bluuebunny/crossref_metadata_2025_split huggingface dataset:
Archaeology within, archaeology without
Authors: Sanders Jeff 
Published: May 2016

AbstractThe rise of the nation state has had a major influence on the development of archaeology. Nation states today, however, differ from their 19th- and 20th-century equivalents, and they both impact upon and use archaeology in different ways. By looking outwards from an individual country within a collective nation state, I will explore the forms that this can take. From a Scotland-based perspective, I will look at how various borders and boundaries, and the aims and objectives of those responsible for them, affect archaeological work. As well as looking at institutional and administrative boundaries and their effect on archaeology, I will also explore how archaeological work, and the stories we produce, can either question or reinforce the nation state. Ultimately, archaeology can be used in a very different way now than in the 19th and 20th centuries: it is less about the specific stories and more about the process of uncovering them. Rather than telling a national story, archaeology can be used as an instrument to deliver on wider objectives.
Is there an alternative to the nation state?
Authors: Prescott Christopher 
Published: May 2016

AbstractAcademic developments, migration and other forces of globalization have ruptured the validity of traditional national and ethnic archaeology in the Scandinavian states. However, this does not mean that the relationship between nation states and archaeology has come to an end. In reference to Norway, this article contends that on a practical level there is no viable alternative to replace the nation state. In terms of archaeological narratives, it is more relevant to adapt archaeological narratives to the evolving state than to advocate abandoning the nation state altogether.
Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus
Authors: Howard-Varona Cristina , Roux Simon , Dore Hugo , Solonenko Natalie E , Holmfeldt Karin , Markillie Lye M , Orr Galya , Sullivan Matthew B 
Published: May 2016

Abstract
Bacteria impact humans, industry and nature, but do so under viral constraints. Problematically, knowledge of viral infection efficiencies and outcomes derives from few model systems that over-represent efficient lytic infections and under-represent virus–host natural diversity. Here we sought to understand infection efficiency regulation in an emerging environmental Bacteroidetes–virus model system with markedly different outcomes on two genetically and physiologically nearly identical host strains. For this, we quantified bacterial virus (phage) and host DNA, transcripts and phage particles throughout both infections. While phage transcriptomes were similar, transcriptional differences between hosts suggested host-derived regulation of infection efficiency. Specifically, the alternative host overexpressed DNA degradation genes and underexpressed translation genes, which seemingly targeted phage DNA particle production, as experiments revealed they were both significantly delayed (by &gt;30 min) and reduced (by &gt;50%) in the inefficient infection. This suggests phage failure to repress early alternative host expression and stress response allowed the host to respond against infection by delaying phage DNA replication and protein translation. Given that this phage type is ubiquitous and abundant in the global oceans and that variable viral infection efficiencies are central to dynamic ecosystems, these data provide a critically needed foundation for understanding and modeling viral infections in nature.
T-bet is a key modulator of IL-23-driven pathogenic CD4+ T cell responses in the intestine
Authors: Krausgruber Thomas , Schiering Chris , Adelmann Krista , Harrison Oliver J. , Chomka Agnieszka , Pearson Claire , Ahern Philip P. , Shale Matthew , Oukka Mohamed , Powrie Fiona 
Published: May 2016

AbstractIL-23 is a key driver of pathogenic Th17 cell responses. It has been suggested that the transcription factor T-bet is required to facilitate IL-23-driven pathogenic effector functions; however, the precise role of T-bet in intestinal T cell responses remains elusive. Here, we show that T-bet expression by T cells is not required for the induction of colitis or the differentiation of pathogenic Th17 cells but modifies qualitative features of the IL-23-driven colitogenic response by negatively regulating IL-23R expression. Consequently, absence of T-bet leads to unrestrained Th17 cell differentiation and activation characterized by high amounts of IL-17A and IL-22. The combined increase in IL-17A/IL-22 results in enhanced epithelial cell activation and inhibition of either IL-17A or IL-22 leads to disease amelioration. Our study identifies T-bet as a key modulator of IL-23-driven colitogenic responses in the intestine and has important implications for understanding of heterogeneity among inflammatory bowel disease patients.
The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa
Authors: Hervella M. , Svensson E. M. , Alberdi A. , Günther T. , Izagirre N. , Munters A. R. , Alonso S. , Ioana M. , Ridiche F. , Soficaru A. , Jakobsson M. , Netea M. G. , de-la-Rua C. 
Published: May 2016

AbstractAfter the dispersal of modern humans (Homo sapiens) Out of Africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into Eurasia. The mitogenome (33-fold coverage) of the Peştera Muierii 1 individual (PM1) from Romania (35 ky cal BP) we present in this article corresponds fully to Homo sapiens, whilst exhibiting a mosaic of morphological features related to both modern humans and Neandertals. We have identified the PM1 mitogenome as a basal haplogroup U6*, not previously found in any ancient or present-day humans. The derived U6 haplotypes are predominantly found in present-day North-Western African populations. Concomitantly, those found in Europe have been attributed to recent gene-flow from North Africa. The presence of the basal haplogroup U6* in South East Europe (Romania) at 35 ky BP confirms a Eurasian origin of the U6 mitochondrial lineage. Consequently, we propose that the PM1 lineage is an offshoot to South East Europe that can be traced to the Early Upper Paleolithic back migration from Western Asia to North Africa, during which the U6 lineage diversified, until the emergence of the present-day U6 African lineages.
Hyponatremia in patients with systemic lupus erythematosus
Authors: Il Shin Jae , Park Se Jin , Suh Chang-Hee , Lee Geum Hwa , Hur Min Woo , Han Song Yi , Kim Dong Soo , Kim Ji Hong 
Published: May 2016

AbstractThe aim of this study was to determine whether decreased serum sodium concentration could be associated with the disease activity in SLE. We retrospectively analyzed the data of the two independent cohorts of children and adults with SLE in two centers. Hyponatremia was associated with serum chloride (p = 0.004), albumin (p = 0.002) and SLE disease activity index (SLEDAI) (p = 0.026) in children with SLE. Serum sodium levels were correlated negatively with ESR (p =0.001) and positively with serum albumin levels (p < 0.0001) and C3 (p = 0.008) in children with SLE and those levels were correlated negatively with serum interleukin-6 levels (p = 0.003) in adults with SLE. Independent risk factors for the development of hyponatremia were the decreased serum C3 levels (OR 1.069, p = 0.031), the decreased serum chloride levels (OR 2.054, p = 0.006) and increased erythrocyte sedimentation rate (ESR) (OR 1.066, p = 0.03) in children with SLE and increased C-reactive protein (CRP) (OR 1.480, p = 0.023) in combined cohorts with SLE by multiple logistic regression analyses. Our study firstly showed that hyponatremia could reflect a disease activity and severe inflammation of SLE.
Development and evaluation of two subunit vaccine candidates containing antigens of hepatitis E virus, rotavirus, and astrovirus
Authors: Xia Ming , Wei Chao , Wang Leyi , Cao Dianjun , Meng Xiang-Jin , Jiang Xi , Tan Ming 
Published: May 2016

AbstractHepatitis E virus (HEV), rotavirus (RV), and astrovirus (AstV) are important pathogens that transmit through a common fecal-oral route, causing hepatitis (HEV) and gastroenteritis (RV and AstV) respectively in humans. In this study, we developed and evaluated two subunit vaccine candidates that consisted of the same protruding or spike protein antigens of the three viruses in two formats, a fusion of the three antigens into one molecule (fused vaccine) vs. a mixture of the three free antigens together (mixed vaccine). Both vaccines were easily made viaE. coliexpression system. Mouse immunization experiments showed that the fused vaccine elicited significantly higher antibody responses against the three viral antigens than those induced by the mixed vaccine. In addition, the mouse post-immune antisera of the fused vaccine revealed significantly higher neutralizing titers against HEV infection in cell culture, as well as significantly higher 50% blocking titers (BT50) against RV VP8-HBGA receptor interactions than those of the post-immune antisera after immunization of the mixed vaccine. Thus, the fused vaccine is a promising trivalent vaccine candidate against HEV, RV, and AstV, which is worth for further development.
Plasma prolactin and breast cancer risk: a meta- analysis
Authors: Wang Minghao , Wu Xiujuan , Chai Fan , Zhang Yi , Jiang Jun 
Published: May 2016

AbstractBreast cancer is the most common cancer among women and its incidence is on a constant rise. Previous studies suggest that higher levels of plasma prolactin are associated with escalated risk of breast cancer, however, these results are contradictory and inconclusive. PubMed and Medline were used to search and identify published observational studies that assessed the relationship between plasma prolactin levels and the risk of breast cancer. The pooled relative risks (RRs) with 95% confidence intervals (CIs) were calculated using a fixed-effects or random-effects model. A total of 7 studies were included in our analysis. For the highest versus lowest levels of plasma prolactin, the pooled RR (95% CI) of breast cancer were 1.16 (1.04, 1.29). In subgroup analyses, we found a positive association between plasma prolactin levels and the risk of breast cancer among the patients who were postmenopausal, ER+/PR+ or in situ and invasive carcinoma. However, this positive association was not detected in the premenopausal and ER-/PR- patients. In conclusion, the present study provides evidence supporting a significantly positive association between plasma prolactin levels and the risk of breast cancer.
Nucleation and growth of (10͞11) semi-polar AlN on (0001) AlN by Hydride Vapor Phase Epitaxy
Authors: Liu Ting , Zhang Jicai , Su Xujun , Huang Jun , Wang Jianfeng , Xu Ke 
Published: May 2016

AbstractWurtzite AlN is widely used for deep ultraviolet optoelectronic devices (DUV), which are generally grown along the [0001]-direction of the wurtzite structure on currently available substrates. However, huge internal electrostatic fields are presented within the material along [0001] axis induced by piezoelectric and spontaneous polarization, which has limited the internal quantum efficiency of AlN based DUV LEDs dramatically. The internal fields can be strongly reduced by changing the epitaxial growth direction from the conventional polar c-direction into less polar crystal directions. Twinned crystal is a crystal consisting of two or more domains with the same crystal lattice and composition but different crystal orientations. In other words, twins can be induced to change crystal directions. In this work we demonstrated that the epitaxial growth of ("Equation missing") semi-polar AlN on (0001) AlN by constructing ("Equation missing") and ("Equation missing") twin structures. This new method is relative feasible than conventional methods and it has huge prospect to develop high-quality semi-polar AlN.
Single molecule targeted sequencing for cancer gene mutation detection
Authors: Gao Yan , Deng Liwei , Yan Qin , Gao Yongqian , Wu Zengding , Cai Jinsen , Ji Daorui , Li Gailing , Wu Ping , Jin Huan , Zhao Luyang , Liu Song , Ge Liangjin , Deem Michael W. , He Jiankui 
Published: May 2016

AbstractWith the rapid decline in cost of sequencing, it is now affordable to examine multiple genes in a single disease-targeted clinical test using next generation sequencing. Current targeted sequencing methods require a separate step of targeted capture enrichment during sample preparation before sequencing. Although there are fast sample preparation methods available in market, the library preparation process is still relatively complicated for physicians to use routinely. Here, we introduced an amplification-free Single Molecule Targeted Sequencing (SMTS) technology, which combined targeted capture and sequencing in one step. We demonstrated that this technology can detect low-frequency mutations using artificially synthesized DNA sample. SMTS has several potential advantages, including simple sample preparation thus no biases and errors are introduced by PCR reaction. SMTS has the potential to be an easy and quick sequencing technology for clinical diagnosis such as cancer gene mutation detection, infectious disease detection, inherited condition screening and noninvasive prenatal diagnosis.
Modified serpinA1 as risk marker for Parkinson’s disease dementia: Analysis of baseline data
Authors: Halbgebauer Steffen , Nagl Magdalena , Klafki Hans , Haußmann Ute , Steinacker Petra , Oeckl Patrick , Kassubek Jan , Pinkhardt Elmar , Ludolph Albert C. , Soininen Hilkka , Herukka Sanna-Kaisa , Wiltfang Jens , Otto Markus 
Published: May 2016

AbstractEarly detection of dementia in Parkinson disease is a prerequisite for preventive therapeutic approaches. Modified serpinA1 in cerebrospinal fluid (CSF) was suggested as an early biomarker for differentiation between Parkinson patients with (PDD) or without dementia (PD). Within this study we aimed to further explore the diagnostic value of serpinA1. We applied a newly developed nanoscale method for the detection of serpinA1 based on automated capillary isoelectric focusing (CIEF). A clinical sample of 102 subjects including neurologically healthy controls (CON), PD and PDD patients was investigated. Seven serpinA1 isoforms of different charge were detected in CSF from all three diagnostic groups. The mean CSF signals of the most acidic serpinA1 isoform differed significantly (p < 0.01) between PDD (n = 29) and PD (n = 37) or CON (n = 36). Patients above the cut-off of 6.4 have a more than six times higher risk for an association with dementia compared to patients below the cut off. We propose this serpinA1 CIEF-immunoassay as a novel tool in predicting cognitive impairment in PD patients and therefore for patient stratification in therapeutic trials.
Fructose, but not glucose, impairs insulin signaling in the three major insulin-sensitive tissues
Authors: Baena Miguel , Sangüesa Gemma , Dávalos Alberto , Latasa María-Jesús , Sala-Vila Aleix , Sánchez Rosa María , Roglans Núria , Laguna Juan Carlos , Alegret Marta 
Published: May 2016

AbstractHuman studies support the relationship between high intake of fructose-sweetened beverages and type 2 diabetes, but there is a debate on whether this effect is fructose-specific or it is merely associated to an excessive caloric intake. Here we investigate the effects of 2 months’ supplementation to female rats of equicaloric 10% w/v fructose or glucose solutions on insulin sensitivity in target tissues. Fructose supplementation caused hepatic deposition of triglycerides and changed the fatty acid profile of this fraction, with an increase in monounsaturated and a decrease in polyunsaturated species, but did not cause inflammation and oxidative stress. Fructose but not glucose-supplemented rats displayed an abnormal glucose tolerance test and did not show increased phosphorylation of V-akt murine thymoma viral oncogene homolog-2 (Akt) in white adipose tissue and liver after insulin administration. In skeletal muscle, phosphorylation of Akt and of Akt substrate of 160 kDA (AS160) was not impaired but the expression of the glucose transporter type 4 (GLUT4) in the plasma membrane was reduced only in fructose-fed rats. In conclusion, fructose but not glucose supplementation causes fatty liver without inflammation and oxidative stress and impairs insulin signaling in the three major insulin-responsive tissues independently from the increase in energy intake.
Illumina MiSeq sequencing disfavours a sequence motif in the GFP reporter gene
Authors: Van den Hoecke Silvie , Verhelst Judith , Saelens Xavier 
Published: May 2016

AbstractGreen fluorescent protein (GFP) is one of the most used reporter genes. We have used next-generation sequencing (NGS) to analyse the genetic diversity of a recombinant influenza A virus that expresses GFP and found a remarkable coverage dip in the GFP coding sequence. This coverage dip was present when virus-derived RT-PCR product or the parental plasmid DNA was used as starting material for NGS and regardless of whether Nextera XT transposase or Covaris shearing was used for DNA fragmentation. Therefore, the sequence coverage dip in the GFP coding sequence was not the result of emerging GFP mutant viruses or a bias introduced by Nextera XT fragmentation. Instead, we found that the Illumina MiSeq sequencing method disfavours the ‘CCCGCC’ motif in the GFP coding sequence.
Mucosal adherent bacterial dysbiosis in patients with colorectal adenomas
Authors: Lu Yingying , Chen Jing , Zheng Junyuan , Hu Guoyong , Wang Jingjing , Huang Chunlan , Lou Lihong , Wang Xingpeng , Zeng Yue 
Published: May 2016

AbstractRecent reports have suggested that the gut microbiota is involved in the progression of colorectal cancer (CRC). The composition of gut microbiota in CRC precursors has not been adequately described. To characterize the structure of adherent microbiota in this disease, we conducted pyrosequencing-based analysis of 16S rRNA genes to determine the bacterial profile of normal colons (healthy controls) and colorectal adenomas (CRC precursors). Adenoma mucosal biopsy samples and adjacent normal colonic mucosa from 31 patients with adenomas and 20 healthy volunteers were profiled using the Illumina MiSeq platform. Principal coordinate analysis (PCoA) showed structural segregation between colorectal adenomatous tissue and control tissue. Alpha diversity estimations revealed higher microbiota diversity in samples from patients with adenomas. Taxonomic analysis illustrated that abundance of eight phyla (Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Chloroflexi, Cyanobacteria, Candidate-division TM7 and Tenericutes) was significantly different. In addition, Lactococcus and Pseudomonas were enriched in preneoplastic tissue, whereas Enterococcus, Bacillus and Solibacillus were reduced. However, both PCoA and cluster tree analyses showed similar microbiota structure between adenomatous and adjacent non-adenoma tissues. These present findings provide preliminary experimental evidence supporting that colorectal preneoplastic lesion may be the most important factor leading to alterations in bacterial community composition.
Proteomic profiling of cellulase-aid-extracted membrane proteins for functional identification of cellulose synthase complexes and their potential associated- components in cotton fibers
Authors: Li Ao , Wang Ruyi , Li Xianliang , Liu Mingyong , Fan Jian , Guo Kai , Luo Bing , Chen Tingting , Feng Shengqiu , Wang Yanting , Wang Bingrui , Peng Liangcai , Xia Tao 
Published: May 2016

AbstractCotton fibers are an excellent model for understanding of cellulose biosynthesis in higher plants. In this study, we determined a high cellulose biosynthesis activity in vitro by optimizing biochemical reaction conditions in cotton fibers. By adding a commercial cellulase enzyme into fibers extraction process, we extracted markedly higher levels of GhCESA1 and GhCESA8 proteins and observed an increase in β-1,4-glucan and β-1,3-glucan products in vitro. LC-MS/MS analysis of anti-GhCESA8-immunoprecipitated proteins showed that 19 proteins could be found in three independent experiments including four CESAs (GhCESA1,2,7,8), five well-known non-CESA proteins, one callose synthase (CALS) and nine novel proteins. Notably, upon the cellulase treatment, four CESAs, one CALS and four novel proteins were measured at relatively higher levels by calculating total peptide counts and distinct peptide numbers, indicating that the cellulase-aid-extracted proteins most likely contribute to the increase in β-glucan products in vitro. These results suggest that the cellulase treatment may aid to release active cellulose synthases complexes from growing glucan chains and make them more amenable to extraction. To our knowledge, it is the first time report about the functional identification of the potential proteins that were associated with plant cellulose and callose synthases complexes by using the cellulase-aided protein extraction.
Quantum coherence and quantum phase transitions
Authors: Li Yan-Chao , Lin Hai-Qing 
Published: May 2016

AbstractWe study the connections between local quantum coherence (LQC) based on Wigner-Yanase skew information and quantum phase transitions (QPTs). When applied on the one-dimensional Hubbard, XY spin chain with three-spin interaction and Su-Schrieffer-Heeger models, the LQC and its derivatives are used successfully to detect different types of QPTs in these spin and fermionic systems. Furthermore, the LQC is effective as the quantum discord (QD) in detecting QPTs at finite temperatures, where the entanglement has lost its effectiveness. We also demonstrate that the LQC can exhibit different behaviors in many forms compared with the QD.
Variation in infection length and superinfection enhance selection efficiency in the human malaria parasite
Authors: Chang Hsiao-Han , Childs Lauren M. , Buckee Caroline O. 
Published: May 2016

AbstractThe capacity for adaptation is central to the evolutionary success of the human malaria parasite Plasmodium falciparum. Malaria epidemiology is characterized by the circulation of multiple, genetically diverse parasite clones, frequent superinfection and highly variable infection lengths, a large number of which are chronic and asymptomatic. The impact of these characteristics on the evolution of the parasite is largely unknown, however, hampering our understanding of the impact of interventions and the emergence of drug resistance. In particular, standard population genetic frameworks do not accommodate variation in infection length or superinfection. Here, we develop a population genetic model of malaria including these variations and show that these aspects of malaria infection dynamics enhance both the probability and speed of fixation for beneficial alleles in complex and non-intuitive ways. We find that populations containing a mixture of short- and long-lived infections promote selection efficiency. Interestingly, this increase in selection efficiency occurs even when only a small fraction of the infections are chronic, suggesting that selection can occur efficiently in areas of low transmission intensity, providing a hypothesis for the repeated emergence of drug resistance in the low transmission setting of Southeast Asia.