bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Book of Psalms and the early modern sonnet
Authors: Serjeantson Deirdre 
Published: July 2015

AbstractPsalms and sonnets were the most popular lyric genres in early modern English writing. Little scholarly attention, however, has been paid to the common ground between the two forms, largely because they have been perceived as incompatible, with one epitomizing the sacred, and the other, the secular, literature of their day. Nonetheless, sixteenth‐century writers often moved from one genre to the other; the first sonnet sequence in English (Anne Lock's A Meditation of a Penitent Sinner, 1560), takes the form of a translation of Psalm 51; and paraphrases of other psalms appear in sonnet sequences by Barnabe Barnes and Henry Lok. The figure of David as psalmist and poet is invoked in sonnets as well as psalms, and the diction of the biblical texts was harnessed and remade for the secular tradition. This essay argues for a close relationship between psalms and sonnets, and through an examination of the influences exerted on both genres, including contemporary poetics and Petrarchism, it suggests that both the biblical Book of Psalms, and the broader tradition of psalm translation, provided an important model for the early modern English sonnet sequence.
Hereditary error and popular culture in Pseudodoxia Epidemica
Authors: Phillips Harriet 
Published: July 2015

AbstractThomas Browne's Pseudodoxia Epidemica (1646) is often described as a major landmark in the emergence of ‘popular culture’ as the object of scholarly scrutiny. This article argues, however, that the drift of Pseudodoxia's argument is to move away from taxonomies of social distinction, and towards a universal errancy. It suggests that Browne's understanding of error is fundamentally Christian and postlapsarian, and therefore also essentially genealogical. This leads him to prefer historical or philological explanations of error, occluding the contemporary and ephemeral, and underpins one of Pseudodoxia's most distinctive features, its persistent derivation of contemporary popular beliefs and practices from antiquity. While tradition is therefore central to the book's conception of popular errors, it is also problematic. It was a commonplace of seventeenth‐century Protestant culture that popular superstitions were relics of Catholicism: a conclusion which Browne, for intellectual and perhaps also personal reasons, was keen to resist. Pseudodoxia's insistent classicizing, therefore, can be seen as a way to evade these rhetorics, and seek a more nuanced and irenic language of preternatural belief. In severing superstition and Catholicism, Pseudodoxia insists on errancy as a shared human inheritance; a source of unity, rather than division.
Brief Exercises Affect Gene Expression in Circulating Monocytes
Authors: Wang D. , Cai F. , Ge J. , Yin L. 
Published: July 2015

AbstractWe aimed to give a systematic hypothesis on the functions of exercise on circulating monocytes by identifying a discrete set of genes in circulating monocytes that were altered by exercise. The microarray expression profile of GSE51835 was downloaded from gene expression omnibus (GEO) database for the identification of differentially expressed genes (DEGs) using limma and affy packages in R language. Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed for DEGs, followed by the construction of co‐expression network and protein–protein interaction (PPI) network. The top 10 nodes in PPI network were screened, and subnetwork was constructed for the key genes identification. Totally, 35 DEGs, including 2 upregulated genes and 33 downregulated genes, were identified. The enriched GO terms were mainly linked to immune response and defence response, and the enriched KEGG pathways were mainly associated with natural killer cell‐mediated cytotoxicity and graft‐versus‐host disease. Dual‐specificity phosphatase 2 (DUSP2) was identified as a key node in the co‐expression network. In the PPI network, CD247 module (CD247), chemokine (C‐X‐C motif) receptor 4 (CXCR4), granzyme B (GZMB) and perforin 1 (PRF1) were identified as key nodes. An important interaction, GZMB/PRF1, was detected. Five key genes, including DUSP2, CD247, CXCR4, GZMB and PRF1, and an interaction of GZMB/PRF1, were significant factors in the immune processes of circulating monocytes, which might be regulated by brief exercises, leading to the enhancement of immune function.
Draft Genome Sequence of Lactobacillus panis DSM 6035
T
, First Isolated from Sourdough
Authors: Zhu Yixin , Fang Daiqiong , Shi Ding , Li Ang , Lv Longxian , Yan Ren , Yao Jian , Hua Dasong , Hu Xinjun , Guo Feifei , Wu Wenrui , Guo Jing , Chen Yanfei , Jiang Xiawei , Chen Xiaoxiao , Li Lanjuan 
Published: July 2015

ABSTRACT

We report a draft genome sequence of
Lactobacillus panis
DSM 6035
T
, isolated from sourdough. The genome of this strain is 2,082,789 bp long, with 47.9% G+C content. A total of 2,047 protein-coding genes were predicted.
Draft Genome Sequence of Mycobacterium europaeum Strain CSUR P1344
Authors: Phelippeau Michael , Croce Olivier , Robert Catherine , Raoult Didier , Drancourt Michel 
Published: July 2015

ABSTRACT

We report the draft genome sequence of
Mycobacterium europaeum
strain CSUR P1344, a slowly growing mycobacterium of the
Mycobacterium simiae
complex and opportunistic respiratory tract colonizer and pathogen. This genome of 6,152,523 bp exhibits a 68.18% G+C content, encoding 5,814 predicted proteins and 74 RNAs.
Draft Genome Sequence of Mycobacterium lentiflavum CSUR P1491
Authors: Phelippeau Michael , Croce Olivier , Robert Catherine , Raoult Didier , Drancourt Michel 
Published: July 2015

ABSTRACT

We announce the draft genome sequence of
Mycobacterium lentiflavum
strain CSUR P1491, a nontuberculous mycobacterium responsible for opportunistic potentially life-threatening infections in immunocompromised patients. The genome described here comprises a 6,818,507-bp chromosome exhibiting a 65.75% G+C content, 6,354 protein-coding genes, and 75 RNA genes.
Transmission and Progression to Disease of Mycobacterium tuberculosis Phylogenetic Lineages in The Netherlands
Authors: Nebenzahl-Guimaraes Hanna , Verhagen Lilly M. , Borgdorff Martien W. , van Soolingen Dick 
Published: July 2015

ABSTRACT

The aim of this study was to determine if mycobacterial lineages affect infection risk, clustering, and disease progression among
Mycobacterium tuberculosis
cases in The Netherlands. Multivariate negative binomial regression models adjusted for patient-related factors and stratified by patient ethnicity were used to determine the association between phylogenetic lineages and infectivity (mean number of positive contacts around each patient) and clustering (as defined by number of secondary cases within 2 years after diagnosis of an index case sharing the same fingerprint) indices. An estimate of progression to disease by each risk factor was calculated as a bootstrapped risk ratio of the clustering index by the infectivity index. Compared to the Euro-American reference,
Mycobacterium africanum
showed significantly lower infectivity and clustering indices in the foreign-born population, while
Mycobacterium bovis
showed significantly lower infectivity and clustering indices in the native population. Significantly lower infectivity was also observed for the East African Indian lineage in the foreign-born population. Smear positivity was a significant risk factor for increased infectivity and increased clustering. Estimates of progression to disease were significantly associated with age, sputum-smear status, and behavioral risk factors, such as alcohol and intravenous drug abuse, but not with phylogenetic lineages. In conclusion, we found evidence of a bacteriological factor influencing indicators of a strain's transmissibility, namely, a decreased ability to infect and a lower clustering index in ancient phylogenetic lineages compared to their modern counterparts. Confirmation of these findings via follow-up studies using tuberculin skin test conversion data should have important implications on
M. tuberculosis
control efforts.
Human Dendritic Cell Response Signatures Distinguish 1918, Pandemic, and Seasonal H1N1 Influenza Viruses
Authors: Hartmann Boris M. , Thakar Juilee , Albrecht Randy A. , Avey Stefan , Zaslavsky Elena , Marjanovic Nada , Chikina Maria , Fribourg Miguel , Hayot Fernand , Schmolke Mirco , Meng Hailong , Wetmur James , García-Sastre Adolfo , Kleinstein Steven H. , Sealfon Stuart C. 
Published: July 2015

ABSTRACTInfluenza viruses continue to present global threats to human health. Antigenic drift and shift, genetic reassortment, and cross-species transmission generate new strains with differences in epidemiology and clinical severity. We compared the temporal transcriptional responses of human dendritic cells (DC) to infection with two pandemic (A/Brevig Mission/1/1918, A/California/4/2009) and two seasonal (A/New Caledonia/20/1999, A/Texas/36/1991) H1N1 influenza viruses. Strain-specific response differences included stronger activation of NF-κB following infection with A/New Caledonia/20/1999 and a unique cluster of genes expressed following infection with A/Brevig Mission/1/1918. A common antiviral program showing strain-specific timing was identified in the early DC response and found to correspond with reported transcript changes in blood during symptomatic human influenza virus infection. Comparison of the global responses to the seasonal and pandemic strains showed that a dramatic divergence occurred after 4 h, with only the seasonal strains inducing widespread mRNA loss.IMPORTANCEContinuously evolving influenza viruses present a global threat to human health; however, these host responses display strain-dependent differences that are incompletely understood. Thus, we conducted a detailed comparative study assessing the immune responses of human DC to infection with two pandemic and two seasonal H1N1 influenza strains. We identified in the immune response to viral infection both common and strain-specific features. Among the stain-specific elements were a time shift of the interferon-stimulated gene response, selective induction of NF-κB signaling by one of the seasonal strains, and massive RNA degradation as early as 4 h postinfection by the seasonal, but not the pandemic, viruses. These findings illuminate new aspects of the distinct differences in the immune responses to pandemic and seasonal influenza viruses.
R5 Macrophage-Tropic HIV-1 in the Male Genital Tract
Authors: Bednar Maria M. , Hauser Blake M. , Ping Li-Hua , Dukhovlinova Elena , Zhou Shuntai , Arrildt Kathryn T. , Hoffman Irving F. , Eron Joseph J. , Cohen Myron S. , Swanstrom Ronald 
Published: July 2015

ABSTRACT

The entry tropism of HIV-1 Env proteins from virus isolated from the blood and genital tract of five men with compartmentalized lineages was determined. The Env proteins isolated from the genital tract of subject C018 were macrophage-tropic proteins, while the remaining cloned
env
genes encoded R5 T cell-tropic proteins. The detection of a macrophage-tropic lineage of HIV-1 within the male genital tract strongly suggests that evolution of macrophage-tropic viruses can occur in anatomically isolated sites outside the central nervous system.
Nintedanib Is a Highly Effective Therapeutic for Neuroendocrine Carcinoma of the Pancreas (PNET) in the Rip1Tag2 Transgenic Mouse Model
Authors: Bill Ruben , Fagiani Ernesta , Zumsteg Adrian , Antoniadis Helena , Johansson David , Haefliger Simon , Albrecht Imke , Hilberg Frank , Christofori Gerhard 
Published: July 2015

Abstract
Purpose: Pancreatic neuroendocrine tumors (PNET) represent a rare but challenging heterogeneous group of cancers with an increasing incidence over the last number of decades. Herein, we report an in-depth evaluation of the new antiangiogenic small-molecule tyrosine kinase inhibitor (TKI) nintedanib in the preclinical Rip1Tag2 transgenic mouse model of neuroendocrine carcinoma of the pancreas (insulinoma).
Experimental Design: We have assessed the antiangiogenic and antitumor activity of nintedanib, in comparison with other antiangiogenic TKI, by treating Rip1Tag2 transgenic mice with different treatment schedules complemented with histopathologic, cell biologic, and biochemical analyses.
Results: Prolonged nintedanib treatment of Rip1Tag2 mice has led to a strong suppression of angiogenesis, accompanied by a reduced tumor burden, which translated into a significant prolongation of survival. Despite nintedanib's inhibitory action on perivascular cells, the blood vessels remaining after therapy displayed a considerably mature phenotype with tight perivascular cell coverage and preserved perfusion. Nintedanib treatment did not increase local tumor invasiveness or metastasis to the liver and pancreatic lymph nodes—a phenomenon that has been observed with antiangiogenic treatments of Rip1Tag2 transgenic mice in other laboratories. In contrast with the strong reduction in blood microvessel densities, nintedanib did not have any impact on tumor lymphangiogenesis.
Conclusions: Based on our findings, we propose the clinical evaluation of the antiangiogenic drug nintedanib as a new treatment modality for PNET patients, notably in a direct comparison with already established therapeutic regimens, such as sunitinib. Clin Cancer Res; 21(21); 4856–67. ©2015 AACR.
R-Ketorolac Targets Cdc42 and Rac1 and Alters Ovarian Cancer Cell Behaviors Critical for Invasion and Metastasis
Authors: Guo Yuna , Kenney S. Ray , Muller Carolyn Y. , Adams Sarah , Rutledge Teresa , Romero Elsa , Murray-Krezan Cristina , Prekeris Rytis , Sklar Larry A. , Hudson Laurie G. , Wandinger-Ness Angela 
Published: July 2015

Abstract
Cdc42 (cell division control protein 42) and Rac1 (Ras-related C3 botulinum toxin substrate 1) are attractive therapeutic targets in ovarian cancer based on established importance in tumor cell migration, adhesion, and invasion. Despite a predicted benefit, targeting GTPases has not yet been translated to clinical practice. We previously established that Cdc42 and constitutively active Rac1b are overexpressed in primary ovarian tumor tissues. Through high-throughput screening and computational shape homology approaches, we identified R-ketorolac as a Cdc42 and Rac1 inhibitor, distinct from the anti-inflammatory, cyclooxygenase inhibitory activity of S-ketorolac. In the present study, we establish R-ketorolac as an allosteric inhibitor of Cdc42 and Rac1. Cell-based assays validate R-ketorolac activity against Cdc42 and Rac1. Studies on immortalized human ovarian adenocarcinoma cells (SKOV3ip) and primary patient-derived ovarian cancer cells show that R-ketorolac is a robust inhibitor of growth factor or serum-dependent Cdc42 and Rac1 activation with a potency and cellular efficacy similar to small-molecule inhibitors of Cdc42 (CID2950007/ML141) and Rac1 (NSC23766). Furthermore, GTPase inhibition by R-ketorolac reduces downstream p21-activated kinases (PAK1/PAK2) effector activation by &gt;80%. Multiple assays of cell behavior using SKOV3ip and primary patient-derived ovarian cancer cells show that R-ketorolac significantly inhibits cell adhesion, migration, and invasion. In summary, we provide evidence for R-ketorolac as a direct inhibitor of Cdc42 and Rac1 that is capable of modulating downstream GTPase-dependent, physiologic responses, which are critical to tumor metastasis. Our findings demonstrate the selective inhibition of Cdc42 and Rac1 GTPases by an FDA-approved drug, racemic ketorolac, that can be used in humans. Mol Cancer Ther; 14(10); 2215–27. ©2015 AACR.
Polarity Protein Scrib Facilitates Endothelial Inflammatory Signaling
Authors: Kruse Christoph , Kurz Angela R.M. , Pálfi Katalin , Humbert Patrick O. , Sperandio Markus , Brandes Ralf P. , Fork Christian , Michaelis U. Ruth 
Published: July 2015

Objective—
The polarity protein Scrib is highly expressed in endothelial cells and is required for planar cell polarity. Scrib also facilitates recycling of integrin α5 to the plasma membrane. Because integrin α5 signals the presence of the inflammatory matrix protein fibronectin, we hypothesized that Scrib contributes to endothelial inflammatory signaling.

Approach and Results—
Cytokine treatment of human umbilical vein endothelial cells induced an inflammatory response as evident by the induction of vascular cell adhesion molecule-1 (VCAM-1). Downregulation of Scrib greatly attenuated this effect. In endothelial-specific conditional Scrib knockout mice, in vivo lipopolysaccharide treatment resulted in an impaired VCAM-1 induction. These effects were functionally relevant because Scrib small interfering RNAs in human umbilical vein endothelial cells attenuated the VCAM-1–mediated leukocyte adhesion in response to tumor necrosis factor-α. In vivo, tamoxifen-induced endothelial-specific deletion of Scrib resulted in a reduced VCAM-1–mediated leukocyte adhesion in response to tumor necrosis factor-α in the mouse cremaster model. This effect was specific for Scrib and not mediated by other polarity proteins. Moreover, it did not involve integrin α5 or classic pathways supporting inflammatory signaling, such as nuclear factor κ light chain enhancer of activated B-cells or MAP kinases. Co-immunoprecipitation/mass spectrometry identified the zinc finger transcription factor GATA-like protein-1 as a novel Scrib interacting protein. Small interfering RNA depletion of GATA-like protein-1 decreased the tumor necrosis factor-α–stimulated VCAM-1 induction to a similar extent as loss of Scrib did. Silencing of Scrib reduced GATA-like protein-1 protein, but not mRNA abundance.

Conclusions—
Scrib is a novel proinflammatory regulator in endothelial cells, which maintains the protein expression of GATA-like protein-1.
Extracranial Systemic Embolic Events in Patients With Nonvalvular Atrial Fibrillation
Authors: Bekwelem Wobo , Connolly Stuart J. , Halperin Jonathan L. , Adabag Selcuk , Duval Sue , Chrolavicius Susan , Pogue Janice , Ezekowitz Michael D. , Eikelboom John W. , Wallentin Lars G. , Yusuf Salim , Hirsch Alan T. 
Published: July 2015

Background—
Nonvalvular atrial fibrillation is a major cause of thromboembolic events. In comparison with atrial fibrillation–related stroke, extracranial systemic embolic events (SEEs) remain poorly defined.

Methods and Results—

All suspected SEEs reported among 37 973 participants of 4 large contemporary randomized clinical trials of anticoagulation in atrial fibrillation were independently readjudicated for clinical and objective evidence of sudden loss of perfusion of a limb or organ. Over 91 746 patient-years of follow-up, 221 SEEs occurred in 219 subjects. The SEE incidence was 0.24 of 100 and stroke incidence was 1.92 of 100 patient-years. In comparison with patients with stroke, those with SEE were more often female (56% versus 47%;
P
=0.01) and had comparable mean age (73.1±8.5 versus 73.5±8.8 years;
P
=0.57) and mean CHADS
2
scores (2.4±1.3 versus 2.5±1.2;
P
=0.33). SEEs more frequently involved the lower extremity (58%) than visceral-mesenteric (31%) or upper extremity (10%). SEE-related care involved clinic assessment alone in 5%, 30% were hospitalized without procedures, 60% underwent endovascular or surgical intervention, and 5% underwent amputation. Within 30 days, 54% of patients recovered fully, 20% survived with deficits, and 25% died. Thirty-day mortality was greater after visceral-mesenteric than lower- or upper-extremity SEE (55%, 17%, and 9%, respectively,
P
≤0.0001). The relative risk of death throughout follow-up was 4.33 (95% confidence interval, 3.29–5.70) after SEE versus 6.79 (95% confidence interval, 6.22–7.41) after stroke in comparison with patients without either event.

Conclusions—
SEE constituted 11.5% of clinically recognized thromboembolic events in patients with atrial fibrillation and was associated with high morbidity and mortality. SEE mortality was comparable to that of ischemic stroke and varied by anatomic site.
Temperature and Precipitation Variability and Its Effects on Streamflow in the Upstream Regions of the Lancang–Mekong and Nu–Salween Rivers
Authors: Fan Hui , He Daming 
Published: July 2015

Abstract
Hydrological regimes of alpine rivers are highly sensitive to climate variability/change. Temperature and precipitation variability and its effects on streamflow in the upstream regions of the Lancang–Mekong River (LMR) and Nu–Salween River (NSR) are examined in this study based on long-term observational data from 16 meteorological stations and 2 hydrological stations between the 1950s and 2010. This study employs the Mann–Kendall nonparametric test, together with the trend-free prewhitening (TFPW) approach to test trends and the Breaks For Additive Season and Trend (BFAST) method to detect abrupt changes in the hydrometeorological time series. The relations between air temperature, precipitation, and streamflow trends are assessed using random forest regression. The results show significant climate warming and related prevalent positive precipitation trends both at the annual and seasonal scale. A substantial precipitation increase paralleling climate warming, especially in spring, was also observed. However, no consistent abrupt change in meteorological time series was found. The increasing trends of streamflow with climate warming are seen both for the outlets of the LMR and NSR upstream regions, with the abrupt changes occurring in the mid-1960s and the late 1990s, respectively. The relation of streamflow to annual and wet season precipitation is pronounced, especially for the upstream region of the LMR with a percent variance explained of more than 65%. However, the relatively minor linkage of streamflow to air temperature and dry season precipitation may be confounded by the climate warming–driven changes in snowpack, permafrost, glacier, and evapotranspiration. These results could provide further a reference for the regional water resources management under climate change scenarios.
Origin and Impact of Initialization Shocks in Coupled Atmosphere–Ocean Forecasts*
Authors: Mulholland David P. , Laloyaux Patrick , Haines Keith , Balmaseda Magdalena Alonso 
Published: July 2015

Abstract
Current methods for initializing coupled atmosphere–ocean forecasts often rely on the use of separate atmosphere and ocean analyses, the combination of which can leave the coupled system imbalanced at the beginning of the forecast, potentially accelerating the development of errors. Using a series of experiments with the European Centre for Medium-Range Weather Forecasts coupled system, the magnitude and extent of these so-called initialization shocks is quantified, and their impact on forecast skill measured. It is found that forecasts initialized by separate oceanic and atmospheric analyses do exhibit initialization shocks in lower atmospheric temperature, when compared to forecasts initialized using a coupled data assimilation method. These shocks result in as much as a doubling of root-mean-square error on the first day of the forecast in some regions, and in increases that are sustained for the duration of the 10-day forecasts performed here. However, the impacts of this choice of initialization on forecast skill, assessed using independent datasets, were found to be negligible, at least over the limited period studied. Larger initialization shocks are found to follow a change in either the atmosphere or ocean model component between the analysis and forecast phases: changes in the ocean component can lead to sea surface temperature shocks of more than 0.5 K in some equatorial regions during the first day of the forecast. Implications for the development of coupled forecast systems, particularly with respect to coupled data assimilation methods, are discussed.