bluuebunny/crossref_metadata_2025_split huggingface dataset:
Involvement of the Global Regulator H-NS in the Survival of Escherichia coli in Stationary Phase
Authors: Chib Savita , Mahadevan Subramony 
Published: July 2012

ABSTRACT

Long-term batch cultures of
Escherichia coli
grown in nutrient-rich medium accumulate mutations that provide a growth advantage in the stationary phase (GASP). We have examined the survivors of prolonged stationary phase to identify loci involved in conferring a growth advantage and show that a mutation in the
hns
gene causing reduced activity of the global regulator H-NS confers a GASP phenotype under specific conditions. The
hns-66
allele bears a point mutation within the termination codon of the H-NS open reading frame, resulting in a longer protein that is partially functional. Although isolated from a long-term stationary-phase culture of the parent carrying the
rpoS819
allele that results in reduced RpoS activity, the
hns-66
survivor showed a growth disadvantage in the early stationary phase (24 to 48 h) when competed against the parent. The
hns-66
mutant is also unstable and reverts at a high frequency in the early stationary phase by accumulating second-site suppressor mutations within the
ssrA
gene involved in targeting aberrant proteins for proteolysis. The mutant was more stable and showed a moderate growth advantage in combination with the
rpoS819
allele when competed against a 21-day-old parent. These studies show that H-NS is a target for mutations conferring fitness gain that depends on the genetic background as well as on the stage of the stationary phase.
Novel Repressor of Escherichia coli O157:H7 Motility Encoded in the Putative Fimbrial Cluster OI-1
Authors: Allison Sarah E. , Silphaduang Uma , Mascarenhas Mariola , Konczy Paulina , Quan Quyen , Karmali Mohamed , Coombes Brian K. 
Published: July 2012

ABSTRACT

Escherichia coli
O157:H7 is a gastrointestinal pathogen that has become a serious public health concern, as it is associated with outbreaks and severe diseases such as hemolytic-uremic syndrome. The molecular basis of its greater virulence than that of other serotypes is not completely known. OI-1 is a putative fimbria-encoding genomic island that is found almost exclusively in O157:H7 Shiga toxin-producing
E. coli
strains and may be associated with the enhanced pathogenesis of these strains. In this study, we identified and characterized a novel repressor of flagellar synthesis encoded by OI-1. We showed that deletion of
Z0021
increased the motility of
E. coli
O157:H7, which correlated with an increase in flagellin production and enhanced assembly of flagella on the cell surface. In contrast, overexpression of
Z0021
inhibited motility. We demonstrated that Z0021 exerted its regulatory effects downstream of the transcription and translation of
flhDC
but prior to the activation of class II/III promoters. Furthermore, the master regulator of flagellar synthesis, FlhD
4
C
2
, was shown to be a high-copy suppressor of the nonmotile phenotype associated with elevated levels of Z0021—a finding consistent with Z0021-FlhD
4
C
2
being a potential regulatory complex. This work provides insight into the mechanism by which Z0021, which we have named
fmrA
, represses flagellar synthesis and is the first report of a fimbrial-operon-encoded inhibitor of motility in
E. coli
O157:H7.
The Genus Corynebacterium and Other Medically Relevant Coryneform-Like Bacteria
Authors: Bernard Kathryn 
Published: July 2012

ABSTRACTCatalase-positive Gram-positive bacilli, commonly called “diphtheroids” or “coryneform” bacteria were historically nearly always dismissed as contaminants when recovered from patients, but increasingly have been implicated as the cause of significant infections. These taxa have been underreported, and the taxa were taxonomically confusing. The mechanisms of pathogenesis, especially for newly described taxa, were rarely studied. Antibiotic susceptibility data were relatively scant. In this minireview, clinical relevance, phenotypic and genetic identification methods, matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) evaluations, and antimicrobial susceptibility testing involving species in the genusCorynebacteriumand other medically relevant Gram-positive rods, collectively called coryneforms, are described.
Evaluation of Double-Disk Potentiation and Disk Potentiation Tests Using Dipicolinic Acid for Detection of Metallo-β-Lactamase-Producing Pseudomonas spp. and Acinetobacter spp
Authors: Yong Dongeun , Lee Yangsoon , Jeong Seok Hoon , Lee Kyungwon , Chong Yunsop 
Published: July 2012

ABSTRACT

Accurate detection of metallo-β-lactamase (MBL)-producing
Pseudomonas
spp. and
Acinetobacter
spp. became very important with the increasing prevalence of carbapenem-nonsusceptible clinical isolates. The performance of phenotypic MBL detection methods may depend on the types of MBL and the characteristics of the isolates. A high false-positive rate is a problem with EDTA-based MBL detection methods. We evaluated the performance of double-disk potentiation tests (DDPTs) and disk potentiation tests (DPTs) with dipicolinic acid (DPA) using 44 isolates of
Pseudomonas
spp. and
Acinetobacter
spp. producing IMP-1-like, VIM-2-like, and SIM-1 type MBLs. Also, we characterized
P. aeruginosa
isolates with positive imipenem (IPM)-DPA DDPT, but negative meropenem (MEM)-DPA DDPT, and determined possibility of improving a DDPT by using MacConkey agar. Among five different DDPT methods, the IPM-DPA 250-μg method showed the highest sensitivity (97.7%) and specificity (100%). Among four DPT tests, the highest sensitivity (100%) was shown by the IPM-EDTA 1,900-μg disk method, but the specificity was very low (11.4%). Five of six
P. aeruginosa
isolates with false-negative DDPTs with MEM-DPA 250-μg disks carried
bla
IMP-6,
and the high level resistance to MEM (MIC ≥ 512 μg/ml) was reduced by the presence of phenylalanine arginine β-naphtylamide. Improvement of DDPTs was observed when MacConkey agar was used instead of Mueller-Hinton agar. In conclusion, DPA is a better MBL inhibitor than EDTA for detection of
Pseudomonas
spp. and
Acinetobacter
spp. with IMP-1-like, VIM-2-like, and SIM-1-type MBLs. In DPA DDPTs, IPM disks perform better than MEM disks when the isolates are highly resistant to MEM due to the overexpression of efflux pumps.
Galactomannan Enzymatic Immunoassay Cross-Reactivity Caused by Prototheca Species
Authors: Van den Bossche D. , De Bel A. , Hendrickx M. , De Becker A. , Jacobs R. , Naessens A. , Piérard D. 
Published: July 2012

ABSTRACT

We report a reactive
Aspergillus
galactomannan enzymatic immunoassay against the serum of a patient with invasive
Prototheca zopfii
infection. Analysis of the supernatants of suspensions of
P. zopfii
and other
Prototheca
isolates revealed positive results as well. These data suggest cross-reactivity with the serum
Aspergillus
galactomannan assay in invasive protothecosis.
Eastern Chimpanzees, but Not Bonobos, Represent a Simian Immunodeficiency Virus Reservoir
Authors: Li Yingying , Ndjango Jean-Bosco , Learn Gerald H. , Ramirez Miguel A. , Keele Brandon F. , Bibollet-Ruche Frederic , Liu Weimin , Easlick Juliet L. , Decker Julie M. , Rudicell Rebecca S. , Inogwabini Bila-Isia , Ahuka-Mundeke Steve , Leendertz Fabian H. , Reynolds Vernon , Muller Martin N. , Chancellor Rebecca L. , Rundus Aaron S. , Simmons Nicole , Worobey Michael , Shaw George M. , Peeters Martine , Sharp Paul M. , Hahn Beatrice H. 
Published: July 2012

ABSTRACT

Chimpanzees in west central Africa (
Pan troglodytes troglodytes
) are endemically infected with simian immunodeficiency viruses (SIVcpz
Ptt
) that have crossed the species barrier to humans and gorillas on at least five occasions, generating pandemic and nonpandemic forms of human immunodeficiency virus type 1 (HIV-1) as well as gorilla SIV (SIVgor). Chimpanzees in east Africa (
Pan troglodytes schweinfurthii
) are also infected with SIVcpz; however, their viruses (SIVcpz
Pts
) have never been found in humans. To examine whether this is due to a paucity of natural infections, we used noninvasive methods to screen wild-living eastern chimpanzees in the Democratic Republic of the Congo (DRC), Uganda, and Rwanda. We also screened bonobos (
Pan paniscus
) in the DRC, a species not previously tested for SIV in the wild. Fecal samples (
n
= 3,108) were collected at 50 field sites, tested for species and subspecies origin, and screened for SIVcpz antibodies and nucleic acids. Of 2,565 samples from eastern chimpanzees, 323 were antibody positive and 92 contained viral RNA. The antibody-positive samples represented 76 individuals from 19 field sites, all sampled north of the Congo River in an area spanning 250,000 km
2
. In this region, SIVcpz
Pts
was common and widespread, with seven field sites exhibiting infection rates of 30% or greater. The overall prevalence of SIVcpz
Pts
infection was 13.4% (95% confidence interval, 10.7% to 16.5%). In contrast, none of the 543 bonobo samples from six sites was antibody positive. All newly identified SIVcpz
Pts
strains clustered in strict accordance to their subspecies origin; however, they exhibited considerable genetic diversity, especially in protein domains known to be under strong host selection pressure. Thus, the absence of SIVcpz
Pts
zoonoses cannot be explained by an insufficient primate reservoir. Instead, greater adaptive hurdles may have prevented the successful colonization of humans by
P. t. schweinfurthii
viruses.
Human Cytomegalovirus Stimulates Monocyte-to-Macrophage Differentiation via the Temporal Regulation of Caspase 3
Authors: Chan Gary , Nogalski Maciej T. , Yurochko Andrew D. 
Published: July 2012

ABSTRACTMonocytes are primary targets for human cytomegalovirus (HCMV) infection and are proposed to be responsible for hematogenous dissemination of the virus. Biologically, monocytes have a short life span of 48 h in the circulation, a period of time during which monocytes must make a cell fate decision on whether to undergo apoptosis or differentiate into a macrophage. We have previously shown that HCMV infection stimulates monocyte-to-macrophage differentiation; however, the mechanism(s) by which HCMV-infected monocytes simultaneously navigate the 48-h “viability gate” and undergo macrophagic differentiation has remained elusive. Studies have demonstrated that the level of caspase 3 and 8 activities in monocytes may mediate the delicate balance between apoptosis and macrophage colony-stimulating factor (M-CSF)-induced myeloid differentiation. Here, we show that HCMV infection, unlike M-CSF treatment, does not induce caspase 8 activity to promote myeloid differentiation. However, HCMV infection does induce a temporal activation of caspase 3, with only a low level of active caspase 3 being observed after the 48-h viability checkpoint. Consistent with the role of a time-dependent activation of caspase 3 in promoting myeloid differentiation, the inhibition of caspase 3 blocked HCMV-induced monocyte-to-macrophage differentiation. Temporal transcriptome and functional analyses identified heat shock protein 27 (HSP27) and Mcl-1, two known regulators of caspase 3 activation, as being upregulated prior to the 48-h viability gate following HCMV infection. Using small interfering RNAs (siRNAs), we demonstrate that HCMV targets the rapid induction of HSP27 and Mcl-1, which cooperatively function to precisely control caspase 3 activity in order to allow for HCMV-infected monocytes to successfully traverse the 48-h cell fate decision checkpoint and commence macrophage maturation. Overall, this study highlights a unique regulatory mechanism employed by HCMV to tightly modulate the caspase 3 activity needed to promote myeloid differentiation, a key process in the viral dissemination and persistence strategy.
Report of two cases of a rare cause of subarachnoid hemorrhage including unusual presentation and an emerging and effective treatment option
Authors: Nyberg Eric MacKenzie , Chaudry M Imran , Turk Aquilla S , Spiotta Alejandro M , Fiorella David , Turner Raymond D 
Published: July 2012

PurposeTo report two cases of a rare cause of subarachnoid hemorrhage (SAH), including unusual presentation and an emerging and effective treatment option.Case reportsRuptured basilar perforator artery aneurysm is a rare cause of SAH. Catheter angiography in the immediate post hemorrhage period may be unrevealing. We report two cases of ruptured basilar pontine perforator aneurysms. In one of these cases the perforator aneurysm was not apparent on the initial or the 1 week follow-up angiograms. Both patients returned for follow-up angiography 2 months later by which time aneurysmal filling and conspicuity had increased. Both patients were treated solely with two overlapping Neuroform stents. Follow-up angiograms demonstrated complete resolution of the aneurysms in both patients.ConclusionsRupture of aneurysms arising from basilar artery perforators is a rare cause of SAH and attention to this area should be part of an interventionist's search pattern. Aneurysms in this area may not be apparent in the immediate post rupture setting and delayed post hemorrhage angiography has a role in detecting this entity. Stent monotherapy may be effective in treating these lesions.
QUANTUM BACKREACTION (CASIMIR) EFFECT WITHOUT INFINITIES: ALGEBRAIC ANALYSIS
Authors: HERDEGEN ANDRZEJ 
Published: July 2012

Casimir effect, in most general terms, is the backreaction of a quantum system responding to an adiabatic change of external conditions. This backreaction is expected to be quantitatively measured by a change in the expectation value of a certain energy observable of the system. However, for this concept to be applicable, the system has to retain its identity in the process. Most prevailing tendencies in the analysis of the effect seem to ignore this question. In general, a quantum theory is defined by an algebra of observables, whose representations by operators in a Hilbert space define concrete physical systems described by the theory. A quantum system retains its identity if both the algebra as well as its representation do not change. We discuss the resulting restrictions for admissible models of changing external conditions. These ideas are applied to quantum field models. No infinities arise, if the algebraic demands are respected.
Recurrent Mutations of MYD88 and TBL1XR1 in Primary Central Nervous System Lymphomas
Authors: Gonzalez-Aguilar Alberto , Idbaih Ahmed , Boisselier Blandine , Habbita Naïma , Rossetto Marta , Laurenge Alice , Bruno Aurélie , Jouvet Anne , Polivka Marc , Adam Clovis , Figarella-Branger Dominique , Miquel Catherine , Vital Anne , Ghesquières Hervé , Gressin Rémy , Delwail Vincent , Taillandier Luc , Chinot Olivier , Soubeyran Pierre , Gyan Emmanuel , Choquet Sylvain , Houillier Caroline , Soussain Carole , Tanguy Marie-Laure , Marie Yannick , Mokhtari Karima , Hoang-Xuan Khê 
Published: July 2012

Abstract
Purpose: Our objective was to identify the genetic changes involved in primary central nervous system lymphoma (PCNSL) oncogenesis and evaluate their clinical relevance.
Experimental Design: We investigated a series of 29 newly diagnosed, HIV-negative, PCNSL patients using high-resolution single-nucleotide polymorphism (SNP) arrays (n = 29) and whole-exome sequencing (n = 4) approaches. Recurrent homozygous deletions and somatic gene mutations found were validated by quantitative real-time PCR and Sanger sequencing, respectively. Molecular results were correlated with prognosis.
Results: All PCNSLs were diffuse large B-cell lymphomas, and the patients received chemotherapy without radiotherapy as initial treatment. The SNP analysis revealed recurrent large and focal chromosome imbalances that target candidate genes in PCNSL oncogenesis. The most frequent genomic abnormalities were (i) 6p21.32 loss (HLA locus), (ii) 6q loss, (iii) CDKN2A homozygous deletions, (iv) 12q12-q22, and (v) chromosome 7q21 and 7q31 gains. Homozygous deletions of PRMD1, TOX, and DOCK5 and the amplification of HDAC9 were also detected. Sequencing of matched tumor and blood DNA samples identified novel somatic mutations in MYD88 and TBL1XR1 in 38% and 14% of the cases, respectively. The correlation of genetic abnormalities with clinical outcomes using multivariate analysis showed that 6q22 loss (P = 0.006 and P = 0.01) and CDKN2A homozygous deletion (P = 0.02 and P = 0.01) were significantly associated with shorter progression-free survival and overall survival.
Conclusions: Our study provides new insights into the molecular tumorigenesis of PCNSL and identifies novel genetic alterations in this disease, especially MYD88 and TBL1XR1 mutations activating the NF-κB signaling pathway, which may be promising targets for future therapeutic strategies. Clin Cancer Res; 18(19); 5203–11. ©2012 AACR.
Evolution of the Arterial Structure and Function From Infancy to Adolescence Is related to Anthropometric and Blood Pressure Changes
Authors: Sarkola Taisto , Manlhiot Cedric , Slorach Cameron , Bradley Timothy J. , Hui Wei , Mertens Luc , Redington Andrew , Jaeggi Edgar 
Published: July 2012

Objective—
To develop a normative data set and to study the relationship among arterial structure, different anthropometric measures, blood pressure, and arterial function during healthy childhood using very-high-resolution ultrasound (25–55 MHz).

Methods and Results—

In 135 healthy children between 0 and 18 years of age, we assessed the structure of the carotid arteries, larger peripheral arteries, aorta, and left ventricle with ultrasound. Arterial stiffness was assessed by pulse wave velocity and endothelial function by brachial flow-mediated dilation. Reference curves adjusted for age and body surface area of arterial lumen diameters, intima-media thickness, and adventitia thickness were developed. Arterial walls thicken during childhood predominantly as a result of a progressive increase in intima-media thickness. There were significant associations among lumen diameter (
R
2
range, 0.20–0.88 for different arteries;
P
<0.001), intima-media thickness (
R
2
range, 0.47–0.85;
P
<0.001), left ventricular mass (
R
2
=0.90;
P
<0.001), and adventitia thickness (
R
2
range, 0.15–0.22;
P
<0.001) with sex, age, body surface, and systolic blood pressure. Arterial wall stress was associated with lumen diameter (
R
2
range, 0.52–0.83;
P
<0.001) and intima-media thickness (
R
2
range, 0.53–0.88;
P
<0.001). Limited relationships were found among arterial wall layer thickness, stiffness, and endothelial function.

Conclusion—
In healthy children, the evolution of the arterial structure is mainly related to anthropometrics and blood pressure.
An Observational Study of Vertical Eddy Diffusivity in the Hurricane Boundary Layer
Authors: Zhang Jun A. , Drennan William M. 
Published: July 2012

Abstract
Although vertical eddy diffusivity or viscosity has been extensively used in theoretical and numerical models simulating tropical cyclones, little observational study has documented the magnitude of the eddy diffusivity in high-wind conditions (&gt;20 m s−1) until now. Through analyzing in situ aircraft data that were collected in the atmospheric boundary layer of four intense hurricanes, this study provides the first estimates of vertical distributions of the vertical eddy diffusivities for momentum, sensible heat, and latent heat fluxes in the surface wind speed range between 18 and 30 m s−1. In this work, eddy diffusivity is determined from directly measured turbulent fluxes and vertical gradients of the mean variable, such as wind speed, temperature, and humidity. The analyses show that the magnitudes of vertical eddy diffusivities for momentum and latent heat fluxes are comparable to each other, but the eddy diffusivity for sensible heat flux is much smaller than that for the latent heat flux. The vertical distributions of the eddy diffusivities are generally alike, increasing from the surface to a maximum value within the thermodynamic mixed layer and then deceasing with height. The results indicate also that momentum and latent heat are mainly transferred downgradient of the mean flow and that countergradient transport of the sensible heat may exist. The observational estimates are compared with the eddy diffusivities derived from different methods as used in planetary boundary layer (PBL) parameterization schemes in numerical models as well as ones used in previous observational studies.
Synoptic Weather Types for the Ross Sea Region, Antarctica
Authors: Cohen Lana , Dean Sam , Renwick James 
Published: July 2012

Abstract
Synoptic classifications over the Southern Ocean in the Ross Sea region of Antarctica (50°S–Antarctic coast, 150°E–90°W) have been derived from NCEP reanalysis data (1979–2011), producing a set of six synoptic types for the region. These types describe realistic synoptic conditions for the region and represent the moisture-bearing low pressure systems that circulate around Antarctica. The types are described as follows: low Bellingshausen/Amundsen (L-BA), low (L), zonal (Z), low Ross (L-R), ridge (R), and low Amundsen (L-A).
Seasonal frequencies of the synoptic types reflect the seasonal zonal shift of the Amundsen Sea low (ASL) and also correlate well with the Southern Oscillation index (SOI) and the southern annular mode (SAM). Variability in the occurrences of the synoptic types L-R and L-BA indicate a shifting of the position of the ASL farther east (west) toward (away from) the Antarctic Peninsula during La Niña (El Niño) and positive (negative) SAM conditions. A joint linear regression of the SOI and SAM indices show the strongest correlations with the types L-BA and L-R in the spring and quantifies the joint forcing effect of these climate cycles on synoptic variability in the region.
As a demonstration of how synoptic classification provides links between large-scale atmospheric circulation and local climate parameters, the synoptic types are related to precipitation and temperature at Roosevelt Island, an ice core site on the Ross Ice Shelf (80°S, 160°W). The synoptic types provide quantification of distinct precipitation and temperature regimes at this site, which allows for more fundamental understanding of the precipitation source regions and transport pathways that drive the variability in snow and ice proxies.
Climate Change on the Northern Tibetan Plateau during 1957–2009: Spatial Patterns and Possible Mechanisms
Authors: Cuo Lan , Zhang Yongxin , Wang Qingchun , Zhang Leilei , Zhou Bingrong , Hao Zhenchun , Su Fengge 
Published: July 2012

Abstract
Gridded daily precipitation, temperature minima and maxima, and wind speed are generated for the northern Tibetan Plateau (NTP) for 1957–2009 using observations from 81 surface stations. Evaluation reveals reasonable quality and suitability of the gridded data for climate and hydrology analysis. The Mann–Kendall trends of various climate elements of the gridded data show that NTP has in general experienced annually increasing temperature and decreasing wind speed but spatially varied precipitation changes. The northwest (northeast) NTP became dryer (wetter), while there were insignificant changes in precipitation in the south. Snowfall has decreased along high mountain ranges during the wet and warm season. Averaged over the entire NTP, snowfall, temperature minima and maxima, and wind speed experienced statistically significant linear trends at rates of −0.52 mm yr−1 (water equivalent), +0.04°C yr−1, +0.03°C yr−1, and −0.01 m s−1 yr−1, respectively. Correlation between precipitation/wind speed and climate indices characterizing large-scale weather systems for four subregions in NTP reveals that changes in precipitation and wind speed in winter can be attributed to changes in the North Atlantic Oscillation (NAO), the Arctic Oscillation (AO), the East Asian westerly jet (WJ), and the El Niño–Southern Oscillation (ENSO) (wind speed only). In summer, the changes in precipitation and wind are only weakly related to these indices. It is speculated that in addition to the NAO, AO, ENSO, WJ, and the East and South Asian summer monsoons, local weather systems also play important roles.