bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autosomal recessive retinitis pigmentosa with homozygous rhodopsin mutation E150K and non-coding cis-regulatory variants in CRX-binding regions of SAMD7
Authors: Van Schil Kristof , Karlstetter Marcus , Aslanidis Alexander , Dannhausen Katharina , Azam Maleeha , Qamar Raheel , Leroy Bart P. , Depasse Fanny , Langmann Thomas , De Baere Elfride 
Published: February 2016

AbstractThe aim of this study was to unravel the molecular pathogenesis of an unusual retinitis pigmentosa (RP) phenotype observed in a Turkish consanguineous family. Homozygosity mapping revealed two candidate genes, SAMD7 and RHO. A homozygous RHO mutation c.448G > A, p.E150K was found in two affected siblings, while no coding SAMD7 mutations were identified. Interestingly, four non-coding homozygous variants were found in two SAMD7 genomic regions relevant for binding of the retinal transcription factor CRX (CRX-bound regions, CBRs) in these affected siblings. Three variants are located in a promoter CBR termed CBR1, while the fourth is located more downstream in CBR2. Transcriptional activity of these variants was assessed by luciferase assays and electroporation of mouse retinal explants with reporter constructs of wild-type and variant SAMD7 CBRs. The combined CBR2/CBR1 variant construct showed significantly decreased SAMD7 reporter activity compared to the wild-type sequence, suggesting a cis-regulatory effect on SAMD7 expression. As Samd7 is a recently identified Crx-regulated transcriptional repressor in retina, we hypothesize that these SAMD7 variants might contribute to the retinal phenotype observed here, characterized by unusual, recognizable pigment deposits, differing from the classic spicular intraretinal pigmentation observed in other individuals homozygous for p.E150K and typically associated with RP in general.
Liver X receptor α is essential for the capillarization of liver sinusoidal endothelial cells in liver injury
Authors: Xing Yan , Zhao Tingting , Gao Xiaoyan , Wu Yuzhang 
Published: February 2016

AbstractLiver X receptors (LXRs) play essential roles in lipogenesis, anti-inflammatory action and hepatic stellate cells (HSCs) activation in the liver. However, the effects of LXRs on the capillarization of liver sinusoidal endothelial cells (LSECs) in liver fibrosis remain undetermined. Here, we demonstrated that LXRα plays an important role in LSECs capillarization in a manner that involved Hedgehog (Hh) signaling. We found that LXRα expression in LSECs was increased in the carbon tetrachloride (CCl4)-induced fibrosis model. LXRα deletion markedly exacerbated CCl4-induced lesions assessed by histopathology, as well as inflammation and collagen deposition. Furthermore, capillarization of the sinusoids was aggravated in CCl4 -treated LXRα-deficient mice, as evidenced by increased CD34 expression, the formation of continuous basement membranes and aggravation of the loss of fenestrae. In vitro, LXR agonist could maintain freshly isolated LSECs differentiation on day 3. Furthermore, LXRα deletion led to increased expression of Hedgehog (Hh)-regulated gene in LSECs in the injured liver. Conversely, the LXR agonist could inhibit the Hh pathway in cultured LSECs. These responses indicated that LXRα suppressed the process of LSECs capillarization by repressing Hh signaling. Overall, our findings suggest that LXRα, by restoring the differentiation of LSECs, may be critical for the regression of liver fibrosis.
Alcoholic hepatitis accelerates early hepatobiliary cancer by increasing stemness and miR-122-mediated HIF-1α activation
Authors: Ambade Aditya , Satishchandran Abhishek , Szabo Gyongyi 
Published: February 2016

AbstractAlcohol-related hepatocellular carcinoma (HCC) develops with advanced alcoholic liver disease and liver fibrosis. Using adult mice, we evaluate the effect of alcoholic steatohepatitis on early hepatobiliary carcinoma after initiation by diethyl-nitrosamine (DEN). Here we show that alcohol-fed DEN-injected mice have higher ALT and liver-to-body weight ratio compared to pair-fed DEN-injected mice. Alcohol feeding results in steatohepatitis indicated by increased pro-inflammatory cytokines and fibrotic genes. MRI and liver histology of alcohol+DEN mice shows hepatobiliary cysts, early hepatic neoplasia and increase in serum alpha-fetoprotein. Proliferation makers (BrdU, cyclin D1, p53) and cancer stem cell markers (CD133 and nanog) are significantly up-regulated in livers of alcohol-fed DEN-injected mice compared to controls. In livers with tumors, loss of miR-122 expression with a significant up-regulation of miR-122 target HIF-1α is seen. We conclude that alcoholic steatohepatitis accelerates hepatobiliary tumors with characteristic molecular features of HCC by up-regulating inflammation, cell proliferation, stemness and miR-122 loss.
Divergence time estimates and the evolution of major lineages in the florideophyte red algae
Authors: Yang Eun Chan , Boo Sung Min , Bhattacharya Debashish , Saunders Gary W. , Knoll Andrew H. , Fredericq Suzanne , Graf Louis , Yoon Hwan Su 
Published: February 2016

AbstractThe Florideophyceae is the most abundant and taxonomically diverse class of red algae (Rhodophyta). However, many aspects of the systematics and divergence times of the group remain unresolved. Using a seven-gene concatenated dataset (nuclear EF2, LSU and SSU rRNAs, mitochondrial cox1, and plastid rbcL, psaA and psbA genes), we generated a robust phylogeny of red algae to provide an evolutionary timeline for florideophyte diversification. Our relaxed molecular clock analysis suggests that the Florideophyceae diverged approximately 943 (817–1,049) million years ago (Ma). The major divergences in this class involved the emergence of Hildenbrandiophycidae [ca. 781 (681–879) Ma], Nemaliophycidae [ca. 661 (597–736) Ma], Corallinophycidae [ca. 579 (543–617) Ma], and the split of Ahnfeltiophycidae and Rhodymeniophycidae [ca. 508 (442–580) Ma]. Within these clades, extant diversity reflects largely Phanerozoic diversification. Divergences within Florideophyceae were accompanied by evolutionary changes in the carposporophyte stage, leading to a successful strategy for maximizing spore production from each fertilization event. Our research provides robust estimates for the divergence times of major lineages within the Florideophyceae. This timeline was used to interpret the emergence of key morphological innovations that characterize these multicellular red algae.
Group precipitation and age hardening of nanostructured Fe-based alloys with ultra-high strengths
Authors: Jiao Z. B. , Luan J. H. , Miller M. K. , Yu C. Y. , Liu C. T. 
Published: February 2016

AbstractThe precipitation of nanoparticles plays a key role in determining the properties of many structural materials and the understanding of their formation and stabilization mechanisms has been a long standing interest in the material field. However, the critical issues involving the group precipitation of various nanoparticles and their cooperative hardening mechanism remain elusive in the newly discovered Fe-based alloys with nanostructures. Here we quantitatively elucidate the nucleation mechanism, evolution kinetics and hardening effects of the group-precipitated nanoparticles in the Fe-Cu-Ni-Al-based alloys by atom probe tomography together with both first-principles and thermodynamic calculations. Our results provide the compelling evidence for two interesting but complex group precipitation pathways of nanoparticles, i.e., the Cu-rich and NiAl-based precipitations. The co-existence of the two precipitation pathways plays a key role in age hardening kinetics and ultimately enhances the hardening response, as compared to the single particle type of strengthening, therefore providing an effective new approach for strengthening materials for structural applications.
Basal ganglia correlates of fatigue in young adults
Authors: Nakagawa Seishu , Takeuchi Hikaru , Taki Yasuyuki , Nouchi Rui , Kotozaki Yuka , Shinada Takamitsu , Maruyama Tsukasa , Sekiguchi Atsushi , Iizuka Kunio , Yokoyama Ryoichi , Yamamoto Yuki , Hanawa Sugiko , Araki Tsuyoshi , Miyauchi Carlos Makoto , Magistro Daniele , Sakaki Kohei , Jeong Hyeonjeong , Sasaki Yukako , Kawashima Ryuta 
Published: February 2016

AbstractAlthough the prevalence of chronic fatigue is approximately 20% in healthy individuals, there are no studies of brain structure that elucidate the neural correlates of fatigue outside of clinical subjects. We hypothesized that fatigue without evidence of disease might be related to changes in the basal ganglia and prefrontal cortex and be implicated in fatigue with disease. We aimed to identify the white matter structures of fatigue in young subjects without disease using magnetic resonance imaging (MRI). Healthy young adults (n = 883; 489 males and 394 females) were recruited. As expected, the degrees of fatigue and motivation were associated with larger mean diffusivity (MD) in the right putamen, pallidus and caudate. Furthermore, the degree of physical activity was associated with a larger MD only in the right putamen. Accordingly, motivation was the best candidate for widespread basal ganglia, whereas physical activity might be the best candidate for the putamen. A plausible mechanism of fatigue may involve abnormal function of the motor system, as well as areas of the dopaminergic system in the basal ganglia that are associated with motivation and reward.
Genome analysis of the kiwifruit canker pathogen Pseudomonas syringae pv. actinidiae biovar 5
Authors: Fujikawa Takashi , Sawada Hiroyuki 
Published: February 2016

AbstractPseudomonas syringae pv. actinidiae (Psa) is a destructive pathogen of kiwifruit bacterial canker disease, causing severe economic losses to kiwifruit industry worldwide. Biovar 5 is the most recently reported biovar of Psa and is found in only a local area of Japan at present. There is not much information of genetic characteristics of biovar 5. Thus, the genome of biovar 5 was sequenced and analyzed to clarify its detailed genetic characteristics. Here, the genomes of strain MAFF 212056 and MAFF 212061 of biovar 5 were estimated to be about 6.3 Mbp and 6.5 Mbp, respectively and their phylogenetic positions were proved to be near that of biovar 2 in the phylogenetic tree. However, it was confirmed that biovar 5 had neither the coronatine biosynthetic genes conserved in biovar 2, its phylogenetic neighbor, nor the phaseolotoxin biosynthetic genes conserved in biovar 1, Japanese native pathogen. In addition, 45 genes of type III secreted effectors were identified in biovar 5 genomes, showing that their composition is different from that in the other biovars. Moreover, some biovar 5-specific regions were identified. Then, biovar 5-specific PCR primers for targeting these regions were designed and proved to be applicable for detecting biovar 5 specifically.
High-internal-phase emulsions stabilized by metal-organic frameworks and derivation of ultralight metal-organic aerogels
Authors: Zhang Bingxing , Zhang Jianling , Liu Chengcheng , Peng Li , Sang Xinxin , Han Buxing , Ma Xue , Luo Tian , Tan Xiuniang , Yang Guanying 
Published: February 2016

AbstractTo design high-internal-phase emulsion (HIPE) systems is of great interest from the viewpoints of both fundamental researches and practical applications. Here we demonstrate for the first time the utilization of metal-organic framework (MOF) for HIPE formation. By stirring the mixture of water, oil and MOF at room temperature, the HIPE stabilized by the assembly of MOF nanocrystals at oil-water interface could be formed. The MOF-stabilized HIPE provides a novel route to produce highly porous metal-organic aerogel (MOA) monolith. After removing the liquids from the MOF-stabilized HIPE, the ultralight MOA with density as low as 0.01 g·cm−3 was obtained. The HIPE approach for MOA formation has unique advantages and is versatile in producing different kinds of ultralight MOAs with tunable porosities and structures.
Electron-phonon interaction and pairing mechanism in superconducting Ca-intercalated bilayer graphene
Authors: Margine E. R. , Lambert Henry , Giustino Feliciano 
Published: February 2016

AbstractUsing the ab initio anisotropic Eliashberg theory including Coulomb interactions, we investigate the electron-phonon interaction and the pairing mechanism in the recently-reported superconducting Ca-intercalated bilayer graphene. We find that C6CaC6 can support phonon-mediated superconductivity with a critical temperature Tc = 6.8–8.1 K, in good agreement with experimental data. Our calculations indicate that the low-energy Caxy vibrations are critical to the pairing and that it should be possible to resolve two distinct superconducting gaps on the electron and hole Fermi surface pockets.
New England harbor seal H3N8 influenza virus retains avian-like receptor specificity
Authors: Hussein Islam T. M. , Krammer Florian , Ma Eric , Estrin Michael , Viswanathan Karthik , Stebbins Nathan W. , Quinlan Devin S. , Sasisekharan Ram , Runstadler Jonathan 
Published: February 2016

AbstractAn influenza H3N8 virus, carrying mammalian adaptation mutations, was isolated from New England harbor seals in 2011. We sought to assess the risk of its human transmissibility using two complementary approaches. First, we tested the binding of recombinant hemagglutinin (HA) proteins of seal H3N8 and human-adapted H3N2 viruses to respiratory tissues of humans and ferrets. For human tissues, we observed strong tendency of the seal H3 to bind to lung alveoli, which was in direct contrast to the human-adapted H3 that bound mainly to the trachea. This staining pattern was also consistent in ferrets, the primary animal model for human influenza pathogenesis. Second, we compared the binding of the recombinant HAs to a library of 610 glycans. In contrast to the human H3, which bound almost exclusively to α-2,6 sialylated glycans, the seal H3 bound preferentially to α-2,3 sialylated glycans. Additionally, the seal H3N8 virus replicated in human lung carcinoma cells. Our data suggest that the seal H3N8 virus has retained its avian-like receptor binding specificity, but could potentially establish infection in human lungs.
Broadening the absorption bandwidth of metamaterial absorbers by transverse magnetic harmonics of 210 mode
Authors: Long Chang , Yin Sheng , Wang Wei , Li Wei , Zhu Jianfei , Guan Jianguo 
Published: February 2016

AbstractBy investigating a square-shaped metamaterial structure we discover that wave diffraction at diagonal corners of such a structure excites transverse magnetic harmonics of 210 mode (TM210 harmonics). Multi-layer overlapping and deliberately regulating period length between adjacent unit cells can significantly enhance TM210 harmonics, leading to a strong absorption waveband. On such a basis, a design strategy is proposed to achieve broadband, thin-thickness multi-layered metamaterial absorbers (MMAs). In this strategy big pyramidal arrays placed in the “white blanks” of a chessboard exhibit two isolated absorption bands due to their fundamental and TM210 harmonics, which are further connected by another absorption band from small pyramidal arrays in the “black blanks” of the chessboard. The as-designed MMA at a total thickness (h) of 4.36 mm shows an absorption of above 0.9 in the whole frequency range of 7–18 GHz, which is 38% broader with respect to previous design methods at the same h. This strategy provides an effective route to extend the absorption bandwidth of MMAs without increasing h.
Determination of thiol metabolites in human urine by stable isotope labeling in combination with pseudo-targeted mass spectrometry analysis
Authors: Liu Ping , Qi Chu-Bo , Zhu Quan-Fei , Yuan Bi-Feng , Feng Yu-Qi 
Published: February 2016

AbstractPrecursor ion scan and multiple reaction monitoring scan (MRM) are two typical scan modes in mass spectrometry analysis. Here, we developed a strategy by combining stable isotope labeling (IL) with liquid chromatography-mass spectrometry (LC-MS) under double precursor ion scan (DPI) and MRM for analysis of thiols in 5 types of human cancer urine. Firstly, the IL-LC-DPI-MS method was applied for non-targeted profiling of thiols from cancer samples. Compared to traditional full scan mode, the DPI method significantly improved identification selectivity and accuracy. 103 thiol candidates were discovered in all cancers and 6 thiols were identified by their standards. It is worth noting that pantetheine, for the first time, was identified in human urine. Secondly, the IL-LC-MRM-MS method was developed for relative quantification of thiols in cancers compared to healthy controls. All the MRM transitions of light and heavy labeled thiols were acquired from urines by using DPI method. Compared to DPI method, the sensitivity of MRM improved by 2.1–11.3 folds. In addition, the concentration of homocysteine, γ-glutamylcysteine and pantetheine enhanced more than two folds in cancer patients compared to healthy controls. Taken together, the method demonstrated to be a promising strategy for identification and comprehensive quantification of thiols in human urines.
Selection of highly efficient sgRNAs for CRISPR/Cas9-based plant genome editing
Authors: Liang Gang , Zhang Huimin , Lou Dengji , Yu Diqiu 
Published: February 2016

AbstractThe CRISPR/Cas9-sgRNA system has been developed to mediate genome editing and become a powerful tool for biological research. Employing the CRISPR/Cas9-sgRNA system for genome editing and manipulation has accelerated research and expanded researchers’ ability to generate genetic models. However, the method evaluating the efficiency of sgRNAs is lacking in plants. Based on the nucleotide compositions and secondary structures of sgRNAs which have been experimentally validated in plants, we instituted criteria to design efficient sgRNAs. To facilitate the assembly of multiple sgRNA cassettes, we also developed a new strategy to rapidly construct CRISPR/Cas9-sgRNA system for multiplex editing in plants. In theory, up to ten single guide RNA (sgRNA) cassettes can be simultaneously assembled into the final binary vectors. As a proof of concept, 21 sgRNAs complying with the criteria were designed and the corresponding Cas9/sgRNAs expression vectors were constructed. Sequencing analysis of transgenic rice plants suggested that 82% of the desired target sites were edited with deletion, insertion, substitution, and inversion, displaying high editing efficiency. This work provides a convenient approach to select efficient sgRNAs for target editing.
FLP-4 neuropeptide and its receptor in a neuronal circuit regulate preference choice through functions of ASH-2 trithorax complex in Caenorhabditis elegans
Authors: Yu Yonglin , Zhi Lingtong , Guan Xiangmin , Wang Daoyong , Wang Dayong 
Published: February 2016

AbstractPreference choice on food is an important response strategy for animals living in the environment. Using assay system of preference choice on bacterial foods, OP50 and PA14, we identified the involvement of ADL sensory neurons in the control of preference choice in Caenorhabditis elegans. Both genetically silencing and ChR2-mediated activation of ADL sensory neurons significantly affected preference choice. ADL regulated preference choice by inhibiting function of G protein-coupled receptor (GPCR)/SRH-220. ADL sensory neurons might regulate preference choice through peptidergic signals of FLP-4 and NLP-10 and function of FLP-4 or NLP-10 in regulating preference choice was regulated by SRH-220. FLP-4 released from ADL sensory neurons further regulated preference choice through its receptor of NPR-4 in AIB interneurons. In AIB interneurons, NPR-4 was involved in the control of preference choice by activating the functions of ASH-2 trithorax complex consisting of SET-2, ASH-2 and WDR-5, implying the crucial role of molecular machinery of trimethylation of histone H3K4 in the preference choice control. The identified novel neuronal circuit and the underlying molecular mechanisms will strengthen our understanding neuronal basis of preference choice in animals.
The N-terminal sequence of the extrinsic PsbP protein modulates the redox potential of Cyt b559 in photosystem II
Authors: Nishimura Taishi , Nagao Ryo , Noguchi Takumi , Nield Jon , Sato Fumihiko , Ifuku Kentaro 
Published: February 2016

AbstractThe PsbP protein, an extrinsic subunit of photosystem II (PSII) in green plants, is known to induce a conformational change around the catalytic Mn4CaO5 cluster securing the binding of Ca2+ and Cl– in PSII. PsbP has multiple interactions with the membrane subunits of PSII, but how these affect the structure and function of PSII requires clarification. Here, we focus on the interactions between the N-terminal residues of PsbP and the α subunit of Cytochrome (Cyt) b559 (PsbE). A key observation was that a peptide fragment formed of the first N-terminal 15 residues of PsbP, ‘pN15’, was able to convert Cyt b559 into its HP form. Interestingly, addition of pN15 to NaCl-washed PSII membranes decreased PSII’s oxygen-evolving activity, even in the presence of saturating Ca2+ and Cl– ions. In fact, pN15 reversibly inhibited the S1 to S2 transition of the OEC in PSII. These data suggest that pN15 can modulate the redox property of Cyt b559 involved in the side-electron pathway in PSII. This potential change of Cyt b559, in the absence of the C-terminal domain of PsbP, however, would interfere with any electron donation from the Mn4CaO5 cluster, leading to the possibility that multiple interactions of PsbP, binding to PSII, have distinct roles in regulating electron transfer within PSII.
Prognostic role of microscopically positive margins for primary gastrointestinal stromal tumors: a systematic review and meta-analysis
Authors: Zhi Xiaofei , Jiang Baofei , Yu Junbo , Røe Oluf Dimitri , Qin Jun , Ni Qingfeng , Sun Luning , Xu Meirong , Zhu Jianwei , Ma Lilin 
Published: February 2016

AbstractThe impact and management of microscopically positive margins in gastrointestinal stromal tumors (GISTs) remain unclear. The aim of this study is to estimate the prognostic value of surgical margins for disease-free survival (DFS) and overall survival (OS) in patients with primary GISTs. Twelve studies with 1985 GIST patients were included. The overall recurrence rate in R1 resection and R0 resection group was 0.364 (95% CI 0.299–0.429) and 0.296 (95% CI 0.161–0.430), respectively. Meta-analysis confirmed that a microscopically positive margin could significantly impact the disease-free survival (HR 1.596, 95% CI 1.128–2.258; I2 = 37.5%, P value = 0.091), but had no influence on overall survival (HR 1.430, 95% CI 0.608–3.363; I2 = 60.8%, P value = 0.013). Importantly, subgroup analysis revealed that adjuvant imatinib treatment could attenuate the risk of recurrence for primary GIST patients who received R1 resection. (HR 1.308, 95% CI 0.583–2.935; I2 = 53.2%, P value = 0.074). The level of evidence achieved in this study was “moderate” for DFS and “low” for OS. In conclusion, this study revealed that a microscopically positive margin is an unfavorable prognostic factor for GIST patients with R1 resection and adjuvant imatinib treatment is proved to be effective.