bluuebunny/crossref_metadata_2025_split huggingface dataset:
Psgl-1 Deficiency is Protective against Stroke in a Murine Model of Lupus
Authors: Wang Hui , Knight Jason S. , Hodgin Jeffrey B. , Wang Jintao , Guo Chiao , Kleiman Kyle , Eitzman Daniel T. 
Published: June 2016

AbstractSystemic lupus erythematosus (SLE) is associated with an elevated risk of vascular complications, including premature stroke. Therapies targeting leukocyte recruitment may be beneficial in reducing vascular complications associated with SLE. Lupus was induced in female wild-type (WT) and P-selectin glycoprotein ligand-1 deficient (Psgl-1−/−) mice with pristane. Stroke was induced following photochemical injury to the middle cerebral artery (MCA). Stroke size was increased in pristane-treated WT mice compared to non-pristane-treated WT controls. However, stroke size was not increased in pristane-treated Psgl-1−/− mice compared to controls, despite evidence of increased nephritis in Psgl-1−/− mice. Pristane-treated WT mice showed elevated anti-dsDNA, anti-snRNP, CXCL1 and MCP-1 levels compared to untreated mice; however levels of anti-snRNP, MCP-1 and CXCL1 were reduced in pristane-treated Psgl-1−/− mice compared to pristane-treated WT mice. Infiltration of neutrophils and macrophages at the cerebral infarction site were reduced in pristane-treated Psgl-1−/− mice compared to pristane-treated WT mice. In conclusion, the increase in stroke size associated with lupus is prevented by Psgl-1 deficiency while nephritis is exacerbated. Therapies targeting Psgl-1 may be useful in the management of SLE patients at high risk of acute vascular complications although elucidation of downstream pathways will be necessary to identify targets that do not promote nephritis.
Phosphoproteomic analysis of Methanohalophilus portucalensis FDF1T identified the role of protein phosphorylation in methanogenesis and osmoregulation
Authors: Wu Wan-Ling , Lai Shu-Jung , Yang Jhih-Tian , Chern Jeffy , Liang Suh-Yuen , Chou Chi-Chi , Kuo Chih-Horng , Lai Mei-Chin , Wu Shih-Hsiung 
Published: June 2016

AbstractMethanogens have gained much attention for their metabolic product, methane, which could be an energy substitute but also contributes to the greenhouse effect. One factor that controls methane emission, reversible protein phosphorylation, is a crucial signaling switch and phosphoproteomics has become a powerful tool for large-scale surveying. Here, we conducted the first phosphorylation-mediated regulation study in halophilic Methanohalophilus portucalensis FDF1T, a model strain for studying stress response mechanisms in osmoadaptation. A shotgun approach and MS-based analysis identified 149 unique phosphoproteins. Among them, 26% participated in methanogenesis and osmolytes biosynthesis pathways. Of note, we uncovered that protein phosphorylation might be a crucial factor to modulate the pyrrolysine (Pyl) incorporation and Pyl-mediated methylotrophic methanogenesis. Furthermore, heterologous expression of glycine sarcosine N-methyltransferase (GSMT) mutant derivatives in the osmosensitive Escherichia coli MKH13 revealed that the nonphosphorylated T68A mutant resulted in increased salt tolerance. In contrast, mimic phosphorylated mutant T68D proved defective in both enzymatic activity and salinity tolerance for growth. Our study provides new insights into phosphorylation modification as a crucial role of both methanogenesis and osmoadaptation in methanoarchaea, promoting biogas production or reducing future methane emission in response to global warming and climate change.
Anti-cancer efficacy of nonthermal plasma dissolved in a liquid, liquid plasma in heterogeneous cancer cells
Authors: Nguyen Ngoc Hoan , Park Hyung Jun , Yang Sang Sik , Choi Kyeong Sook , Lee Jong-Soo 
Published: July 2016

AbstractThe therapeutic potential of nonthermal plasma for cancer treatment has been reported recently. The heterogeneity of cancer cells need to be addressed to design effective anticancer treatments. Here, we show that treatment with nonthermal atmospheric-pressure plasma dissolved in a liquid (liquid plasma) induces oxidative stress in heterogeneous populations of cancer cells and ultimately kills these cells via apoptosis, regardless of genetic status, e.g., mutations in p53 and other DNA-damage-response genes. We found that liquid plasma markedly increased the concentration of intracellular and mitochondrial reactive oxygen species (ROS), reflecting an influx from the extracellular milieu. Liquid plasma contributed to mitochondrial accumulation of ROS and depolarization of mitochondrial membrane potential with consequent cell death. Healthy normal cells, however, were hardly affected by the liquid-plasma treatment. The antioxidant N-acetylcysteine blocked liquid-plasma-induced cell death. A knockdown of CuZn-superoxide dismutase or Mn-SOD enhanced the plasma-induced cell death, whereas expression of exogenous CuZn-SOD, Mn-SOD, or catalase blocked the cell death. These results suggest that the mitochondrial dysfunction mediated by ROS production is a key contributor to liquid-plasma-induced apoptotic cell death, regardless of genetic variation. Thus, liquid plasma may have clinical applications, e.g., the development of therapeutic strategies and prevention of disease progression despite tumor heterogeneity.
A novel AhR ligand, 2AI, protects the retina from environmental stress
Authors: Gutierrez Mark A. , Davis Sonnet S. , Rosko Andrew , Nguyen Steven M. , Mitchell Kylie P. , Mateen Samiha , Neves Joana , Garcia Thelma Y. , Mooney Shaun , Perdew Gary H. , Hubbard Troy D. , Lamba Deepak A. , Ramanathan Arvind 
Published: July 2016

AbstractVarious retinal degenerative diseases including dry and neovascular age-related macular degeneration (AMD), retinitis pigmentosa, and diabetic retinopathy are associated with the degeneration of the retinal pigmented epithelial (RPE) layer of the retina. This consequently results in the death of rod and cone photoreceptors that they support, structurally and functionally leading to legal or complete blindness. Therefore, developing therapeutic strategies to preserve cellular homeostasis in the RPE would be a favorable asset in the clinic. The aryl hydrocarbon receptor (AhR) is a conserved, environmental ligand-dependent, per ARNT-sim (PAS) domain containing bHLH transcription factor that mediates adaptive response to stress via its downstream transcriptional targets. Using in silico, in vitro and in vivo assays, we identified 2,2′-aminophenyl indole (2AI) as a potent synthetic ligand of AhR that protects RPE cells in vitro from lipid peroxidation cytotoxicity mediated by 4-hydroxynonenal (4HNE) as well as the retina in vivo from light-damage. Additionally, metabolic characterization of this molecule by LC-MS suggests that 2AI alters the lipid metabolism of RPE cells, enhancing the intracellular levels of palmitoleic acid. Finally, we show that, as a downstream effector of 2AI-mediated AhR activation, palmitoleic acid protects RPE cells from 4HNE-mediated stress, and light mediated retinal degeneration in mice.
Realized niche shift associated with the Eurasian charophyte Nitellopsis obtusa becoming invasive in North America
Authors: Escobar Luis E. , Qiao Huijie , Phelps Nicholas B. D. , Wagner Carli K. , Larkin Daniel J. 
Published: July 2016

AbstractNitellopsis obtusa(starry stonewort) is a dioecious green alga native to Europe and Asia that has emerged as an aquatic invasive species in North America.Nitellopsis obtusais rare across large portions of its native range, but has spread rapidly in northern-tier lakes in the United States, where it can interfere with recreation and may displace native species. Little is known about the invasion ecology ofN. obtusa, making it difficult to forecast future expansion. Using ecological niche modeling we investigated environmental variables associated with invasion risk. We used species records, climate data, and remotely sensed environmental variables to characterize the species’ multidimensional distribution. We found thatN. obtusais exploiting novel ecological niche space in its introduced range, which may help explain its invasiveness. While the fundamental niche ofN. obtusamay be stable, there appears to have been a shift in its realized niche associated with invasion in North America. Large portions of the United States are predicted to constitute highly suitable habitat forN. obtusa. Our results can inform early detection and rapid response efforts targetingN. obtusaand provide testable estimates of the physiological tolerances of this species as a baseline for future empirical research.
Stimulated emission of Cooper pairs in a high-temperature cuprate superconductor
Authors: Zhang Wentao , Miller Tristan , Smallwood Christopher L. , Yoshida Yoshiyuki , Eisaki Hiroshi , Kaindl R. A. , Lee Dung-Hai , Lanzara Alessandra 
Published: July 2016

AbstractThe concept of stimulated emission of bosons has played an important role in modern science and technology and constitutes the working principle for lasers. In a stimulated emission process, an incoming photon enhances the probability that an excited atomic state will transition to a lower energy state and generate a second photon of the same energy. It is expected, but not experimentally shown, that stimulated emission contributes significantly to the zero resistance current in a superconductor by enhancing the probability that scattered Cooper pairs will return to the macroscopically occupied condensate instead of entering any other state. Here, we use time- and angle-resolved photoemission spectroscopy to study the initial rise of the non-equilibrium quasiparticle population in a Bi2Sr2CaCu2O8+δ cuprate superconductor induced by an ultrashort laser pulse. Our finding reveals significantly slower buildup of quasiparticles in the superconducting state than in the normal state. The slower buildup only occurs when the pump pulse is too weak to deplete the superconducting condensate and for cuts inside the Fermi arc region. We propose this is a manifestation of stimulated recombination of broken Cooper pairs and signals an important momentum space dichotomy in the formation of Cooper pairs inside and outside the Fermi arc region.
Time resolved X-ray Dark-Field Tomography Revealing Water Transport in a Fresh Cement Sample
Authors: Prade Friedrich , Fischer Kai , Heinz Detlef , Meyer Pascal , Mohr Jürgen , Pfeiffer Franz 
Published: June 2016

AbstractGrating-based X-ray dark-field tomography is a promising technique for biomedical and materials research. Even if the resolution of conventional X-ray tomography does not suffice to resolve relevant structures, the dark-field signal provides valuable information about the sub-pixel microstructural properties of the sample. Here, we report on the potential of X-ray dark-field imaging to be used for time-resolved three-dimensional studies. By repeating consecutive tomography scans on a fresh cement sample, we were able to study the hardening dynamics of the cement paste in three dimensions over time. The hardening of the cement was accompanied by a strong decrease in the dark-field signal pointing to microstructural changes within the cement paste. Furthermore our results hint at the transport of water from certain limestone grains, which were embedded in the sample, to the cement paste during the process of hardening. This is indicated by an increasing scattering signal which was observed for two of the six tested limestone grains. Electron microscopy images revealed a distinct porous structure only for those two grains which supports the following interpretation of our results. When the water filled pores of the limestone grains empty during the experiment the scattering signal of the grains increases.
Specificity and mechanism of action of alpha-helical membrane-active peptides interacting with model and biological membranes by single-molecule force spectroscopy
Authors: Sun Shiyu , Zhao Guangxu , Huang Yibing , Cai Mingjun , Shan Yuping , Wang Hongda , Chen Yuxin 
Published: July 2016

AbstractIn this study, to systematically investigate the targeting specificity of membrane-active peptides on different types of cell membranes, we evaluated the effects of peptides on different large unilamellar vesicles mimicking prokaryotic, normal eukaryotic, and cancer cell membranes by single-molecule force spectroscopy and spectrum technology. We revealed that cationic membrane-active peptides can exclusively target negatively charged prokaryotic and cancer cell model membranes rather than normal eukaryotic cell model membranes. Using Acholeplasma laidlawii, 3T3-L1, and HeLa cells to represent prokaryotic cells, normal eukaryotic cells, and cancer cells in atomic force microscopy experiments, respectively, we further studied that the single-molecule targeting interaction between peptides and biological membranes. Antimicrobial and anticancer activities of peptides exhibited strong correlations with the interaction probability determined by single-molecule force spectroscopy, which illustrates strong correlations of peptide biological activities and peptide hydrophobicity and charge. Peptide specificity significantly depends on the lipid compositions of different cell membranes, which validates the de novo design of peptide therapeutics against bacteria and cancers.
Integrative analysis of cancer genes in a functional interactome
Authors: Ung Matthew H. , Liu Chun-Chi , Cheng Chao 
Published: June 2016

AbstractThe post-genomic era has resulted in the accumulation of high-throughput cancer data from a vast array of genomic technologies including next-generation sequencing and microarray. As such, the large amounts of germline variant and somatic mutation data that have been generated from GWAS and sequencing projects, respectively, show great promise in providing a systems-level view of these genetic aberrations. In this study, we analyze publicly available GWAS, somatic mutation and drug target data derived from large databanks using a network-based approach that incorporates directed edge information under a randomized network hypothesis testing procedure. We show that these three classes of disease-associated nodes exhibit non-random topological characteristics in the context of a functional interactome. Specifically, we show that drug targets tend to lie upstream of somatic mutations and disease susceptibility germline variants. In addition, we introduce a new approach to measuring hierarchy between drug targets, somatic mutants and disease susceptibility genes by utilizing directionality and path length information. Overall, our results provide new insight into the intrinsic relationships between these node classes that broaden our understanding of cancer. In addition, our results align with current knowledge on the therapeutic actionability of GWAS and somatic mutant nodes, while demonstrating relationships between node classes from a global network perspective.
Longitudinal Comparison of Auditory Steady-State Evoked Potentials in Preterm and Term Infants: The Maturation Process
Authors: Sousa Ana , Didoné Dayane , Sleifer Pricila 
Published: July 2016

Introduction Preterm neonates are at risk of changes in their auditory system development, which explains the need for auditory monitoring of this population. The Auditory Steady-State Response (ASSR) is an objective method that allows obtaining the electrophysiological thresholds with greater applicability in neonatal and pediatric population.
Objective The purpose of this study is to compare the ASSR thresholds in preterm and term infants evaluated during two stages.
Method The study included 63 normal hearing neonates: 33 preterm and 30 term. They underwent assessment of ASSR in both ears simultaneously through insert phones in the frequencies of 500 to 4000Hz with the amplitude modulated from 77 to 103Hz. We presented the intensity at a decreasing level to detect the minimum level of responses. At 18 months, 26 of 33 preterm infants returned for the new assessment for ASSR and were compared with 30 full-term infants. We compared between groups according to gestational age.
Results Electrophysiological thresholds were higher in preterm than in full-term neonates (p < 0.05) at the first testing. There were no significant differences between ears and gender. At 18 months, there was no difference between groups (p > 0.05) in all the variables described.
Conclusion In the first evaluation preterm had higher thresholds in ASSR. There was no difference at 18 months of age, showing the auditory maturation of preterm infants throughout their development.
Algorithmic methods to infer the evolutionary trajectories in cancer progression
Authors: Caravagna Giulio , Graudenzi Alex , Ramazzotti Daniele , Sanz-Pamplona Rebeca , De Sano Luca , Mauri Giancarlo , Moreno Victor , Antoniotti Marco , Mishra Bud 
Published: June 2016

SignificanceA causality-based machine learning Pipeline for Cancer Inference (PiCnIc) is introduced to infer the underlying somatic evolution of ensembles of tumors from next-generation sequencing data. PiCnIc combines techniques for sample stratification, driver selection, and identification of fitness-equivalent exclusive alterations to exploit an algorithm based on Suppes’ probabilistic causation. The accuracy and translational significance of the results are studied in detail, with an application to colorectal cancer. The PiCnIc pipeline has been made publicly accessible for reproducibility, interoperability, and future enhancements.
Solid tumor therapy by selectively targeting stromal endothelial cells
Authors: Liu Shihui , Liu Jie , Ma Qian , Cao Liu , Fattah Rasem J. , Yu Zuxi , Bugge Thomas H. , Finkel Toren , Leppla Stephen H. 
Published: June 2016

Significance
Anthrax toxin proteins engineered to require activation by tumor-associated proteases show high specificity and potency in suppression of solid tumor growth through actions on tumor endothelial cells. The toxin strongly inhibits proliferation of tumor endothelial cells. Importantly, an immunosuppressive regimen (pentostatin plus cyclophosphamide) not only prevents induction of toxin-neutralizing antibodies, allowing multiple courses of toxin treatment, but also has strong synergy with the toxin on solid tumors. The ability to give repeated doses of toxins, coupled with the specific targeting of tumor endothelium, suggests that our strategy should be efficacious for a wide range of solid tumors, meriting its clinical evaluation.
Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia
Authors: Hatzenpichler Roland , Connon Stephanie A. , Goudeau Danielle , Malmstrom Rex R. , Woyke Tanja , Orphan Victoria J. 
Published: June 2016

SignificanceOne of the biggest challenges in environmental microbiology is to determine the activity of uncultured cells directly in their habitat. We report on the application of bioorthogonal noncanonical amino acid tagging (BONCAT), a high-throughput approach to detecting protein synthesis in individual cells by fluorescence staining, on deep-sea methane seep sediments. By combining BONCAT with fluorescence in situ hybridization, we visualized active archaeal−bacterial consortia catalyzing the anaerobic oxidation of methane. We further developed a novel approach that combines BONCAT with fluorescence-activated cell sorting (FACS) to separate translationally active cells from complex samples. BONCAT-FACS enabled us to directly link the identities of anaerobic methane-oxidizing archaea with their partner bacteria for individual active consortia, uncovering previously unknown interactions between these archaea andVerrucomicrobia.
Gpr161 anchoring of PKA consolidates GPCR and cAMP signaling
Authors: Bachmann Verena A. , Mayrhofer Johanna E. , Ilouz Ronit , Tschaikner Philipp , Raffeiner Philipp , Röck Ruth , Courcelles Mathieu , Apelt Federico , Lu Tsan-Wen , Baillie George S. , Thibault Pierre , Aanstad Pia , Stelzl Ulrich , Taylor Susan S. , Stefan Eduard 
Published: June 2016

Significance
At the plasma membrane an array of more than 800 G protein-coupled receptors (GPCRs) receive, convert, amplify, and transmit incoming signals. Activated GPCRs team-up with intracellular scaffolding proteins to compartmentalize signal transmission. Scaffolds, such as β-arrestin and A-kinase anchoring proteins (AKAPs), function as a physical nexus between receptors and molecular switches. Typically, these receptor-bound AKAPs recruit protein kinase A (PKA) to assemble dedicated polyvalent signaling complexes that are spatially and temporally confined. Here, we report that the orphan GPCR, Gpr161, is a PKA substrate and also has an AKAP motif embedded in its C-terminal tail. Our results suggest that Gpr161, by directly recruiting type I PKA holoenzymes to the receptor, creates a cAMP-sensing signalosome. Furthermore, we propose that Gpr161 plays a role in recruiting isoform-specific PKA complexes to primary cilia.
Genome engineering uncovers 54 evolutionarily conserved and testis-enriched genes that are not required for male fertility in mice
Authors: Miyata Haruhiko , Castaneda Julio M. , Fujihara Yoshitaka , Yu Zhifeng , Archambeault Denise R. , Isotani Ayako , Kiyozumi Daiji , Kriseman Maya L. , Mashiko Daisuke , Matsumura Takafumi , Matzuk Ryan M. , Mori Masashi , Noda Taichi , Oji Asami , Okabe Masaru , Prunskaite-Hyyrylainen Renata , Ramirez-Solis Ramiro , Satouh Yuhkoh , Zhang Qian , Ikawa Masahito , Matzuk Martin M. 
Published: June 2016

Significance
In the mouse genome, thousands of genes are predominantly expressed in the testis, where these genes are thought to play important roles in spermatogenesis and fertilization. However, in this study, we report that 54 evolutionarily conserved and testis-enriched genes are not essential individually for male mouse fertility. Because the recent development of the CRISPR/Cas9 system has made it faster and easier to produce knockout mice, our results suggest that one should determine whether a gene of interest is essential for male fertility in vivo before spending significant effort to analyze the molecular function of the gene in vitro.
For richer, for poorer: why ethnicity often trumps economic cleavages in Kenya
Authors: Bedasso Biniam E. 
Published: June 2016

ABSTRACT
This article aims to examine why ethnic allegiances have persisted as the most dominant platform used by the elites to organise collective action in Kenya. The author formulates a broad theoretical framework centred around the organisational role of ethnicity in negotiating social orders. Empirically, it is shown that ethnic allegiances in Kenya are deeply rooted in group inequalities and feelings of historical injustice. Moreover, the historical structure of the economy has skewed the distribution of economic rents toward group-specific activities and resources. Therefore, the early institutions of the country were designed in such a way that the stability of political order would depend on the elites’ ability to use ethnicity as a bargaining chip. Ethnicity continues to be politically salient partly because economic rents are not individualised enough to sustainably support trans-ethnic forms of organisation.
Diamond pricing and valuation in South Africa’s extractive political economy
Authors: Sharife Khadija , Bracking Sarah 
Published: June 2016

ABSTRACT
This article explores the valuation and marketisation of diamonds in South Africa from 2004 to 2012. It argues that there is no positivist foundation for a ‘real’ or ‘fair’ price from which derogations can be measured, which constitutes a challenge for establishing transfer pricing in the context of tax justice. Instead, there is a performative valuation process wherein artificial underlying values are assigned which then condition prices and tax liabilities. Thus it is not the essential nature of diamonds per se that conditions a ‘resource curse’, but corporate control over the marketisation process in the context of enclavity and oligopoly.