marco , Husi Holger 
Published: January 2017

AbstractComplex human traits such as chronic kidney disease (CKD) are a major health and financial burden in modern societies. Currently, the description of the CKD onset and progression at the molecular level is still not fully understood. Meanwhile, the prolific use of high-throughput omic technologies in disease biomarker discovery studies yielded a vast amount of disjointed data that cannot be easily collated. Therefore, we aimed to develop a molecule-centric database featuring CKD-related experiments from available literature publications. We established the Chronic Kidney Disease database CKDdb, an integrated and clustered information resource that covers multi-omic studies (microRNAs, genomics, peptidomics, proteomics and metabolomics) of CKD and related disorders by performing literature data mining and manual curation. The CKDdb database contains differential expression data from 49395 molecule entries (redundant), of which 16885 are unique molecules (non-redundant) from 377 manually curated studies of 230 publications. This database was intentionally built to allow disease pathway analysis through a systems approach in order to yield biological meaning by integrating all existing information and therefore has the potential to unravel and gain an in-depth understanding of the key molecular events that modulate CKD pathogenesis.
Predicting drug-target interactions by dual-network integrated logistic matrix factorization
Authors: Hao Ming , Bryant Stephen H. , Wang Yanli 
Published: January 2017

AbstractIn this work, we propose a dual-network integrated logistic matrix factorization (DNILMF) algorithm to predict potential drug-target interactions (DTI). The prediction procedure consists of four steps: (1) inferring new drug/target profiles and constructing profile kernel matrix; (2) diffusing drug profile kernel matrix with drug structure kernel matrix; (3) diffusing target profile kernel matrix with target sequence kernel matrix; and (4) building DNILMF model and smoothing new drug/target predictions based on their neighbors. We compare our algorithm with the state-of-the-art method based on the benchmark dataset. Results indicate that the DNILMF algorithm outperforms the previously reported approaches in terms of AUPR (area under precision-recall curve) and AUC (area under curve of receiver operating characteristic) based on the 5 trials of 10-fold cross-validation. We conclude that the performance improvement depends on not only the proposed objective function, but also the used nonlinear diffusion technique which is important but under studied in the DTI prediction field. In addition, we also compile a new DTI dataset for increasing the diversity of currently available benchmark datasets. The top prediction results for the new dataset are confirmed by experimental studies or supported by other computational research.
Galectin-3 as a marker of interstitial atrial remodelling involved in atrial fibrillation
Authors: Hernández-Romero Diana , Vílchez Juan Antonio , Lahoz Álvaro , Romero-Aniorte Ana I. , Jover Eva , García-Alberola Arcadio , Jara-Rubio Rubén , Martínez Carlos M. , Valdés Mariano , Marín Francisco 
Published: January 2017

AbstractRemodelling in the atria could appear as a result of hypertension, diabetes or ischaemic heart disease. Galectin-3 (Gal-3) is a mediator of profibrotic pathways and a potential biomarker of cardiac remodelling. We prospectively recruited consecutive patients undergoing elective cardiac surgery. Preoperative Gal-3 levels were determined from serum samples, and the presence of fibrosis was assessed from atrial appendage tissue samples obtained during cardiac surgery. We included 100 patients with aortic valve or ischaemic heart diseases and 15 controls with permanent AF. Gal-3 levels were associated with sex, left atrial volume, previous cardiac disease, diabetes mellitus, hypertension, NYHA and NT-proBNP. We observed differences in serum Gal-3 concentrations between patients and controls with permanent AF (p = 0.020). We performed ROC curves related to fibrosis and established a cutoff point for Gal-3 >13.65 ng/ml. Multivariate analyses showed previous cardiac disease, NYHA scale and high Gal-3 to be independent predictors of fibrosis. After adjustment for confounding factors, atrial fibrosis remained the only independent factor for the development of AF (p = 0.022). High Gal-3 serum levels predict fibrosis of the atrial appendage. NYHA scale and previous cardiac disease were also associated with tissue fibrosis in patients undergoing surgery. Atrial fibrosis was the only independent predictor for post-operative AF occurrence in our model after correcting for confounding factors.