bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conservation of Genomic Localization and Sequence Content of Sau3AI-Like Restriction-Modification Gene Cassettes amongListeria monocytogenesEpidemic Clone I and Selected Strains of Serotype 1/2a
Authors: Yildirim Suleyman , Elhanafi Driss , Lin Wen , Hitchins Anthony D. , Siletzky Robin M. , Kathariou S. 
Published: June 2010

ABSTRACTListeria monocytogenesis a food-borne pathogen with a clonal population structure and apparently limited gene flow between strains of different lineages. Strains of epidemic clone I (ECI) have been responsible for numerous outbreaks and invariably have DNA that is resistant to digestion by Sau3AI, suggesting methylation of cytosine at GATC sites. A putative restriction-modification (RM) gene cassette has been identified in the genome of the ECI strain F2365 and all other tested ECI strains but is absent from other strains of the same serotype (4b). Homologous RM cassettes have not been reported amongL. monocytogenesisolates of other serotypes. Furthermore, conclusive evidence for the involvement of this RM cassette in the Sau3AI resistance phenotype of ECI strains has been lacking. In this study, we describe a highly conserved RM cassette in certain strains of serotypes 1/2a and 4a that have Sau3AI-resistant DNA. In these strains the RM cassette was in the same genomic location as in the ECI reference strain F2365. The cassette included a gene encoding a putative recombinase, suggesting insertion via site-specific recombination. Deletion of the RM cassette in the ECI strain F2365 and the serotype 1/2a strain A7 rendered the DNA of both strains susceptible to Sau3AI digestion, providing conclusive evidence that the cassette includes a gene required for methylation of cytosine at GATC sites in both strains. The findings suggest that, in addition to its presence in ECI strains, this RM cassette and the accompanying genomic DNA methylation is also encountered among selected strains of other lineages.
Method for Designing and Optimizing Random-Search Libraries for Strain Improvement
Authors: Klein-Marcuschamer Daniel , Stephanopoulos Gregory 
Published: June 2010

ABSTRACT
Random searches have been the hallmark of directed evolution and have been extensively employed in the improvement of complex or poorly understood phenotypes such as tolerance to toxic compounds in the context of cellular engineering. While genome-wide mutagenesis followed by selection or screening has been a traditional means of phenotype improvement, the list of experimental methods for cellular engineering based on random searches is rapidly expanding. Adding to the confusion is the element of chance, which lengthens the process and most notably adds to the cost of phenotypic improvement programs. Here we present a method to systematize the effort of finding superior mutants by successively improving random libraries. The method, based on the quantification of phenotypic diversity, is then used to isolate more-robust strains.
Detection of Human Intestinal Catalase-Negative, Gram-Positive Cocci by rRNA-Targeted Reverse Transcription-PCR
Authors: Kubota Hiroyuki , Tsuji Hirokazu , Matsuda Kazunori , Kurakawa Takashi , Asahara Takashi , Nomoto Koji 
Published: June 2010

ABSTRACT

An analytical system based on rRNA-targeted reverse transcription-quantitative PCR (RT-qPCR) for enumeration of catalase-negative, Gram-positive cocci was established. Subgroup- or species-specific primer sets targeting 16S or 23S rRNA from
Enterococcus
,
Streptococcus
, and
Lactococcus
were newly developed. The RT-qPCR method using these primers together with the previously reported primer sets specific for the
Enterococcus
genus, the
Streptococcus
genus, and several
Streptococcus
species was found to be able to quantify the target populations with detection limits of 10
3
to 10
4
cells per gram feces, which was more than 100 times as sensitive as the qPCR method (10
6
to 10
8
cells per gram feces). The RT-qPCR analysis of fecal samples from 24 healthy adult volunteers using the genus-specific primer sets revealed that
Enterococcus
and
Streptococcus
were present as intestinal commensals at population levels of log
10
6.2 ± 1.4 and 7.5 ± 0.9 per gram feces (mean ± standard deviation [SD]), respectively. Detailed investigation using species- or subgroup-specific primer sets revealed that the volunteers harbored unique
Enterococcus
species, including the
E. avium
subgroup, the
E. faecium
subgroup,
E. faecalis
, the
E. casseliflavus
subgroup, and
E. caccae
, while the dominant human intestinal
Streptococcus
species was found to be
S. salivarius
. Various
Lactococcus
species, such as
L. lactis
subsp.
lactis
or
L. lactis
subsp.
cremoris
,
L. garvieae
,
L. piscium
, and
L. plantarum
, were also detected but at a lower population level (log
10
4.6 ± 1.2 per gram feces) and prevalence (33%). These results suggest that the RT-qPCR method enables the accurate and sensitive enumeration of human intestinal subdominant but still important populations, such as Gram-positive cocci.
Cellular and Molecular Remodeling of the Endocytic Pathway during Differentiation of Trypanosoma brucei Bloodstream Forms
Authors: Vanhollebeke Benoit , Uzureau Pierrick , Monteyne Daniel , Pérez-Morga David , Pays Etienne 
Published: June 2010

ABSTRACT

During the course of mammalian infection, African trypanosomes undergo extensive cellular differentiation, as actively dividing long slender (SL) forms progressively transform into intermediate (I) forms and finally quiescent G
1
/G
0
-locked short stumpy (ST) forms. ST forms maintain adaptations compatible with their survival in the mammalian bloodstream, such as high endocytic activity, but they already show preadaptations to the insect midgut conditions. The nutritional requirements of ST forms must differ from those of SL forms because the ST forms stop multiplying. We report that the uptake of several ligands was reduced in ST forms compared with that in SL forms. In particular, the haptoglobin-hemoglobin (Hp-Hb) complex was no longer taken up due to dramatic downregulation of its cognate receptor, TbHpHbR. As this receptor also allows uptake of trypanolytic particles from human serum, ST forms were resistant to trypanolysis by human serum lipoproteins. These observations allowed both flow cytometry analysis of SL-to-ST differentiation and the generation of homogeneous ST populations after positive selection upon exposure to trypanolytic particles. In addition, we observed that in ST forms the lysosome relocates anterior to the nucleus. Altogether, we identified novel morphological and molecular features that characterize SL-to-ST differentiation.
Geobacter uraniireducensNikR Displays a DNA Binding Mode Distinct from Other Members of the NikR Family
Authors: Benanti Erin L. , Chivers Peter T. 
Published: June 2010

ABSTRACTNikR is a nickel-responsive ribbon-helix-helix transcription factor present in many bacteria and archaea. The DNA binding properties ofEscherichia coliandHelicobacter pyloriNikR (factors EcNikR and HpNikR, respectively) have revealed variable features of DNA recognition. EcNikR represses a single operon by binding to a perfect inverted repeat sequence, whereas HpNikR binds to promoters from multiple genes that contain poorly conserved inverted repeats. These differences are due in large part to variations in the amino acid sequences of the DNA-contacting β-sheets, as well as residues preceding the β-sheets of these two proteins. We present here evidence of another variation in DNA recognition by the NikR protein fromGeobacter uraniireducens(GuNikR). GuNikR has an Arg-Gly-Ser β-sheet that binds specifically to an inverted repeat sequence distinct from those recognized by Ec- or HpNikR. The N-terminal residues that precede the GuNikR β-sheet residues are required for high-affinity DNA binding. Mutation of individual arm residues dramatically reduced the affinity of GuNikR for specific DNA. Interestingly, GuNikR tetramers are capable of binding cooperatively to the promoter regions of two different genes,nik(MN)1andnik(MN)2. Cooperativity was not observed for the closely relatedG. bemidjiensisNikR, which recognizes the same operator sequence. The cooperative mode of DNA binding displayed by GuNikR could affect the sensitivity of transporter gene expression to changes in intracellular nickel levels.
On the Weak Relatively Nonexpansive Mappings in Banach Spaces
Authors: Xu Yongchun , Su Yongfu 
Published: June 2010

AbstractIn recent years, the definition of weak relatively nonexpansive mapping has been presented and studied by many authors. In this paper, we give some results about weak relatively nonexpansive mappings and give two examples which are weak relatively nonexpansive mappings but not relatively nonexpansive mappings in Banach space "Equation missing" and "Equation missing".
On Uniformly Generalized Lipschitzian Mappings
Authors: Imdad M , Soliman AhmedH 
Published: June 2010

AbstractWe consider another class of generalized Lipschitzian type mappings and utilize the same to prove fixed point theorems for asymptotically regular and uniformly generalized Lipschitzian one-parameter semigroups of self-mappings defined on bounded metric spaces equipped with uniform normal structure which yield corresponding results in respect of semigroup of iterates of a self-mapping as corollaries. Our results also generalize some relevant results due to the work of Lim and Xu (1995), Yao and Zeng (2007), and Soliman (2009).
Spatially Variable Advection Correction of Radar Data. Part I: Theoretical Considerations
Authors: Shapiro Alan , Willingham Katherine M. , Potvin Corey K. 
Published: June 2010

Abstract
Radar data–based analysis products, such as accumulated rainfall maps, dual-Doppler wind syntheses, and thermodynamic retrievals, are prone to substantial error if the temporal sampling interval is too coarse. Techniques to mitigate these errors typically make use of advection-correction procedures (space-to-time conversions) in which the analyzed radial velocity or reflectivity field is idealized as a pattern of unchanging form that translates horizontally at constant speed. The present study is concerned with an advection-correction procedure for the reflectivity field in which the pattern-advection components vary spatially. The analysis is phrased as a variational problem in which errors in the frozen-turbulence constraint are minimized subject to smoothness constraints. The Euler–Lagrange equations for this problem are derived and a solution is proposed in which the trajectories, pattern-advection fields, and reflectivity field are analyzed simultaneously using a combined analytical and numerical procedure. The potential for solution nonuniqueness is explored.
The Role of Linear Interference in the Annular Mode Response to Extratropical Surface Forcing
Authors: Smith Karen L. , Fletcher Christopher G. , Kushner Paul J. 
Published: June 2010

AbstractThe classical problem of predicting the atmospheric circulation response to extratropical surface forcing is revisited in the context of the observed connection between autumnal snow cover anomalies over Siberia and wintertime anomalies of the northern annular mode (NAM). Previous work has shown that in general circulation model (GCM) simulations in which autumnal Siberian snow forcing is prescribed, a vertically propagating Rossby wave train is generated that propagates into the stratosphere, drives dynamical stratospheric warming, and induces a negative NAM response that couples to the troposphere. Important questions remain regarding the dynamics of the response to this surface cooling. It is shown that previously unexplained aspects of the evolution of the response in a comprehensive GCM can be explained by examining the time evolution of the phasing, and hence the linear interference, between the Rossby wave response and the background climatological stationary wave. When the wave response and background wave are in phase, wave activity into the stratosphere is amplified and the zonal-mean stratosphere–troposphere NAM response displays a negative tendency; when they are out of phase, wave activity into the stratosphere is reduced and the NAM response displays a positive tendency. The effects of linear interference are probed further in a simplified GCM, where an imposed lower tropospheric cooling is varied in position, strength, and sign. As in the comprehensive GCM, linear interference strongly influences the response over a realistic range of forcing strengths. The transition from linear to nonlinear behavior is shown to depend simply on forcing strength.
Assessment of disease severity and outcome in patients with systemic light-chain amyloidosis by the high-sensitivity troponin T assay
Authors: Kristen Arnt V. , Giannitsis Evangelos , Lehrke Stephanie , Hegenbart Ute , Konstandin Matthias , Lindenmaier David , Merkle Corina , Hardt Stefan , Schnabel Philipp A. , Röcken Christoph , Schonland Stefan O. , Ho Anthony D. , Dengler Thomas J. , Katus Hugo A. 
Published: June 2010

Abstract
Cardiac biomarkers provide prognostic information in light-chain amyloidosis (AL). Thus, a novel high-sensitivity cardiac troponin T (hs-TnT) assay may improve risk stratification. hs-TnT was assessed in 163 patients. Blood levels were higher with cardiac than renal or other organ involvement and were related to the severity of cardiac involvement. Increased sensitivity was not associated with survival benefit. Forty-seven patients died during follow-up (22.3 ± 1.0 months). Nonsurvivors had higher hs-TnT than survivors. Outcome was worse if hs-TnT more than or equal to 50 ng/L and best less than 3 ng/L. Survival of patients with hs-TnT 3 to 14 ng/L did not differ from patients with moderately increased hs-TnT (14-50 ng/L), but was worse if interventricular septum was more than or equal to 15 mm. Discrimination according to the Mayo staging system was only achieved by the use of the hs-TnT assay, but not by the fourth-generation troponin T assay. Multivariate analysis revealed hs-TnT, NT-proBNP, and left ventricular impairment as independent risk factors for survival. hs-TnT and NT-proBNP predicted survival, even after exclusion of patients with impaired renal function. Plasma levels of the hs-TnT assay are associated with the clinical, morphologic, and functional severity of cardiac AL amyloidosis and could provide useful information for clinicians on cardiac involvement and outcome.
Thymic and peripheral microenvironments differentially mediate development and maturation of iNKT cells by IL-15 transpresentation
Authors: Castillo Eliseo F. , Acero Luis F. , Stonier Spencer W. , Zhou Dapeng , Schluns Kimberly S. 
Published: June 2010

Abstract
Invariant NKT (iNKT) cells are an innate type of T cells, which respond rapidly on activation. iNKT cells acquire these innate-like abilities during development; however, the signals driving development and functional maturation remain only partially understood. Because interleukin-15 (IL-15) is crucial for iNKT development and is delivered by transpresentation, we set out to identify the cell types providing IL-15 to developing iNKT cells and determine their role at the various states of development and maturation. We report here that transpresentation of IL-15 by parenchymal cells was crucial for generating normal number of iNKTs in the thymus, whereas both hematopoietic and parenchymal cells regulated iNKT cell numbers in the periphery, particularly in the liver. Specifically, dendritic cells contributed to peripheral iNKT cell numbers by up-regulating Bcl-2 expression and promoting extrathymic iNKT cell ex-pansion and their homeostatic proliferation. Whether IL-15 affects functional maturation of iNKT cells was also examined. In IL-15Rα−/− mice, CD44HighNK1.1+ iNKT cells displayed decreased T-bet expression and in response to α-galactosylceramide, had deficient interferon-γ expression. Such defects could be reversed by exogenous IL-15 signals. Overall, these studies identify stage-specific functions of IL-15, which are determined by the tissue microenvironment and elucidate the importance of IL-15 in functional maturation.
Genetic diversity of Mycobacterium tuberculosis Complex in Jos, Nigeria
Authors: Ani Agatha , Bruvik Torbjørn , Okoh Yetunde , Agaba Patricia , Agbaji Oche , Idoko John , Dahle Ulf R 
Published: June 2010

Abstract

Background
Nigeria has a high tuberculosis incidence, and genotyping studies of Mycobacterium tuberculosis Complex (MTC) in the country are necessary in order to improve our understanding of the epidemic.

Methods
Isolates of MTC were isolated from cases of pulmonary tuberculosis in Jos, North Central region of Nigeria during 2006-2008. Drug susceptibility test (DST) was performed on 77 of 111 isolates by proportion method on Lowenstein Jensen (LJ) slope while genotyping of mycobacterial DNA was performed by spoligotyping. The SpolDB4 database and the model-based program 'spotclust' were used to assign isolates to families, subfamilies and variants.

Results
A total of 111 pulmonary isolates from consecutive tuberculosis patients in the city of Jos, Plateau State, Nigeria were spoligotyped. A total of 84 (76%) of the isolates belonged to the Latin American Mediterranean (LAM) family. Of these, 78 isolates were assigned to the LAM10 lineage. Among these, 66 exhibited identical spoligopatterns. Drug susceptibility profiles obtained were not consistently associated with any spoligopattern.

Conclusions
The dominance of few M. tuberculosis lineages suggests either a high rate of transmission, frequent import of closely related strains, or a highly conserved genotype. It remains to be confirmed whether the predominance of identical LAM10 represent an outbreak.
Spoligotyping was useful to gain an overall understanding of the local TB epidemic. This study demonstrated that the incidence of TB in Jos, Nigeria may be caused by a few successful M. tuberculosis families, dominated by the LAM10 family.
Methylation-mediated silencing and tumour suppressive function of hsa-miR-124 in cervical cancer
Authors: Wilting Saskia M , van Boerdonk Robert AA , Henken Florianne E , Meijer Chris JLM , Diosdado Begoňa , Meijer Gerrit A , le Sage Carlos , Agami Reuven , Snijders Peter JF , Steenbergen Renske DM 
Published: June 2010

Abstract

Background
A substantial number of microRNAs (miRNAs) is subject to epigenetic silencing in cancer. Although epigenetic silencing of tumour suppressor genes is an important feature of cervical cancer, little is known about epigenetic silencing of miRNAs. Since DNA methylation-based silencing of hsa-miR-124 occurs in various human cancers, we studied the frequency and functional effects of hsa-miR-124 methylation in cervical carcinogenesis.

Results
Quantitative MSP analysis of all 3 loci encoding the mature hsa-miR-124 (hsa-miR-124-1/-2/-3) showed methylation in cervical cancer cell lines SiHa, CaSki and HeLa as well as in late passages of human papillomavirus (HPV) type 16 or 18 immortalised keratinocytes. Treatment of SiHa cells with a demethylating agent reduced hsa-miR-124 methylation levels and induced hsa-miR-124 expression. In HPV-immortalised keratinocytes increased methylation levels were related to reduced hsa-miR-124 expression and higher mRNA expression of IGFBP7, a potential hsa-miR-124 target gene. Ectopic hsa-miR-124 expression in SiHa and CaSki cells decreased proliferation rates and migratory capacity. Combined hsa-miR-124-1 and/or hsa-miR-124-2 methylation analysis of 139 cervical tissue specimens showed an increasing methylation frequency from 0% in normal tissues up to 93% in cervical carcinomas. Increased methylation levels of hsa-miR-124-1 and hsa-miR-124-2 were significantly correlated with reduced hsa-miR-124 expression in cervical tissue specimens. Combined hsa-miR-124-1 and/or hsa-miR-124-2 methylation analysis of 43 cervical scrapes of high-risk HPV positive women was predictive of underlying high-grade lesions.

Conclusions
DNA methylation-based silencing of hsa-miR-124 is functionally involved in cervical carcinogenesis and may provide a valuable marker for improved detection of cervical cancer and its high-grade precursor lesions.
Prognostic value of HMGB1 overexpression in resectable gastric adenocarcinomas
Authors: Bao Guoqiang , Qiao Qing , Zhao Huadong , He Xianli 
Published: June 2010

Abstract

Introduction
HMGB1(High mobility group box 1), originally described as a nuclear protein, is now regarded as a multifunctional protein with a paradoxical dual effect in tumors. In the present study, HMGB1 overexpression and its correlation with the clinicopathologic characteristics and recurrence-free survival were evaluated in gastric adenocarcinomas.

Methods
76 gastric adenocarcinomas surgically removed entered the study. The immunohistochemical staining was used to assess HMGB1 expression through tissue microarray procedure. The clinicopathologic characteristics of all patients were recorded, and the regular follow-up was made for all patients.

Results
Almost all the gastric adenocarcinomas showed HMGB1 positive staining mainly in the nucleus, and the overexpression of HMGB1 was found in cancerous tissues with higher strong reactivity rate, compared with non-cancerous tissues (total expression score ≥ 9, 42.0% vs. 9.0%, P < 0.001). Survival analysis revealed that tumor stage negatively correlated with cancer-free survival (P = 0.022). Furthermore, HMGB1 overexpression positively associated with cancer-free survival of resectable gastric adenocarcinomas (P = 0.023).

Conclusions
The overexpression of HMGB1 protein indicates that HMGB1 may play a role in the tumorigenesis of gastric adenocarcinomas. And the overexpression of HMGB1 may be a marker of good prognosis of gastric adenocarcinoma given curative resection combined with adjuvant chemotherapy.
Acute camptocormia induced by olanzapine: a case report
Authors: Robert Florence , Koenig Martial , Robert Aurélie , Boyer Stéphane , Cathébras Pascal , Camdessanché Jean-Philippe 
Published: June 2010

Abstract

Introduction
Camptocormia refers to an abnormal posture with flexion of the thoraco-lumbar spine which increases during walking and resolves in supine position. This symptom is an increasingly recognized feature of parkinsonian and dystonic disorders, but may also be caused by neuromuscular diseases. There is recent evidence that both central and peripheral mechanisms may be involved in the pathogenesis of camptocormia. We report a case of acute onset of camptocormia, a rare side effect induced by olanzapine, a second-generation atypical anti-psychotic drug with fewer extra-pyramidal side-effects, increasingly used as first line therapy for schizophrenia, delusional disorders and bipolar disorder.

Case presentation
A 73-year-old Caucasian woman with no history of neuromuscular disorder, treated for chronic delusional disorder for the last ten years, received two injections of long-acting haloperidol. She was then referred for fatigue. Physical examination showed a frank parkinsonism without other abnormalities. Routine laboratory tests showed normal results, notably concerning creatine kinase level. Fatigue was attributed to haloperidol which was substituted for olanzapine. Our patient left the hospital after five days without complaint. She was admitted again three days later with acute back pain. Examination showed camptocormia and tenderness in paraspinal muscles. Creatine kinase level was elevated (2986 UI/L). Magnetic resonance imaging showed necrosis and edema in paraspinal muscles. Olanzapine was discontinued. Pain resolved quickly and muscle enzymes were normalized within ten days. Risperidone was later introduced without significant side-effect. The camptocormic posture had disappeared when the patient was seen as an out-patient one year later.

Conclusions
Camptocormia is a heterogeneous syndrome of various causes. We believe that our case illustrates the need to search for paraspinal muscle damage, including drug-induced rhabdomyolysis, in patients presenting with acute-onset bent spine syndrome. Although rare, the occurrence of camptocormia induced by olanzapine must be considered.