bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applying additive modelling and gradient boosting to assess the effects of watershed and reach characteristics on riverine assemblages
Authors: Maloney Kelly O. , Schmid Matthias , Weller Donald E. 
Published: June 2011

Summary1. Issues with ecological data (e.g. non‐normality of errors, nonlinear relationships and autocorrelation of variables) and modelling (e.g. overfitting, variable selection and prediction) complicate regression analyses in ecology. Flexible models, such as generalized additive models (GAMs), can address data issues, and machine learning techniques (e.g. gradient boosting) can help resolve modelling issues. Gradient boosted GAMs do both. Here, we illustrate the advantages of this technique using data on benthic macroinvertebrates and fish from 1573 small streams in Maryland, USA.2. We assembled a predictor matrix of 15 watershed attributes (e.g. ecoregion and land use), 15 stream attributes (e.g. width and habitat quality) and location (latitude and longitude). We built boosted and conventionally estimated GAMs for macroinvertebrate richness and for the relative abundances of macroinvertebrates in the Orders Ephemeroptera, Plecoptera and Trichoptera (%EPT); individuals that cling to substrate (%Clingers); and individuals in the collector/gatherer functional feeding group (%Collectors). For fish, models were constructed for taxonomic richness, benthic species richness, biomass and the relative abundance of tolerant individuals (%Tolerant Fish).3. For several of the responses, boosted GAMs had lower pseudo R2s than conventional GAMs for in‐sample data but larger pseudo R2s for out‐of‐bootstrap data, suggesting boosted GAMs do not overfit the data and have higher prediction accuracy than conventional GAMs. The models explained most variation in fish richness (pseudo R2 = 0·97), least variation in %Clingers (pseudo R2 = 0·28) and intermediate amounts of variation in the other responses (pseudo R2s between 0·41 and 0·60). Many relationships of macroinvertebrate responses to anthropogenic measures and natural watershed attributes were nonlinear. Fish responses were related to system size and local habitat quality.4. For impervious surface, models predicted below model‐average macroinvertebrate richness at levels above c. 3·0%, lower %EPT above c. 1·5%, and lower %Clingers for levels above c. 2·0%. Impervious surface did not affect %Collectors or any fish response. Prediction functions for %EPT and fish richness increased linearly with log10 (watershed area), %Tolerant Fish decreased with log10 (watershed area), and benthic fish richness and biomass both increased nonlinearly with log10 (watershed area).5. Gradient boosting optimizes the predictive accuracy of GAMs while preserving the structure of conventional GAMs, so that predictor–response relationships are more interpretable than with other machine learning methods. Boosting also avoids overfitting the data (by shrinking effect estimates towards zero and by performing variable selection), thus avoiding spurious predictor effects and interpretations. Thus, in many ecological settings, it may be reasonable to use boosting instead of conventional GAMs.
HERODOTUS AND SAMOS
Authors: PELLING CHRISTOPHER 
Published: June 2011

Abstract
What role does Samos play in Herodotus' narrative? Sometimes he shows the ‘warm sympathy’ that scholars have claimed, but more often Samian dysfunctionality is in point. Often events in Samos prepare for later episodes where Greek states offer more spirited, committed, or organised opposition to external threats; but the threat that they too might collapse into the Samian pattern is never far away. There are ways too in which Samos points forward to events beyond the end of Herodotus' text, especially the Samian defection from Athens in 440–39. It is difficult, though, to extract a single or simple moral from the Samian past for Herodotus' present; a series of conversations are reconstructed where very different conclusions could be drawn for events in the mid-430s and late-410s.
Clinical Significance of Interleukin-2/Gamma Interferon Ratios in Mycobacterium tuberculosis-Specific T-Cell Signatures
Authors: Suter-Riniker Franziska , Berger Antonia , Mayor Désirée , Bittel Pascal , Iseli Patricia , Bodmer Thomas 
Published: June 2011

ABSTRACTThe simultaneous determination of interleukin-2 (IL-2) and gamma interferon (IFN-γ) in QuantiFERON-TB test plasma supernatants permitted the detection of shifts inMycobacterium tuberculosis-specific T-cell signatures. A subset of the 84 subjects tested revealed a significantly elevated IL-2/IFN-γ ratio, which may be a marker for the successful elimination ofM. tuberculosisinfection.
Practical Approach for Reliable Detection of AmpC Beta-Lactamase-Producing Enterobacteriaceae
Authors: Polsfuss Silke , Bloemberg Guido V. , Giger Jacqueline , Meyer Vera , Böttger Erik C. , Hombach Michael 
Published: June 2011

ABSTRACTIn this prospective study allEnterobacteriaceaeisolates (n= 2,129) recovered in the clinical microbiology laboratory during October 2009 to April 2010 were analyzed for AmpC production. Clinical and Laboratory Standards Institute (CLSI) cefoxitin and cefotetan susceptibility breakpoints and CLSI critical ESBL diameters were used to screen for potential AmpC producers. In total, 305 isolates (211 potential AmpC producers and 94 AmpC screen-negative isolates as a control group) were further analyzed by multiplex PCR for the detection of plasmid-encodedampCbeta-lactamase genes and byampCpromoter sequence analysis (considered as the gold standard). Cefoxitin and cefotetan were assessed as primary screening markers. The sensitivities of cefoxitin and cefotetan for the detection of AmpC production were 97.4 and 52.6%, respectively, and the specificities were 78.7 and 99.3%, respectively. As a phenotypic confirmation test, the Etest AmpC and the cefoxitin-cloxacillin double-disk synergy method (CC-DDS) were compared. The sensitivities for the Etest AmpC and the CC-DDS method were 77.4 and 97.2%, respectively, and the specificity was 100% for both methods. The results of the Etest AmpC were inconclusive for 10 isolates. With the CC-DDS method 2 inconclusive results were observed. Based on this study, we propose a comprehensive diagnostic flow chart for the detection of AmpC production consisting of a simple phenotypic screening and a single phenotypic confirmation test with inconclusive results being resolved by molecular analysis. For the proposed flow chart using (i) cefoxitin as a screening marker for AmpC production, (ii) the CC-DDS method as phenotypic confirmation, and (iii) molecular methods in case of inconclusive results, the sensitivity and specificity for AmpC detection would have been 97.4 and 100%, respectively, with respect to the studied isolates. The phenotypic methods used in the AmpC algorithm are simple to perform and easy to implement in the diagnostic laboratory.
Evaluation of a New DNA Test for Detection of Carcinogenic Human Papillomavirus
Authors: Castle Philip E. , Gutierrez Erin C. , Leitch Sharon V. , Maus Courtney E. , McMillian Ray A. , Nussbaumer William A. , Vaughan Laurence M. , Wheeler Cosette M. , Gravitt Patti E. , Schiffman Mark 
Published: June 2011

ABSTRACT

Using archived specimens, we evaluated a new automated real-time PCR assay (BD Diagnostics) that detects all carcinogenic human papillomaviruses (HPV) and provides HPV genotyping for seven of them, including HPV16 and HPV18, the two most carcinogenic HPV genotypes. We found comparable results with Hybrid Capture 2 (HC2) for detection of carcinogenic HPV (
n
= 473) and with Linear Array and Line Blot Assay (
n
= 371) for detection of individual HPV genotypes.
Comparative Evaluation of Combined-Disk Tests Using Different Boronic Acid Compounds for Detection of Klebsiella pneumoniae Carbapenemase-Producing Enterobacteriaceae Clinical Isolates
Authors: Tsakris Athanassios , Themeli-Digalaki Katerina , Poulou Aggeliki , Vrioni Georgia , Voulgari Evangelia , Koumaki Vasiliki , Agodi Antonella , Pournaras Spyros , Sofianou Danai 
Published: June 2011

ABSTRACT

The accurate phenotypic detection of
Klebsiella pneumoniae
carbapenemase (KPC)-producing
Enterobacteriaceae
is an increasing necessity worldwide. We evaluated the performance of boronic acid combined-disk tests using as substrate imipenem or meropenem and as inhibitor of KPC production 300 μg aminophenylboronic acid (APBA), 600 μg APBA, or 400 μg phenylboronic acid (PBA). Tests were considered positive when an increase in the growth-inhibitory zone around a carbapenem disk with KPC inhibitor was 5 mm or greater of the growth-inhibitory zone diameter around the disk containing carbapenem alone. The comparison of the combined-disk tests was performed with 112 genotypically confirmed KPC-possessing
Enterobacteriaceae
isolates. To measure the specificity of the tests, 127 genotypically confirmed KPC-negative
Enterobacteriaceae
isolates that were nonsusceptible to at least one carbapenem were chosen for testing. Using disks containing imipenem without and with 300 μg APBA, 600 μg APBA, or 400 μg PBA, 72, 92, and 112 of the KPC producers, respectively, gave positive results (sensitivities, 64.3%, 82.1%, and 100%, respectively). Using disks containing meropenem without and with 300 μg APBA, 600 μg APBA, or 400 μg PBA, 87, 108, and 112 of the KPC producers, respectively, gave positive results (sensitivities, 77.7%, 96.4%, and 100%, respectively). Among KPC producers, the disk potentiation tests using meropenem and PBA demonstrated the largest differences in inhibition zones (
P
< 0.001). All combined-disk tests correctly identified 124 of the 127 non-KPC producers (specificity, 97.6%). This comparative study showed that PBA is the most effective inhibitor of KPC enzymes, and its use in combined-disk tests with meropenem may give the most easily interpreted results.
Use of Modified PCR Ribotyping for Direct Detection of Clostridium difficile Ribotypes in Stool Samples
Authors: Janežič Sandra , Štrumbelj Iztok , Rupnik Maja 
Published: June 2011

ABSTRACT

PCR ribotyping was modified to allow direct detection of
Clostridium difficile
from stool samples. Direct PCR ribotyping was possible in 86 out of 99
C. difficile
-positive stool samples, and in 84 cases (84.8%), the ribotype determined directly from the stool sample was identical to the ribotype of the strain isolated from the same stool sample.
Evaluation of Two Molecular Assays for Rapid Detection of Mycobacterium tuberculosis Resistance to Fluoroquinolones in High-Tuberculosis and -Multidrug-Resistance Settings
Authors: Kontsevaya I. , Mironova S. , Nikolayevskyy V. , Balabanova Y. , Mitchell S. , Drobniewski F. 
Published: June 2011

ABSTRACT

The Russian Federation is a high-tuberculosis (TB)-burden country with high rates of drug resistance, including multidrug and extensive drug resistance to TB (M/XDRTB). Rapid diagnosis of resistance to fluoroquinolones (FQs) using molecular assays is essential for the implementation of appropriate drug regimens and prevention of the transmission of XDR strains. A total of 51 individual MDRTB strains were tested by pyrosequencing of the quinolone resistance determining region of the
gyrA
gene and the GenoType MTBDR
sl
assay (Hain Lifescience, GmbH, Nehren, Germany), and the results were evaluated against those obtained by phenotypic drug susceptibility testing (DST). Mutations were detected in 25 (78.1%) FQ-resistant strains, with the majority of mutations (
n
= 19 [73.0%]) found in codon 94 of the
gyrA
gene; the novel mutation 1457 C→Τ was found in the
gyrB
gene. Three mixed allelic variants were detected, which is a well-known phenomenon in areas with high TB and drug-resistant TB rates. The sensitivity and specificity of pyrosequencing (86.2 and 100%, respectively) and MTBDR
sl
(86.2 and 100%, respectively) were high; however, the results for 5.9% of the analyzed strains were unreadable when MTBDR
sl
was used. The MTBDR
sl
and pyrosequencing assays offer a rapid and accurate means for diagnosing resistance to FQs in high-TB-burden areas.
Adenovirus Structural Protein IIIa Is Involved in the Serotype Specificity of Viral DNA Packaging
Authors: Ma Hsin-Chieh , Hearing Patrick 
Published: June 2011

ABSTRACT

The packaging of the adenovirus (Ad) genome into a capsid displays serotype specificity. This specificity has been attributed to viral packaging proteins, the IVa2 protein and the L1-52/55K protein. We previously found that the Ad17 L1-52/55K protein was not able to complement the growth of an Ad5 L1-52/55K mutant virus, whereas two other Ad17 packaging proteins, IVa2 and L4-22K, could complement the growth of Ad5 viruses with mutations in the respective genes. In this report, we investigated why the Ad17 L1-52/55K protein was not able to complement the Ad5 L1-52/55K mutant virus. We demonstrate that the Ad17 L1-52/55K protein binds to the Ad5 IVa2 protein
in vitro
and the Ad5 packaging domain
in vivo
, activities previously associated with packaging function. The Ad17 L1-52/55K protein also associates with empty Ad5 capsids. Interestingly, we find that the Ad17 L1-52/55K protein is able to complement the growth of an Ad5 L1-52/55K mutant virus in conjunction with the Ad17 structural protein IIIa. The same result was found with the L1-52/55K and IIIa proteins of several other Ad serotypes, including Ad3 and Ad4. The Ad17 IIIa protein associates with empty Ad5 capsids. Consistent with the complementation results, we find that the IIIa protein interacts with the L1-52/55K protein
in vitro
and associates with the viral packaging domain
in vivo
. These results underscore the complex nature of virus assembly and genome encapsidation and provide a new model for how the viral genome may tether to the empty capsid during the encapsidation process.
Differentiated Neuroblastoma Cells Provide a Highly Efficient Model for Studies of Productive Varicella-Zoster Virus Infection of Neuronal Cells
Authors: Christensen Jenna , Steain Megan , Slobedman Barry , Abendroth Allison 
Published: June 2011

ABSTRACT
Varicella-zoster virus (VZV) is a highly species-specific herpesvirus that targets sensory ganglionic neurons. This species specificity has limited the study of many aspects of VZV pathogenesis, including neuronal infection. We report development of a highly efficient neuroblastoma cell model to study productive VZV infection of neuronal cells. We show that differentiation of SH-SY5Y neuroblastoma cells yields a homogenous population of neuron-like cells that are permissive to the full VZV replicative cycle. These cells supported productive infection by both laboratory and clinical VZV isolates, including the live varicella vaccine. This model may enable rapid identification of genetic determinants facilitating VZV neurotropism.
Modulation of TRIM5α Activity in Human Cells by Alternatively Spliced TRIM5 Isoforms
Authors: Battivelli Emilie , Migraine Julie , Lecossier Denise , Matsuoka Saori , Perez-Bercoff Danielle , Saragosti Sentob , Clavel François , Hance Allan J. 
Published: June 2011

ABSTRACT

TRIM5α is a restriction factor that can block an early step in the retroviral life cycle by recognizing and causing the disassembly of incoming viral capsids, thereby preventing the completion of reverse transcription. Numerous other isoforms of human TRIM5 exist, and isoforms lacking a C-terminal SPRY domain can inhibit the activity of TRIM5α. Thus, TRIM5α activity in a given cell type could be dependent on the relative proportions of TRIM5 isoforms expressed, but little information concerning the relative expression of TRIM5 isoforms in human cells is available. In this study, we demonstrate that mRNAs coding for TRIM5α represent only 50% of total TRIM5 transcripts in human cell lines, CD4
+
T cells, and macrophages. Transcripts coding for, in order of abundance, TRIM5ι (TRIM5-iota), a previously uncharacterized isoform, TRIM5γ, TRIM5δ, and TRIM5κ are also present. Like TRIM5γ and TRIM5δ, TRIM5ι and TRIM5κ do not inhibit HIV-1 replication, but both have dominant-negative activity against TRIM5α. Specific knockdown of TRIM5ι increases TRIM5α activity in human U373-X4 cells, indicating that physiological levels of expression of truncated TRIM5 isoforms in human cells can reduce the activity of TRIM5α.
The Herpes Simplex Virus 1 UL17 Protein Is the Second Constituent of the Capsid Vertex-Specific Component Required for DNA Packaging and Retention
Authors: Toropova Katerina , Huffman Jamie B. , Homa Fred L. , Conway James F. 
Published: June 2011

ABSTRACT

The herpes simplex virus (HSV) UL17 and UL25 minor capsid proteins are essential for DNA packaging. They are thought to comprise a molecule arrayed in five copies around each of the capsid vertices. This molecule was initially termed the “C-capsid-specific component” (CCSC) (B. L. Trus et al., Mol. Cell
26:
479-489, 2007), but as we have subsequently observed this feature on reconstructions of A, B, and C capsids, we now refer to it more generally as the “capsid vertex-specific component” (CVSC) (S. K. Cockrell et al., J. Virol.
85:
4875-4887, 2011). We previously confirmed that UL25 occupies the vertex-distal region of the CVSC density by visualizing a large UL25-specific tag in reconstructions calculated from cryo-electron microscopy (cryo-EM) images. We have pursued the same strategy to determine the capsid location of the UL17 protein. Recombinant viruses were generated that contained either a small tandem affinity purification (TAP) tag or the green fluorescent protein (GFP) attached to the C terminus of UL17. Purification of the TAP-tagged UL17 or a similarly TAP-tagged UL25 protein clearly demonstrated that the two proteins interact. A cryo-EM reconstruction of capsids containing the UL17-GFP protein reveals that UL17 is the second component of the CVSC and suggests that UL17 interfaces with the other CVSC component, UL25, through its C terminus. The portion of UL17 nearest the vertex appears to be poorly constrained, which may provide flexibility in interacting with tegument proteins or the DNA-packaging machinery at the portal vertex. The exposed locations of the UL17 and UL25 proteins on the HSV-1 capsid exterior suggest that they may be attractive targets for highly specific antivirals.
Establishment of the Black-Tailed Prairie Dog (Cynomys ludovicianus) as a Novel Animal Model for Comparing Smallpox Vaccines Administered Preexposure in both High- and Low-Dose Monkeypox Virus Challenges
Authors: Keckler M. S. , Carroll D. S. , Gallardo-Romero N. F. , Lash R. R. , Salzer J. S. , Weiss S. L. , Patel N. , Clemmons C. J. , Smith S. K. , Hutson C. L. , Karem K. L. , Damon I. K. 
Published: June 2011

ABSTRACT

The 2003 monkeypox virus (MPXV) outbreak and subsequent laboratory studies demonstrated that the black-tailed prairie dog is susceptible to MPXV infection and that the ensuing rash illness is similar to human systemic orthopoxvirus (OPXV) infection, including a 7- to 9-day incubation period and, likely, in some cases a respiratory route of infection; these features distinguish this model from others. The need for safe and efficacious vaccines for OPVX in areas where it is endemic or epidemic is important to protect an increasingly OPXV-naïve population. In this study, we tested current and investigational smallpox vaccines for safety, induction of anti-OPXV antibodies, and protection against mortality and morbidity in two MPXV challenges. None of the smallpox vaccines caused illness in this model, and all vaccinated animals showed anti-OPXV antibody responses and neutralizing antibody. We tested vaccine efficacy by challenging the animals with 10
5
or 10
6
PFU Congo Basin MPXV 30 days postvaccination and evaluating morbidity and mortality. Our results demonstrated that vaccination with either Dryvax or Acambis2000 protected the animals from death with no rash illness. Vaccination with IMVAMUNE also protected the animals from death, albeit with (modified) rash illness. Based on the results of this study, we believe prairie dogs offer a novel and potentially useful small animal model for the safety and efficacy testing of smallpox vaccines in pre- and postexposure vaccine testing, which is important for public health planning.
Assessment of children's capacity to consent for research: a descriptive qualitative study of researchers' practices: Table 1
Authors: Gibson Barbara E , Stasiulis Elaine , Gutfreund Shawna , McDonald Maria , Dade Lauren 
Published: June 2011

BackgroundIn Canadian jurisdictions without specific legislation pertaining to research consent, the onus is placed on researchers to determine whether a child is capable of independently consenting to participate in a research study. Little, however, is known about how child health researchers are approaching consent and capacity assessment in practice. The aim of this study was to explore and describe researchers' current practices.MethodsThe study used a qualitative descriptive design consisting of 14 face-to-face interviews with child health researchers and research assistants in Southern Ontario. Transcribed interviews were analysed for common themes.ResultsProcedures for assessing capacity varied considerably from the use of age cutoffs to in-depth engagement with each child. Three key issues emerged from the accounts: (1) requirements that consent be provided by a single person thwarted researchers' abilities to support family decision-making; (2) little practical distinction was made between assessing if a child was capable, versus determining if study information had been adequately explained by the researcher; and (3) participants' perceived that review boards' requirements may conflict with what they considered ethical consent practices.ConclusionThe results suggest that researchers' consent and capacity knowledge and skills vary considerably. Perceived discrepancies between ethical practice and ethics boards' requirements suggest the need for dialogue, education and possibly ethics board reforms. Furthermore we propose, where appropriate, a ‘family decision-making’ model that allows parents and their children to consent together, thereby shifting the focus from separate assent and consent procedures to approaches that appropriately engage the child and family.
Effects of a music intervention on patients undergoing cerebral angiography: a pilot study
Authors: Vanderboom Teresa L , Arcari Patricia M , Duffy Mary E , Somarouthu B , Rabinov James D , Yoo Albert J , Hirsch Joshua A 
Published: June 2011

PurposeTo test the effect of a music intervention on procedural anxiety, stress response and medication requirements in participants with a cerebral aneurysm or arteriovenous malformation (AVM) undergoing cerebral angiography.Method and materialsA prospective pilot study was conducted using an experimental two group pre-test, post-test design. 48 participants were randomly assigned to a control group (standard care) or experimental group (standard care plus self-selected music via overhead stereo system). The stress response was measured by heart rate (HR) and systolic blood pressure (SBP) at baseline, and during and following the procedure. Anxiety was measured by the State Trait Anxiety Inventory for Adults (STAI) before and after the procedure, and total medications administered periprocedurally were recorded.Results24 participants in each group were enrolled. R-ANCOVA revealed non-significant findings for HR (F=1.4; p=0.27; power=0.38) and SBP (F=2.1; p=0.10; power=0.57). The ANCOVA for anxiety revealed significantly lower STAI scores in the control group (F=3.8; p=0.003) compared with the experimental group. Independent t test analysis for the total doses of fentanyl and midazolam were found to be F=0.08, p=0.78 and F=0.38, p=0.54, respectively.ConclusionA music intervention on participants with a brain aneurysm or AVM undergoing cerebral angiography did not have a statistically significant impact on reducing the stress response, anxiety or medication requirements. Interestingly, participants in the control group had significantly less anxiety after their angiogram than did participants in the experimental group. This pilot study sets the stage for future research to further examine these findings.