bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cranial biomechanics in basal urodeles: the Siberian salamander (Salamandrella keyserlingii) and its evolutionary and developmental implications
Authors: Zhou Zupeng , Fortuny Josep , Marcé-Nogué Jordi , Skutschas Pavel P. 
Published: August 2017

AbstractDevelopmental changes in salamander skulls, before and after metamorphosis, affect the feeding capabilities of these animals. How changes in cranial morphology and tissue properties affect the function of the skull are key to decipher the early evolutionary history of the crown-group of salamanders. Here, 3D cranial biomechanics of the adultSalamandrella keyserlingiiwere analyzed under different tissue properties and ossification sequences of the cranial skeleton. This helped unravel that: (a) Mechanical properties of tissues (as bone, cartilage or connective tissue) imply a consensus between the stiffness required to perform a function versus the fixation (and displacement) required with the surrounding skeletal elements. (b) Changes on the ossification pattern, producing fontanelles as a result of bone loss or failure to ossify, represent a trend toward simplification potentially helping to distribute stress through the skull, but may also imply a major destabilization of the skull. (c) Bone loss may be originated due to biomechanical optimization and potential reduction of developmental costs. (d) Hynobiids are excellent models for biomechanical reconstruction of extinct early urodeles.
Efficient laser-driven proton acceleration from cylindrical and planar cryogenic hydrogen jets
Authors: Obst Lieselotte , Göde Sebastian , Rehwald Martin , Brack Florian-Emanuel , Branco João , Bock Stefan , Bussmann Michael , Cowan Thomas E. , Curry Chandra B. , Fiuza Frederico , Gauthier Maxence , Gebhardt René , Helbig Uwe , Huebl Axel , Hübner Uwe , Irman Arie , Kazak Lev , Kim Jongjin B. , Kluge Thomas , Kraft Stephan , Loeser Markus , Metzkes Josefine , Mishra Rohini , Rödel Christian , Schlenvoigt Hans-Peter , Siebold Mathias , Tiggesbäumker Josef , Wolter Steffen , Ziegler Tim , Schramm Ulrich , Glenzer Siegfried H. , Zeil Karl 
Published: August 2017

AbstractWe report on recent experimental results deploying a continuous cryogenic hydrogen jet as a debris-free, renewable laser-driven source of pure proton beams generated at the 150 TW ultrashort pulse laser Draco. Efficient proton acceleration reaching cut-off energies of up to 20 MeV with particle numbers exceeding 109 particles per MeV per steradian is demonstrated, showing for the first time that the acceleration performance is comparable to solid foil targets with thicknesses in the micrometer range. Two different target geometries are presented and their proton beam deliverance characterized: cylindrical (∅ 5 μm) and planar (20 μm × 2 μm). In both cases typical Target Normal Sheath Acceleration emission patterns with exponential proton energy spectra are detected. Significantly higher proton numbers in laser-forward direction are observed when deploying the planar jet as compared to the cylindrical jet case. This is confirmed by two-dimensional Particle-in-Cell (2D3V PIC) simulations, which demonstrate that the planar jet proves favorable as its geometry leads to more optimized acceleration conditions.
Metagenomic evidence of stronger effect of stylo (legume) than bahiagrass (grass) on taxonomic and functional profiles of the soil microbial community
Authors: Zhou Yang , Zhu Honghui , Fu Shenglei , Yao Qing 
Published: August 2017

AbstractPlants are key determinants of soil microbial community (SMC). Legumes and grasses are distinct groups in various ecosystems; however, how they differentially shape SMC structure and functioning has yet to be explored. Here, we investigate SMC in soils grown with stylo (legume) or bahiagrass (grass). Soil metagenomic sequencing indicates that Archaea was more abundant in unplanted soils than in planted soils, and that stylo selected higher abundance of fungi than bahiagrass. When the stylo soils enriched Streptomyces, Frankia, Mycobacterium and Amycolatopsis, the bahiagrass soils enriched Sphingomonas and Sphingobium. NMDS reveals that the legume shaped SMC more greatly than the grass (P < 0.004). SMC functional profiles (KEGG and CAZy) were also greatly altered by plants with the legume being more effective (P < 0.000 and P < 0.000). The abundant microbial taxa contributed to the main community functions, with Conexibacter, Sphingomonas, and Burkholderia showing multifunctionality. Moreover, soil chemical property showed much higher direct effect on SMC structure and functional profiles than soil extracts, although the soil total nitrogen and some compounds (e.g. heptadecane, 1-pentadecyne and nonanoic acid) in soil extracts were best correlated with SMC structure and functional profiles. These findings are the first to suggest that legume species shape SMC more greatly than grass species.
Optimal achieved blood pressure for patients with stable coronary artery disease
Authors: Huang Chin-Chou , Leu Hsin-Bang , Yin Wei-Hsian , Tseng Wei-Kung , Wu Yen-Wen , Lin Tsung-Hsien , Yeh Hung-I , Chang Kuan-Cheng , Wang Ji-Hung , Wu Chau-Chung , Chen Jaw-Wen 
Published: August 2017

AbstractWe aimed to investigate the ideal achieved blood pressure (BP) in ethnic Chinese patients with stable coronary artery disease (CAD) in Taiwan. A total of 2,045 patients (age 63.5 ± 11.9 years, 1,722 male [84.2%]) with stable CAD who had undergone percutaneous coronary interventions were enrolled. The achieved systolic BP was 130.6 ± 17.7 mmHg and diastolic BP was 74.9 ± 12.0 mmHg. In 12 months, patients with systolic BP < 120 mmHg and systolic BP ≥ 160 mmHg had increased risk of total cardiovascular events when compared to those with systolic BP 120–139 mmHg. In 24 months, patients with systolic BP < 120 mmHg and systolic BP ≥ 160 mmHg had increased risk of total cardiovascular events when compared to those with systolic BP 120–139 mmHg; patients with diastolic BP < 70 mmHg had increased risk of total cardiovascular events when compared to those with diastolic BP 70–79 mmHg. In conclusion, systolic BP < 120 mmHg and ≥160 mmHg or diastolic BP < 70 mmHg is associated with increased cardiovascular events, supporting that the optimal BP control should also be justified for stable CAD in non-western cohorts.
Entropy spikes as a signature of Lifshitz transitions in the Dirac materials
Authors: Tsaran V. Yu. , Kavokin A. V. , Sharapov S. G. , Varlamov A. A. , Gusynin V. P. 
Published: August 2017

AbstractWe demonstrate theoretically that the characteristic feature of a 2D system undergoing N consequent Lifshitz topological transitions is the occurrence of spikes of entropy per particle s of a magnitude ±ln2/(J − 1/2) with 2 ≤ J ≤ N at low temperatures. We derive a general expression for s as a function of chemical potential, temperature and gap magnitude for the gapped Dirac materials. Inside the smallest gap, the dependence of s on the chemical potential exhibits a dip-and-peak structure in the temperature vicinity of the Dirac point. The spikes of the entropy per particles can be considered as a signature of the Dirac materials. These distinctive characteristics of gapped Dirac materials can be detected in transport experiments where the temperature is modulated in gated structures.
Functional validation of novel MKS3/TMEM67 mutations in COACH syndrome
Authors: Lee So-Hyun , Nam Tai-Seung , Li Wenting , Kim Jung Ha , Yoon Woong , Choi Yoo-Duk , Kim Kun-Hee , Cai Hua , Kim Min Jung , Kim Changsoo , Choy Hyon E. , Kim Nacksung , Chay Kee Oh , Kim Myeong-Kyu , Choi Seok-Yong 
Published: August 2017

AbstractCOACH syndrome is an autosomal recessive developmental disorder, a subtype of Joubert syndrome and related disorders, characterized by cerebellar vermis hypoplasia, oligophrenia, ataxia, coloboma, and hepatic fibrosis. Although mutations in TMEM67 (transmembrane protein 67)/MKS3 (Meckel-Gruber syndrome, type 3) were reported to cause COACH syndrome, this causality has not verified by functional studies. In a 20-year-old Korean man, we found cerebellar ataxia, isolated elevation in serum γ-glutamyl transpeptidase (γ-GTP) activity, oligophrenia, the molar tooth sign (MTS) in the brain MR images and congenital hepatic fibrosis (CHF). Two novel compound heterozygous mutations were found in TMEM67 in the patient: i) missense mutation (c.395 G > C and p.Gly132Ala) in exon 3, and ii) deletion in exon 26 (c.2758delT and p.Tyr920ThrfsX40). Western blotting showed that the p.Tyr920ThrfsX40 mutation accelerates turnover of the TMEM67 protein. Although wild-type human TMEM67 RNA rescued phenotypes of zebrafish embryos injected with anti-sense oligonucleotide morpholinos against tmem67, the two human TMEM67 RNAs individually harboring the two mutations did not. Finally, Wnt signaling, but not Hedgehog signaling, was suppressed in tmem67 morphants. To the best of our knowledge, this is the first report verifying the causality between COACH syndrome and TMEM67, which will further our understanding of molecular pathogenesis of the syndrome.
Inert Gas Deactivates Protein Activity by Aggregation
Authors: Zhang Lijuan , Zhang Yuebin , Cheng Jie , Wang Lei , Wang Xingya , Zhang Meng , Gao Yi , Hu Jun , Zhang Xuehua , Lü Junhong , Li Guohui , Tai Renzhong , Fang Haiping 
Published: August 2017

AbstractBiologically inert gases play important roles in the biological functionality of proteins. However, researchers lack a full understanding of the effects of these gases since they are very chemically stable only weakly absorbed by biological tissues. By combining X-ray fluorescence, particle sizing and molecular dynamics (MD) simulations, this work shows that the aggregation of these inert gases near the hydrophobic active cavity of pepsin should lead to protein deactivation. Micro X-ray fluorescence spectra show that a pepsin solution can contain a high concentration of Xe or Kr after gassing, and that the gas concentrations decrease quickly with degassing time. Biological activity experiments indicate a reversible deactivation of the protein during this gassing and degassing. Meanwhile, the nanoparticle size measurements reveal a higher number of “nanoparticles” in gas-containing pepsin solution, also supporting the possible interaction between inert gases and the protein. Further, MD simulations indicate that gas molecules can aggregate into a tiny bubble shape near the hydrophobic active cavity of pepsin, suggesting a mechanism for reducing their biological function.
Involvement of mTOR-autophagy in the selection of primitive mesenchymal stem cells in chitosan film 3-dimensional culture
Authors: Chiu Hsiao-Ying , Tsay Yeou-Guang , Hung Shih-Chieh 
Published: August 2017

AbstractMesenchymal stem cells (MSCs) in conventional monolayer culture are heterogeneous and contain a significant portion of senescent cells. MSCs cultured on chitosan film form 3-dimenional spheres, increase in stemness and differentiation capability; however, the underlying mechanisms remain elusive. We first demonstrate chitosan film culture induces apoptosis at 2 days, with specificity in late senescent cells. Especially in senescent cells, chitosan film culture activates mTOR, which activates S6K/S6/4E-BP1 to enhance fibronection synthesis and peripheral dead cell attachment, and phosphorylates ULK1 at S757 to further inactivate ULK1, LC3A and autophagy, thereby inducing apoptosis. Combination of chitosan film culture with mTOR inhibition prevents peripheral dead cell attachment, thereby further increasing pluripotent gene expression, in vitro osteogenesis and in vivo bone formation. These data successfully figure out the role of mTOR signaling in chitosan film culture and develop a method by combination of rapamycin treatment for promoting stemness and differentiation capability in MSCs.
Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids (Diaphorina citri) from California Were Related to Those from Florida
Authors: Wu Fengnian , Kumagai Luci , Cen Yijing , Chen Jianchi , Wallis Christopher M. , Polek MaryLou , Jiang Hongyan , Zheng Zheng , Liang Guangwen , Deng Xiaoling 
Published: August 2017

AbstractAsian citrus psyllid (ACP, Diaphorina citri Kuwayama) transmits “Candidatus Liberibacter asiaticus” (CLas), an unculturable alpha-proteobacterium associated with citrus Huanglongbing (HLB). CLas has recently been found in California. Understanding ACP population diversity is necessary for HLB regulatory practices aimed at reducing CLas spread. In this study, two circular ACP mitogenome sequences from California (mt-CApsy, ~15,027 bp) and Florida (mt-FLpsy, ~15,012 bp), USA, were acquired. Each mitogenome contained 13 protein coding genes, 2 ribosomal RNA and 22 transfer RNA genes, and a control region varying in sizes. The Californian mt-CApsy was identical to the Floridian mt-FLpsy, but different from the mitogenome (mt-GDpsy) of Guangdong, China, in 50 single nucleotide polymorphisms (SNPs). Further analyses were performed on sequences in cox1 and trnAsn regions with 100 ACPs, SNPs in nad1-nad4-nad5 locus through PCR with 252 ACP samples. All results showed the presence of a Chinese ACP cluster (CAC) and an American ACP cluster (AAC). We proposed that ACP in California was likely not introduced from China based on our current ACP collection but somewhere in America. However, more studies with ACP samples from around the world are needed. ACP mitogenome sequence analyses will facilitate ACP population research.
PIK3CA exon9 mutations associate with reduced survival, and are highly concordant between matching primary tumors and metastases in endometrial cancer
Authors: Mjos Siv , Werner Henrica M. J. , Birkeland Even , Holst Frederik , Berg Anna , Halle Mari K. , Tangen Ingvild L. , Kusonmano Kanthida , Mauland Karen K. , Oyan Anne M. , Kalland Karl-Henning , Lewis Aurélia E. , Mills Gordon B. , Krakstad Camilla , Trovik Jone , Salvesen Helga B. , Hoivik Erling A. 
Published: August 2017

AbstractMutations of the phosphoinositide-3-kinase (PI3K) catalytic subunit alpha gene (PIK3CA) are frequent in endometrial cancer. We sequenced exon9 and exon20 of PIK3CA in 280 primary endometrial cancers to assess the relationship with clinicopathologic variables, patient survival and associations with PIK3CA mRNA and phospho-AKT1 by gene expression and protein data, respectively. While PIK3CA mutations generally had no impact on survival, and were not associated with clinicopathological variables, patients with exon9 charge-changing mutations, providing a positive charge at the substituted amino acid residue, were associated with poor survival (p = 0.018). Furthermore, we characterized PIK3CA mutations in the metastatic setting, including 32 patients with matched primary tumors and metastases, and found a high level of concordance (85.7%; 6 out of 7 patients), suggesting limited heterogeneity. PIK3CA mRNA levels were increased in metastases compared to the primary tumors (p = 0.031), independent of PIK3CA mutation status, which rather associated with reduced PIK3CA mRNA expression. PIK3CA mutated tumors expressed higher p-AKT/AKT protein levels, both within primary (p < 0.001) and metastatic lesion (p = 0.010). Our results support the notion that the PI3K signaling pathway might be activated, both dependent- and independently of PIK3CA mutations, an aspect that should be considered when designing PIK3 pathway targeting strategies in endometrial cancer.
De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide
Authors: Entzminger Kevin C. , Hyun Jeong-min , Pantazes Robert J. , Patterson-Orazem Athena C. , Qerqez Ahlam N. , Frye Zach P. , Hughes Randall A. , Ellington Andrew D. , Lieberman Raquel L. , Maranas Costas D. , Maynard Jennifer A. 
Published: August 2017

AbstractComputational antibody engineering efforts to date have focused on improving binding affinities or biophysical characteristics. De novo design of antibodies binding specific epitopes could greatly accelerate discovery of therapeutics as compared to conventional immunization or synthetic library selection strategies. Here, we employed de novo complementarity determining region (CDR) design to engineer targeted antibody–antigen interactions using previously described in silico methods. CDRs predicted to bind the minimal FLAG peptide (Asp–Tyr–Lys–Asp) were grafted onto a single-chain variable fragment (scFv) acceptor framework. Fifty scFvs comprised of designed heavy and light or just heavy chain CDRs were synthesized and screened for peptide binding by phage ELISA. Roughly half of the designs resulted in detectable scFv expression. Four antibodies, designed entirely in silico, bound the minimal FLAG sequence with high specificity and sensitivity. When reformatted as soluble antigen-binding fragments (Fab), these clones expressed well, were predominantly monomeric and retained peptide specificity. In both formats, the antibodies bind the peptide only when present at the amino-terminus of a carrier protein and even conservative peptide amino acid substitutions resulted in a complete loss of binding. These results support in silico CDR design of antibody specificity as an emerging antibody engineering strategy.
Evidence for rangewide panmixia despite multiple barriers to dispersal in a marine mussel
Authors: Lourenço Carla R. , Nicastro Katy R. , McQuaid Christopher D. , Chefaoui Rosa M. , Assis Jorge , Taleb Mohammed Z. , Zardi Gerardo I. 
Published: August 2017

AbstractOceanographic features shape the distributional and genetic patterns of marine species by interrupting or promoting connections among populations. Although general patterns commonly arise, distributional ranges and genetic structure are species-specific and do not always comply with the expected trends. By applying a multimarker genetic approach combined with Lagrangian particle simulations (LPS) we tested the hypothesis that oceanographic features along northeastern Atlantic and Mediterranean shores influence dispersal potential and genetic structure of the intertidal musselPerna perna. Additionally, by performing environmental niche modelling we assessed the potential and realized niche ofP.pernaalong its entire native distributional range and the environmental factors that best explain its realized distribution.Perna pernashowed evidence of panmixia across >4,000 km despite several oceanographic breaking points detected by LPS. This is probably the result of a combination of life history traits, continuous habitat availability and stepping-stone dynamics. Moreover, the niche modelling framework depicted minimum sea surface temperatures (SST) as the major factor shapingP.pernadistributional range limits along its native areas. Forthcoming warming SST is expected to further change these limits and allow the species to expand its range polewards though this may be accompanied by retreat from warmer areas.
Endolysin LysEF-P10 shows potential as an alternative treatment strategy for multidrug-resistant Enterococcus faecalis infections
Authors: Cheng Mengjun , Zhang Yufeng , Li Xinwei , Liang Jiaming , Hu Liyuan , Gong Pengjuan , Zhang Lei , Cai Ruopeng , Zhang Hao , Ge Jinli , Ji Yalu , Guo Zhimin , Feng Xin , Sun Changjiang , Yang Yongjun , Lei Liancheng , Han Wenyu , Gu Jingmin 
Published: August 2017

AbstractPhage-derived lysins can hydrolyse bacterial cell walls and show great potential for combating Gram-positive pathogens. In this study, the potential of LysEF-P10, a new lysin derived from a isolated Enterococcus faecalis phage EF-P10, as an alternative treatment for multidrug-resistant E. faecalis infections, was studied. LysEF-P10 shares only 61% amino acid identity with its closest homologues. Four proteins were expressed: LysEF-P10, the cysteine, histidine-dependent amidohydrolase/peptidase (CHAP) domain (LysEF-P10C), the putative binding domain (LysEF-P10B), and a fusion recombination protein (LysEF-P10B-green fluorescent protein). Only LysEF-P10 showed highly efficient, broad-spectrum bactericidal activity against E. faecalis. Several key functional residues, including the Cys-His-Asn triplet and the calcium-binding site, were confirmed using 3D structure prediction, BLAST and mutation analys. We also found that calcium can switch LysEF-P10 between its active and inactive states and that LysEF-P10B is responsible for binding E. faecalis cells. A single administration of LysEF-P10 (5 μg) was sufficient to protect mice against lethal vancomycin-resistant Enterococcus faecalis (VREF) infection, and LysEF-P10-specific antibody did not affect its bactericidal activity or treatment effect. Moreover, LysEF-P10 reduced the number of Enterococcus colonies and alleviated the gut microbiota imbalance caused by VREF. These results indicate that LysEF-P10 might be an alternative treatment for multidrug-resistant E. faecalis infections.
Discovery of human-like L-asparaginases with potential clinical use by directed evolution
Authors: Rigouin Coraline , Nguyen Hien Anh , Schalk Amanda M. , Lavie Arnon 
Published: August 2017

AbstractL-asparaginase is a chemotherapy drug used to treat acute lymphoblastic leukemia (ALL). The main prerequisite for clinical efficacy of L-asparaginases is micromolar KM for asparagine to allow for complete depletion of this amino acid in the blood. Since currently approved L-asparaginases are of bacterial origin, immunogenicity is a challenge, which would be mitigated by a human enzyme. However, all human L-asparaginases have millimolar KM for asparagine. We recently identified the low KM guinea pig L-asparaginase (gpASNase1). Because gpASNase1 and human L-asparaginase 1 (hASNase1) share ~70% amino-acid identity, we decided to humanize gpASNase1 by generating chimeras with hASNase1 through DNA shuffling. To identify low KM chimeras we developed a suitable bacterial selection system (E. coli strain BW5Δ). Transforming BW5Δ with the shuffling libraries allowed for the identification of several low KM clones. To further humanize these clones, the C-terminal domain of gpASNase1 was replaced with that of hASNase1. Two of the identified clones, 63N-hC and 65N-hC, share respectively 85.7% and 87.1% identity with the hASNase1 but have a KM similar to gpASNase1. These clones possess 100–140 fold enhanced catalytic efficiency compared to hASNase1. Notably, we also show that these highly human-like L-asparaginases maintain their in vitro ALL killing potential.
Predicting hidden bulk phases from surface phases in bilayered Sr3Ru2O7
Authors: Rivero Pablo , Jin Rongying , Chen Chen , Meunier Vincent , Plummer E. W. , Shelton William 
Published: August 2017

AbstractThe ability to predict hidden phases under extreme conditions is not only crucial to understanding and manipulating materials but it could also lead to insight into new phenomena and novel routes to synthesize new phases. This is especially true for Ruddlesden-Popper perovskite phases that possess interesting properties ranging from superconductivity and colossal magnetoresistance to photovoltaic and catalytic activities. In particular, the physical properties of the bilayer perovskite Sr3Ru2O7 at the surface are intimately tied to the rotation and tilt of the RuO6 octahedra. To take advantage of the extra degree of freedom associated with tilting we have performed first principles hybrid density functional simulations of uniaxial pressure applied along the c-axis of bulk Sr3Ru2O7 where we find that the octahedra become tilted, leading to two phase transitions. One is a structural transition at $$\simeq $$
≃
1.5 GPa, and the other is from a ferromagnetic (FM) metal to an antiferromagnetic (AFM) insulator at $$\simeq $$
≃
21 GPa whose AFM spin configuration is different from the AFM state near the FM ground state.