bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of the Bispectral Index by Anesthesiologists
Authors: Bottros Michael M. , Palanca Ben Julian A. , Mashour George A. , Patel Ami , Butler Catherine , Taylor Amanda , Lin Nan , Avidan Michael S. 
Published: April 2011

Background
Processed electroencephalographic indices, such as the bispectral index (BIS), are potential adjuncts for assessing anesthetic depth. While BIS® monitors might aid anesthetic management, unprocessed or nonproprietary electroencephalographic data may be a rich source of information for clinicians. We hypothesized that anesthesiologists, after training in electroencephalography interpretation, could estimate the index of a reference BIS as accurately as a second BIS® monitor (twin BIS®) (Covidien Medical, Boulder, CO) when provided with clinical and electroencephalographic data.

Methods
Two sets of electrodes connected to two separate BIS® monitors were placed on the foreheads of 10 surgical patients undergoing general anesthesia. Electroencephalographic parameters, vital signs, and end-tidal anesthetic gas concentrations were recorded at prespecified time points, and were provided to two sets of anesthesiologists. Ten anesthesiologists received brief structured training in electroencephalograph interpretation and 10 were untrained. Although electroencephalographic waveforms and open-source processed electroencephalograph metrics were provided from the reference BIS®, both groups were blinded to BIS values and were asked to estimate BIS.

Results
The trained anesthesiologists averaged as close to or closer to the reference BIS® compared with the twin BIS® monitor for 34% of their BIS estimates versus 26% for the untrained anesthesiologists. Using linear mixed effects model analysis, there was a statistically significant difference between the trained and untrained anesthesiologists (P = 0.02), but no difference between the twin BIS® monitor and trained anesthesiologists (P = 0.9).

Conclusion
With limited electroencephalography training and access to clinical data, anesthesiologists can estimate the BIS almost as well as a second BIS® monitor. These results reinforce the potential utility of training anesthesia practitioners in unprocessed electroencephalogram interpretation.
Time-Lapse Imaging of Postimplantation Mouse Embryos
Authors: Garcia Monica D. , Udan Ryan S. , Hadjantonakis Anna-Katerina , Dickinson Mary E. 
Published: April 2011

INTRODUCTIONGenetic manipulation methods allow fluorescent labeling of virtually any cell type or protein of interest in developing embryos, providing powerful insights into morphogenetic events at cellular and subcellular resolutions. The development of ex vivo embryo culture methods combined with high-resolution imaging provides a strong platform for observing morphogenetic events as they occur within the developing embryo. In this protocol, postimplantation mouse embryos are cultured directly on the microscope stage under conditions that carefully control temperature, humidity, and gas exchange. This permits time-lapse imaging of developing mouse embryos.
Megaselia abdita: Fixing and Devitellinizing Embryos: Figure 1.
Authors: Rafiqi Ab. Matteen , Lemke Steffen , Schmidt-Ott Urs 
Published: April 2011

INTRODUCTIONThis protocol describes a combined heat/formaldehyde fixation procedure, as well as a manual devitellinization procedure, for pregastrular Megaselia abdita embryos.
IgG Affinity Capture of TAP-tagged Protein Complexes from Cell Extracts: Affinity Purification Step 1
Authors: Link Andrew J. , Weaver Connie , Farley Adam 
Published: April 2011

INTRODUCTIONOne approach to identifying protein–protein interactions is the biochemical purification of a target protein from cells or tissues under nondenaturing conditions, followed by the mass spectrometric identification of the components of the purified protein complex. The combination of highly specific protein purification strategies and mass spectrometry has proven to be a very successful approach for identifying protein–protein interactions. The tandem affinity purification (TAP) affinity tag and purification method allows efficient recovery of proteins present at low cellular concentrations under native conditions. Expressing the target protein at its natural levels avoids the assembly of overexpressed proteins into nonphysiological complexes. This protocol describes the immunoglobulin G (IgG) affinity capture of TAP-tagged complexes. This procedure is followed by calmodulin affinity purification.
Affinity Capture of TAP-tagged Protein Complexes: Affinity Purification Step 2
Authors: Link Andrew J. , Weaver Connie , Farley Adam 
Published: April 2011

INTRODUCTIONOne approach to identifying protein–protein interactions is the biochemical purification of a target protein from cells or tissues under nondenaturing conditions, followed by the mass spectrometric identification of the components of the purified protein complex. The combination of highly specific protein purification strategies and mass spectrometry has proven to be a very successful approach for identifying protein–protein interactions. The tandem affinity purification (TAP) affinity tag and purification method allows efficient recovery of proteins present at low cellular concentrations under native conditions. Expressing the target protein at its natural levels avoids the assembly of overexpressed proteins into nonphysiological complexes. This protocol describes calmodulin affinity capture of the TAP-tagged complexes after immunoglobulin G (IgG) affinity purification has been performed. These complexes can then be analyzed by methods such as high-sensitivity liquid chromatography coupled with tandem mass spectrometry and/or multidimensional protein identification technology (MudPIT) analysis.
Imaging Gene Expression in Live Cells and Tissues
Authors: Hong Hao , Yang Yunan , Cai Weibo 
Published: April 2011

INTRODUCTIONMonitoring gene expression is crucial for studying the responses of gene therapy and clarifying gene function in various environments. Molecular imaging is a powerful tool for noninvasive visualization of gene expression. This article summarizes the current status of fluorescence and bioluminescence imaging (BLI) of gene expression in live cells and tissues, with the emphasis mainly on the early studies that pioneered the field. First, we describe fluorescence imaging of gene expression with a wide variety of fluorescent proteins. Next, we discuss the strategies for BLI of gene expression. Besides incorporating the reporter gene into the host DNA, mRNA-based BLI of gene expression is also briefly mentioned. Last, the construction of double- and triple-fusion reporter genes is presented. Because no single imaging modality is perfect and sufficient to obtain all of the necessary information for a given question, combinations of multiple molecular imaging modalities can offer synergistic advantages over any modality alone. Noninvasive optical imaging of gene expression has revolutionized biomedical research, and the progress made over the last decade should allow molecular imaging to play a major role in the field of gene therapy. For basic and preclinical research, optical imaging is indispensable for imaging gene expression. However, for clinical imaging of gene expression, positron emission tomography (PET) holds the greatest promise.
Live Imaging of Mouse Embryos
Authors: Garcia Monica D. , Udan Ryan S. , Hadjantonakis Anna-Katerina , Dickinson Mary E. 
Published: April 2011

INTRODUCTIONThe development of the mouse embryo is a dynamic process that requires the spatial and temporal coordination of multiple cell types as they migrate, proliferate, undergo apoptosis, and differentiate to form complex structures. However, the confined nature of embryos as they develop in utero limits our ability to observe these morphogenetic events in vivo. Previous work has used fixed samples and histological methods such as immunofluorescence or in situ hybridization to address expression or localization of a gene of interest within a developmental time line. However, such methods do not allow us to follow the complex, dynamic movements of individual cells as the embryo develops. Genetic manipulation methods now allow us to label virtually any cell type or protein of interest fluorescently, providing powerful insights into morphogenetic events at cellular and subcellular resolutions. The development of ex vivo embryo culture methods combined with high-resolution imaging now provides a strong platform for observing morphogenetic events as they occur within the developing embryo. In this article, we discuss the advantages of live embryo imaging for observing dynamic morphogenetic events in vivo.
Modernization of the small-angle neutron scattering spectrometer SANS-U by upgrade to a focusing SANS spectrometer
Authors: Iwase Hiroki , Endo Hitoshi , Katagiri Masaki , Shibayama Mitsuhiro 
Published: April 2011

The small-angle neutron scattering spectrometer SANS-U at the research reactor (JRR-3) of the Japan Atomic Energy Agency, Tokai, Japan, has been successfully upgraded. This major upgrade was undertaken in order to install a high-resolution position-sensitive detector consisting of a cross-wired position-sensitive photomultiplier tube combined with a ZnS/6LiF scintillator on the SANS-U spectrometer. Without changing the total length of the spectrometer, the aim was to extend the accessible low-Qlimit (Qis the magnitude of the scattering vector) and to shorten the measurement time by employing focusing small-angle neutron scattering (FSANS). By using both spherical MgF2biconcave lenses and the new high-resolution position-sensitive detector, the accessible low-Qlimit was extended from 2.5 × 10−3to 3.8 × 10−4 Å−1. As a result, SANS-U can continuously cover a wideQrange from 3.8 × 10−4to 0.35 Å−1with a wavelength of 7 Å. FSANS can be utilized not only to improve the accessible low-Qlimit but also to increase the intensity of incident neutrons passing through the sample in the conventionalQrange from 2.5 × 10−3to 0.35 Å−1. The use of `high-intensity' FSANS also allowed a reduction of the measuring time by approximately 1/3.16 by increasing the incident neutron intensity.
Identification of de novo mutations and rare variants in hypoplastic left heart syndrome
Authors: Iascone M , Ciccone R , Galletti L , Marchetti D , Seddio F , Lincesso AR , Pezzoli L , Vetro A , Barachetti D , Boni L , Federici D , Soto AM , Comas JV , Ferrazzi P , Zuffardi O 
Published: April 2011

Iascone M, Ciccone R, Galletti L, Marchetti D, Seddio F, Lincesso AR, Pezzoli L, Vetro A, Barachetti D, Boni L, Federici D, Soto AM, Comas JV, Ferrazzi P, Zuffardi O. Identification of de novo mutations and rare variants in hypoplastic left heart syndrome.Hypoplastic left heart syndrome (HLHS) is one of the most severe congenital heart malformations, characterized by underdevelopment of the structures in the left heart–aorta complex. The majority of cases are sporadic. Although multiple genetic loci have been tentatively implicated in HLHS, no gene or pathway seems to be specifically associated with the disease. To elucidate the genetic basis of HLHS, we analyzed 53 well‐characterized patients with isolated HLHS using an integrated genomic approach that combined DNA sequencing of five candidate genes (NKX2‐5, NOTCH1, HAND1, FOXC2 and FOXL1) and genome‐wide screening by high‐resolution array comparative genomic hybridization. In 30 patients, we identified two novel de novo mutations in NOTCH1, 23 rare patients inherited gene variants in NOTCH1, FOXC2 and FOXL1, and 33 rare patients mostly inherited copy‐number variants. Some of the identified variations coexisted in the same patient. The biological significance of such rare variations is unknown, but our findings strengthen the role of NOTCH pathway in cardiac valve development, indicating that HLHS is, at least in part, a ‘valve’ disease. This is the first report of de novo mutations associated with isolated HLHS. Moreover, the coexistence of multiple rare variants suggests in some cases a cumulative effect, as shown for other complex disease.
Urinary angiotensin‐converting enzyme 2 in patients with CKD
Authors: MIZUIRI SONOO , AOKI TOSHIYUKI , HEMMI HIROMICHI , ARITA MICHITSUNE , SAKAI KEN , AIKAWA ATSUSHI 
Published: April 2011

ABSTRACT:Aim:  Angiotensin‐converting enzyme 2 (ACE2) is a type I membrane protein that antagonizes the action of angiotensin II. Because of the need for invasive kidney biopsy, little is known about the role of renal ACE2 in human kidney diseases. The authors studied if urinary ACE2 could provide a novel clue to renal ACE2 in chronic kidney disease (CKD).Methods:  Subjects were 190 patients with CKD including 38 patients with diabetic nephropathy and 36 healthy subjects. Parameters were urinary ACE2 by enzyme‐linked immunosorbent assay, blood pressure, casual plasma glucose, proteinuria, microalbuminuria, serum creatinine and estimated glomerular filtration rate. Urine and serum samples were also subjected to western blotting of ACE2.Results:  Western blotting confirmed increased urinary ACE2 levels in patients with CKD. Urinary ACE2 was significantly higher in patients with CKD than healthy subjects (median 9.64 (interquartile range, 4.41–16.89) vs 1.50 (0.40–2.33) mg/g·creatinine, P < 0.001) and in patients with diabetic nephropathy than patients without diabetic nephropathy (median 13.16 (interquartile range 6.81–18.70) vs 8.90 (4.19–16.67) mg/g·creatinine, P < 0.05). No significant difference in urinary ACE2 was observed by the use of angiotensin‐converting enzyme inhibitor and angiotensin receptor blocker.Conclusion:  Urinary ACE2 could be used as a non‐invasive marker to understand the role of renal ACE2 in CKD.
Gene acquisition, duplication and metabolic specification: the evolution of fungal methylisocitrate lyases
Authors: Müller Sebastian , Fleck Christian B. , Wilson Duncan , Hummert Christian , Hube Bernhard , Brock Matthias 
Published: April 2011

SummaryGene duplication represents an evolutionary mechanism for expanding metabolic potential. Here we analysed the evolutionary relatedness of isocitrate and methylisocitrate lyases, which are key enzymes of the glyoxylate and methylcitrate cycle respectively. Phylogenetic analyses imply that ancient eukaryotes acquired an isocitrate lyase gene from a prokaryotic source, but it was lost in some eukaryotic lineages. However, protists, oomycetes and most fungi maintained this gene and successfully integrated the corresponding enzyme into the glyoxylate cycle. A second gene, encoding a highly related enzyme, is present in fungi, but absent from other eukaryotes. This methylisocitrate lyase is specifically involved in propionyl‐CoA degradation via the methylcitrate cycle. Although bacteria possess methylisocitrate lyases with a structural fold similar to that of isocitrate lyases, their sequence identity to fungal methylisocitrate lyases is low. Phylogenetic analyses imply that fungal methylisocitrate lyases arose from gene duplication of an ancient isocitrate lyase gene from the basidiomycete lineage. Mutagenesis of active‐site residues of a bacterial and fungal isocitrate lyase, which have been predicted to direct the substrate specificity of iso‐ and methylisocitrate lyases, experimentally confirmed the possibility of direct evolution of methylisocitrate lyases from isocitrate lyases. Thus, gene duplication has increased the metabolic capacity of fungi.
Whole‐genome expression analysis reveals a role for death‐related genes in stress acclimation of the diatom Thalassiosira pseudonana
Authors: Thamatrakoln Kimberlee , Korenovska Olga , Niheu A. Kalani , Bidle Kay D. 
Published: April 2011

SummaryLow iron (Fe) availability critically limits diatom distribution and productivity in vast regions of the modern ocean, such as open‐ocean, high nutrient low chlorophyll areas and coastal regimes characterized as Fe limitation ‘mosaics’. While unique strategies of Fe uptake and storage confer competitive advantages to pennate diatoms, the molecular determinants of low Fe acclimation are largely unknown in centric diatoms. We combined genome‐wide and targeted comparative transcriptomic analysis with diagnostic biochemistry and in vivo cell staining as a platform to identify the suite of genes involved in acclimation to Fe and associated oxidative stress in Thalassiosira pseudonana. A total of 1312 genes, nearly 12% of the total genome content, responded to Fe starvation in growing cells characterized by low photosynthetic efficiency and enhanced oxidative stress, caspase activity and metacaspase expression. While 82% of the most highly upregulated genes were also represented in EST libraries derived from diverse diatoms grown under various stress conditions (e.g. silicon, CO2 and nitrogen limitation), our analysis suggests that T. pseudonana mounts a unique molecular response to Fe starvation that includes a number of genes distinct from those of the model pennate diatom, Phaeodactylum tricornutum, which diverged ∼90 million years ago. Homologues to ∼50% of the upregulated genes were also identified in a metatranscriptome of eukaryotic phytoplankton communities from a chronically Fe‐limited region in the Northeast Pacific. Furthermore, we provide experimental evidence that a subset of putative death‐related genes participate in the cellular acclimation to low Fe and associated oxidative damage, suggesting that they co‐evolved with other metabolic pathways and play adaptive roles in the success of diatoms.
CD4+ and CD8+ T‐lymphocyte scores cannot reliably predict progression in patients with benign prostatic hyperplasia
Authors: Lamb Alastair D. , Qadan Motaz , Roberts Simon , Timlin Hannah , Vowler Sarah L. , Campbell Fiona M. , Grigor Ken , Bartlett John M. S. , McNeill S. Alan 
Published: April 2011

OBJECTIVETo determine whether the density of CD4+ and CD8+ T‐lymphocytes in a transrectal ultrasonography (TRUS) biopsy of the prostate can be used to predict the progression of lower urinary tract symptoms (LUTS) in benign prostatic hyperplasia (BPH).PATIENTS AND METHODSIn total, 100 patients were randomly selected from a pool of patients with histologically proven, benign TRUS biopsy specimens. There were seven full years of follow‐up available. Clinical data were recorded, including prostate volume, International Prostate Symptom Score (IPSS), prostate‐specific antigen, urine flow rate, postvoid residual urine volume and previous prostate surgery. Markers of disease progression included the subsequent development of acute urinary retention (AUR), ≥4 point rise in IPSS, prescription of medical therapy (α‐blocker or 5‐α‐reductase inhibitor) and bladder outlet surgery. Four patients’ specimens were unsuitable for analysis. Biopsy sections from 96 patients were immunohistochemically stained for the presence of CD4+ and CD8+ T‐lymphocytes and the density of infiltrate was assessed using random field sampling and point counting.RESULTSSome 29% of patients (28/96) did not have BPH at the time of biopsy. Of all patients, 41% (39/96) progressed, 10% of whom (4/39) did not have BPH at the time of biopsy. A further 10% (10/96) developed AUR, 7% (7/96) had a ≥4 point rise in IPSS, 33% (32/96) required medical therapy for BPH and 11% (11/96) required bladder outlet surgery. There was low correlation between CD4+ and CD8+ densities in paired sections. CD4+ and CD8+ densities did not provide any significant predictive function in the progression of BPH, nor was their any predictive association noted between CD4+ and CD8+ scores and the development of prostate cancer. Sub‐analysis did show that a threshold mean of ≥1.35 CD8+ cells per field predicted progression to AUR with a sensitivity of 60% (95% confidence interval, CI, 26.2–87.8), specificity of 73.3% (95% CI 62.6–82.2) but a positive predictive value of 20.6% (95% CI 8.0–39.7). CD4+ infiltrate density suggested a trend to general progression but without statistical significance.CONCLUSIONThe present study, despite certain trends, shows no evidence for an association between CD4+ and CD8+ T‐lymphocytes and the progression of LUTS in BPH.
Allomorphy, autonomous morphology and phonological conditioning in the history of the Daco‐Romance present and subjunctive
Authors: Maiden Martin 
Published: April 2011

AbstractDaco‐Romance dialects inherited the effects of two distinct sound changes which coincidentally gave rise to almost identical distributional patterns of alternation in the inflectional paradigm of the verb. Once the original phonological conditioning of the alternants (apparently) ceased to operate, what was left was a frequently encountered yet ‘nonsensical’ pattern of paradigmatic distribution, irreducible to any coherent common set of morphosyntactic features. It appears to have been, in the terminology of Aronoff, ‘morphomic’. Drawing on a large body of historical and comparative dialectological data, I chart the history of this apparently morphomic pattern. For much of the history of Daco‐Romance, it constitutes a kind of leitmotiv of paradigmatic organisation, practically inviolable in its distribution and providing a recurrent distributional model for novel types of alternation, unconnected with the original sound change. Yet, in relatively recent times, the distributional coherence has collapsed in apparent chaos. My analysis of these diachronic facts will suggest that there are morphological phenomena which may properly be seen as morphomic while also retaining elements of extramorphological, phonological conditioning.
Overlapping dual ERP responses to low cloze probability sentence continuations
Authors: Delong Katherine A. , Urbach Thomas P. , Groppe David M. , Kutas Marta 
Published: April 2011

AbstractIn 2005, DeLong, Urbach, and Kutas took advantage of the a/an English indefinite article phonological alternation and the sensitivities of the N400 ERP component to show that readers can neurally preactivate individual words of a sentence (including nouns and their prenominal indefinite articles) in a graded fashion with a likelihood estimated from the words' offline probabilities as sentence continuations. Here we report an additional finding from that study: a prolonged ERP frontal positivity to less probable noun continuations. We suggest that this positivity is consistent with hypotheses that additional neural processing may be invoked when highly expected continuations are not encountered in the input and speculate briefly on possible functional correlates.
Estimation of soil organic carbon stock and its spatial distribution in the Republic of Ireland
Authors: Xu X. , Liu W. , Zhang C. , Kiely G. 
Published: April 2011

AbstractData scarcity often prevents the estimate of regional (or national) scale soil organic carbon (SOC) stock and its spatial distribution. This study attempts to overcome the data limitations by combining two existing Irish soil databases [SoilC and national soil database (NSD)] at the national scale, to create an improved estimate of the national SOC stock. Representative regression models between the near‐surface SOC concentration and those of deeper depths, and between SOC concentration and bulk density (BD) were developed based on the SoilC database. These regression models were then applied to the NSD derived SOC concentration map, resulting in an improved SOC stock and spatial distribution map for the top 10 cm, 30 cm and 50 cm depths. Western Ireland, particularly coastal areas, was found to have higher SOC densities than eastern Ireland, corresponding to the spatial distribution of peatland. We estimated the national SOC stock at 383 ± 38 Tg for the near‐surface of 0–10 cm depth; 1016 ± 118 Tg for 0–30 cm depth; and 1474 ± 181 Tg for 0–50 cm depth.