bluuebunny/crossref_metadata_2025_split huggingface dataset:
Case‐control study of cases of bovine spongiform encephalopathy born after July 31, 1996 (BARB cases) in Great Britain
Authors: Ortiz‐Pelaez A. , Stevenson M. A. , Wilesmith J. W. , Ryan J. B. M. , Cook A. J. C. 
Published: January 2012

This paper reports the results of a case‐control study of the bovine spongiform encephalopathy (BSE) cases born in Great Britain after the statutory reinforcement of the ban (BARB) on the feeding of mammalian‐derived meat and bone meal on 31 July 1996.A total of 499 suspect clinical cases of BSE, born after 31 July 1996, and reported negative by July 31, 1996 and were compared with the set of 164 confirmed Great BARB cases in Great Britain detected by both passive and active surveillance. Animal‐level risk factors (age and type of feed offered) and herd‐level risk factors (herd size and type, number of prereinforced feed ban BSE cases born on the holding, the presence of other domestic species and waste management) were obtained for the analysis.BARB cases were 2.56 times (95 per cent CI 1.29 to 5.07) more likely to be exposed to homemix or a combination of homemix and proprietary feeds were 0.59 times (95 per cent CI 0.50 to 0.69) as less likely to be exposed to the unit increases in the number of prereinforced feed ban BSE cases diagnosed on the natal holding. A supplementary spatial analysis of these cases revealed three areas of excess BARB density: Northwest and Southwest of Wales and Northeast of Scotland.
YANGIANS IN INTEGRABLE FIELD THEORIES, SPIN CHAINS AND GAUGE-STRING DUALITIES
Authors: SPILL FABIAN 
Published: January 2012

In the following paper, which is based on the author's PhD thesis submitted to Imperial College London, we explore the applicability of Yangian symmetry to various integrable models, in particular, in relation with S-matrices. One of the main themes in this work is that, after a careful study of the mathematics of the symmetry algebras one finds that in an integrable model, one can directly reconstruct S-matrices just from the algebra. It has been known for a long time that S-matrices in integrable models are fixed by symmetry. However, Lie algebra symmetry, the Yang–Baxter equation, crossing and unitarity, which constrain the S-matrix in integrable models, are often taken to be separate, independent properties of the S-matrix. Here, we construct scattering matrices purely from the Yangian, showing that the Yangian is the right algebraic object to unify all required symmetries of many integrable models. In particular, we reconstruct the S-matrix of the principal chiral field, and, up to a CDD factor, of other integrable field theories with 𝔰𝔲(n) symmetry. Furthermore, we study the AdS/CFT correspondence, which is also believed to be integrable in the planar limit. We reconstruct the S-matrices at weak and at strong coupling from the Yangian or its classical limit. We give a pedagogical introduction into the subject, presenting a unified perspective of Yangians and their applications in physics. This paper should hence be accessible to mathematicians who would like to explore the application of algebraic objects to physics as well as to physicists interested in a deeper understanding of the mathematical origin of physical quantities.
Activation of PI3K Signaling in Merkel Cell Carcinoma
Authors: Nardi Valentina , Song Youngchul , Santamaria-Barria Juan A. , Cosper Arjola K. , Lam Quynh , Faber Anthony C. , Boland Genevieve M. , Yeap Beow Y. , Bergethon Kristin , Scialabba Vanessa L. , Tsao Hensin , Settleman Jeffrey , Ryan David P. , Borger Darrell R. , Bhan Atul K. , Hoang Mai P. , Iafrate Anthony J. , Cusack James C. , Engelman Jeffrey A. , Dias-Santagata Dora 
Published: January 2012

Abstract
Purpose: Merkel cell carcinoma (MCC) is an aggressive cutaneous neuroendocrine tumor, often metastatic at presentation, for which current chemotherapeutic regimens are largely ineffective. As its pathogenesis is still unknown, we hypothesized that deregulation of signaling pathways commonly activated in cancer may contribute to MCC tumorigenesis and may provide insights into targeted therapy approaches for this malignancy.
Experimental Design: We retrospectively profiled 60 primary MCC samples using a SNaPshot-based tumor genotyping assay to screen for common mutations in 13 cancer genes.
Results: We identified mutations in 9 (15%) MCC primary tumors, including mutations in TP53 (3 of 60) and activating mutations in the PIK3CA gene (6 of 60). Sanger sequencing of the primary MCC tumors detected one additional PIK3CA mutation (R19K) that had not been previously described in cancer. Merkel cell polyoma virus (MCPyV) was detected in 38 (66%) MCC cases and patients with MCPyV-positive cancers showed a trend toward better survival. With one exception, the presence of MCPyV and activating mutations in PIK3CA appeared mutually exclusive. We observed that signaling through the PI3K/pAKT pathway was active in one MCPyV-positive and in all MCPyV-negative MCC cell lines, as evidenced by AKT phosphorylation. Importantly, the presence of a PIK3CA-activating mutation was associated with sensitivity to treatment with ZST474, a specific phosphoinositide 3-kinase (PI3K) inhibitor, and to NVP-BEZ235, a dual PI3K/mTOR inhibitor, targeted agents under active clinical development.
Conclusions: PI3K pathway activation may drive tumorigenesis in a subset of MCC and screening these tumors for PIK3CA mutations could help identify patients who may respond to treatment with PI3K pathway inhibitors. Clin Cancer Res; 18(5); 1227–36. ©2012 AACR.
Where the Mass Counts: Common Cortical Activation for Different Kinds of Nonsingularity
Authors: Domahs Frank , Nagels Arne , Domahs Ulrike , Whitney Carin , Wiese Richard , Kircher Tilo 
Published: January 2012

Abstract
Typically, plural nouns are morphosyntactically marked for the number feature, whereas mass nouns are morphosyntactically singular. However, both plural count nouns and mass nouns can be semantically interpreted as nonsingular. In this study, we investigated the hypothesis that their commonality in semantic interpretation may lead to common cortical activation for these different kinds of nonsingularity. To this end, we examined brain activation patterns related to three types of nouns while participants were listening to a narrative. Processing of plural compared with singular nouns was related to increased activation in the left angular gyrus. Processing of mass nouns compared with singular count nouns was related to increased activity bilaterally in the superior temporal cortex and also in the left angular gyrus. No significant activation was observed in the direct comparison between plural and mass nouns. We conclude that the left angular gyrus, also known to be relevant for numerical cognition, is involved in the semantic interpretation of different kinds of nonsingularity.
Sirt1 protects against thrombomodulin down-regulation and lung coagulation after particulate matter exposure
Authors: Wu Zhuang , Liu Ming-Cheh , Liang Mei , Fu Jian 
Published: January 2012

Abstract
Exposure to ambient particulate matter (PM) air pollution has been reported to trigger inflammation and thrombosis. However, molecular mechanisms underlying the modulation of coagulation pathways in PM-induced thrombosis remain largely unknown. We report here that Sirt1, a member of class III histone deacetylase, controls lung inflammation and coagulation after PM exposure. Sirt1 knock-out mice exhibited aggravated lung vascular leakage and inflammation after PM exposure, which was correlated with increased NF-κB acetylation and activation. Furthermore, Sirt1 knock-out mice were highly susceptible to PM-induced lung coagulation as demonstrated by increased fibrin formation. The increased fibrin formation was associated with reduced tissue factor pathway inhibitor (TFPI) expression and increased plasminogen activator inhibitor-1 (PAI-1) activity in the lungs, thus favoring elevated coagulation and disrupted fibrinolysis responses. Thrombomodulin (TM), a central player of the anticoagulant protein C system, is regulated by Kruppel-like factor 2 (KLF2) at the transcriptional level. Our data show that PM exposure led to decreased lung KLF2 and TM expression in wild-type mice, and lung KLF2 and TM protein levels were further decreased in Sirt1 knock-out mice. Importantly, Sirt1 gene delivery inhibited TM and KLF2 down-regulation and reduced lung coagulation after PM exposure. Collectively, our studies indicate that Sirt1 functions as a suppressor of coagulation after particulate matter exposure.
TDT-HET: A new transmission disequilibrium test that incorporates locus heterogeneity into the analysis of family-based association data
Authors: Londono Douglas , Buyske Steven , Finch Stephen J , Sharma Swarkar , Wise Carol A , Gordon Derek 
Published: January 2012

AbstractBackgroundLocus heterogeneity is one of the most documented phenomena in genetics. To date, relatively little work had been done on the development of methods to address locus heterogeneity in genetic association analysis. Motivated by Zhou and Pan's work, we present a mixture model of linked and unlinked trios and develop a statistical method to estimate the probability that a heterozygous parent transmits the disease allele at a di-allelic locus, and the probability that any trio is in the linked group. The purpose here is the development of a test that extends the classic transmission disequilibrium test (TDT) to one that accounts for locus heterogeneity.ResultsOur simulations suggest that, for sufficiently large sample size (1000 trios) our method has good power to detect association even the proportion of unlinked trios is high (75%). While the median difference (TDT-HETempirical power -TDTempirical power) is approximately 0 for all MOI, there are parameter settings for which the power difference can be substantial. Our multi-locus simulations suggest that our method has good power to detect association as long as the markers are reasonably well-correlated and the genotype relative risk are larger. Results of both single-locus and multi-locus simulations suggest our method maintains the correct type I error rate.Finally, theTDT-HETstatistic shows highly significant p-values for most of the idiopathic scoliosis candidate loci, and for some loci, the estimated proportion of unlinked trios approaches or exceeds 50%, suggesting the presence of locus heterogeneity.ConclusionsWe have developed an extension of theTDTstatistic (TDT-HET) that allows for locus heterogeneity among coded trios. Benefits of our method include: estimates of parameters in the presence of heterogeneity, and reasonable power even when the proportion of linked trios is small. Also, we have extended multi-locus methods toTDT-HETand have demonstrated that the empirical power may be high to detect linkage. Last, given that we obtain PPBs, we conjecture that theTDT-HETmay be a useful method for correctly identifying linked trios. We anticipate that researchers will find this property increasingly useful as they apply next-generation sequencing data in family based studies.
Constitutive activity of NF-kappa B in myeloid cells drives pathogenicity of monocytes and macrophages during autoimmune neuroinflammation
Authors: Ellrichmann Gisa , Thöne Jan , Lee De-Hyung , Rupec Rudolph A , Gold Ralf , Linker Ralf A 
Published: January 2012

AbstractThe NF-κB/REL-family of transcription factors plays a central role in coordinating the expression of a wide variety of genes controlling immune responses including autoimmunity of the central nervous system (CNS). The inactive form of NF-κB consists of a heterodimer which is complexed with its inhibitor, IκB. Conditional knockout-mice for IκBα in myeloid cells (lysMCreIκBαfl/fl) have been generated and are characterized by a constitutive activation of NF-κB proteins allowing the study of this transcription factor in myelin-oligodendrocyte-glycoprotein induced experimental autoimmune encephalomyelitis (MOG-EAE), a well established experimental model for autoimmune demyelination of the CNS.In comparison to controls, lysMCreIκBαfl/flmice developed a more severe clinical course of EAE. Upon histological analysis on day 15 p.i., there was an over two fold increased infiltration of T-cells and macrophages/microglia. In addition, lysMCreIκBαfl/flmice displayed an increased expression of the NF-κB dependent factor inducible nitric oxide synthase in inflamed lesions. These changes in the CNS are associated with increased numbers of CD11b positive splenocytes and a higher expression of Ly6c on monocytes in the periphery. Well in accordance with these changes in the myeloid cell compartment, there was an increased production of the monocyte cytokines interleukin(IL)-12 p70, IL-6 and IL-1beta in splenocytes. In contrast, production of the T-cell associated cytokines interferon gamma (IFN-gamma) and IL-17 was not influenced.In summary, myeloid cell derived NF-κB plays a crucial role in autoimmune inflammation of the CNS and drives a pathogenic role of monocytes and macrophages independently from T-cells.
Tight regulation of wingless-type signaling in the articular cartilage - subchondral bone biomechanical unit: transcriptomics in Frzb-knockout mice
Authors: Lodewyckx Liesbet , Cailotto Frédéric , Thysen Sarah , Luyten Frank P , Lories Rik J 
Published: January 2012

Abstract
Introduction
The aim of this research was to study molecular changes in the articular cartilage and subchondral bone of the tibial plateau from mice deficient in frizzled-related protein (Frzb) compared to wild-type mice by transcriptome analysis.

Methods
Gene-expression analysis of the articular cartilage and subchondral bone of three wild-type and three Frzb
-/-
mice was performed by microarray. Data from three wild-type and two Frzb
-/-
samples could be used for pathway analysis of differentially expressed genes and were explored with PANTHER, DAVID and GSEA bioinformatics tools. Activation of the wingless-type (WNT) pathway was analysed using Western blot. The effects of Frzb gain and loss of function on chondrogenesis and cell proliferation was examined using ATDC5 micro-masses and mouse ribcage chondrocytes.

Results
Extracellular matrix-associated integrin and cadherin pathways, as well as WNT pathway genes were up-regulated in Frzb
-/-
samples. Several WNT receptors, target genes and other antagonists were up-regulated, but no difference in active β-catenin was found. Analysis of ATDC5 cell micro-masses overexpressing FRZB indicated an up-regulation of aggrecan and Col2a1, and down-regulation of molecules related to damage and repair in cartilage, Col3a1 and Col5a1. Silencing of Frzb resulted in down-regulation of aggrecan and Col2a1. Pathways associated with cell cycle were down-regulated in this transcriptome analysis. Ribcage chondrocytes derived from Frzb
-/-
mice showed decreased proliferation compared to wild-type cells.

Conclusions
Our analysis provides evidence for tight regulation of WNT signalling, shifts in extracellular matrix components and effects on cell proliferation and differentiation in the articular cartilage - subchondral bone unit in Frzb
-/-
mice. These data further support an important role for FRZB in joint homeostasis and highlight the complex biology of WNT signaling in the joint.
Study of Nano-Mechanics of Collagen I Triple-helices by Computerized Processing of AFM Images
Authors: Bitler Arkady , Perugia Emanuel , Cohen Sidney R. 
Published: January 2012

ABSTRACTWe used atomic force microscope (AFM) to acquire high-resolution images of collagen type I triple-helices under ambient conditions in tapping mode. Angles between consecutive fixed-length segments were measured and analyzed to yield persistence length and elastic constant. Changing the segment length allowed exploring the mechanics at various scales. Understanding the mechanical properties of collagen molecules could serve to elucidate mechanisms of complex mechanical properties of interest in nanomedicine and nanotechnology.
Isomorphism relations on computable structures
Authors: Fokina Ekaterina B. , Friedman Sy-David , Harizanov Valentina , Knight Julia F. , Mccoy Charles , Montalbán Antonio 
Published: January 2012

AbstractWe study the complexity of the isomorphism relation on classes of computable structures. We use the notion of FF-reducibility introduced in [9] to show completeness of the isomorphism relation on many familiar classes in the context of all equivalence relations on hyperarithmetical subsets of ω.
Finding generically stable measures
Authors: Simon Pierre 
Published: January 2012

AbstractThis work builds on previous papers by Hrushovski, Pillay and the author where Keisler measures over NIP theories are studied. We discuss two constructions for obtaining generically stable measures in this context. First, we show how to symmetrize an arbitrary invariant measure to obtain a generically stable one from it. Next, we show that suitable sigma-additive probability measures give rise to generically stable Keisler measures. Also included is a proof that generically stable measures over o-minimal theories and the p-adics are smooth.
Some Examples of Stationary Planetary Flow Patterns in Bounded Basins
Authors: Stommel Henry , Arons A. B. , Faller A. J. 
Published: January 2012

A simple regime of fluid flow is defined. This regime can occur in a homogeneous layer of fluid (i) of uniform depth on a rotating sphere and bounded by meridional barriers (ii) of uniform depth on a betaplane and bounded by barriers running north-south (iii) of radially non-uniform depth on a rotating plane and bounded by radial barriers. The essential elements defining the regime are: (a) the flow in the whole layer is steady and geostrophic except and only (b) at the western boundary where a narrow, intense western boundary current is permitted to depart markedly from geostrophy, and (c) the system, which would otherwise be at rest, is driven by a distribution of sources and sinks of fluid (this includes driving agents such as the wind, which can be expressed in terms of source and sink distributions).
Predictions concerning patterns of flow have been deduced from the defined regime and verified experimentally on a rotating model of type (iii). Certain results obtained were by no means intuitively obvious from a priori considerations.
On the Influence of Cosmic Radiation on the Isotopic Composition of the Elements
Authors: Johansson Sven A. E. 
Published: January 2012

When cosmic radiation interacts with the atomic nuclei of the atmosphere, it produces a great number of stable as well as radioactive isotopes. The radioactive isotopes are fairly easy to detect but the production of stable isotopes can only be detected by the changes in isotopic composition of the elements that might be caused by this effect. The amounts of Li6, Ne21, and A36 that are produced in this way have been calculated. If the mean intensity of cosmic radiation in the past has been the same as at present it turns out that the production of these isotopes causes a change in isotopic composition which is barely detectable.
A study of this effect gives a possibility of obtaining information about the cosmic-ray intensity in the past. If no cosmic-ray effect is found, it shows that the mean cosmic-ray intensity in the past could not have been considerably higher than at present. If the cosmic-ray intensity during the earlier stages in the earth's evolution were higher than at present, one could expect easily detectable changes in the isotopic composition of some elements.
Fission Product Radioactivity in the Air along the 80th Meridian — January–June 1957
Authors: Lockhart, Jr. L. B. , Baus R. A. , Blifford, Jr. I. H. 
Published: January 2012

Measurements of gross fission product radioactivity in the air at a number of sites along the 80th meridian (west) are reported for the period January–June 1957.
The concentration of long-lived radioactive products (primarly fission products) in the air continues to remain considerably higher in the Northern than in the Southern Hemisphere. Among the more interesting developments, there has been obtained a definite inverse relation between the air concentration of radioactivity and rainfall during the dry and rainy seasons at Panama.
The use of “radioactivity profiles” (plots of latitude vs fission product concentration) to represent a cross section of the average air concentrations of fission products along the 80th meridian for any given period offers a ready means to obtain the total burden of such activity in the atmosphere for such a period and to follow its increase or decrease with time.
Uninodal Seiches in the Oscillation System Baltic proper—Gulf of Finland
Authors: Lisitzin Eugenie 
Published: January 2012

Seventeen cases of regular sea level oscillations with at least four distinctly developed periods recorded at Hamina (Fredrikshamn) in the east part of the Gulf of Finland during the years 1952–1954 were selected and the period corresponding to the maximum amplitude computed numerically. The results show that this period is fairly constant with an average of 26.2 (± 0.2) hours. Sea level records at Władysławowo on the Polish coast confirm this period as a uninodal seiche in the oscillation system Baltic proper—Gulf of Finland.
In the paper is also discussed the possible occurrence of transversal oscillations in the Gulf of Finland and the probability of the participation of the Bay of Kiel at the named seiches in the Baltic.
Solar Disturbances and the Cosmic Ray Equator
Authors: Pomerantz M. A. , Sandström A. E. , Potnis V. R. , Rose D. C. 
Published: January 2012

The location of the cosmic ray equator off the west coast of Africa has been established from measurements obtained with a shipboard neutron monitor which made ten crossings between November, 1956, and October, 1958. From the individual determinations of the point of minimum cosmic ray intensity, the mean geographical position was 6.7 ± 0.8° N at 14° W. Direct measurements of zero magnetic inclination were made at the same time in the immediate vicinity of this point.
Although solar and geophysical activity varied considerably during this period, the location of the cosmic ray equator appears to have remained fixed within approximately 1°. However, the possibility of a small progressive change of about the magnitude of the uncertainty cannot be precluded.
Comparison of the results with plots of measurements of the magnetic elements along the ship’s route reveals a significant difference between the location of the points of maximum horizontal intensity and minimum cosmic ray intensity.
Meteorological Fractionation of Nuclear Bomb Debris
Authors: Storebö Per B. 
Published: January 2012

Radioactive particles are produced by nuclear bomb explosions which are widely different in size and nature. Systematic differences in properties are expected for particles formed under different conditions. Differences in particle properties may cause sorting during deposition because of systematic differences in weather trends at different geographical locations and thus bring to light information about the particles.
Deposits at a mountain station in Norway appear to have contained more short-lived fission products than those at lowland stations, especially during periods when considerable fresh fission products have been present in the atmosphere. This could be due to a substantial chemical fractionation on particle sizes taking place during formation, or to the general formation of particles somewhat larger than 0.5 micron diameter during high-yield explosions.