bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new mib allele with a chromosomal deletion covering foxc1a exhibits anterior somite specification defect
Authors: Hsu Chia-Hao , Lin Ji-Sheng , Po Lai Keng , Li Jing-Woei , Chan Ting-Fung , You May-Su , Tse William Ka Fai , Jiang Yun-Jin 
Published: June 2015

Abstractmibnn2002, found from an allele screen, showed early segmentation defect and severe cell death phenotypes, which are different from previously known mib mutants. Despite distinct morphological phenotypes, the typical mib molecular phenotypes: her4 down-regulation, neurogenic phenotype and cold sensitive dlc expression pattern, still remained. The linkage analysis also indicated that mibnn2002 is a new mib allele. Failure of specification in anterior 7-10 somites is likely due to lack of foxc1a expression in mibnn2002 homozygotes. Somites and somite markers gradually appeared after 7-10 somite stage, suggesting that foxc1a is only essential for the formation of anterior 7-10 somites. Apoptosis began around 16-somite stage with p53 up-regulation. To find the possible links of mib, foxc1a and apoptosis, transcriptome analysis was employed. About 140 genes, including wnt3a, foxc1a and mib, were not detected in the homozygotes. Overexpression of foxc1a mRNA in mibnn2002 homozygotes partially rescued the anterior somite specification. In the process of characterizing mibnn2002 mutation, we integrated the scaffolds containing mib locus into chromosome 2 (or linkage group 2, LG2) based on synteny comparison and transcriptome results. Genomic PCR analysis further supported the conclusion and showed that mibnn2002 has a chromosomal deletion with the size of about 9.6 Mbp.
Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the “Finished” C. elegans Genome
Authors: Li Runsheng , Hsieh Chia-Ling , Young Amanda , Zhang Zhihong , Ren Xiaoliang , Zhao Zhongying 
Published: June 2015

AbstractMost next-generation sequencing platforms permit acquisition of high-throughput DNA sequences, but the relatively short read length limits their use in genome assembly or finishing. Illumina has recently released a technology called Synthetic Long-Read Sequencing that can produce reads of unusual length, i.e., predominately around 10 Kb. However, a systematic assessment of their use in genome finishing and assembly is still lacking. We evaluate the promise and deficiency of the long reads in these aspects using isogenic C. elegans genome with no gap. First, the reads are highly accurate and capable of recovering most types of repetitive sequences. However, the presence of tandem repetitive sequences prevents pre-assembly of long reads in the relevant genomic region. Second, the reads are able to reliably detect missing but not extra sequences in the C. elegans genome. Third, the reads of smaller size are more capable of recovering repetitive sequences than those of bigger size. Fourth, at least 40 Kbp missing genomic sequences are recovered in the C. elegans genome using the long reads. Finally, an N50 contig size of at least 86 Kbp can be achieved with 24×reads but with substantial mis-assembly errors, highlighting a need for novel assembly algorithm for the long reads.
Association of mtDNA M/N haplogroups with systemic lupus erythematosus: a case-control study of Han Chinese women
Authors: Tang Youzhou , Wang Li , Zhu Min , Yang Ming , Zhong Kuangbiao , Du Qing , Zhang Hao , Gui Ming 
Published: June 2015

AbstractTo investigate whether mitochondrial DNA haplogroups M or N are related to occurrence or manifestations of systemic lupus erythematosus (SLE), we collected M/N haplogrouping and clinical characteristics from 868 Han Chinese women with SLE, as well as for 870 age-matched healthy Han Chinese control women. M/N haplogroups were determined in all subjects using allele-specific amplification. The frequency of M haplogroup in all patients was 429 (49.4%) and the frequency of N haplogroup, 439 (50.6%). The corresponding frequencies in controls were 456 (52.4%) and 414 (47.6%) (P = 0.213). Among women older than 50 years at onset age, the N haplogroup was significantly higher in patients than in healthy controls (59.6% vs 41.7%, P = 0.042). The N haplogroup was associated with significantly higher risk for certain SLE characteristics: hematological system damage (OR 2.128, 95%CI 1.610 to 2.813), skin impairment (OR 1.873, 95%CI 1.428 to 2.457), neurological disturbance (OR 3.956, 95%CI 1.874 to 8.352) and alopecia (OR 1.322, 95%CI 1.007 to 1.737 ). Our results suggest that in Han Chinese women, the mtDNA N haplogroup is associated with higher risk of late-onset SLE, skin impairment, neurological disturbance, hematological system damage and alopecia.
Low-glucose enhances keratocyte-characteristic phenotype from corneal stromal cells in serum-free conditions
Authors: Foster James W. , Gouveia Ricardo M. , Connon Che J. 
Published: June 2015

AbstractThe avascular cornea is a uniquely-isolated organ, with its stroma constituting a nutrient-poor environment. Consequently, the availability of metabolites such as glucose to corneal stromal cells is considerably reduced compared with other tissues, or indeed with media commonly used to culture these cells in vitro. However, the role of glucose in the behaviour of human corneal keratocytes has been overlooked. As such, we sought to investigate the effects of low-glucose formulations on the phenotype of human corneal stromal cells. Cells cultured in low-glucose were able to survive for extended periods when compared to high-glucose, serum-free conditions. Furthermore, low-glucose enhanced their reversal to a keratocyte-characteristic phenotype. Specifically, cells within low-glucose medium assumed dendritic morphologies, with bean-shaped condensed nuclei, absence of alpha-smooth muscle actin or stress fibres and a corresponding reduction in migratory and contractile activities when compared with high-glucose, serum-free conditions. Moreover, cells within low-glucose uniquely recovered the ability to express a robust keratocyte-characteristic marker, CD34, while still expressing elevated levels of other representative phenotypic markers such as keratocan, lumican, ALDH1A1 and ALDH3A1. These results indicate that low-glucose enhances keratocyte-characteristic phenotype above and beyond established media formulations and thus has important implications for corneal biology in health and disease.
KA1-targeted regulatory domain mutations activate Chk1 in the absence of DNA damage
Authors: Gong Eun-Yeung , Smits Veronique A. J. , Fumagallo Felipe , Piscitello Desiree , Morrice Nick , Freire Raimundo , Gillespie David A. 
Published: June 2015

AbstractThe Chk1 protein kinase is activated in response to DNA damage through ATR-mediated phosphorylation at multiple serine-glutamine (SQ) residues within the C-terminal regulatory domain, however the molecular mechanism is not understood. Modelling indicates a high probability that this region of Chk1 contains a kinase-associated 1 (KA1) domain, a small, compact protein fold found in multiple protein kinases including SOS2, AMPK and MARK3. We introduced mutations into Chk1 designed to disrupt specific structural elements of the predicted KA1 domain. Remarkably, six of seven Chk1 KA1 mutants exhibit constitutive biological activity (Chk1-CA) in the absence of DNA damage, profoundly arresting cells in G2 phase of the cell cycle. Cell cycle arrest induced by selected Chk1-CA mutants depends on kinase catalytic activity, which is increased several-fold compared to wild-type, however phosphorylation of the key ATR regulatory site serine 345 (S345) is not required. Thus, mutations targeting the putative Chk1 KA1 domain confer constitutive biological activity by circumventing the need for ATR-mediated positive regulatory phosphorylation.
Biased random walk model for the prioritization of drug resistance associated proteins
Authors: Guo Hao , Dong Jiaqiang , Hu Sijun , Cai Xiqiang , Tang Guangbo , Dou Jianhua , Tian Miaomiao , He Fuchu , Nie Yongzhan , Fan Daiming 
Published: June 2015

AbstractMulti-drug resistance is the main cause of treatment failure in cancer patients. How to identify molecules underlying drug resistance from multi-omics data remains a great challenge. Here, we introduce a data biased strategy, ProteinRank, to prioritize drug-resistance associated proteins in cancer cells. First, we identified differentially expressed proteins in Adriamycin and Vincristine resistant gastric cancer cells compared to their parental cells using iTRAQ combined with LC-MS/MS experiments and then mapped them to human protein-protein interaction network; second, we applied ProteinRank to analyze the whole network and rank proteins similar to known drug resistance related proteins. Cross validations demonstrated a better performance of ProteinRank compared to the method without usage of MS data. Further validations confirmed the altered expressions or activities of several top ranked proteins. Functional study showed PIM3 or CAV1 silencing was sufficient to reverse the drug resistance phenotype. These results indicated ProteinRank could prioritize key proteins related to drug resistance in gastric cancer and provided important clues for cancer research.
First-principles study of the influence of different interfaces and core types on the properties of CdSe/CdS core-shell nanocrystals
Authors: Kocevski V. , Rusz J. , Eriksson O. , Sarma D.D. 
Published: June 2015

AbstractWith the expanding field of nanoengineering and the production of nanocrystals (NCs) with higher quality and tunable size, having reliable theoretical calculations to complement the experimental results is very important. Here we present such a study of CdSe/CdS core-shell NCs using density functional theory, where we focus on dependence of the properties of these NCs on core types and interfaces between the core and the shell, as well as on the core/shell ratio. We show that the density of states and the absorption indices depend rather weakly on the type of interface and core type. We demonstrate that the HOMO wavefunction is mainly localised in the core of the nanocrystal, depending primarily on the core/shell ratio. On the other hand the LUMO wavefunction spreads more into the shell of the nanocrystal, where its confinement in the core is almost the same in each of the studied structural models. Furthermore, we show that the radiative lifetimes decrease with increasing core sizes due to changes in the dipolar overlap integral of the HOMO and LUMO wavefunctions. In addition, the electron-hole Coulomb interaction energies follow a similar pattern as the localisation of the wavefunctions, with the smaller NCs having higher Coulomb interaction energies.
A repeat unit of Vibrio diarrheal T3S effector subverts cytoskeletal actin homeostasis via binding to interstrand region of actin filaments
Authors: Nishimura Mitsuhiro , Fujii Takashi , Hiyoshi Hirotaka , Makino Fumiaki , Inoue Hajime , Motooka Daisuke , Kodama Toshio , Ohkubo Tadayasu , Kobayashi Yuji , Nakamura Shota , Namba Keiichi , Iida Tetsuya 
Published: June 2015

AbstractA novel bacterial type III secretion effector, VopV, from the enteric pathogen Vibrio parahaemolyticus has been identified as a key factor in pathogenicity due to its interaction with cytoskeletal actin. One of the repeat units in the long repetitive region of VopV, named VopVrep1, functions as an actin-binding module. Despite its importance in pathogenesis, the manner in which the effector binds to actin and the subsequent effects on actin dynamics remain unclear. Here, we report the molecular basis of the VopVrep1/actin interaction. VopVrep1 exists as an unstructured protein in solution but potently and specifically binds filamentous actin (F-actin) and not globular actin (G-actin). The F-actin/VopVrep1 complex was directly visualized at 9.6-Å resolution using electron cryomicroscopy (cryoEM) and helical image reconstitution. The density map revealed the binding site of VopVrep1 at the interface between two actin strands, which is close to the binding site of the bicyclic heptapeptide toxin phalloidin. Consistent with this observation, VopVrep1 alone prevented the depolymerization of F-actin. Overall, VopVrep1 demonstrated unique characteristics in comparison to known actin-binding proteins, but was relatively similar to phalloidin. The phalloidin-like behavior, targeting the interstrand region of actin filaments to stabilize the filament structure, likely contributes to the pathogenicity of V. parahaemolyticus.
A New Approach to Reduce Toxicities and to Improve Bioavailabilities of Platinum-Containing Anti-Cancer Nanodrugs
Authors: Liu Li , Ye Qing , Lu Maggie , Lo Ya-Chin , Hsu Yuan-Hung , Wei Ming-Cheng , Chen Yu-Hsiang , Lo Shen-Chuan , Wang Shian-Jy , Bain Daniel J. , Ho Chien 
Published: June 2015

AbstractPlatinum (Pt) drugs are the most potent and commonly used anti-cancer chemotherapeutics. Nanoformulation of Pt drugs has the potential to improve the delivery to tumors and reduce toxic side effects. A major challenge for translating nanodrugs to clinical settings is their rapid clearance by the reticuloendothelial system (RES), hence increasing toxicities on off-target organs and reducing efficacy. We are reporting that an FDA approved parenteral nutrition source, Intralipid 20%, can help this problem. A dichloro (1, 2-diaminocyclohexane) platinum (II)-loaded and hyaluronic acid polymer-coated nanoparticle (DACHPt/HANP) is used in this study. A single dose of Intralipid (2 g/kg, clinical dosage) is administrated [intravenously (i. v.), clinical route] one hour before i.v. injection of DACHPt/HANP. This treatment can significantly reduce the toxicities of DACHPt/HANP in liver, spleen, and, interestingly, kidney. Intralipid can decrease Pt accumulation in the liver, spleen and kidney by 20.4%, 42.5% and 31.2% at 24-hr post nanodrug administration, respectively. The bioavailability of DACHPt/HANP increases by 18.7% and 9.4% during the first 5 and 24 hr, respectively.
Realization of high-luminous-efficiency InGaN light-emitting diodes in the “green gap” range
Authors: Jiang Yang , Li Yangfeng , Li Yueqiao , Deng Zhen , Lu Taiping , Ma Ziguang , Zuo Peng , Dai Longgui , Wang Lu , Jia Haiqiang , Wang Wenxin , Zhou Junming , Liu Wuming , Chen Hong 
Published: June 2015

AbstractLight-emitting diodes (LEDs) in the wavelength region of 535–570 nm are still inefficient, which is known as the “green gap” problem. Light in this range causes maximum luminous sensation in the human eye and is therefore advantageous for many potential uses. Here, we demonstrate a high-brightness InGaN LED with a normal voltage in the “green gap” range based on hybrid multi-quantum wells (MQWs). A yellow-green LED device is successfully fabricated and has a dominant wavelength, light output power, luminous efficiency and forward voltage of 560 nm, 2.14 mW, 19.58 lm/W and 3.39 V, respectively. To investigate the light emitting mechanism, a comparative analysis of the hybrid MQW LED and a conventional LED is conducted. The results show a 2.4-fold enhancement of the 540-nm light output power at a 20-mA injection current by the new structure due to the stronger localization effect and such enhancement becomes larger at longer wavelengths. Our experimental data suggest that the hybrid MQW structure can effectively push the efficient InGaN LED emission toward longer wavelengths, connecting to the lower limit of the AlGaInP LEDs’ spectral range, thus enabling completion of the LED product line covering the entire visible spectrum with sufficient luminous efficacy.
A rapid, efficient and facile solution for dental hypersensitivity: The tannin–iron complex
Authors: Oh Dongyeop X. , Prajatelistia Ekavianty , Ju Sung-Won , Jeong Kim Hyo , Baek Soo-Jin , Joon Cha Hyung , Ho Jun Sang , Ahn Jin-Soo , Soo Hwang Dong 
Published: June 2015

AbstractDental hypersensitivity due to exposure of dentinal tubules under the enamel layer to saliva is a very popular and highly elusive technology priority in dentistry. Blocking water flow within exposed dentinal tubules is a key principle for curing dental hypersensitivity. Some salts used in “at home” solutions remineralize the tubules inside by concentrating saliva ingredients. An “in-office” option of applying dense resin sealants on the tubule entrance has only localized effects on well-defined sore spots. We report a self-assembled film that was formed by facile, rapid (4 min) and efficient (approximately 0.5 g/L concentration) dip-coating of teeth in an aqueous solution containing a tannic acid–iron(III) complex. It quickly and effectively occluded the dentinal tubules of human teeth. It withstood intense tooth brushing and induced hydroxyapatite remineralisation within the dentinal tubules. This strategy holds great promise for future applications as an effective and user-friendly desensitizer for managing dental hypersensitivity.
Gene Perturbation Atlas (GPA): a single-gene perturbation repository for characterizing functional mechanisms of coding and non-coding genes
Authors: Xiao Yun , Gong Yonghui , Lv Yanling , Lan Yujia , Hu Jing , Li Feng , Xu Jinyuan , Bai Jing , Deng Yulan , Liu Ling , Zhang Guanxiong , Yu Fulong , Li Xia 
Published: June 2015

AbstractGenome-wide transcriptome profiling after gene perturbation is a powerful means of elucidating gene functional mechanisms in diverse contexts. The comprehensive collection and analysis of the resulting transcriptome profiles would help to systematically characterize context-dependent gene functional mechanisms and conduct experiments in biomedical research. To this end, we collected and curated over 3000 transcriptome profiles in human and mouse from diverse gene perturbation experiments, which involved 1585 different perturbed genes (microRNAs, lncRNAs and protein-coding genes) across 1170 different cell lines/tissues. For each profile, we identified differential genes and their associated functions and pathways, constructed perturbation networks, predicted transcription regulation and cancer/drug associations and assessed cooperative perturbed genes. Based on these transcriptome analyses, the Gene Perturbation Atlas (GPA) can be used to detect (i) novel or cell-specific functions and pathways affected by perturbed genes, (ii) protein interactions and regulatory cascades affected by perturbed genes and (iii) perturbed gene-mediated cooperative effects. The GPA is a user-friendly database to support the rapid searching and exploration of gene perturbations. Particularly, we visualized functional effects of perturbed genes from multiple perspectives. In summary, the GPA is a valuable resource for characterizing gene functions and regulatory mechanisms after single-gene perturbations. The GPA is freely accessible at http://biocc.hrbmu.edu.cn/GPA/.
Genetically assembled fluorescent biosensor for in situ detection of bio-synthesized alkanes
Authors: Wu Wei , Zhang Lei , Yao Lun , Tan Xiaoming , Liu Xufeng , Lu Xuefeng 
Published: June 2015

AbstractConstruction of highly efficient microbial cell factories producing drop-in biofuel alkanes is severely limited due to the lack of a fast detection method against alkanes. Here we first developed a sensitive fluorescent biosensor for rapid and in situ monitoring of intracellular alkane synthesis. Using GFP as reporter, the biosensor could actively respond to the intracellular alkane products, especially for the mid- and long-chain alkanes synthesized in the recombinant Escherichia coli and give a concentration-dependent fluorescence response. Our results also suggested the feasibility of developing high-throughput strategies basing on the alkane biosensor device in E. coli and thus will greatly facilitate the application of directed evolution strategies to further improve the alkane-producing microbial cell factories.
Dual yolk-shell structure of carbon and silica-coated silicon for high-performance lithium-ion batteries
Authors: Yang L. Y. , Li H. Z. , Liu J. , Sun Z. Q. , Tang S. S. , Lei M. 
Published: June 2015

AbstractSilicon batteries have attracted much attention in recent years due to their high theoretical capacity, although a rapid capacity fade is normally observed, attributed mainly to volume expansion during lithiation. Here, we report for the first time successful synthesis of Si/void/SiO2/void/C nanostructures. The synthesis strategy only involves selective etching of SiO2in Si/SiO2/C structures with hydrofluoric acid solution. Compared with reported results, such novel structures include a hard SiO2-coated layer, a conductive carbon-coated layer and two internal void spaces. In the structures, the carbon can enhance conductivity, the SiO2layer has mechanically strong qualities and the two internal void spaces can confine and accommodate volume expansion of silicon during lithiation. Therefore, these specially designed dual yolk-shell structures exhibit a stable and high capacity of 956 mA h g−1after 430 cycles with capacity retention of 83%, while the capacity of Si/C core-shell structures rapidly decreases in the first ten cycles under the same experimental conditions. The novel dual yolk-shell structures developed for Si can also be extended to other battery materials that undergo large volume changes.
Efficacy comparison between cryoablation and radiofrequency ablation for patients with cavotricuspid valve isthmus dependent atrial flutter: a meta-analysis
Authors: Chen Yi-He , Lin Hui , Xie Cheng-Long , Zhang Xiao-Ting , Li Yi-Gang 
Published: June 2015

AbstractWe perform this meta-analysis to compare the efficacy and safety of cryoablation versus radiofrequency ablation for patients with cavotricuspid valve isthmus dependent atrial flutter. By searching EMBASE, MEDLINE, PubMed and Cochrane electronic databases from March 1986 to September 2014, 7 randomized clinical trials were included. Acute (risk ratio[RR]: 0.93; P = 0.14) and long-term (RR: 0.94; P = 0.08) success rate were slightly lower in cryoablation group than in radiofrequency ablation group, but the difference was not statistically significant. Additionally, the fluoroscopy time was nonsignificantly reduced (weighted mean difference[WMD]: −2.83; P = 0.29), whereas procedure time was significantly longer (WMD: 25.95; P = 0.01) in cryoablation group compared with radiofrequency ablation group. Furthermore, Pain perception during the catheter ablation was substantially less in cryoabaltion group than in radiofrequency ablation group (standardized mean difference[SMD]: −2.36; P < 0.00001). Thus, our meta-analysis demonstrated that cryoablation and radiofrequency ablation produce comparable acute and long-term success rate for patients with cavotricuspid valve isthmus dependent atrial flutter. Meanwhile, cryoablation ablation tends to reduce the fluoroscopy time and significantly reduce pain perception in cost of significantly prolonged procedure time.
Plant tolerance to excess light energy and photooxidative damage relies on plastoquinone biosynthesis
Authors: Ksas Brigitte , Becuwe Noëlle , Chevalier Anne , Havaux Michel 
Published: June 2015

AbstractPlastoquinone-9 is known as a photosynthetic electron carrier to which has also been attributed a role in the regulation of gene expression and enzyme activities via its redox state. Here, we show that it acts also as an antioxidant in plant leaves, playing a central photoprotective role. When Arabidopsis plants were suddenly exposed to excess light energy, a rapid consumption of plastoquinone-9 occurred, followed by a progressive increase in concentration during the acclimation phase. By overexpressing the plastoquinone-9 biosynthesis gene SPS1 (SOLANESYL DIPHOSPHATE SYNTHASE 1) in Arabidopsis, we succeeded in generating plants that specifically accumulate plastoquinone-9 and its derivative plastochromanol-8. The SPS1-overexpressing lines were much more resistant to photooxidative stress than the wild type, showing marked decreases in leaf bleaching, lipid peroxidation and PSII photoinhibition under excess light. Comparison of the SPS1 overexpressors with other prenyl quinone mutants indicated that the enhanced phototolerance of the former plants is directly related to their increased capacities for plastoquinone-9 biosynthesis.