bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the size distortion of tests after an overidentifying restrictions pretest
Authors: Guggenberger Patrik , Kumar Gitanjali 
Published: June 2011

SUMMARYIn the linear instrumental variables model, we provide theoretical and Monte Carlo evidence for the size distortion of a two‐stage hypothesis test that uses a test of overidentifying restrictions (OR) in the first stage. We derive a lower bound for the asymptotic size of the two‐stage test. The lower bound is given by the asymptotic size of a test that rejects the null hypothesis when two conditions are met: the test of OR used in the first stage does not reject and the test in the second stage rejects. This lower bound can be as large as 1 − εP, where εP is the pretest nominal size, for a parameter space that allows for local non‐exogeneity of the instruments but rules out weak instruments. Copyright © 2011 John Wiley & Sons, Ltd.
An essential role for the association of CD47 to SHPS-1 in skeletal remodeling
Authors: Maile Laura A , DeMambro Victoria E , Wai Christine , Aday Ariel W , Capps Byron E , Beamer Wesley G , Rosen Clifford J , Clemmons David R 
Published: June 2011

Abstract
Integrin-associated protein (IAP/CD47) has been implicated in macrophage-macrophage fusion. To understand the actions of CD47 on skeletal remodeling, we compared Cd47−/− mice with Cd47+/+ controls. Cd47−/− mice weighed less and had decreased areal bone mineral density compared with controls. Cd47−/− femurs were shorter in length with thinner cortices and exhibited lower trabecular bone volume owing to decreased trabecular number and thickness. Histomorphometry revealed reduced bone-formation and mineral apposition rates, accompanied by decreased osteoblast numbers. No differences in osteoclast number were observed despite a nonsignificant but 40% decrease in eroded surface/bone surface in Cd47−/− mice. In vitro, the number of functional osteoclasts formed by differentiating Cd47−/− bone marrow cells was significantly decreased compared with wild-type cultures and was associated with a decrease in bone-resorption capacity. Furthermore, by disrupting the CD47–SHPS-1 association, we found that osteoclastogenesis was markedly impaired. Assays for markers of osteoclast maturation suggested that the defect was at the point of fusion and not differentiation and was associated with a lack of SHPS-1 phosphorylation, SHP-1 phosphatase recruitment, and subsequent dephosphorylation of non–muscle cell myosin IIA. We also demonstrated a significant decrease in osteoblastogenesis in bone marrow stromal cells derived from Cd47−/− mice. Our finding of cell-autonomous defects in Cd47−/− osteoblast and osteoclast differentiation coupled with the pronounced skeletal phenotype of Cd47−/− mice support the conclusion that CD47 plays an important role in regulating skeletal acquisition and maintenance through its actions on both bone formation and bone resorption. © 2011 American Society for Bone and Mineral Research
Construct drift in the MMPI‐2 restructured clinical scales: further evidence and a possible historic example
Authors: Kevin Bolinskey P. , Nichols David S. 
Published: June 2011

AbstractConstruct drift (Nichols, 2006) describes the possibility that the MMPI‐2 Reconstructed Clinical (RC) scales are less accurate measures of the primary traits than the original Clinical scales. The authors review the development of RC scales RC4, RC7, and RC9 and provide further evidence that these scales measure traits and behaviors that are not necessarily equivalent to those assessed by the original scales. Further, the development of the original Clinical Scale 7 is reviewed and evidence is provided that suggests that construct drift is not a new phenomenon, but may have been present in the development of the original scales. Suggestions for future research as well as cautions with regard to the clinical interpretation of the RC scales are provided. © 2011 Wiley Periodicals, Inc. J Clin Psychol 67:1–11, 2011.
CID of singly charged antioxidants applied in lubricants by means of a 3D ion trap and a linear ion trap–Orbitrap mass spectrometer
Authors: Kassler Alexander , Pittenauer Ernst , Doerr Nicole , Allmaier Guenter 
Published: June 2011

AbstractThe aim of this study was to investigate the fragmentation behavior induced by low‐energy collision‐induced dissociation (LE‐CID) of four selected antioxidants applied in lubricants, by two different types of ion trap mass spectrometers: a three‐dimensional ion trap (3D‐IT) and a linear IT (LIT) Orbitrap MS. Two sterically hindered phenols and two aromatic amines were selected as model compounds representing different antioxidant classes and were characterized by positive‐ion electrospray ionization (ESI) and LE‐CID. Various types of molecular ions (e.g. [M]+•, [M + H]+, [M + NH4]+ or [M + Na]+) were used as precursor ions generating a significant number of structurally relevant product ions. Furthermore, the phenolic compounds were analyzed by negative‐ion ESI. For both IT types applied for fragmentation, the antioxidants exhibited the same unusual LE‐CID behavior: (1) they formed stable radical product ions and (2) CC bond cleavages of aliphatic substituents were observed and their respective cleavage sites depended on the precursor ion selected. This fragmentation provided information on the type of structural isomer usually not obtainable for branched aliphatic substituents utilizing LE‐CID. Comparing the two instruments, the main benefit of applying the LIT‐Orbitrap was direct access to elemental composition of product ions enabling unambiguous interpretation of fragmentation trees not obtainable by the 3D‐IT device (e.g. loss of isobaric neutrals). It should be emphasized that the types of product ions formed do not depend on the type of IT analyzer applied. For characterizing degradation products of antioxidants, the LIT‐Orbitrap hybrid system, allowing the determination of accurate m/z values for product ions, is the method of choice. Copyright © 2011 John Wiley & Sons, Ltd.
Proton transfer reactions for improved peptide characterisation
Authors: Rožman Marko , Schneider Andrea , Gaskell Simon J. 
Published: June 2011

AbstractThe combination of deprotonation (via ion/molecule and ion/ion reactions) and low‐energy collision‐induced dissociation (CID) has been explored for the enhanced characterisation of tryptic peptides via access to different precursor charge states. This approach allows instant access to fragmentation properties of singly and doubly protonated precursors (arising from the availability of mobile protons) in a single experiment. Considering both charge states extended our base of structurally informative data (in comparison with considering just a single charge state) due to generation of additional sequence ions and by obtaining supplementary structural information derived from selective cleavages. Roughly 37% of combined data sets (CID spectra of doubly and singly charged precursor) showed a greater database identification confidence than each set alone. Moreover, comparison between a number of sequence ions of the singly charged precursor and the doubly charged precursor provided a mean of distinguishing the two classes of tryptic peptides (arginine or lysine containing). Copyright © 2011 John Wiley & Sons, Ltd.
It is time for a paradigm shift in drug discovery bioanalysis: from SRM to HRMS
Authors: Ramanathan Ragu , Jemal Mohammed , Ramagiri Suma , Xia Yuan‐Qing , Humpreys W. Griffith , Olah Timothy , Korfmacher Walter A. 
Published: June 2011

AbstractIt can be argued that the last true paradigm shift in the bioanalytical (BA) arena was the shift from high‐performance liquid chromatography (HPLC) with ultraviolet (UV) detection to HPLC with tandem mass spectrometry (MS/MS) detection after the commercialization of the triple quadrupole mass spectrometer in the 1990s. HPLC‐MS/MS analysis based on selected reaction monitoring (SRM) has become the gold standard for BA assays and is used by all the major pharmaceutical companies for the quantitative analysis of new drug entities (NCEs) as part of the new drug discovery and development process. While LC‐MS/MS continues to be the best tool for drug discovery bioanalysis, a new paradigm involving high‐resolution mass spectrometry (HRMS) and ultrahigh‐pressure liquid chromatography (uHPLC) is starting to make inroads into the pharmaceutical industry. The ability to collect full scan spectra, with excellent mass accuracy, mass resolution, 10–250 ms scan speeds and no NCE‐related MS parameter optimization, makes the uHPLC‐HRMS techniques suitable for quantitative analysis of NCEs while preserving maximum qualitative information about other drug‐related and endogenous components such as metabolites, degradants, biomarkers and formulation materials. In this perspective article, we provide some insight into the evolution of the hybrid quadrupole‐time‐of‐flight (Qq‐TOF) mass spectrometer and propose some of the desirable specifications that such HRMS systems should have to be integrated into the drug discovery bioanalytical workflow for performing integrated qualitative and quantitative bioanalysis of drugs and related components. Copyright © 2011 John Wiley & Sons, Ltd.
A neutralization–reionization and reactivity mass spectrometry study of the generation of neutral hydroxymethylene
Authors: Lin Yawei , Crestoni Maria Elisa , Fornarini Simonetta , Mayer Paul M. 
Published: June 2011

AbstractNeutral hydroxymethylene HCOH is an important intermediate in several chemical reactions; however, it is difficult to observe due to its high reactivity. In this work, neutral hydroxymethylene and formaldehyde were generated by charge exchange neutralization of their respective ionic counterparts and then were reionized and detected as positive‐ion recovery signals in neutralization–reionization mass spectrometry in a magnetic sector instrument of BEE geometry. The reionized species were characterized by their subsequent collision‐induced dissociation mass spectra. The transient hydroxymethylene neutral was observed to isomerize to formaldehyde with an experimental time span exceeding 13.9 µs. The vertical neutralization energy of the HCOH+• ion has also been assayed using charge transfer reactions between the fast ions and stationary target gases of differing ionization energy. The measured values match the result of ab initio calculations at the QCISD/6‐311 + G(d,p) and CCSD(T)/6‐311 + + G(3df,2p) levels of theory. Neutral hydroxymethylene was also produced by proton transfer from CH2OH+ to a strong base such as pyridine, confirmed by appropriate isotopic labeling. There is a kinetic isotope effect (KIE) for H+ versus D+ transfer from the C atom of the hydroxymethyl cation of ∼3, consistent with a primary KIE of a nearly thermoneutral reaction. Copyright © 2011 John Wiley & Sons, Ltd.
Gaseous cation chemistry and chain‐length effects in electron ionization and collision‐induced dissociation mass spectraof symmetric 1,n‐bis(9‐anthracenyl)alkanes
Authors: Schildcrout Steven M. , Masnovi John 
Published: June 2011

AbstractThe behavior of the gaseous cations resulting from EI (30 and 70 eV) of the bichromophoric title compounds 1–5 (for n = 1–5, respectively) is examined by ion‐trap mass spectrometry, including collision‐induced dissociation (CID) with variation in collision energy. These results are compared with those from anthracene and 9‐methylanthracene and with previously reported mass spectrometric results for 3 and dicarbazolylalkanes. Rather than using the kinetic method to obtain ion energetics where the fragmentation mechanism is clear, as commonly done, the method is used here with relative complementary‐ion abundances from CID to test the proposed fragmentation mechanisms using B3LYP calculations of relative ionization energies and optimized geometries of ionic and neutral fragments. Hydrogen migrations are common, and skeletal rearrangements including formation of expanded, fused and spiro rings are proposed in several cases. Of the chain cleavages, α‐homolysis giving C15H11+, likely as dibenzotropylium, is most important for each of 1–5 except 3, where β‐cleavage to C16H13+ dominates with a proposed methyldibenzotropylium structure. α‐Cleavage was important also in the dicarbazolylalkanes. A previous inference of a McLafferty rearrangement to explain C15H12+• from 3 is not supported by the present results. The fragmentation behavior of 1–5 depends strongly on n and implies significant interchromophoric interaction between anthracenyl groups. Copyright © 2011 John Wiley & Sons, Ltd.
Characterization of the human serum depletome by label‐free shotgun proteomics
Authors: Koutroukides Theodoros A. , Guest Paul C. , Leweke F. Markus , Bailey David M. D. , Rahmoune Hassan , Bahn Sabine , Martins‐de‐Souza Daniel 
Published: June 2011

AbstractWhile it is known that immunoaffinity depletion of abundant proteins in serum removes additional proteins beyond those targeted, there has been little characterization of the co‐depleted proteins in the high abundant fraction, which we refer to here as the “depletome”. We present evidence of co‐depletion of non‐targeted proteins in human serum using a top‐20 immunodepletion column, as shown by label‐free liquid chromatography mass spectrometry (LC‐MSE) profiling. This led to identification of 147 proteins which were specific for this fraction and comprised proteins with functions predominantly in binding and transport of nucleotides, metal ions, carbohydrates and lipids. These results suggest that further studies on this commonly ignored serum fraction may provide new insights into clinical proteomics.
Predicting spatial distribution of human–black bear interactions in urban areas
Authors: Merkle Jerod A. , Krausman Paul R. , Decesare Nicholas J. , Jonkel James J. 
Published: June 2011

AbstractHuman–wildlife interactions are often associated with a myriad of stakeholder groups, intense political scrutiny, and limited biological data, creating complex decision‐making situations for wildlife management agencies. Limited research exists on the development and testing of tools (e.g., models to predict the spatial distribution of interactions) to reduce human–black bear (Ursus americanus) interactions (HBI). Available models predicting spatial distribution of HBI are usually developed at scales too large to predict across urban areas, are rarely tested against independent data sets, and usually do not incorporate both landscape and anthropogenic variables. Our objective was to develop a predictive modeling tool that could identify areas of high conflict potential across urban landscapes. We compared locations of HBI in Missoula, MT, recorded by Montana Fish, Wildlife & Parks from 2003 to 2008, to random locations using logistic regression. The final model discriminated the relative spatial probability of HBI within Missoula well, and a second study area moderately. The probability of HBI in Missoula increased when residents lived close to forested patches and major rivers and streams and in intermediate housing densities (approx. 6.59 houses/ha). Our results provide a wildlife management tool and a repeatable statistical framework that predicts spatial distribution of HBI using only a small set of variables. © 2011 The Wildlife Society.
ASSESSING LANDSLIDE SUSCEPTIBILITY BY INCORPORATING THE SURFACE COVER INDEX AS A MEASUREMENT OF VEGETATIVE COVER
Authors: Miller A. J. 
Published: June 2011

ABSTRACTLocal environmental conditions are known to be the most influential in landslide dynamics. Some variables, such as slope, elevation, lithology, vegetative cover, and soil type, are more common and influential than others. Every variable, except for vegetative cover, has been incorporated into many different statistical models as a continuous variable showing nuances and differentiation among the data. In regions where vegetative cover is the single most important variable in determining slope stability, a land cover classification cannot provide the level of information required for efficient modeling of landslide events. It is hoped that the surface cover index (SCI) can be used to numerically assess vegetative cover by using Landsat imagery and sub‐pixel analysis. Two models utilizing simple raster calculations involving slope and the SCI were created. Each model was then assessed and validated for accuracy by using a user‐created multi‐temporal landslide inventory of the Dominical, Costa Rica area. Results determined that normalized inputs of slope and SCI can produce an algorithm with a high degree of accuracy and proved that the SCI can be used in assessing landslide hazard in a tropical forest environment. Copyright © 2011 John Wiley & Sons, Ltd.
Odor identification deficits identify Parkinson's disease patients with poor cognitive performance
Authors: Damholdt Malene Flensborg , Borghammer Per , Larsen Lars , Østergaard Karen 
Published: June 2011

AbstractOlfactory dysfunction is a prodromal and prevalent nonmotor symptom of Parkinson's disease. Unlike olfactory dysfunction in Alzheimer's disease, it is believed to be unrelated to cognitive impairment. However, recent research has implicated cholinergic denervation in Parkinson's disease hyposmia and linked it to verbal memory. This research hypothesized that severe odor identification deficits may identify patients with Parkinson's disease at risk for cognitive impairment. The current study tested this hypothesis by comparing 24 functionally anosmic, nondemented patients with Parkinson's disease and 39 nonanosmic, nondemented patients with Parkinson's disease with 29 healthy control participants on composite scores of memory, processing speed, executive function, and language. The functionally anosmic group had significantly poorer visual and verbal memory than the nonanosmic group, which was indistinguishable from the control group. Furthermore, the functionally anosmic group had reduced processing speed compared with the nonanosmic patients with Parkinson's disease, who, in turn, were outperformed by the control group. On the composite language score, the score of the functionally anosmic group was significantly reduced compared with that of the control group, whereas the nonanosmic group scored in the medium range. The 2 patient groups did not differ on executive functioning. These findings demonstrate co‐occurrence between reduced cognitive function and olfactory deficits in functionally anosmic patients with Parkinson's disease and support the notion of more severe cognitive deficits in this group. © 2011 Movement Disorder Society
Dietary‐resistant starch improves maternal glycemic control in Goto–Kakizaki rat
Authors: Shen Li , Keenan Michael J. , Raggio Anne , Williams Cathy , Martin Roy J. 
Published: June 2011

AbstractScope: Dietary prebiotics show potential in anti‐diabetes. Dietary resistant starch (RS) has a favorable impact on gut hormone profiles, including glucagon‐like peptide‐1 (GLP‐1) consistently released, a potent anti‐diabetic incretin. Also RS reduced body fat and improved glucose tolerance in rats and mice. In the current project, we hypothesize that dietary‐resistant starch can improve insulin sensitivity and pancreatic β cell mass in a type 2 diabetic rat model. Altered gut fermentation and microbiota are the initial mechanisms, and enhancement in serum GLP‐1 is the secondary mechanism.Methods and results: In this study, GK rats were fed an RS diet with 30% RS and an energy control diet. After 10 wk, these rats were mated and went through pregnancy and lactation. At the end of the study, pancreatic β cell mass, insulin sensitivity, pancreatic insulin content, total GLP‐1 levels, cecal short‐chain fatty acid concentrations and butyrate producing bacteria in cecal contents were greatly improved by RS feeding. The offspring of RS‐fed dams showed improved fasting glucose levels and normal growth curves.Conclusion: Dietary RS is potentially of great therapeutic importance in the treatment of diabetes and improvement in outcomes of pregnancy complicated by diabetes.
Response of a Lactobacillus plantarum human isolate to tannic acid challenge assessed by proteomic analyses
Authors: Curiel José Antonio , Rodríguez Héctor , de las Rivas Blanca , Anglade Patricia , Baraige Fabienne , Zagorec Monique , Champomier‐Vergès Marie , Muñoz Rosario , de Felipe Félix López 
Published: June 2011

AbstractScope: To gain insight on the mechanisms used by intestinal bacteria to adapt and resist the antimicrobial action of dietary tannins and identify targets for tannic acid in Lactobacillus plantarum. Methods and results: A proteomic analysis of an L. plantarum human isolate exposed to the tannic acid challenge was undertaken. Tannic acid targeted proteins involved in outstanding processes for bacterial stress resistance including cyclopropanation of membrane lipids, stress response at population scale and maintenance of cell shape. To respond to this aggression, tannic acid‐misfit cells of L. plantarum challenged with tannic acid reorganized their metabolic capacity to economize energy and express proteins involved in oxidative stress defense and cell wall biogenesis, indicating that the injury incurred by tannic acid was based on oxidative damage and disruption of the cell envelope. The induction of 3‐octaprenyl‐4‐hydroxybenzoate carboxy‐lyase, which is sensitive to changes in redox conditions and involved in ubiquinone biosynthesis in other bacteria, suggests for a tannic acid‐induced redox imbalance. Conclusion: The results reveal the adaptation of a gastrointestinal isolate of L. plantarum to tannic acid and identify antibacterial targets for this dietary compound. This provides the basis for the selection of tannin‐resistant microorganisms and their use to obtain health benefits from tannin‐containing diets.
Eomesodermin, HAND1, and CSH1 proteins are induced by cellular stress in a stress‐activated protein kinase‐dependent manner
Authors: Awonuga A.O. , Zhong W. , Abdallah M.E. , Slater J.A. , Zhou S.C. , Xie Y.F. , Puscheck E.E. , Rappolee D.A. 
Published: June 2011

AbstractEomesodermin (Eomes) is a transcription factor essential for trophoblast development. Stress stimuli activate stress‐activated protein kinase (MAPK8/9) and modulate transcription factors in trophoblast stem cells (TSC). In this study, we test the hypothesis that stress‐induced Eomes upregulation and downstream trophoblast development are MAPK8/9‐dependent. Immunocytochemical and immunoblot assays suggest that Eomes is induced by hyperosmolar stress in a dose‐ and time‐dependent manner. Two MAPK8/9 inhibitors that work by different mechanisms, LJNKl1 and SP600125, block induction of Eomes protein by stress. During normal TSC differentiation, the transcription factor heart and neural crest derivatives expressed 1 (HAND1) is dependent on Eomes, and chorionic somatomammotropin hormone 1 (CSH1) expression is dependent on HAND1. Similar to Eomes, HAND1 and CSH1 induction by stress are MAPK8/9‐dependent, and CSH1 is induced in nearly all stressed TSC. CSH1 induction normally requires downregulation of the transcription factor inhibitor of differentiation 2 (ID2) as well as HAND1 upregulation. It was shown previously that hyperosmolar stress induces AMP‐activated protein kinase (PRKAA1/2)‐dependent ID2 loss in a MAPK8/9‐independent manner. Inhibition of PRKAA1/2 with compound C and LJNKl1, more than MAPK8/9 inhibitors alone, inhibits the induction of CSH1 by stress. Taken together these data suggest that stress‐induced MAPK8/9 and PRKAA1/2 regulate transcription factors Eomes/HAND1 and ID2, respectively. Together this network mediates induction of CSH1 by stress. Therefore, stress triggers a proportional increase in a normal early TSC differentiation event that could be adaptive in inducing CSH1. But the flexibility of TSC to undergo stress‐induced differentiation could lead to pathophysiological consequences if stress endured and TSC differentiation became unbalanced. Mol. Reprod. Dev. 78:519–528, 2011. © 2011 Wiley‐Liss, Inc.