bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lake sediments as natural seismographs: A compiled record of Late Quaternary earthquakes in Central Switzerland and its implication for Alpine deformation
Authors: Strasser Michael , Monecke Katrin , Schnellmann Michael , Anselmetti Flavio S. 
Published: October 2012

AbstractCentral Switzerland lies tectonically in an intraplate area and recurrence rates of strong earthquakes exceed the time span covered by historic chronicles. However, many lakes are present in the area that act as natural seismographs: their continuous, datable and high‐resolution sediment succession allows extension of the earthquake catalogue to pre‐historic times. This study reviews and compiles available data sets and results from more than 10 years of lacustrine palaeoseismological research in lakes of northern and Central Switzerland. The concept of using lacustrine mass‐movement event stratigraphy to identify palaeo‐earthquakes is showcased by presenting new data and results from Lake Zurich. The Late Glacial to Holocene mass‐movement units in this lake document a complex history of varying tectonic and environmental impacts. Results include sedimentary evidence of three major and three minor, simultaneously triggered basin‐wide lateral slope failure events interpreted as the fingerprints of palaeoseismic activity. A refined earthquake catalogue, which includes results from previous lake studies, reveals a non‐uniform temporal distribution of earthquakes in northern and Central Switzerland. A higher frequency of earthquakes in the Late Glacial and Late Holocene period documents two different phases of neotectonic activity; they are interpreted to be related to isostatic post‐glacial rebound and relatively recent (re‐)activation of seismogenic zones, respectively. Magnitudes and epicentre reconstructions for the largest identified earthquakes provide evidence for two possible earthquake sources: (i) a source area in the region of the Alpine or Sub‐Alpine Front due to release of accumulated north‐west/south‐east compressional stress related to an active basal thrust beneath the Aar massif; and (ii) a source area beneath the Alpine foreland due to reactivation of deep‐seated strike‐slip faults. Such activity has been repeatedly observed instrumentally, for example, during the most recent magnitude 4·2 and 3·5 earthquakes of February 2012, near Zug. The combined lacustrine record from northern and Central Switzerland indicates that at least one of these potential sources has been capable of producing magnitude 6·2 to 6·7 events in the past.
Simultaneous cutaneous infection due to Paecilomyces lilacinus and Alternaria in a heart transplant patient
Authors: Lavergne R.A. , Cassaing S. , Nocera T. , Pauwels C. , Cointault O. , Basse G. , Lavayssière L. , Berry A. , Kamar N. , Lamant L. , Iriart X. , Linas M.D. , Valentin A. , Fillaux J. , Paul C. , Magnaval J.F. 
Published: October 2012

AbstractPaecilomyces lilacinus is an emerging pathogen in immunocompromised patients. We report here a case of cutaneous hyphomycosis in a 63‐year‐old heart transplant recipient caused by the simultaneous presence of 2 molds: Paecilomyces lilacinus and Alternaria alternata. The infection was successfully treated with local voriconazole followed by oral terbinafine.
A pencil beam algorithm for helium ion beam therapy
Authors: Fuchs Hermann , Ströbele Julia , Schreiner Thomas , Hirtl Albert , Georg Dietmar 
Published: October 2012

Purpose:To develop a flexible pencil beam algorithm for helium ion beam therapy. Dose distributions were calculated using the newly developed pencil beam algorithm and validated using Monte Carlo (MC) methods.Methods:The algorithm was based on the established theory of fluence weighted elemental pencil beam (PB) kernels. Using a new real‐time splitting approach, a minimization routine selects the optimal shape for each sub‐beam. Dose depositions along the beam path were determined using a look‐up table (LUT). Data for LUT generation were derived from MC simulations in water using GATE 6.1. For materials other than water, dose depositions were calculated by the algorithm using water‐equivalent depth scaling. Lateral beam spreading caused by multiple scattering has been accounted for by implementing a non‐local scattering formula developed by Gottschalk. A new nuclear correction was modelled using a Voigt function and implemented by a LUT approach. Validation simulations have been performed using a phantom filled with homogeneous materials or heterogeneous slabs of up to 3 cm. The beams were incident perpendicular to the phantoms surface with initial particle energies ranging from 50 to 250 MeV/A with a total number of 107 ions per beam. For comparison a special evaluation software was developed calculating the gamma indices for dose distributions.Results:In homogeneous phantoms, maximum range deviations between PB and MC of less than 1.1% and differences in the width of the distal energy falloff of the Bragg‐Peak from 80% to 20% of less than 0.1 mm were found. Heterogeneous phantoms using layered slabs satisfied a γ‐index criterion of 2%/2mm of the local value except for some single voxels. For more complex phantoms using laterally arranged bone‐air slabs, the γ‐index criterion was exceeded in some areas giving a maximum γ‐index of 1.75 and 4.9% of the voxels showed γ‐index values larger than one. The calculation precision of the presented algorithm was considered to be sufficient for clinical practice. Although only data for helium beams was presented, the performance of the pencil beam algorithm for proton beams was comparable.Conclusions:The pencil beam algorithm developed for helium ions presents a suitable tool for dose calculations. Its calculation speed was evaluated to be similar to other published pencil beam algorithms. The flexible design allows easy customization of measured depth‐dose distributions and use of varying beam profiles, thus making it a promising candidate for integration into future treatment planning systems. Current work in progress deals with RBE effects of helium ions to complete the model.
A real‐time in vivo dosimetric verification method for high‐dose rate intracavitary brachytherapy of nasopharyngeal carcinoma
Authors: Qi Zhen‐Yu , Deng Xiao‐Wu , Cao Xin‐ping , Huang Shao‐Min , Lerch Michael , Rosenfeld Anatoly 
Published: October 2012

Purpose:A real‐timein vivo dosimetric verification method using metal‐oxide‐semiconductor field effect transistor (MOSFET) dosimeters has been developed for patient dosimetry in high‐dose rate (HDR) intracavitary brachytherapy of nasopharyngeal carcinoma (NPC).Methods:The necessary calibration and correction factors for MOSFET measurements in192Iridium source were determined in a water phantom. With the detector placed inside a custom‐made nasopharyngeal applicator, the actual dose delivered to the tumor was measured in vivo and compared to the calculated values using a commercial brachytherapy planning system.Results:Five MOSFETs were independently calibrated with the HDR source, yielding calibration factors of 0.48 ± 0.007 cGy/mV. The maximum sensitivity variation was no more than 7% in the clinically relevant distance range of 1–5 cm from the source. A total of 70in vivo measurements in 11 NPC patients demonstrated good agreement with the treatment planning. The mean differences between the planned and the actually delivered dose within a single treatment fraction were −0.1% ± 3.8% and −0.1% ± 3.7%, respectively, for right and left side assessments. The maximum dose deviation was less than 8.5%.Conclusions:In vivo measurement using the real‐time MOSFET dosimetry system is possible to evaluate the actual dose to the tumor received by the patient during a treatment fraction and thus can offer another line of security to detect and prevent large errors.
In VivoEfficacy of a Chimeric Peptide Derived from the Conserved Region of the M Protein against Group C and G Streptococci
Authors: Nordström Therese , Malcolm Jessica , Magor Graham , Good Michael F. , Batzloff Michael R. 
Published: October 2012

ABSTRACTThe J8 peptide from the conserved region of the M protein protects against group A streptococcus infections. In this study, we demonstrate that vaccination with a J8-containing formulation induces IgG that recognizes and binds group C and G streptococci. Moreover, this formulation has the potential to provide protection against infections caused by these organisms.
False Daptomycin-Nonsusceptible MIC Results by Microscan Panel PC 29 Relative to Etest Results for Staphylococcus aureus and Enterococci
Authors: Palavecino Elizabeth L. , Burnell Jacqueline M. 
Published: October 2012

ABSTRACT

This study correlated the daptomycin MIC results obtained by Microscan and by Etest in
Staphylococcus aureus
and enterococci and found that the Microscan panel GP 29 had a high rate of false nonsusceptible results. Of the isolates interpreted as nonsusceptible by Microscan, 87% of
Staphylococcus aureus
, 90% of
Enterococcus faecalis
, and 88% of
Enterococcus faecium
isolates were interpreted as susceptible by Etest. In turn, Etest also has false nonsusceptible results compared to reference methods.
Comparison of Ahlstrom Grade 226, Munktell TFN, and Whatman 903 Filter Papers for Dried Blood Spot Specimen Collection and Subsequent HIV-1 Load and Drug Resistance Genotyping Analysis
Authors: Rottinghaus Erin , Bile Ebi , Modukanele Mosetsanagape , Maruping Maruping , Mine Madisa , Nkengasong John , Yang Chunfu 
Published: October 2012

ABSTRACTDried blood spots (DBS) collected onto filter paper have eased the difficulty of blood collection in resource-limited settings. Currently, Whatman 903 (W-903) filter paper is the only filter paper that has been used for HIV load and HIV drug resistance (HIVDR) testing. We therefore evaluated two additional commercially available filter papers, Ahlstrom grade 226 (A-226) and Munktell TFN (M-TFN), for viral load (VL) testing and HIVDR genotyping using W-903 filter paper as a comparison group. DBS specimens were generated from 344 adult patients on antiretroviral therapy (ART) in Botswana. The VL was measured with NucliSENS EasyQ HIV-1 v2.0, and genotyping was performed for those specimens with a detectable VL (≥2.90 log10copies/ml) using an in-house method. Bland-Altman analysis revealed a strong concordance in quantitative VL analysis between W-903 and A-226 (bias = −0.034 ± 0.246 log10copies/ml [mean difference ± standard deviation]) and W-903 and M-TFN (bias = −0.028 ± 0.186 log10copies/ml) filter papers, while qualitative VL analysis for virological failure determination, defined as a VL of ≥3.00 log10copies/ml, showed low sensitivities for A-266 (71.54%) and M-TFN (65.71%) filter papers compared to W-903 filter paper. DBS collected on M-TFN filter paper had the highest genotyping efficiency (100%) compared to W-903 and A-226 filter papers (91.7%) and appeared more sensitive in detecting major HIVDR mutations. DBS collected on A-226 and M-TFN filter papers performed similarly to DBS collected on W-903 filter paper for quantitative VL analysis and HIVDR detection. Together, the encouraging genotyping results and the variability observed in determining virological failure from this small pilot study warrant further investigation of A-226 and M-TFN filter papers as specimen collection devices for HIVDR monitoring surveys.
Neutralizing DNA Aptamers against Swine Influenza H3N2 Viruses
Authors: Wongphatcharachai Manoosak , Wang Ping , Enomoto Shinichiro , Webby Richard J. , Gramer Marie R. , Amonsin Alongkorn , Sreevatsan Srinand 
Published: October 2012

ABSTRACT

Triple reassortant influenza A viruses (IAVs) of swine, particularly the North American H3N2 subtype, circulate in swine herds and may reassort and result in the emergence of novel zoonotic strains. Current diagnostic tools rely on isolation of the viruses, followed by serotyping by hemagglutination or genome sequencing, both of which can be expensive and time-consuming. Thus, novel subtype-specific ligands and methods are needed for rapid testing and subtyping of IAVs in the field. To address this need, we selected DNA aptamers against the recombinant HA protein from swine IAV H3 cluster IV using systematic evolution of ligands by exponential enrichment (SELEX). Four candidate aptamers (HA68, HA7, HA2a, and HA2b) were identified and characterized. The dissociation constants (
K

d

) of aptamers HA68, HA7, HA2a, and HA2b against recombinant H3 protein were 7.1, 22.3, 16.0, and 3.7 nM, respectively. The binding site of HA68 to H3 was identified to be between nucleotide residues 8 and 40. All aptamers inhibited H3 hemagglutination. HA68 was highly specific to all four lineages within the North American H3N2 subtype. Further, the other three aptamers specifically identified live viruses belonging to the phylogenetic clusters I, II/III, and IV especially the virus that closely related to the recent H3N2 variant (H3N2v). Aptamer HA68 was also able to bind and detect H3N2v isolated from recent human cases. In conclusion, we provide subtype-specific aptamers against H3N2 IAVs of swine that can now be used in rapid detection and typing protocols for field applications.
Rapid Detection and Statistical Differentiation of KPC Gene Variants in Gram-Negative Pathogens by Use of High-Resolution Melting and ScreenClust Analyses
Authors: Roth Amanda L. , Hanson Nancy D. 
Published: October 2012

ABSTRACT

In the United States, the production of the
Klebsiella pneumoniae
carbapenemase (KPC) is an important mechanism of carbapenem resistance in Gram-negative pathogens. Infections with KPC-producing organisms are associated with increased morbidity and mortality; therefore, the rapid detection of KPC-producing pathogens is critical in patient care and infection control. We developed a real-time PCR assay complemented with traditional high-resolution melting (HRM) analysis, as well as statistically based genotyping, using the Rotor-Gene ScreenClust HRM software to both detect the presence of
bla
KPC
and differentiate between KPC-2-like and KPC-3-like alleles. A total of 166 clinical isolates of
Enterobacteriaceae
,
Pseudomonas aeruginosa
, and
Acinetobacter baumannii
with various β-lactamase susceptibility patterns were tested in the validation of this assay; 66 of these organisms were known to produce the KPC β-lactamase. The real-time PCR assay was able to detect the presence of
bla
KPC
in all 66 of these clinical isolates (100% sensitivity and specificity). HRM analysis demonstrated that 26 had KPC-2-like melting peak temperatures, while 40 had KPC-3-like melting peak temperatures. Sequencing of 21 amplified products confirmed the melting peak results, with 9 isolates carrying
bla
KPC-2
and 12 isolates carrying
bla
KPC-3
. This PCR/HRM assay can identify KPC-producing Gram-negative pathogens in as little as 3 h after isolation of pure colonies and does not require post-PCR sample manipulation for HRM analysis, and ScreenClust analysis easily distinguishes
bla
KPC-2-like
and
bla
KPC-3-like
alleles. Therefore, this assay is a rapid method to identify the presence of
bla
KPC
enzymes in Gram-negative pathogens that can be easily integrated into busy clinical microbiology laboratories.
Interplay between Polyadenylate-Binding Protein 1 and Kaposi's Sarcoma-Associated Herpesvirus ORF57 in Accumulation of Polyadenylated Nuclear RNA, a Viral Long Noncoding RNA
Authors: Massimelli Maria J. , Majerciak Vladimir , Kruhlak Michael , Zheng Zhi-Ming 
Published: October 2012

ABSTRACT

Polyadenylate-binding protein cytoplasmic 1 (PABPC1) is a cytoplasmic-nuclear shuttling protein important for protein translation initiation and both RNA processing and stability. We report that PABPC1 forms a complex with the Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 protein, which allows ORF57 to interact with a 9-nucleotide (nt) core element of KSHV
p
oly
a
denylated
n
uclear (PAN) RNA, a viral long noncoding RNA (lncRNA), and increase PAN stability. The N-terminal RNA recognition motifs (RRMs) of PABPC1 are necessary for the direct interaction with ORF57. During KSHV lytic infection, the expression of viral ORF57 leads to a substantial decrease in overall PABPC1 expression, along with a shift in the cellular distribution of the remaining PABPC1 to the nucleus. Interestingly, PABPC1 and ORF57 have opposing functions in modulating PAN steady-state accumulation. The suppressive effect of PABPC1 specific to PAN expression is alleviated by small interfering RNA knockdown of PABPC1 or by overexpression of ORF57. Conversely, ectopic PABPC1 reduces ORF57 steady-state protein levels and induces aberrant polyadenylation of PAN and thereby indirectly inhibits ORF57-mediated PAN accumulation. However, E1B-AP5 (heterogeneous nuclear ribonucleoprotein U-like 1), which interacts with a region outside the 9-nt core to stimulate PAN expression, does not interact or even colocalize with ORF57. Unlike PABPC1, the nuclear distribution of E1B-AP5 remains unchanged by viral lytic infection or overexpression of ORF57. Together, these data indicate that PABPC1 is an important cellular target of viral ORF57 to directly upregulate PAN accumulation during viral lytic infection, and the ability of host PABPC1 to disrupt ORF57 expression is a strategic host counterbalancing mechanism.
TRIM Protein-Mediated Regulation of Inflammatory and Innate Immune Signaling and Its Association with Antiretroviral Activity
Authors: Uchil Pradeep D. , Hinz Angelika , Siegel Steven , Coenen-Stass Anna , Pertel Thomas , Luban Jeremy , Mothes Walther 
Published: October 2012

ABSTRACT

Members of the
tri
partite interaction
m
otif (TRIM) family of E3 ligases are emerging as critical regulators of innate immunity. To identify new regulators, we carried out a screen of 43 human TRIM proteins for the ability to activate NF-κB, AP-1, and interferon, hallmarks of many innate immune signaling pathways. We identified 16 TRIM proteins that induced NF-κB and/or AP-1. We found that one of these, TRIM62, functions in the TRIF branch of the TLR4 signaling pathway. Knockdown of TRIM62 in primary macrophages led to a defect in TRIF-mediated late NF-κB, AP-1, and interferon production after lipopolysaccharide challenge. We also discovered a role for TRIM15 in the RIG-I-mediated interferon pathway upstream of MAVS. Knockdown of TRIM15 limited virus/RIG-I ligand-induced interferon production and enhanced vesicular stomatitis virus replication. In addition, most TRIM proteins previously identified to inhibit murine leukemia virus (MLV) demonstrated an ability to induce NF-κB/AP-1. Interfering with the NF-κB and AP-1 signaling induced by the antiretroviral TRIM1 and TRIM62 proteins rescued MLV release. In contrast, human immunodeficiency virus type 1 (HIV-1) gene expression was increased by TRIM proteins that induce NF-κB. HIV-1 resistance to inflammatory TRIM proteins mapped to the NF-κB sites in the HIV-1 long terminal repeat (LTR) U3 and could be transferred to MLV. Thus, our work identifies new TRIM proteins involved in innate immune signaling and reinforces the striking ability of HIV-1 to exploit innate immune signaling for the purpose of viral replication.
Dissection of Functional Sites in Herpesvirus Saimiri Complement Control Protein Homolog
Authors: Reza Malik Johid , Kamble Ashish , Ahmad Muzammil , Krishnasastry Musti V. , Sahu Arvind 
Published: October 2012

ABSTRACTHerpesvirus saimiri is known to encode a homolog of human complement regulators named complement control protein homolog (CCPH). We have previously reported that this virally encoded inhibitor effectively inactivates complement by supporting factor I-mediated inactivation of complement proteins C3b and C4b (termed cofactor activity), as well as by accelerating the irreversible decay of the classical/lectin and alternative pathway C3 convertases (termed decay-accelerating activity). To fine map its functional sites, in the present study, we have generated a homology model of CCPH and performed substitution mutagenesis of its conserved residues. Functional analyses of 24 substitution mutants of CCPH indicated that (i) amino acids R118 and F144 play a critical role in imparting C3b and C4b cofactor activities, (ii) amino acids R35, K142, and K191 are required for efficient decay of the C3 convertases, (iii) positively charged amino acids of the linker regions, which are dubbed to be critical for functioning in other complement regulators, are not crucial for its function, and (iv) S100K and G110D mutations substantially enhance its decay-accelerating activities without affecting the cofactor activities. Overall, our data point out that ionic interactions form a major component of the binding interface between CCPH and its interacting partners.
The Compensatory G88R Change Is Essential in Restoring the Normal Functions of Influenza A/WSN/33 Virus Matrix Protein 1 with a Disrupted Nuclear Localization Signal
Authors: Xie Hang , Lin Zhengshi , Mosier Philip D. , Desai Umesh R. , Gao Yamei 
Published: October 2012

ABSTRACT

G88R emerged as a compensatory mutation in matrix protein 1 (M1) of influenza virus A/WSN/33 when its nuclear localization signal (NLS) was disrupted by R101S and R105S substitutions. The resultant M1 triple mutant M(NLS-88R) regained replication efficiency
in vitro
while remaining attenuated
in vivo
with the potential of being a live vaccine candidate. To understand why G88R was favored by the virus as a compensatory change for the NLS loss and resultant replication deficiency, three more M1 triple mutants with an alternative G88K, G88V, or G88E change in addition to R101S and R105S substitutions in the NLS were generated. Unlike the other M1 triple mutants, M(NLS-88R) replicated more efficiently
in vitro
and
in vivo
. The G88R compensatory mutation not only restored normal functions of M1 in the presence of a disrupted NLS but also resulted in a strong association of M1 with viral ribonucleoprotein. Under a transmission electron microscope, only the M1 layer of the M(NLS-88R) virion exhibited discontinuous fingerprint-like patterns with average thicknesses close to that of wild-type A/WSN/33. Computational modeling suggested that the compensatory G88R change could reestablish the integrity of the M1 layer through new salt bridges between adjacent M1 subunits when the original interactions were interrupted by simultaneous R101S and R105S replacements in the NLS. Our results suggested that restoring the normal functions of M1 was crucial for efficient virus replication.