bluuebunny/crossref_metadata_2025_split huggingface dataset:
DOBRE-2 WARR profile: the Earth's upper crust across Crimea between the Azov Massif and the northeastern Black Sea
Authors: Starostenko V. , Janik T. , Stephenson R. , Gryn D. , Rusakov O. , Czuba W. , Środa P. , Grad M. , Guterch A. , Flüh E. , Thybo H. , Artemieva I. , Tolkunov A. , Sydorenko G. , Lysynchuk D. , Omelchenko V. , Kolomiyets K. , Legostaeva O. , Dannowski A. , Shulgin A. 
Published: February 2016

Abstract
The DOBRE-2 wide-angle reflection and refraction profile was acquired in June 2007 as a direct, southwestwards prolongation of the 1999 DOBREfraction'99 that crossed the Donbas Foldbelt in eastern Ukraine. It crosses the Azov Massif of the East European Craton, the Azov Sea, the Kerch Peninsula (the easternmost part of Crimea) and the northern East Black Sea Basin, thus traversing the entire Crimea–Caucasus compressional zone centred on the Kerch Peninsula. The DOBRE-2 profile recorded a mix of onshore explosive sources as well as airguns at sea. A variety of single-component recorders were used on land and ocean bottom instruments were deployed offshore and recovered by ship. The DOBRE-2 datasets were degraded by a lack of shot-point reversal at the southwestern terminus and by some poor signal registration elsewhere, in particular in the Black Sea. Nevertheless, they allowed a robust velocity model of the upper crust to be constructed along the entire profile as well as through the entire crust beneath the Azov Massif. A less well constrained model was constructed for much of the crust beneath the Azov Sea and the Kerch Peninsula. The results showed that there is a significant change in the upper crustal lithology in the northern Azov Sea, expressed in the near surface as the Main Azov Fault; this boundary can be taken as the boundary between the East European Craton and the Scythian Platform. The upper crustal rocks of the Scythian Platform in this area probably consist of metasedimentary rocks. A narrow unit as shallow as about 5 km and characterized by velocities typical of the crystalline basement bounds the metasedimentary succession on its southern margin and also marks the northern margin of the northern foredeep and the underlying successions of the Crimea–Caucasus compressional zone in the southern part of the Azov Sea. A broader and somewhat deeper basement unit (about 11 km) with an antiformal shape lies beneath the northern East Black Sea Basin and forms the southern margin of the Crimea–Caucasus compressional zone. The depth of the underlying Moho discontinuity increases from 40 km beneath the Azov Massif to 47 km beneath the Crimea–Caucasus compressional zone.
Phase I Safety, Pharmacokinetic, and Pharmacodynamic Study of the Poly(ADP-ribose) Polymerase (PARP) Inhibitor Veliparib (ABT-888) in Combination with Irinotecan in Patients with Advanced Solid Tumors
Authors: LoRusso Patricia M. , Li Jing , Burger Angelika , Heilbrun Lance K. , Sausville Edward A. , Boerner Scott A. , Smith Daryn , Pilat Mary Jo , Zhang Jie , Tolaney Sara M. , Cleary James M. , Chen Alice P. , Rubinstein Lawrence , Boerner Julie L. , Bowditch Adam , Cai Dongpo , Bell Tracy , Wolanski Andrew , Marrero Allison M. , Zhang Yiping , Ji Jiuping , Ferry-Galow Katherine , Kinders Robert J. , Parchment Ralph E. , Shapiro Geoffrey I. 
Published: February 2016

Abstract
Purpose: PARP is essential for recognition and repair of DNA damage. In preclinical models, PARP inhibitors modulate topoisomerase I inhibitor–mediated DNA damage. This phase I study determined the MTD, dose-limiting toxicities (DLT), pharmacokinetics (PK), and pharmacodynamics (PD) of veliparib, an orally bioavailable PARP1/2 inhibitor, in combination with irinotecan.
Experimental Design: Patients with advanced solid tumors were treated with 100 mg/m2 irinotecan on days 1 and 8 of a 21-day cycle. Twice-daily oral dosing of veliparib (10–50 mg) occurred on days 3 to 14 (cycle 1) and days −1 to 14 (subsequent cycles) followed by a 6-day rest. PK studies were conducted with both agents alone and in combination. Paired tumor biopsies were obtained after irinotecan alone and veliparib/irinotecan to evaluate PARP1/2 inhibition and explore DNA damage signals (nuclear γ-H2AX and pNBS1).
Results: Thirty-five patients were treated. DLTs included fatigue, diarrhea, febrile neutropenia, and neutropenia. The MTD was 100 mg/m2 irinotecan (days 1 and 8) combined with veliparib 40 mg twice daily (days −1–14) on a 21-day cycle. Of 31 response-evaluable patients, there were six (19%) partial responses. Veliparib exhibited linear PK, and there were no apparent PK interactions between veliparib and irinotecan. At all dose levels, veliparib reduced tumor poly(ADP-ribose) (PAR) content in the presence of irinotecan. Several samples showed increases in γ-H2AX and pNBS1 after veliparib/irinotecan compared with irinotecan alone.
Conclusions: Veliparib can be safely combined with irinotecan at doses that inhibit PARP catalytic activity. Preliminary antitumor activity justifies further evaluation of the combination. Clin Cancer Res; 22(13); 3227–37. ©2016 AACR.
Immune Signatures Following Single Dose Trastuzumab Predict Pathologic Response to PreoperativeTrastuzumab and Chemotherapy in HER2-Positive Early Breast Cancer
Authors: Varadan Vinay , Gilmore Hannah , Miskimen Kristy L.S. , Tuck David , Parsai Shikha , Awadallah Amad , Krop Ian E. , Winer Eric P. , Bossuyt Veerle , Somlo George , Abu-Khalaf Maysa M. , Fenton Mary Anne , Sikov William , Harris Lyndsay N. 
Published: February 2016

Abstract
Purpose: Recent data suggest that intrinsic subtype and immune cell infiltration may predict response to trastuzumab-based therapy. We studied the interaction between these factors, changes in immune signatures following brief exposure to trastuzumab, and achievement of pathologic complete response (pCR) to subsequent preoperative trastuzumab and chemotherapy in HER2-positive breast cancer.
Experimental Design: In patients enrolled on two multicenter trials (03-311 and 211B), tumor core biopsies were obtained at baseline and after brief exposure to single-agent trastuzumab or nab-paclitaxel. Gene expression profiles were assessed to assign PAM50 subtypes, measure immune cell activation, and were correlated with response.
Results: The pCR rate was significantly higher in HER2-enriched tumors in the Discovery, 03-311 (36%, P = 0.043) dataset, as compared with other subtypes, which validated in 211B (50%, P = 0.048). Significant increases in a signature of immune cell admixture (Immune Index) were observed only following brief exposure to trastuzumab in HER2-enriched tumors (Discovery/03-311, P = 0.05; Validation/211B, P = 0.02). Increased Immune Index was predictive of response after brief exposure (03-311, P = 0.03; 211B, P = 0.04), but not at baseline, in addition to increased expression of a CD4+ follicular helper T-cell signature (03-311, P = 0.05; 211B, P = 0.04). Brief exposure to trastuzumab significantly increased gene expression of the T-cell marker PD-1 in HER2-enriched tumors (Discovery/03-311, P = 0.045) and PD-1 positivity by IHC (Validation/211B, P = 0.035).
Conclusions: Correlations between pCR rates, increases in Immune Index and markers of T-cell activity following brief exposure to trastuzumab in HER2-enriched tumors provide novel insights into the interaction between tumor biology, antitumor immunity, and response to treatment, and suggest potential clinically useful biomarkers in HER2+ breast cancers. Clin Cancer Res; 22(13); 3249–59. ©2016 AACR.
PreImplantation factor prevents atherosclerosis via its immunomodulatory effects without affecting serum lipids
Authors: Chih Chen Yung , Rivera Jennifer , Fitzgerald Melissa , Hausding Christian , Ying Ya-Lan , Wang Xiaowei , Todorova Krassimira , Hayrabedyan Soren , Barnea Eytan R. , Peter Karlheinz 
Published: February 2016

SummaryPreImplantation factor (PIF) is a 15-amino acid peptide endogenously secreted by viable embryos, regulating/enabling maternal (host) acceptance/tolerance to the “invading” embryo (allograft) all-while preserving maternal immunity to fight infections. Such attributes make PIF a potential therapeutic agent for chronic inflammatory diseases. We investigated whether PIF’s immunomodulatory properties prevent progression of atherosclerosis in the hyper-cholesterolaemic ApoEdeficient murine model. Male, high-fat diet fed, ApoE-deficient (ApoE-/-) mice were administered either PBS, scrambled PIF (0.3–3 mg/kg) or PIF (0.3–3 mg/kg) for seven weeks. After treatment, PIF (3 mg/kg)-treated ApoE-/- mice displayed significantly reduced atherosclerosis lesion burden in the aortic sinus and aortic arch, without any effect on lipid profile. PIF also caused a significant reduction in infiltration of macrophages, decreased expression of pro-inflammatory adhesion molecules, cytokines and chemokines in the plaque, and reduced circulating IFN-γ levels. PIF preferentially binds to monocytes/neutrophils. In vitro, PIF attenuated monocyte migration (MCP-1-induced chemotaxis assay) and in vivo in LPS peritonitis model. Also PIF prevented leukocyte extravasation (peritonitis thioglycollate-induced model), demonstrating that PIF exerts its effect in part by modulation of monocyte function. Inhibition of the potassium channel KCNAB3 (Kv1.3) and of the insulin degrading enzyme (IDE) was demonstrated as potential mechanism of PIF’s immunomodulatory effects. In conclusion, PIF regulates/lowers inflammation and prevents atherosclerosis development without affecting circulating lipids. Overall our findings establish PIF as a strong immunomodulatory drug candidate for atherosclerosis therapy.Supplementary Material to this article is available online at www.thrombosis-online.com.
Integration of flow studies for robust selection of mechanoresponsive genes
Authors: Maimari Nataly , Pedrigi Ryan M. , Russo Alessandra , Broda Krysia , Krams Rob 
Published: February 2016

SummaryBlood flow is an essential contributor to plaque growth, composition and initiation. It is sensed by endothelial cells, which react to blood flow by expressing > 1000 genes. The sheer number of genes implies that one needs genomic techniques to unravel their response in disease. Individual genomic studies have been performed but lack sufficient power to identify subtle changes in gene expression. In this study, we investigated whether a systematic meta-analysis of available microarray studies can improve their consistency. We identified 17 studies using microarrays, of which six were performed in vivo and 11 in vitro. The in vivo studies were disregarded due to the lack of the shear profile. Of the in vitro studies, a cross-platform integration of human studies (HUVECs in flow cells) showed high concordance (> 90 %). The human data set identified > 1600 genes to be shear responsive, more than any other study and in this gene set all known mechanosensitive genes and pathways were present. A detailed network analysis indicated a power distribution (e. g. the presence of hubs), without a hierarchical organisation. The average cluster coefficient was high and further analysis indicated an aggregation of 3 and 4 element motifs, indicating a high prevalence of feedback and feed forward loops, similar to prokaryotic cells. In conclusion, this initial study presented a novel method to integrate human-based mechanosensitive studies to increase its power. The robust network was large, contained all known mechanosensitive pathways and its structure revealed hubs, and a large aggregate of feedback and feed forward loops.Supplementary Material to this article is available online at www.thrombosis-online.com.
Counting the platelets: a robust and sensitive quantification method for thrombus formation
Authors: Lindahl Tomas , Faxälv Lars , Claesson Kjersti 
Published: February 2016

SummaryFlow chambers are common tools used for studying thrombus formation in vitro. However, the use of such devices is not standardised and there is a large diversity among the flow chamber systems currently used, and also in the methods used for quantifying the thrombus development. It was the study objective to evaluate a new method for analysis and quantification of platelet thrombus formation that can facilitate comparison of results between research groups. Whole blood was drawn over a collagen patch in commercial Ibid or in-house constructed PDMS flow chambers. Five percent of the platelets were fluorescently labelled and z-stack time-lapse images were captured during thrombus formation. Images were processed in a Python script in which the number of platelets and their respective x-, yand z-positions were obtained. For comparison with existing methods the platelets were also labelled and quantified using fluorescence intensity and thrombus volume estimations by confocal microscopy. The presented method was found less sensitive to microscope and image adjustments and provides more details on thrombus development dynamics than the methods for measuring fluorescence intensity and thrombus volume estimation. The platelet count method produced comparable results with commercial and PDMS flow chambers, and could also obtain information regarding the stability of each detected platelet in the thrombus. In conclusion, quantification of thrombus formation by platelet count is a sensitive and robust method that enables measurement of platelet accumulation and platelet stability in an absolute scale that could be used for comparisons between research groups.
The Artist and Politics (1954)
Authors: Ecevit Bülent 
Published: February 2016

Abstract
This essay analyzes three polemic newspaper articles written in the early 1950s by the art critic, gallerist, and future Turkish prime minister Bülent Ecevit (1925–2006), “Artistic Awakening in Ankara” (1953), “The Artist and Politics” (1954), and “The Burden of the Intellectual” (1956). It argues that Ecevit's articles document a local intelligentsia's efforts to theorize the role of art in Turkish society at a crucial moment of political transformation. As Turkey abandoned its authoritarian past in order to conduct its inaugural experiment with multi-party democracy, Ecevit's columns took up two of the period's most pressing questions: the extent to which the state should control the local art world, and in what ways Turkey's newly enfranchised citizens might enact their individual rights within the realm of culture. The essay also demonstrates the importance of these three articles to Ecevit's subsequent political and intellectual trajectory: they were central to his lifelong efforts to continue the progressive social and political modernization project of the early Turkish Republic, while developing new forums for its critique, reinterpretation, and reinvigoration.
The Burden of the Intellectual (1956)
Authors: Ecevit Bülent 
Published: February 2016

Abstract
This essay analyzes three polemic newspaper articles written in the early 1950s by the art critic, gallerist, and future Turkish prime minister Bülent Ecevit (1925–2006), “Artistic Awakening in Ankara” (1953), “The Artist and Politics” (1954), and “The Burden of the Intellectual” (1956). It argues that Ecevit's articles document a local intelligentsia's efforts to theorize the role of art in Turkish society at a crucial moment of political transformation. As Turkey abandoned its authoritarian past in order to conduct its inaugural experiment with multi-party democracy, Ecevit's columns took up two of the period's most pressing questions: the extent to which the state should control the local art world, and in what ways Turkey's newly enfranchised citizens might enact their individual rights within the realm of culture. The essay also demonstrates the importance of these three articles to Ecevit's subsequent political and intellectual trajectory: they were central to his lifelong efforts to continue the progressive social and political modernization project of the early Turkish Republic, while developing new forums for its critique, reinterpretation, and reinvigoration.
Molecular phylogenetic analysis of Sciadophycus stellatus (Rhodymeniales, Rhodophyta) supports its placement in the family Rhodymeniaceae
Authors: Hughey Jeffery R , Miller Kathy Ann 
Published: February 2016

The marine red alga Sciadophycus stellatus E.Y.Dawson (1945) (Figure 1) was described from specimens dredged at 40–50 meters from the Kellett Channel, south shore of Cerros Island (also known as Cedros Island), Baja California, Mexico (Dawson 1945). This uncommon subtidal species occurs in southern California, Baja California, Mexico and Isla Floreana, Galapagos Islands (as Fauchea rhizophylla Taylor) (Dawson 1945, Abbott and Hollenberg 1976, Millar 2001, Aguilar-Rosas et al. 2010). In California, S. stellatus has been collected in San Diego County (UC2003699) and Palos Verdes Peninsula, Los Angeles County (UC1882843), on the mainland coast of southern California and, more commonly, offshore from Santa Catalina (UC1471598), Santa Barbara (UC2034301), Anacapa (WTU-A-012879) and Santa Cruz Islands (UC1965240). In Mexico, in addition to the type locality, it has been collected from Isla Los Coronados (UC1574390), La Bufadora (Aguilar-Rosas et al. 2010), Isla Natividad (UC1882846), Punta Eugenia (US13095) and Bahia Tortugas (US42090), Baja California (distribution records, unless otherwise cited, are based on specimens in herbaria at the University of California at Berkeley [UC], University of Washington [WTU-A], and the Smithsonian Institution [US]).
Open-Ocean Submesoscale Motions: A Full Seasonal Cycle of Mixed Layer Instabilities from Gliders
Authors: Thompson Andrew F. , Lazar Ayah , Buckingham Christian , Naveira Garabato Alberto C. , Damerell Gillian M. , Heywood Karen J. 
Published: February 2016

AbstractThe importance of submesoscale instabilities, particularly mixed layer baroclinic instability and symmetric instability, on upper-ocean mixing and energetics is well documented in regions of strong, persistent fronts such as the Kuroshio and the Gulf Stream. Less attention has been devoted to studying submesoscale flows in the open ocean, far from long-term, mean geostrophic fronts, characteristic of a large proportion of the global ocean. This study presents a year-long, submesoscale-resolving time series of near-surface buoyancy gradients, potential vorticity, and instability characteristics, collected by ocean gliders, that provides insight into open-ocean submesoscale dynamics over a full annual cycle. The gliders continuously sampled a 225 km2 region in the subtropical northeast Atlantic, measuring temperature, salinity, and pressure along 292 short (~20 km) hydrographic sections. Glider observations show a seasonal cycle in near-surface stratification. Throughout the fall (September–November), the mixed layer deepens, predominantly through gravitational instability, indicating that surface cooling dominates submesoscale restratification processes. During winter (December–March), mixed layer depths are more variable, and estimates of the balanced Richardson number, which measures the relative importance of lateral and vertical buoyancy gradients, depict conditions favorable to symmetric instability. The importance of mixed layer instabilities on the restratification of the mixed layer, as compared with surface heating and cooling, shows that submesoscale processes can reverse the sign of an equivalent heat flux up to 25% of the time during winter. These results demonstrate that the open-ocean mixed layer hosts various forced and unforced instabilities, which become more prevalent during winter, and emphasize that accurate parameterizations of submesoscale processes are needed throughout the ocean.
Hydrography, Circulation, and Mixing at the Calypso Deep (the Deepest Mediterranean Trough) during 2006–09
Authors: Kontoyiannis H. , Lykousis V. , Papadopoulos V. , Stavrakakis S. , Anassontzis E. G. , Belias A. , Koutsoukos S. , Resvanis L. K. 
Published: February 2016

AbstractThe mass and flow fields from June 2006 to May 2009 in the Calypso Deep (bottom depth ~5.2 km) are investigated using eddy-resolving surface-to-bottom hydrography (station grid spacing ~0.2°) and two tall moorings yielding current-meter records at depths from 700 m to near bottom. A salty warm lens (excess core salinity and temperature are ~0.01 and 0.025°C relative to the surrounding water) of Cretan Deep Water with a core at ~3000 m and a horizontal (vertical) scale of ~50 km (1.5 km) is identified in June 2006 to be locked over the trough. The lens coincides with local maxima in dissolved oxygen. In October 2006 the salinity content of the lens and of all deeper layers is increased; the oxygen maxima are shifted to the bottom layers, indicating an episodic intrusion of higher-density ventilated Adriatic water. The circulation changes from anticyclonic at all depths in June 2006 to cyclonic below ~2.5 km in October 2006, whereas after January 2007 it is cyclonic at all instrumented depths. The measured currents are weak (mean speeds < 5 cm s−1) and persistent in direction, being mostly along the bottom topography at all current-meter depths. After October 2006, the lens erodes due to salt/heat loss caused predominantly by lateral (intrusive) mixing, which works from the outside toward the lens center. The horizontal diffusivity is on the order of ~10 m2 s−1, near the center of the lens, and ~102 to 103 m2 s−1, at its periphery, with an average error ~15 times the diffusivity value. In the deepest part of the trough and in periods of predominance of vertical mixing the vertical diffusivity at 4400 m is ~(4 ± 3) × 10−3 m2 s−1.
Role of E-selectin for diagnosing myocardial injury in paediatric patients with mycoplasma pneumoniae pneumonia
Authors: Deng Ming-Hong , Lin Chun-Wang , Sun Yan-Na , Zeng Xiang-Lin , Wen Fang 
Published: February 2016

Backgrounds Effects of myocardial injury on E-selectin remain unclear. Thus, we investigated the diagnostic value of E-selectin for myocardial injury in paediatric patients with mycoplasma pneumoniae pneumonia. Methods In this prospective and blinded clinical study, plasma E-selectin, cardiac troponin I, creatine kinase isoenzyme MB, interleukin-6 and tumor necrosis factor alpha concentrations were measured in paediatric patients with mycoplasma pneumoniae pneumonia (MPP group, n = 138). The control group comprised 120 healthy children. The definition of cardiac injury was based on cardiac troponin I or CK-MB (with or possibly without abnormal electrocardiogram evidence). Diagnostic value of E-selectin for myocardial injury was determined by analysing receiver operating characteristic curves. Results Among the 138 mycoplasma pneumoniae pneumonia patients, 40 patients were identified with myocardial injury, while 98 patients were identified without myocardial injury. Plasma E-selectin concentrations were: 40.22 ± 4.80 ng/mL, in patients with myocardial injury; 18.55 ± 2.16 ng/mL, in patients without myocardial injury and 12.39 ± 3.27 ng/mL, in healthy children. For the 40 patients identified with myocardial injury, area under the receiver operating characteristic curve value for plasma E-selectin concentrations was 0.945 (95% CI: 0.899–0.991), and optimal diagnostic cut-off value was 29.93 ng/mL (positive likelihood ratio = 72.5). Conclusion E-selectin was shown to be an effective index for myocardial injury in paediatric patients with mycoplasma pneumoniae pneumonia, and its role in other causes of myocardial injury warrants further investigation.