bluuebunny/crossref_metadata_2025_split huggingface dataset:
Root‐related rhodochrosite and concretionary siderite formation in oxygen‐deficient conditions induced by a ground‐water table rise
Authors: Bojanowski Maciej J. , Jaroszewicz Elżbieta , Košir Adrijan , Łoziński Maciej , Marynowski Leszek , Wysocka Anna , Derkowski Arkadiusz 
Published: August 2015

AbstractSedimentological, mineralogical, stable carbon and oxygen isotope determinations and biomarker analyses were performed on siderite concretions occurring in terrestrial silts to understand their formation and to characterize the sedimentary and diagenetic conditions favouring their growth. High δ13C values (6·4‰ on average) indicate that siderite precipitated in an anoxic environment where bacterial methanogenesis operated. The development of anoxic conditions during shallow burial was induced by a change in sedimentary environment from flood plain to swamp, related to a rise of the ground‐water table. Large amounts of decaying plant debris led to efficient oxygen consumption within the pore‐water in the peat. Oxygen depletion, in combination with a decrease in sedimentation rate, promoted anoxic diagenetic conditions under the swamp and favoured abundant siderite precipitation. This shows how a change in sedimentary conditions can have a profound impact on the early‐diagenetic environment and carbonate authigenesis. The concretions contain numerous rhizoliths; they are cemented with calcium‐rhodochrosite, a feature which has not been reported before. The rhodochrosite cement has negative δ13C values (−16·5‰ on average) and precipitated in suboxic conditions due to microbial degradation of roots coupled to manganese reduction. The exceptional preservation of the epidermis/exodermis and xylem vessels of former root tissues indicates that the rhodochrosite formed shortly after the death of a root in water‐logged sediments. Rhodochrosite precipitated during the initial stages of concretionary growth in suboxic microenvironments within roots, while siderite cementation occurred simultaneously around them in anoxic conditions. These suboxic microenvironments developed because oxygen was transported from the overlying oxygenated soil into sediments saturated with anoxic water via roots acting as permeable conduits. This model explains how separate generations of carbonate cements having different mineralogy and isotopic compositions, which would conventionally be regarded as cements precipitated sequentially in different diagenetic zones during gradual burial, can form simultaneously in shallow burial settings where strong redox gradients exist around vertically oriented permeable root structures.
Tissue Distribution Dynamics of Human NK Cells Inferred from Peripheral Blood Depletion Kinetics after Sphingosine‐1‐Phosphate Receptor Blockade
Authors: Mehling M. , Burgener A.‐V. , Brinkmann V. , Bantug G. R. , Dimeloe S. , Hoenger G. , Kappos L. , Hess C. 
Published: August 2015

AbstractHuman natural killer (NK) cell subsets differentially distribute throughout the organism. While CD56dim and CD56bright NK cell subsets similarly reside in the bone marrow (BM), the CD56dim population predominantly accumulates in non‐lymphoid tissues and the CD56bright counterpart in lymphoid tissue (LT). The dynamics with which these NK cell subsets redistribute to tissues remains unexplored. Here, we studied individuals newly exposed to fingolimod, a drug that efficiently blocks sphingosine‐1‐phosphate (S1P)‐directed lymphocyte – including NK cell – egress from tissue to blood. During an observation period of 6h peripheral blood depletion of CD56bright NK cells was observed 3 h after first dose of fingolimod, with 40–50% depletion after 6 h, while a decrease of the numbers of CD56dim NK cells did not reach the level of statistical significance. In vitro, CD56bright and CD56dim NK cells responded comparably to the BM‐homing chemokine CXCL12, while CD56bright NK cells migrated more efficiently in gradients of the LT‐homing chemokines CCL19 and CCL21. In conjuncture with these in vitro studies, the indirectly observed subset‐specific depletion kinetics from blood are compatible with preferential and more rapid redistribution of CD56bright NK cells from blood to peripheral tissue such as LT and possibly also the inflamed central nervous system. These data shed light on an unexplored level at which access of NK cells to LT, and thus, for example antigen‐presenting cells, is regulated.
Religion and Nationalism: Contradictions of Islamic Origins and Secular Nation‐Building in Turkey, Algeria, and Pakistan*
Authors: Akturk Sener 
Published: August 2015

ObjectivesTurkey, Algeria, and Pakistan have been persistently challenged, since their founding, by both Islamist and ethnic separatist movements. These challenges claimed the lives of tens of thousands of people in each country. I investigate the causes behind the concurrence of Islamist and ethnic separatist challenges to the state in Turkey, Algeria, and Pakistan.MethodThis research employs comparative historical analysis, and more specifically, a most different systems design. In addition to small‐Ncross‐national comparison, I also designed an intertemporal comparison, whereby Turkish, Algerian, and Pakistani history is divided into four periods, corresponding to preindependence, mobilization for independence, postindependence secular nation‐building, and Islamist and ethnic separatist challenge periods.ResultsContrary to the prevailing view in the scholarship, this article formulates an alternative reinterpretation of Turkish, Algerian, and Pakistani nation‐state formation. These three states were founded on the basis of an Islamic mobilization against non‐Muslim opponents, but having successfully defeated these non‐Muslim opponents, their political elites chose a secular and monolingual nation‐state model, which they thought would maximize their national security and improve the socioeconomic status of their Muslim constituencies. The choice of a secular and monolingual nation‐state model led to recurrent challenges of increasing magnitude to the state in the form of Islamist and ethnic separatist movements. The causal mechanism outlined in this article resembles what has been metaphorically described as a “meteorite” (Pierson,), where the cause is short term (secular nationalist turn after independence) but the outcome unfolds over the long term (Islamist and ethnic separatist challenges).ConclusionA distinct and counterintuitive path of nation‐state formation has been identified based on the cases of Turkey, Algeria, and Pakistan. This research demonstrates that a contradiction between the goals of the original mobilization that establishes the state and policies of its postindependence governments can be a major structural source of instability and violence in the long run. These findings suggest that theories of nationalism that were developed based on the European experience of ethnic or linguistic nationalism need to be modified in explaining the religious nationalism that is found in the origins of some of the major nation‐states in the Muslim world.
Aspergillus thyroiditis: first antemortem case diagnosed by fine‐needle aspiration culture in a pediatric stem cell transplant patient
Authors: Badawy S.M. , Becktell K.D. , Muller W.J. , Schneiderman J. 
Published: August 2015

AbstractAspergillus thyroiditis (AT) has historically been considered a postmortem diagnosis in immunocompromised patients; most have disseminated disease. This report summarizes the clinical challenge of diagnosing AT. It also highlights the value of the early use of thyroid fine‐needle aspiration culture and the need for a high index of suspicion to reach the final diagnosis before disease dissemination.
Dried blood spots of pooled samples for RHD gene screening in blood donors of mixed ancestry
Authors: Silva‐Malta M. C. F. , Fidélis Araujo N. C. , Neves Vieira O. V. , Cayres Schmidt L. , de Cassia Gonçalves P. , Lobato Martins M. 
Published: August 2015

SUMMARYObjectivesIn this study, we present a strategy for RHD gene screening based on real‐time polymerase chain reaction (PCR) using dried blood spots of pooled samples.BackgroundMolecular analysis of blood donors may be used to detect RHD variants among the presumed D‐negative individuals. RHD genotyping using pooled samples is a strategy to test a large number of samples at a more reasonable cost.Materials and MethodsRHD gene detection based on real‐time PCR using dried blood spots of pooled samples was standardised and used to evaluate 1550 Brazilian blood donors phenotyped as RhD‐negative. Positive results were re‐evaluated by retesting single samples using real‐time PCR and conventional multiplex PCR to amplify five RHD‐specific exons. PCR‐sequence‐specific primers was used to amplify RHDψ allele.ResultsWe devised a strategy for RHD gene screening using dried blood spots of five pooled samples. Among 1550 serologically D‐negative blood donors, 58 (3·74%) had the RHD gene. The non‐functional RHDψ allele was detected in 47 samples (3·02%).ConclusionThe present method is a promising strategy to detect the RHD gene among presumed RhD‐negative blood donors, particularly for populations with African ancestry.
Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome
Authors: Faino Luigi , Seidl Michael F. , Datema Erwin , van den Berg Grardy C. M. , Janssen Antoine , Wittenberg Alexander H. J. , Thomma Bart P. H. J. 
Published: August 2015

ABSTRACT

Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus
Verticillium dahliae
. Compared with Illumina-based assemblies of the
V. dahliae
genome, hybrid assemblies that also include PacBio-generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete
V. dahliae
genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully appreciate an organism's biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes.

IMPORTANCE
Studying whole-genome sequences has become an important aspect of biological research. The advent of next-generation sequencing (NGS) technologies has nowadays brought genomic science within reach of most research laboratories, including those that study nonmodel organisms. However, most genome sequencing initiatives typically yield (highly) fragmented genome assemblies. Nevertheless, considerable relevant information related to genome structure and evolution is likely hidden in those nonassembled regions. Here, we investigated a diverse set of strategies to obtain gapless genome assemblies, using the genome of a typical ascomycete fungus as the template. Eventually, we were able to show that a combination of PacBio-generated long reads and optical mapping yields a gapless telomere-to-telomere genome assembly, allowing in-depth genome analyses to facilitate functional studies into an organism's biology.
Accelerator physics and technology challenges of very high energy hadron colliders
Authors: Shiltsev Vladimir D. 
Published: August 2015

High energy hadron colliders have been in the forefront of particle physics for more than three decades. At present, international particle physics community considers several options for a 100 TeV proton–proton collider as a possible post-LHC energy frontier facility. The method of colliding beams has not fully exhausted its potential but has slowed down considerably in its progress. This paper briefly reviews the accelerator physics and technology challenges of the future very high energy colliders and outlines the areas of required research and development towards their technical and financial feasibility.
Palaeomagnetic data from the Precordillera fold and thrust belt constraining Neogene foreland evolution of the Pampean flat-slab segment (Central Andes, Argentina)
Authors: Japas Maria S. , Ré Guillermo H. , Oriolo Sebastián , Vilas Juan F. 
Published: August 2015

Abstract
Available and new palaeomagnetic data reveal transpressional deformation in the Argentine Precordillera fold and thrust belt contemporaneous with Juan Fernández ridge subduction. Localized changes in the orientation of palaeomagnetic directions indicate a vertical axis rotation pattern linked to local, oblique brittle-ductile shear zones that overprint the regional structure. The nearly homogeneous clockwise block rotation pattern from Western-Central Precordillera shows localized rotation nulls along NNW-trending left-lateral oblique belts, revealing that overprinting anticlockwise tectonic rotations could have balanced previous clockwise rotations. Conversely, clockwise rotations in Eastern Precordillera are only localized in the vicinity of these NNW-trending structures, and are controlled by rigid block rotations linked to basement-involved deformation.These results combined with available regional palaeomagnetic data in the forearc would indicate a regional bending of the upper plate margin between 27° S and 33° S that seems to be related to the subduction of the Juan Fernández aseismic ridge.
Relationship between Complete Pathologic Response to Neoadjuvant Chemotherapy and Survival in Triple-Negative Breast Cancer
Authors: Hatzis Christos , Symmans W. Fraser , Zhang Ya , Gould Rebekah E. , Moulder Stacy L. , Hunt Kelly K. , Abu-Khalaf Maysa , Hofstatter Erin W. , Lannin Donald , Chagpar Anees B. , Pusztai Lajos 
Published: August 2015

AbstractPurpose: Pathologic complete response (pCR) to neoadjuvant chemotherapy reflects the cytotoxic efficacy of a drug, but patient survival is influenced by many other factors. The purpose of this study was to assess the relationship between increased pCR rate and trial-level survival benefit in triple-negative breast cancer (TNBC).Experimental Design: We used bootstrap resampling from a neoadjuvant trial to simulate trials with different pCR rates. We used estimates from Adjuvant!Online to simulate trial populations with different baseline prognosis and estimated survival improvements associated with changes in pCR rate.Results: Assuming that survival is similar for patients with pCR regardless of treatment arm, a linear relationship exists between increasing pCR rate and increasing recurrence-free survival (RFS). The slope is equal to the difference in survival between those with pCR and residual disease, which in turn is influenced by (i) the baseline prognosis of the trial population, (ii) interactions between prognostic variables and pCR, and (iii) the efficacy of the postneoadjuvant therapies. For example, if the pCR rates are 30% and 60% (OR = 3.5) and the 10-year RFS of the control arm is 0.74, the trial would require 3,550 patients per arm, whereas if the RFS is 0.54, the trial would require only 425 patients per arm to detect significant survival benefit.Conclusions: We provide a framework for understanding the relationship between pCR and overall survival benefit that can help inform the design of neoadjuvant trials aiming to demonstrate improved survival from a regimen that results in higher pCR rate. Clin Cancer Res; 22(1); 26–33. ©2015 AACR.See related commentary by Berry, p. 3
Low Socioeconomic Status, Adverse Gene Expression Profiles, and Clinical Outcomes in Hematopoietic Stem Cell Transplant Recipients
Authors: Knight Jennifer M. , Rizzo J. Douglas , Logan Brent R. , Wang Tao , Arevalo Jesusa M.G. , Ma Jeffrey , Cole Steve W. 
Published: August 2015

Abstract
Purpose: Low socioeconomic status (SES) is associated with adverse outcomes among unrelated donor hematopoietic stem cell transplant (HCT) recipients, but the biologic mechanisms contributing to this health disparity are poorly understood. Therefore, we examined whether social environment affects expression of a stress-related gene expression profile known as the conserved transcriptional response to adversity (CTRA), which involves upregulation of proinflammatory genes and downregulation of genes involved in type I IFN response and antibody synthesis.
Experimental Design: We compared pretransplant leukocyte CTRA gene expression between a group of 78 high versus low SES recipients of unrelated donor HCT for acute myelogenous leukemia in first remission. Post hoc exploratory analyses also evaluated whether CTRA gene expression was associated with poor clinical outcomes.
Results: Peripheral blood mononuclear cells collected pre-HCT from low SES individuals demonstrated significant CTRA upregulation compared with matched HCT recipients of high SES. Promoter-based bioinformatics implicated distinct patterns of transcription factor activity, including increased CREB signaling and decreased IRF and GR signaling. High expression of the CTRA gene profile was also associated with increased relapse risk and decreased leukemia-free survival.
Conclusions: Low SES is associated with increased expression of the CTRA gene profile, and CTRA gene expression is associated with adverse HCT clinical outcomes. These findings provide a biologic framework within which to understand how social environmental conditions may influence immune function and clinical outcomes in allogeneic HCT. Clin Cancer Res; 22(1); 69–78. ©2015 AACR.
See related commentary by Turcotte and Verneris, p. 6
Abstract AS20: DNA-PKcs is amplified in high grade serous ovarian cancer (HGSC), correlates with poor outcome and drives resistance to platinum therapy via the AKT signaling pathway
Authors: Curry E , Cheraghchi-Bashi-Astaneh A , Chen M , Cunnea P , De Sousa C , Maginn E , Dai Y , Liu E , Wasan H , Mills G , Bowtell D , Gabra H , Stronach EA 
Published: August 2015

Abstract
High grade serous ovarian cancer is typified by p53 mutation, high degrees of genomic instability and the development of chemo-resistance. Genomic translocations result from incorrectly repaired DNA double strand breaks (DSBs). DNA-PKcs is a central catalytic component of the error prone non-homologous end joining (NHEJ) DSB repair mechanism. We report here that DNA-PKcs is frequently amplified in copy number in HGSC and that amplification correlates with higher DNA-PKcs gene expression and poorer patient outcome (PFS/OS) using both in-house and publicly available datasets (TCGA). Targeting DNA-PKcs, pharmacologically or by RNAi, enhances apoptosis in response to platinum treatment in platinum resistant cell lines and primary models. Furthermore we report that inhibition of DNA-PK restores response to cisplatin in chemoresistant ovarian cancer cells in vivo. SKOV-3 tumor xenografts were implanted subcutaneously into Balb/c Nu/Nu mice and treated with DNA-PKcs inhibitor NU7441 for 2 weeks alone or in combination with cisplatin. DNA-PK inhibition or cisplatin treatment alone were ineffective however in combination they decreased tumor growth at 14 days by 90%, relative to platinum only treatment. On investigating the mechanism of DNA-PKcs mediated chemoresistance we revealed that, in response to DNA damage, DNA-PKcs phosphorylates AKT on serine residue 473 in the nucleus of platinum resistant ovarian tumor cells, but not sensitive cells from the same patient. Phosphorylation at AKT threonine 308 is unaffected and DNA-PK inhibition does not interfere with insulin-mediated phosphorylation of AKT S473. DNA-PK mediated AKT activation in chemoresistant cells results in inhibitory phosphorylation of the pro-apoptotic protein BAD and stabilisation of the anti-apoptotic Bcl-2 protein resulting in the observed attenuation of apoptotic response to platinum treatment. DNA-PK inhibition is an attractive therapeutic strategy for resensitising resistant tumors to platinum based therapy, directly linking the DNA damage caused by platinum to the pro-survival AKT pathway, without interfering with normal physiological roles of AKT.
Citation Format: Curry E, Cheraghchi-Bashi-Astaneh A, Chen M, Cunnea P, De Sousa C, Maginn E, Dai Y, Liu E, Wasan H, Mills G, Bowtell D, Gabra H & Stronach EA. DNA-PKcs is amplified in high grade serous ovarian cancer (HGSC), correlates with poor outcome and drives resistance to platinum therapy via the AKT signaling pathway [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr AS20.
Abstract AS23: Microenvironment mediated downregulation of miR-193b promotes ovarian cancer metastasis
Authors: Mitra AK , Chiang CY , Tiwari P , Peter ME , Lengyel E 
Published: August 2015

Abstract
The cross-talk between ovarian cancer cells with the microenvironment of the site of metastasis is an essential determinant of successful metastatic colonization. microRNAs have been well established to play critical roles in various stages of cancer progression, including metastasis. However, the role of the signals from the microenvironment in regulating key microRNAs in metastasizing cancer cells has not been studied. Using a 3D culture model mimicking the human omentum, one of the principal sites of ovarian cancer metastasis, we have identified the microenvironment-induced downregulation of a tumor suppressor microRNA miR-193b in the metastasizing ovarian cancer cells. The direct interaction of the ovarian cancer cells with the mesothelial cells covering the surface of the omentum caused DNA methyltransferase 1 (DNMT1) mediated methylation and decreased expression of miR-193b. The reduction in miR-193b enabled the metastasizing cancer cells to invade and proliferate in the omentum both in vitro and in a mouse xenograft model of ovarian cancer metastasis. The functional effects of miR-193b were mediated at least partly through the concomitant increased expression of its target urokinase-type plasminogen activator (uPA). Our findings link paracrine signals from the microenvironment with the regulation of a key microRNA in cancer cells that is essential for the initial steps of ovarian cancer metastatic colonization. Targeting miR-193b would be a promising approach to treat ovarian cancer metastasis.
Citation Format: AK Mitra, CY Chiang, P Tiwari, ME Peter, E Lengyel. Microenvironment mediated downregulation of miR-193b promotes ovarian cancer metastasis [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr AS23.