bluuebunny/crossref_metadata_2025_split huggingface dataset:
A versatile protein microarray platform enabling antibody profiling against denatured proteins
Authors: Wang Jie , Barker Kristi , Steel Jason , Park Jin , Saul Justin , Festa Fernanda , Wallstrom Garrick , Yu Xiaobo , Bian Xiaofang , Anderson Karen S. , Figueroa Jonine D. , LaBaer Joshua , Qiu Ji 
Published: October 2012

PurposeWe aim to develop a protein microarray platform capable of presenting both natural and denatured forms of proteins for antibody biomarker discovery. We will further optimize plasma screening protocols to improve detection.Experimental designWe developed a new covalent capture protein microarray chemistry using HaloTag fusion proteins and ligand. To enhance protein yield, we used HeLa cell lysate as an in vitro transcription translation (IVTT) system. Escherichia coli lysates were added to the plasma blocking buffer to reduce nonspecific background. These protein microarrays were probed with plasma samples and autoantibody responses were quantified and compared with or without denaturing buffer treatment.ResultsWe demonstrated that protein microarrays using the covalent attachment chemistry endured denaturing conditions. Blocking with E. coli lysates greatly reduced the background signals and expression with IVTT based on HeLa cell lysates significantly improved the antibody signals on protein microarrays probed with plasma samples. Plasma samples probed on denatured protein arrays produced autoantibody profiles distinct from those probed on natively displayed proteins.Conclusions and clinical relevanceThis versatile protein microarray platform allows the display of both natural and denatured proteins, offers a new dimension to search for disease‐specific antibodies, broadens the repertoire of potential biomarkers, and will potentially yield clinical diagnostics with greater performance.
Measurement Invariance of the Perceived Stress Scale and Latent Mean Differences across Gender and Time
Authors: Barbosa‐Leiker Celestina , Kostick Marylynne , Lei Ming , McPherson Sterling , Roper Virginia , Hoekstra Trynke , Wright Bruce 
Published: October 2012

AbstractMeasurement invariance of the 2‐factor model of the Perceived Stress Scale—10‐item version (Cohen & Williamson, 1988) was tested across men and women at two time points and in the combined total sample over a 2‐year time frame (n = 871). Measurement invariance results indicated that the scale measured the latent factors, stress and counter‐stress, equivalently in men and women and over time. With measurement invariance demonstrated, differences in latent means were tested. Results indicated that men had lower levels of frequencies of stressors, and at one time point, higher levels of counter‐stress, when compared with women. When examining change in frequencies of stressors and counter‐stress over 2 years with the combined male and female sample, stressors remained stable, yet counter‐stress increased over time. These findings may aid in the interpretation of results when examining stressors and counter‐stress in clinical samples where one would expect stress to increase, whereas positive psychological states decrease. Copyright © 2012 John Wiley & Sons, Ltd.
Functional characterization of novel genotypes and cellular oxidative stress studies in propionic acidemia
Authors: Gallego‐Villar Lorena , Pérez‐Cerdá Celia , Pérez Belén , Abia David , Ugarte Magdalena , Richard Eva , Desviat Lourdes R. 
Published: October 2012

AbstractPropionic acidemia (PA), caused by a deficiency of the mitochondrial biotin dependent enzyme propionyl‐CoA carboxylase (PCC) is one of the most frequent organic acidurias in humans. PA is caused by mutations in either the PCCA or PCCB genes encoding the α‐ and β‐subunits of the PCC enzyme which are assembled as an α6β6 dodecamer. In this study we have investigated the molecular basis of the defect in ten fibroblast samples from PA patients. Using homology modeling with the recently solved crystal structure of the PCC holoenzyme and a eukaryotic expression system we have analyzed the structural and functional effect of novel point mutations, also revealing a novel splice defect by minigene analysis. In addition, we have investigated the contribution of oxidative stress to cellular damage measuring reactive oxygen species (ROS) levels and apoptosis parameters in patient fibroblasts, as recent studies point to a secondary mitochondrial dysfunction as pathophysiological mechanism in this disorder. The results show an increase in intracellular ROS content compared to controls, correlating with the activation of the JNK and p38 signaling pathways. Highest ROS levels were present in cells harboring functionally null mutations, including one severe missense mutation. This work provides molecular insight into the pathogenicity of PA variants and indicates that oxidative stress may be a major contributing factor to the cellular damage, supporting the proposal of antioxidant strategies as novel supplementary therapy in this rare disease.
Maternal morbidity in early pregnancy in rural northern Bangladesh
Authors: Kim Julia M. , Labrique Alain , West Keith P. , Rashid Mahbubur , Shamim Abu A. , Ali Hasmot , Ullah Barkat , Wu Lee , Massie Allan , Mehra Sucheta , Klemm Rolf , Christian Parul 
Published: October 2012

AbstractObjectiveTo determine the burden of maternal morbidity in early pregnancy in rural northern Bangladesh.MethodsA cross‐sectional analysis was performed on baseline morbidity data from 42 896 pregnant women enrolled in a vitamin A supplementation trial. One‐week histories for 31 defined symptoms were collected at 5–12 weeks of gestation. Ten illnesses were defined, compatible with ICD‐10 diagnoses and WHO definitions. Prevalence, duration, and treatment‐seeking behaviors were determined for each symptom and illness. Risk of wasting malnutrition was compared between symptomatic and asymptomatic women.ResultsIn total, 93.1% of women reported at least 1 symptom. The most frequent symptoms were poor appetite (53.3%), vaginal discharge (48.7%), and nausea (48.1%), each of which lasted 22–27 days. The most prevalent illnesses were anemia (36.4%), morning sickness (17.2%), excessive vomiting (7.0%), and reproductive tract infections (6.7%). Symptoms that prompted treatment seeking included jaundice, high‐grade fever, and swelling of hands and face. Odds ratios for malnutrition were higher among women with symptoms of anemia (1.30; 95% confidence interval [CI], 1.24–1.36), vaginal discharge (1.37; 95% CI, 1.31–1.43), and high‐grade fever (1.23; 95% CI, 1.10–1.37) than among those without symptoms.ConclusionWomen in rural Bangladesh report substantial morbidity in the first trimester.
Three-Dimensional Synchrotron Virtual Paleohistology: A New Insight into the World of Fossil Bone Microstructures
Authors: Sanchez Sophie , Ahlberg Per E. , Trinajstic Katherine M. , Mirone Alessandro , Tafforeau Paul 
Published: October 2012

AbstractThe recent developments of phase-contrast synchrotron imaging techniques have been of great interest for paleontologists, providing three-dimensional (3D) tomographic images of anatomical structures, thereby leading to new paleobiological insights and the discovery of new species. However, until now, it has not been used on features smaller than 5–7 μm voxel size in fossil bones. Because much information is contained within the 3D histological architecture of bone, including an ontogenetic record, crucial for understanding the paleobiology of fossil species, the application of phase-contrast synchrotron tomography to bone at higher resolutions is potentially of great interest. Here we use this technique to provide new 3D insights into the submicron-scale histology of fossil and recent bones, based on the development of new pink-beam configurations, data acquisition strategies, and improved processing tools. Not only do the scans reveal by nondestructive means all of the major features of the histology at a resolution comparable to that of optical microscopy, they provide 3D information that cannot be obtained by any other method.
Strain Measurement in Semiconductor Heterostructures by Scanning Transmission Electron Microscopy
Authors: Müller Knut , Rosenauer Andreas , Schowalter Marco , Zweck Josef , Fritz Rafael , Volz Kerstin 
Published: October 2012

AbstractThis article deals with the measurement of strain in semiconductor heterostructures from convergent beam electron diffraction patterns. In particular, three different algorithms in the field of (circular) pattern recognition are presented that are able to detect diffracted disc positions accurately, from which the strain in growth direction is calculated. Although the three approaches are very different as one is based on edge detection, one on rotational averages, and one on cross correlation with masks, it is found that identical strain profiles result for an InxGa1−xNyAs1−y/GaAs heterostructure consisting of five compressively and tensile strained layers. We achieve a precision of strain measurements of 7–9·10−4 and a spatial resolution of 0.5–0.7 nm over the whole width of the layer stack which was 350 nm. Being already very applicable to strain measurements in contemporary nanostructures, we additionally suggest future hardware and software designs optimized for fast and direct acquisition of strain distributions, motivated by the present studies.
Copper‐nickel‐rich, amalgamated ferromanganese crust‐nodule deposits from Shatsky Rise, NW Pacific
Authors: Hein J. R. , Conrad T. A. , Frank M. , Christl M. , Sager W. W. 
Published: October 2012

A unique set of ferromanganese crusts and nodules collected from Shatsky Rise (SR), NW Pacific, were analyzed for mineralogical and chemical compositions, and dated using Be isotopes and cobalt chronometry. The composition of these midlatitude, deep‐water deposits is markedly different from northwest‐equatorial Pacific (PCZ) crusts, where most studies have been conducted. Crusts and nodules on SR formed in close proximity and some nodule deposits were cemented and overgrown by crusts, forming amalgamated deposits. The deep‐water SR crusts are high in Cu, Li, and Th and low in Co, Te, and Tl concentrations compared to PCZ crusts. Thorium concentrations (ppm) are especially striking with a high of 152 (mean 56), compared to PCZ crusts (mean 11). The deep‐water SR crusts show a diagenetic chemical signal, but not a diagenetic mineralogy, which together constrain the redox conditions to early oxic diagenesis. Diagenetic input to crusts is rare, but unequivocal in these deep‐water crusts. Copper, Ni, and Li are strongly enriched in SR deep‐water deposits, but only in layers older than about 3.4 Ma. Diagenetic reactions in the sediment and dissolution of biogenic calcite in the water column are the likely sources of these metals. The highest concentrations of Li are in crust layers that formed near the calcite compensation depth. The onset of Ni, Cu, and Li enrichment in the middle Miocene and cessation at about 3.4 Ma were accompanied by changes in the deep‐water environment, especially composition and flow rates of water masses, and location of the carbonate compensation depth.
Genetic analysis of Atlantic salmon captured in a netting station reveals multiple escapement events from commercial fish farms
Authors: Zhang Z. , Glover K. A. , Wennevik V. , Svåsand T. , Sørvik A. G. E. , Fiske P. , Karlsson S. , Skaala Ø. 
Published: October 2012

AbstractMicrosatellite DNA analysis and statistical assignment methods were implemented to identify the origin of 190 farmed escaped Atlantic salmon recaptured over a period of 2 months at a netting station located in Trondheim fjord, Norway. Samples were also collected from farms within the region. The escapees originated from a minimum of two sources, separated in time of capture at the netting station. The majority of the escapees captured in the early period probably originated from a single farm within the region, while escapees captured in later period probably originated from multiple farms, including from outside of the region. Biological data from the escapees supported these conclusions. This study serves to exemplify the use of genetic methods to assist fisheries management.
Effect of activated human polymorphonuclear leucocytes on T lymphocyte proliferation and viability
Authors: Hock Barry D. , Taylor Karen G. , Cross Nicholas B. , Kettle Anthony J. , Hampton Mark B. , McKenzie Judith L. 
Published: October 2012

SummaryHuman polymorphonuclear leucocytes (PMN) are thought to be immunosuppressive. The suppressive mechanism(s) used by PMN are, however, not well defined and in this study they were analysed using T‐cell responses to CD3+ CD28 monoclonal antibodies (mAb) as a readout. We demonstrate that in vitro activated PMN (PMNact) can, without any T‐cell interaction, induce apparent T‐cell suppression by inhibiting the stimulatory capacity of the CD3 mAb. However, a cell‐directed suppression of T‐cell proliferation was observed when PMNact were added to pre‐activated T cells that are already committed to polyclonal proliferation. This suppression was partially reversed by catalase addition (P < 0·01) and largely reversed by addition of exogenous interleukin‐2 (P < 0·001) but was not significantly reduced by nitric oxide synthase inhibition, myeloperoxidase inhibition or addition of excess arginine. Following removal of PMNact, suppressed T cells could respond normally to further stimulation. In addition to suppressing proliferation, co‐culture with PMNact also induced a significant decrease in T‐cell viability that was reversed by catalase addition (P < 0·05). The addition of the arginase inhibitor N‐hydroxy‐nor‐l‐arginine induced both a further significant, catalase‐sensitive, loss in T‐cell viability and increased nitrite release (P < 0·001). These data demonstrate that PMN, when activated, can both induce T‐cell death and reversibly inhibit proliferation of activated T cells. The mechanisms underlying these distinct processes and the effects of arginase inhibitors on PMN induced cytotoxicity merit further investigation.
Homunculus Warping: Conveying importance using self‐intersection‐free non‐homogeneous mesh deformation
Authors: Reinert Bernhard , Ritschel Tobias , Seidel Hans‐Peter 
Published: October 2012

AbstractSize matters. Human perception most naturally relates relative extent, area or volume to importance, nearness and weight. Reversely, conveying importance of something by depicting it at a different size is a classic artistic principle, in particular when importance varies across a domain. One striking example is the neuronal homunculus; a human figure where the size of each body part is proportional to the neural density on that part. In this work we propose an approach which changes local size of a 2D image or 3D surface and, at the same time, minimizes distortion, prevails smoothness, and, most importantly, avoids fold‐overs (collisions). We employ a parallel, two‐stage optimization process, that scales the shape non‐uniformly according to an interactively‐defined importance map and then solves for a nearby, self‐intersection‐free configuration. The results include an interactive 3D‐rendered version of the classic sensorical homunculus but also a range of images and surfaces with different importance maps.
Word fluency performance and strategies in children with cochlear implants: age‐dependent effects?
Authors: LÖFKVIST ULRIKA , ALMKVIST OVE , LYXELL BJÖRN , TALLBERG ING‐MARI 
Published: October 2012

Löfkvist, U., Almkvist, O., Lyxell, B. & Tallberg, I.‐M. (2012). Word fluency performance and strategies in children with cochlear implants: age‐dependent effects? Scandinavian Journal of Psychology 53, 467–474.Word fluency was examined in 73 Swedish children aged 6–9 years divided into two age groups, 6–7 and 8–9 years; 34 deaf children with cochlear implants (CI) (15 girls/19 boys) and 39 age‐matched children with normal hearing (NH) (20 girls/19 boys). One purpose was to compare the ability to retrieve words in two different word fluency tasks; one phonemically based (FAS letter fluency) and one semantically based (animal fluency). A second purpose was to examine retrieval strategies in the two tasks by conducting an analysis of clustering and switching of word sequences. In general we found that age was an important factor for word fluency ability, in both the CI and the NH groups. It was also demonstrated that children with CI aged 8–9 years retrieved significantly fewer words and used less efficient strategies in the retrieval process, especially on the phonemically based task compared to children with NH of the same ages, whereas children 6–7 years performed similarly in both groups regarding number of retrieved words and use of strategies. The results are discussed with respect to factors such as age differences in performance for children with CI, especially for the phonemically based task.
THE MISSING NARRATIVIST TURN IN THE HISTORIOGRAPHY OF SCIENCE
Authors: KUUKKANEN JOUNI‐MATTI 
Published: October 2012

ABSTRACTThe narrativist turn of the 1970s and 1980s transformed the discussion of general history. With the rejection of Rankean historical realism, the focus shifted to the historian as a narrator and on narratives as literary products. Oddly, the historiography of science took a turn in the opposite direction at the same time. The social turn in the historiography of science emphasized studying science as a material and practical activity with traceable and documentable traits. This empirization of the field has led to an understanding that history of science could be directly describable from scientific practice alone without acknowledging the role of the historian as a constructor of narratives about these practices. Contemporary historians of science tend to be critical of science's ability to describe its object—nature, as it is—but they often are not similarly skeptical of their own abilities to describe their object: past science, as it is. I will argue that historiography of science can only gain from a belated narrativist turn.
Individual dolphins as tools for conservation
Authors: Wells R. S. 
Published: October 2012

Read the Feature Paper: The social side of human‐wildlife interaction: wildlife can learn harmful behaviours from each otherOther Commentaries on this paper: Wildlife social learning should inform sustainable tourism management; Conservation issues arising from maladaptive behaviours spreading sociallyResponse from the authors: Social learning of risky behaviour: importance for impact assessments, conservation and management of human‐wildlife interactions
Wildlife social learning should inform sustainable tourism management
Authors: Higham James E. S. 
Published: October 2012

Read the Feature Paper: The social side of human‐wildlife interaction: wildlife can learn harmful behaviours from each otherOther Commentaries on this paper: Individual dolphins as tools for conservation; Conservation issues arising from maladaptive behaviours spreading sociallyResponse from the authors: Social learning of risky behaviour: importance for impact assessments, conservation and management of human‐wildlife interactions
In vivo imaging of glia activation using 1H‐magnetic resonance spectroscopy to detect putative biomarkers of tissue epileptogenicity
Authors: Filibian Marta , Frasca Angelisa , Maggioni Daniela , Micotti Edoardo , Vezzani Annamaria , Ravizza Teresa 
Published: October 2012

SummaryPurpose:  Long‐lasting activation of glia occurs in brain during epileptogenesis, which develops after various central nervous system (CNS) injuries. Glia is the cell source of the biosynthesis and release of molecules that play a role in seizure recurrence and may contribute to epileptogenesis, thus representing a putative biomarker of epilepsy development and severity. In this study, we set up an in vivo longitudinal study using 1H‐magnetic resonance spectroscopy (MRS) to measure metabolite content in the rat hippocampus that could reflect the extent and the duration of glia activation. Our aim was to explore if glia activation during epileptogenesis, or in the chronic epileptic phase, can be used as a biomarker of tissue epileptogenicity (i.e., a measure of epilepsy severity).Methods:  1H‐MRS measurements were done in the adult rat hippocampus every 24 h for 7 days after status epilepticus (SE) and in chronic epileptic rats, using a 7 T Bruker Biospec MRI (magnetic resonance imaging)/MRS scanner. We studied changes in metabolite levels that reflect astrocytes (myo‐inositol, mIns; glutathione, GSH), microglia/macrophage activation and the associated neuronal cell injury/dysfunction (lactate, Lac; N‐acetyl‐aspartate, NAA). 1H‐MRS results were validated by post hoc immunohistochemistry using cell‐specific markers. Data analysis was done to determine whether correlations exist between the metabolite changes and spontaneous seizure frequency or the extent of neuronal cell loss.Key Findings:  The analysis of 1H‐MRS spectra showed a progressive increase in mIns and GSH levels after SE, which was maintained in epileptic rats. Lac signal transiently increased during epileptogenesis being undetectable in chronic epileptic tissue. NAA levels were chronically reduced from day 2 post‐SE. Immunohistochemistry confirmed the activation of microglia and astrocytes and the progressive neuronal cell loss. GSH levels during epileptogenesis showed a negative correlation with the frequency of spontaneous seizures, whereas S100β levels in epileptic tissue were positively correlated with this outcome measure. A negative correlation was also found between GSH or mIns levels during epileptogenesis and the extent of neurodegeneration in hippocampus of epileptic rats.Significance:  1H‐MRS is a valuable in vivo technique for determining the extent and temporal profile of glia activation after an epileptogenic injury. S100β levels measured in the epileptic tissue may represent a biomarker of seizure frequency, whereas GSH levels during epileptogenesis could serve as a predictive marker of seizure frequency. Both mIns and GSH levels measured before the onset of spontaneous seizures predict the extent of neuronal cell loss in epileptic tissue. These findings highlight the potential of serial 1H‐MRS analysis for searching epilepsy biomarkers for prognostic, diagnostic, or therapeutic purposes.