bluuebunny/crossref_metadata_2025_split huggingface dataset:
A catalogue of late Cenozoic tephra beds in the Klondike goldfields and adjacent areas, Yukon Territory1Yukon Geological Survey Contribution 010.
Authors: Preece S.J. , Westgate J.A. , Froese D.G. , Pearce N.J.G. , Perkins W.T. 
Published: October 2011

Many distal tephra beds exist in the late Cenozoic sediments of the Klondike goldfields and nearby areas. They come from volcanoes in the Wrangell volcanic field and the eastern Aleutian arc and represent large-magnitude eruptions. During the course of our tephrochronological studies in this region over the last 40 years, we have discovered 196 tephra occurrences and 50 distinctive tephra beds. The location of these sites and the distinguishing features of each of these tephra beds are presented in the form of a catalogue, which we hope will provide a stimulus for present and future tephrochronological studies in the Yukon Territory. These data are presented as a series of tables, as follows: location, stratigraphic context, petrography, geochemical characteristics, including major- and trace-element composition of glass shards, major-element composition of Fe–Ti oxides, classification, and age determinations. A new classification scheme is presented in which the rhyolitic and dacitic tephra beds are grouped into three classes: adakite, transitional, and typical arc.
Classification of Epstein–Barr Virus–Positive Gastric Cancers by Definition of DNA Methylation Epigenotypes
Authors: Matsusaka Keisuke , Kaneda Atsushi , Nagae Genta , Ushiku Tetsuo , Kikuchi Yasuko , Hino Rumi , Uozaki Hiroshi , Seto Yasuyuki , Takada Kenzo , Aburatani Hiroyuki , Fukayama Masashi 
Published: October 2011

Abstract
Epstein–Barr virus (EBV) is associated with Burkitt lymphoma, nasopharyngeal carcinoma, opportunistic lymphomas in immunocompromised hosts, and a fraction of gastric cancers. Aberrant promoter methylation accompanies human gastric carcinogenesis, though the contribution of EBV to such somatic methylation changes has not been fully clarified. We analyzed promoter methylation in gastric cancer cases with Illumina's Infinium BeadArray and used hierarchical clustering analysis to classify gastric cancers into 3 subgroups: EBV−/low methylation, EBV−/high methylation, and EBV+/high methylation. The 3 epigenotypes were characterized by 3 groups of genes: genes methylated specifically in the EBV+ tumors (e.g., CXXC4, TIMP2, and PLXND1), genes methylated both in EBV+ and EBV−/high tumors (e.g., COL9A2, EYA1, and ZNF365), and genes methylated in all of the gastric cancers (e.g., AMPH, SORCS3, and AJAP1). Polycomb repressive complex (PRC) target genes in embryonic stem cells were significantly enriched among EBV−/high-methylation genes and commonly methylated gastric cancer genes (P = 2 × 10−15 and 2 × 10−34, respectively), but not among EBV+ tumor-specific methylation genes (P = 0.2), suggesting a different cause for EBV+-associated de novo methylation. When recombinant EBV was introduced into the EBV−/low-methylation epigenotype gastric cancer cell, MKN7, 3 independently established subclones displayed increases in DNA methylation. The promoters targeted by methylation were mostly shared among the 3 subclones, and the new methylation changes caused gene repression. In summary, DNA methylation profiling classified gastric cancer into 3 epigenotypes, and EBV+ gastric cancers showed distinct methylation patterns likely attributable to EBV infection. Cancer Res; 71(23); 7187–97. ©2011 AACR.
Epithelial Junction Opener JO-1 Improves Monoclonal Antibody Therapy of Cancer
Authors: Beyer Ines , van Rensburg Ruan , Strauss Robert , Li ZongYi , Wang Hongjie , Persson Jonas , Yumul Roma , Feng Qinghua , Song Hui , Bartek Jiri , Fender Pascal , Lieber André 
Published: October 2011

AbstractThe efficacy of monoclonal antibodies (mAb) used to treat solid tumors is limited by intercellular junctions which tightly link epithelial tumor cells to each another. In this study, we define a small, recombinant adenovirus serotype 3-derived protein, termed junction opener 1 (JO-1), which binds to the epithelial junction protein desmoglein 2 (DSG2). In mouse xenograft models employing Her2/neu- and EGFR-positive human cancer cell lines, JO-1 mediated cleavage of DSG2 dimers and activated intracellular signaling pathways which reduced E-cadherin expression in tight junctions. Notably, JO-1-triggered changes allowed for increased intratumoral penetration of the anti-Her2/neu mAb trastuzumab (Herceptin) and improved access to its target receptor, Her2/neu, which is partly trapped in tight junctions. This effect translated directly into increased therapeutic efficacy of trastuzumab in mouse xenograft models using breast, gastric, and ovarian cancer cells that were Her2/neu-positive. Furthermore, combining JO-1 with the EGFR-targeting mAb cetuximab (Erbitux) greatly improved therapeutic outcomes in a metastatic model of EGFR-positive lung cancer. A combination of JO-1 with an approach that triggered transient degradation of tumor stroma proteins elicited eradication of tumors. Taken together, our findings offer preclinical proof of concept to employ JO-1 in combination with mAb therapy. Cancer Res; 71(22); 7080–90. ©2011 AACR.
Survival Benefit With Drug-Eluting Stents in Observational Studies
Authors: Venkitachalam Lakshmi , Lei Yang , Magnuson Elizabeth A. , Chan Paul S. , Stolker Joshua M. , Kennedy Kevin F. , Kleiman Neal S. , Cohen David J. 
Published: October 2011

Background—
Recently, there has been increased interest in leveraging observational studies for comparative effectiveness research. Without robust and valid risk adjustment, however, findings from these nonrandomized studies may remain biased. Previous studies examining long-term mortality with drug-eluting stents (DESs) have demonstrated discordant results between randomized trials and observational studies. To examine the impact of treatment selection bias on these findings, we used data from a prospective percutaneous coronary intervention (PCI) registry (EVENT [Evaluation of Drug Eluting Stents and Ischemic Events]) to compare clinical outcomes between DESs and bare metal stents (BMSs) using conventional (multivariable regression and propensity matching) and novel (instrumental variable analysis) risk-adjustment techniques.

Methods and Results—

The study population consisted of 9266 patients who underwent nonemergent PCI with stent placement at 55 US centers between 2004 and 2007. All-cause mortality and target lesion revascularization (TLR) were assessed prospectively over 1 year of follow-up. Overall, 8171 patients (88%) received DES, but this proportion substantially differed by treatment year (93% in 2004–2006 and 73% in 2007;
P
<0.001). One-year rates of death and TLR were significantly lower with DES versus BMS (death, 2.5% versus 5.6%; TLR, 4.2% versus 6.9%;
P
<0.001 for both), findings that persisted in both multivariable-adjusted and propensity-matched analyses. In contrast, instrumental variable analysis, using enrollment period (2004–2006 versus 2007) as the instrument, demonstrated no significant difference in 1-year mortality (predicted absolute difference, 2.0%; 95% CI, -1.8% to 5.7%;
P
=0.30) and a strong trend toward reduced TLR with DES use (predicted absolute difference, -4.2%; 95% CI, -8.8% to 0.4%;
P
=0.07).

Conclusions—
Among unselected PCI patients in contemporary practice, DES use tended to be associated with a consistent reduction in TLR regardless of risk-adjustment method but showed discordant effects on mortality with conventional risk adjustment compared with instrumentable variable analysis. These findings underscore the limitations of standard risk-adjustment methods to adequately address treatment selection bias in nonrandomized studies and have important implications for comparative effectiveness research using observational data.
The calling songs of male spring field crickets (Gryllus veletis) change as males age
Authors: Bertram Susan M. , Fitzsimmons Lauren P. 
Published: October 2011

AbstractSexual traits are typically thought to convey information about a male's quality or condition. Female preference for older males has been documented in many taxa, but the evidence that males signal their age is inconclusive. We investigated lifetime patterns of acoustic mate attraction signalling in a longitudinal study of the spring field cricket, Gryllus veletis. We recorded males continuously throughout their lives, such that every pulse of sound produced by every male was analyzed. Our study answers two main questions: (1) Do calls change as males age? Our results reveal that the calls of male spring field crickets change with age; the calls of older males were quieter, with more silent periods within and between chirps, and produced less often than those of younger males. As males aged most of the changes in call structure reflect decreased calling effort. (2) What is the relationship between calling effort and longevity? Lifetime calling effort was positively related to longevity, such that males that called the most over their life also lived longer than males that called less. Together, our findings provide the most thorough exploration of lifetime signalling patterns in crickets to date.
Infant bystanders modulate the influence of ovarian hormones on female socio-sexual behaviour in free-ranging rhesus macaques
Authors: Mandalaywala Tara M. , Higham James P. , Heistermann Michael , Maestripieri Dario 
Published: October 2011

AbstractIt has long been established that one of the driving factors underlying changes in female socio-sexual behaviour across the ovarian cycle is variation in the hormones oestrogen and progesterone. However, the effect that the social environment, and specifically con-specific bystanders, exerts on social relationships is far less clear. Here we explore the modulating effects of infant bystanders on relationships between female ovarian cycling and socio-sexual behaviour in free-ranging rhesus macaques during the 6-month mating season on Cayo Santiago, Puerto Rico. We used non-invasive hormone assessment to time ovulation in females, and analysed measures of social and sexual behaviour with respect to a 2-day ovulation window. Rates of copulation and ejaculation varied relative to ovulation, with female–male sexual interactions peaking around ovulation. Moreover, the presence of an infant bystander affected these rates, with fewer sexual interactions occurring for a given day with respect to ovulation when infant bystanders were more frequently in close proximity to the female. Other bystander categories (adult females, adult males, and adult female & infant groupings) did not have the same effect on female mating behaviour. These results suggest that mother–offspring conflict might manifest not only as direct interactions between mother and infant (e.g., weaning or carrying conflict), but also through indirect interactions.
The Rituals of Renaissance: Liturgy and Mythic History in The Marvels of Rome
Authors: Hamilton Louis I. 
Published: October 2011

AbstractThe Mirabilia urbis romae offers us insight into the symbolic meaning of the streetscape of Rome from the perspective of a canon of St. Peter’s. It should be read alongside the contemporary Roman Ordo with which it was certainly associated in the twelfth century. When read in that context, the Mirabilia serves as a kind of direct and indirect commentary on the papal liturgy. The papal liturgies at Easter and Christmas moved through an environment that was “re-written” by the Mirabilia as a narrative of Christian Roman renewal and of triumph throughout the Mediterranean world. The Mirabilia celebrates both Roman renewal and hegemony in the eastern Mediterranean, giving heightened significance to the liturgical life of the twelfth-century papacy. The papal liturgy, at these most triumphant processional moments, celebrated that historic and, ultimately, eschatological triumph.
Viewing Rome from the Roman Empires
Authors: Albu Emily 
Published: October 2011

AbstractTwelfth-century German and Byzantine emperors vied with each other—and with the popes in Rome—for imperial status, each of the three seeing himself as the legitimate heir of ancient Roman imperium. From the court at Constantinople, historians Anna Komnene and John Kinnamos leveled a venomous critique against the west, surveying Rome through the lens of religious disputes, Crusade, and the hated Latin presence in the East. The Byzantine narratives have left a gritty view of their contemporary Rome, a violent and cruel city of illicit popes and anti-popes, anarchy, and barbarism. The Peutinger map, by contrast, seems but an innocent relic of the past, a map of the inhabited world as known to the pagan Romans. Typically considered an ancient Roman artifact and product of Roman culture, the surviving map actually dates from the very end of the long twelfth century. Produced in Swabia, it continued the anti-papal assault as a fresh salvo in a long-lived Battle of the Maps between Church and secular imperium. This display map, like its lost prototype, advertised the supreme authority of Roman imperial power with claims much more venerable than those of the papacy. Its visual narrative implicitly contradicted the power of papal Rome by foregrounding ancient Rome as the centerpiece of an intricately connected oikoumene, a world that should be ruled by Rome’s German heirs. For Germans as for Byzantines, Rome still mattered. Even while assailing a resurgent imperial papacy, neither secular emperor nor their courts could ignore the power exercised by pagan Rome and papal Rome over twelfth-century imaginations.
Decoding the Labyrinth: Rome in Arabic and Persian Medieval Literature
Authors: Casari Mario 
Published: October 2011

AbstractThe city of Rome is described in a number of Arabic and Persian geographical and historical texts produced between the ninth and thirteenth centuries. Despite the chronological range and geographical distances that separate many of these texts, a common thread of transmission unites them, testament to the fact that very few eyewitness accounts of the city were used. Instead, the descriptions of Rome drew on the authority of more ancient literary accounts, that were reproduced with variations and additions deriving from a number of different origins. While it is not possible to identify the exact web of sources used, nor whether some descriptions refer to Old Rome—the city of the Pope—or to the new Rome on the Bosporus, Constantinople, these texts nevertheless reveal a substantial knowledge of the city’s symbolic features. Indeed, it appears that accurate physical descriptions of Rome were considered less important than exemplary representations of the city. One of the figurative details assumes the iconographic form of a labyrinth, at times identified as a map of the city of Rome, and at other times as a prison located in the city. In this paper, it will be argued that the labyrinth icon is drawn from one of Rome’s own myths concerning the founding of the city by complex and at times obscure means that offer promising directions for further research. More generally, it would appear that the Arabic and Persian sources considered here share a view of the city of Rome that is nourished by a great respect and admiration.
Serum Immunoglobulin G Analysis to Establish a Delayed Diagnosis of Chronic Cough due to Bordetella pertussis
Authors: Bock Jonathan M. , Burtis Charles C. , Poetker David M. , Blumin Joel H. , Frank Michael O. 
Published: October 2011

ObjectivesIncidence of Bordetella pertussis infection among adults has risen significantly throughout the United States, but pertussis is not often considered in the differential diagnosis of chronic cough in adults. The authors hypothesized that serum IgG testing can establish a diagnosis of pertussis infection late in disease presentation when cultures and polymerase chain reaction (PCR) testing are not reliable.Study DesignCase series with chart review.SettingTertiary care hospital.Subjects and MethodsInstitutional B pertussis serum IgG and PCR tests were reviewed since 2007. Clinical factors assessed included vaccination history, duration and severity of cough, and general medical history.ResultsForty‐eight patients had B pertussis fimbrial agglutinogen IgG levels tested since 2007, with a significant increase in positive IgG tests (>27 IU/mL, 3 times the upper limit of normal) since fall 2009. Nineteen patients (39.5%) met IgG criteria for likely recent pertussis infection. Six IgG‐positive patients also had PCR swab testing performed, with 50% positive for B pertussis. IgG values were similar for patients with positive or negative B pertussis PCR testing with positive IgG titers. IgG‐positive patients were much more likely to have posttussive syncope. Recent vaccination for pertussis within the 3 years prior to IgG testing did not significantly increase IgG levels.ConclusionsOne‐time B pertussis serum IgG testing and patient history can establish a likely diagnosis of recent pertussis infection in the adult patient with chronic cough late in disease presentation when PCR testing is often negative. Pertussis should be considered in the differential diagnosis of all patients with chronic cough.
Liver Function Tests
Authors: Deal Allison M. , Patel Mihir R. , Thorp Brian D. , Cannon Trinitia Y. , Shores Carol G. , Zanation Adam M. 
Published: October 2011

ObjectiveReport the prevalence and risk factors of liver metastasis in head and neck squamous cell carcinoma (HNSCC) while evaluating the utility of liver function tests (LFTs) in detection of such metastases.Study DesignCase series with chart review.SettingTertiary referral center.Subjects and MethodsOf 745 patients with newly diagnosed HNSCC (oral cavity, oropharynx, hypopharynx, larynx) treated at University of North Carolina hospitals from 1989 to 2005, 655 had sufficient data for analysis.ResultsPrevalence of liver metastasis was 3% (20/655) with 7 patients demonstrating early metastasis and 12 with late metastasis. Oropharyngeal and hypopharyngeal lesions constituted 65% of identified liver metastasis but only 39% of the study population. Patients with oropharyngeal lesions were most likely to develop liver metastasis (P =. 047). Abnormal LFTs were seen in 26% of all patients. Overall sensitivity and specificity were 45% and 75%. Seventy‐five percent of patients with liver metastasis had stage IV disease at diagnosis and were more likely to have abnormal LFTs than other stages (P =. 048). In these patients, 2.2% (8/365) had liver metastases and abnormal LFTs, whereas 1.9% (7/365) had liver metastases and normal LFTs. Sensitivity for alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, and lactate dehydrogenase 0%, 10%, 20%, and 30%, respectively. Specificities ranged from 88.0% to 94.3%. Positive predictive values were poor, with the highest being 10.5%.ConclusionsLiver metastases are rare in HNSCC and often delayed in presentation. This study clearly reveals that LFTs do not reliably identify patients with liver metastasis and do not provide physicians with an adequate screening modality in this population.
Transcriptomic analysis of the interaction between Helianthus annuus and its obligate parasite Plasmopara halstedii shows single nucleotide polymorphisms in CRN sequences
Authors: As-sadi Falah , Carrere Sébastien , Gascuel Quentin , Hourlier Thibaut , Rengel David , Le Paslier Marie-Christine , Bordat Amandine , Boniface Marie-Claude , Brunel Dominique , Gouzy Jérôme , Godiard Laurence , Vincourt Patrick 
Published: October 2011

Abstract

Background
Downy mildew in sunflowers (Helianthus annuus L.) is caused by the oomycete Plasmopara halstedii (Farl.) Berlese et de Toni. Despite efforts by the international community to breed mildew-resistant varieties, downy mildew remains a major threat to the sunflower crop. Very few genomic, genetic and molecular resources are currently available to study this pathogen. Using a 454 sequencing method, expressed sequence tags (EST) during the interaction between H. annuus and P. halstedii have been generated and a search was performed for sites in putative effectors to show polymorphisms between the different races of P. halstedii.

Results
A 454 pyrosequencing run of two infected sunflower samples (inbred lines XRQ and PSC8 infected with race 710 of P. halstedii, which exhibit incompatible and compatible interactions, respectively) generated 113,720 and 172,107 useable reads. From these reads, 44,948 contigs and singletons have been produced. A bioinformatic portal, HP, was specifically created for in-depth analysis of these clusters. Using in silico filtering, 405 clusters were defined as being specific to oomycetes, and 172 were defined as non-specific oomycete clusters. A subset of these two categories was checked using PCR amplification, and 86% of the tested clusters were validated. Twenty putative RXLR and CRN effectors were detected using PSI-BLAST. Using corresponding sequences from four races (100, 304, 703 and 710), 22 SNPs were detected, providing new information on pathogen polymorphisms.

Conclusions
This study identified a large number of genes that are expressed during H. annuus/P. halstedii compatible or incompatible interactions. It also reveals, for the first time, that an infection mechanism exists in P. halstedii similar to that in other oomycetes associated with the presence of putative RXLR and CRN effectors. SNPs discovered in CRN effector sequences were used to determine the genetic distances between the four races of P. halstedii. This work therefore provides valuable tools for further discoveries regarding the H. annuus/P. halstedii pathosystem.