bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long‐ and short‐term intravital imaging reveals differential spatiotemporal recruitment and function of myelomonocytic cells after spinal cord injury
Authors: Fenrich Keith K. , Weber Pascal , Rougon Geneviève , Debarbieux Franck 
Published: August 2013

Key points
Inflammatory cells such as myelomonocytic cells are key players in the progression and recovery from spinal cord injury (SCI).
However, the precise spatiotemporal distributions and roles of different subpopulations of myelomonocytic cells remain unclear in part because their dynamics have not been examined in vivo.
Using chronic in vivo two‐photon microscopy techniques in adult transgenic mice with SCI, we show that infiltrating and resident myelomonocytic cells have differential spatiotemporal distribution patterns to injury sites.
We also show that infiltrating myelomonocytic cells are associated with the collapse of certain cut axon terminals thus potentially impeding recovery, whereas resident myelomonocytic cells clear axon debris, which may be important for axon regrowth and recovery.
These results set a framework to understand the roles of different subpopulations of myelomonocytic cells in SCI, and may be important for the development of therapies that target specific immune cell populations at precise times post‐injury.
Abstract  After spinal cord injury (SCI), resident and peripheral myelomonocytic cells are recruited to the injury site and play a role in injury progression. These cells are important for clearing cellular debris, and can modulate the retraction and growth of axons in vitro. However, their precise spatiotemporal recruitment dynamics is unknown, and their respective roles after SCI remain heavily debated. Using chronic, quantitative intravital two‐photon microscopy of adult mice with SCI, here we show that infiltrating lysozyme M (LysM(+)) and resident CD11c(+) myelomonocytic cells have distinct spatiotemporal recruitment profiles, and exhibit changes in morphology, motility, phagocytic activity and axon interaction patterns over time. This study provides the first in vivo description of the influx of inflammatory and resident myelomonocytic cells into the injured spinal cord and their interactions with cut axons, and underscores the importance of precise timing and targeting of specific cell populations in developing therapies for SCI.
A comparative study of automatic thresholding approaches for 3D x‐ray microtomography of trabecular bone
Authors: Gómez W. , Sales E. , Lopes R. T. , Pereira W. C. A. 
Published: August 2013

Purpose:This paper presents a comparative study of automatic thresholding algorithms for segmenting trabecular bone volume in x‐ray microtomography (μ CT).Methods:First, a preprocessing stage was established, which considered noise reduction by applying anisotropic diffusion filtering and contrast enhancement by using morphological top‐hats. Next, four automatic thresholding algorithms were implemented: clustering, maximum entropy, moment preservation, and concavity‐based. These approaches analyze the preprocessed 3Dμ CT image histogram to optimize some parameters to find the best gray‐level threshold. Thirty‐eight vertebra bone samples were acquired from 19 normal Wistar rats, specifically the L3 and L4 vertebrae. The μ CT images were acquired with a microfocus x‐ray device at 100 slices/sample. Next, three human operators segmented the entire 3D μ CT images manually to establish ground‐truth segmentations so as to associate the segmentation problem with perceptual grouping. The normalized probabilistic Rand index (NPRI) was used to quantify the agreement between each computerized segmentation and the corresponding set of three ground‐truth segmentations. Hence, the NPRI value should tend toward unity for an acceptable performance. Finally, a statistical analysis was done to determine which thresholding approach achieved the best performance. Besides, 3D morphometric indices were also measured.Results:The Games‐Howell test (α = 0.05) was used to compare the equality of means from the NPRI results considering the four thresholding algorithms (multiple comparisons). This statistical analysis indicated that the clustering and moment preservation techniques performed similarly, with NPRI values of 0.594 ± 0.126 and 0.607 ± 0.127, respectively.Conclusions:The main advantage of computerized segmentation is that it is fully automatic; that is, no interaction with the user is required. Thus, the method could be considered objective. Besides, the proposed preprocessing stage plays an important role in enhancing theμ CT image quality to achieve better separation between the background volume and the trabecular bone volume.
Mechanism of Action of T-705 Ribosyl Triphosphate against Influenza Virus RNA Polymerase
Authors: Sangawa Hidehiro , Komeno Takashi , Nishikawa Hiroshi , Yoshida Atsushi , Takahashi Kazumi , Nomura Nobuhiko , Furuta Yousuke 
Published: August 2013

ABSTRACT

T-705 (favipiravir; 6-fluoro-3-hydroxy-2-pyrazinecarboxamide) selectively and strongly inhibits replication of the influenza virus
in vitro
and
in vivo
. T-705 has been shown to be converted to T-705-4-ribofuranosyl-5-triphosphate (T-705RTP) by intracellular enzymes and then functions as a nucleotide analog to selectively inhibit RNA-dependent RNA polymerase (RdRp) of the influenza virus. To elucidate these inhibitory mechanisms, we analyzed the enzyme kinetics of inhibition using Lineweaver-Burk plots of four natural nucleoside triphosphates and conducted polyacrylamide gel electrophoresis of the primer extension products initiated from
32
P-radiolabeled 5′Cap1 RNA. Enzyme kinetic analysis demonstrated that T-705RTP inhibited the incorporation of ATP and GTP in a competitive manner, which suggests that T-705RTP is recognized as a purine nucleotide by influenza virus RdRp and inhibited the incorporation of UTP and CTP in noncompetitive and mixed-type manners, respectively. Primer extension analysis demonstrated that a single molecule of T-705RTP was incorporated into the nascent RNA strand of the influenza virus and inhibited the subsequent incorporation of nucleotides. These results suggest that a single molecule of T-705RTP is incorporated into the nascent RNA strand as a purine nucleotide analog and inhibits strand extension, even though the natural ribose of T-705RTP has a 3′-OH group, which is essential for forming a covalent bond with the phosphate group.
Pharmacokinetic Properties of Artemether, Dihydroartemisinin, Lumefantrine, and Quinine in Pregnant Women with Uncomplicated Plasmodium falciparum Malaria in Uganda
Authors: Tarning Joel , Kloprogge Frank , Dhorda Mehul , Jullien Vincent , Nosten Francois , White Nicholas J. , Guerin Philippe J. , Piola Patrice 
Published: August 2013

ABSTRACT

Pregnancy alters the pharmacokinetic properties of many drugs used in the treatment of malaria, usually resulting in lower drug exposures. This increases the risks of treatment failure, adverse outcomes for the fetus, and the development of resistance. The pharmacokinetic properties of artemether and its principal metabolite dihydroartemisinin (
n
= 21), quinine (
n
= 21), and lumefantrine (
n
= 26) in pregnant Ugandan women were studied. Lumefantrine pharmacokinetics in a nonpregnant control group (
n
= 17) were also studied. Frequently sampled patient data were evaluated with noncompartmental analysis. No significant correlation was observed between estimated gestational age and artemether, dihydroartemisinin, lumefantrine, or quinine exposures. Artemether/dihydroartemisinin and quinine exposures were generally low in these pregnant women compared to values reported previously for nonpregnant patients. Median day 7 lumefantrine concentrations were 488 (range, 30.7 to 3,550) ng/ml in pregnant women compared to 720 (339 to 2,150) ng/ml in nonpregnant women (
P
= 0.128). There was no statistical difference in total lumefantrine exposure or maximum concentration. More studies with appropriate control groups in larger series are needed to characterize the degree to which pregnant women are underdosed with current antimalarial dosing regimens.
Characterization of Fecal Extended-Spectrum-β-Lactamase-Producing Escherichia coli in a Remote Community during a Long Time Period
Authors: Woerther Paul-Louis , Angebault Cécile , Jacquier Hervé , Clermont Olivier , El Mniai Assyia , Moreau Brigitte , Djossou Félix , Peroz Gilles , Catzeflis François , Denamur Erick , Andremont Antoine 
Published: August 2013

ABSTRACT

Carriage of extended-spectrum beta-lactamase-producing enterobacteria (ESBL-E) has increased in community settings. Little is known about their long-term evolution. French Guiana Amerindians living in a very remote village, already sampled in 2001 and 2006 for ESBL-E fecal carriage, were screened again in October 2010. Sociodemographic data and antibiotic intake data were collected during the previous year. ESBL-E strains collected in 2010 and their plasmid contents were typed. The results were compared to those of the previous campaigns. The prevalence of ESBL-E carriage in 2010 was 5.3%, whereas it was 8.0% and 3.2% in 2006 and 2001, respectively. As previously determined, no individual factor was associated with carriage, including personal antibiotic exposure. However, overall antibiotic use had decreased to a 0.67 treatments/subject/year in 2010 versus 1.09 in 2006 (
P
< 0.001), which supports the idea that population exposure to antibiotics impacts on ESBL-E community carriage rates. A wide diversity of ESBL
Escherichia coli
strains belonging to the A
0
, A
1
, B1, and D
2
phylogroups and producing the CTX-M-1, CTX-M-2, and CTX-M-8 enzymes were isolated. Despite the overall genetic diversity of the strains evaluated by repetitive extragenic palindromic PCR (rep-PCR) and multilocus sequence typing, two CTX-M-1-producing clones were found to have spread. In contrast, similar ESBL-bearing I1/Iγ plasmids were present in various strains both within and between carriers, suggesting high rates of plasmid transfer. Our results suggest that overall antibiotic exposure affects ESBL-E fecal carriage in the community. ESBL-E spread may be the result of both strain dissemination and the transfer of plasmids in intestinal microbiota.
Human Biotransformation of the Nonnucleoside Reverse Transcriptase Inhibitor Rilpivirine and a Cross-Species Metabolism Comparison
Authors: Lade Julie M. , Avery Lindsay B. , Bumpus Namandjé N. 
Published: August 2013

ABSTRACTRilpivirine is a nonnucleoside reverse transcriptase inhibitor used to treat HIV-1. In the present study, the pathways responsible for the biotransformation of rilpivirine were defined. Using human liver microsomes, the formation of two mono- and two dioxygenated metabolites were detected via ultra high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). Mass spectral analysis of the products suggested that these metabolites resulted from oxygenation of the 2,6-dimethylphenyl ring and methyl groups of rilpivirine. Chemical inhibition studies and cDNA-expressed cytochrome P450 (CYP) assays indicated that oxygenations were catalyzed primarily by CYP3A4 and CYP3A5. Glucuronide conjugates of rilpivirine and a monomethylhydroxylated metabolite of rilpivirine were also detected and were found to be formed by UDP-glucuronosyltransferases (UGTs) UGT1A4 and UGT1A1, respectively. All metabolites that were identifiedin vitrowere detectablein vivo. Further, targeted UHPLC-MS/MS-basedin vivometabolomics screening revealed that rilpivirine treatment versus efavirenz treatment may result in differential levels of endogenous metabolites, including tyrosine, homocysteine, and adenosine. Rilpivirine biotransformation was also assessed across species using liver microsomes isolated from a range of mammals, and the metabolite profile identified using human liver microsomes was largely conserved for both oxidative and glucuronide metabolite formation. These studies provide novel insight into the metabolism of rilpivirine and the potential differential effects of rilpivirine- and efavirenz-containing antiretroviral regimens on the endogenous metabolome.
Characterization of Botulinum Neurotoxin A Subtypes 1 Through 5 by Investigation of Activities in Mice, in Neuronal Cell Cultures, and
In Vitro
Authors: Whitemarsh Regina C. M. , Tepp William H. , Bradshaw Marite , Lin Guangyun , Pier Christina L. , Scherf Jacob M. , Johnson Eric A. , Pellett Sabine 
Published: August 2013

ABSTRACT

Botulinum neurotoxins (BoNTs) are synthesized by
Clostridium botulinum
and exist as seven immunologically distinct serotypes designated A through G. For most serotypes, several subtypes have now been described based on nominal differences in the amino acid sequences. BoNT/A1 is the most well-characterized subtype of the BoNT/A serotype, and many of its properties, including its potency, its prevalence as a food poison, and its utility as a pharmaceutical, have been thoroughly studied. In contrast, much remains unknown of the other BoNT/A subtypes. In this study, BoNT/A subtype 1 (BoNT/A1) to BoNT/A5 were characterized utilizing a mouse bioassay, an
in vitro
cleavage assay, and several neuronal cell-based assays. The data indicate that BoNT/A1 to -5 have distinct
in vitro
and
in vivo
toxicological properties and that, unlike those for BoNT/A1, the neuronal and mouse results for BoNT/A2 to -5 do not correlate with their enzymatic activity. These results indicate that BoNT/A1 to -5 have distinct characteristics, which are of importance for a greater understanding of botulism and for pharmaceutical applications.
Deletion of
arcD
in Streptococcus pneumoniae D39 Impairs Its Capsule and Attenuates Virulence
Authors: Gupta Radha , Yang Jun , Dong Yimin , Swiatlo Edwin , Zhang Jing-Ren , Metzger Dennis W. , Bai Guangchun 
Published: August 2013

ABSTRACT

The arginine deiminase system (ADS) is associated with arginine catabolism and plays a role in virulence of several pathogenic bacteria. In
Streptococcus pneumoniae
, the ADS genes exist as a locus consisting of
arcABCDT
. A recent genome-wide mutagenesis approach revealed that both
arcD
and
arcT
are potentially essential in a chinchilla otitis media (OM) model. In the present study, we generated Δ
arcD
, Δ
arcT
, and Δ
arcDT
mutants by homologous recombination and evaluated their infectivity. Our results showed that only
arcD
, and not
arcT
, of an OM isolate is required during chinchilla middle ear infection. Additionally, D39 Δ
arcD
exhibited enhanced nasopharyngeal colonization and was attenuated in both mouse pneumonia and bacteremia models.
In vitro
, D39 Δ
arcD
displayed enhanced adherence to A549 epithelial cells and increased phagocytosis by J774A.1 macrophages compared to those with the parental strain. This mutant also exhibited an impaired capsule, as detected using electron microscopy, immunofluorescence, and a capsule assay. We demonstrated that the capsule defect in the D39 Δ
arcD
mutant may not be associated with a deficiency in arginine but rather is likely caused by a loss of interaction between the capsule and the transmembrane protein ArcD.
Leptospiral LruA Is Required for Virulence and Modulates an Interaction with Mammalian Apolipoprotein AI
Authors: Zhang Kunkun , Murray Gerald L. , Seemann Torsten , Srikram Amporn , Bartpho Thanatchaporn , Sermswan Rasana W. , Adler Ben , Hoke David E. 
Published: August 2013

ABSTRACT

Leptospirosis is a worldwide zoonosis caused by spirochetes of the genus
Leptospira
. While understanding of pathogenesis remains limited, the development of mutagenesis in
Leptospira
has provided a powerful tool for identifying novel virulence factors. LruA is a lipoprotein that has been implicated in leptospiral uveitis as a target of the immune response. In this study, two
lruA
mutants, M754 and M765, generated by transposon mutagenesis from
Leptospira interrogans
serovar Manilae, were characterized. In M754, the transposon inserted in the middle of
lruA
, resulting in no detectable expression of LruA. In M765, the transposon inserted toward the 3′ end of the gene, resulting in expression of a truncated protein. LruA was demonstrated to be on the cell surface in M765 and the wild type (WT). M754, but not M765, was attenuated in a hamster model of acute infection. A search for differential binding to human serum proteins identified a serum protein of around 30 kDa bound to the wild type and the LruA deletion mutant (M754), but not to the LruA truncation mutant (M765). Two-dimensional separation of proteins from leptospiral cells incubated with guinea pig serum identified the 28-kDa apolipoprotein A-I (ApoA-I) as a major mammalian serum protein that binds
Leptospira
in vitro
. Interestingly, M754 (with no detectable LruA) bound more ApoA-I than did the LruA-expressing strains Manilae wild type and M765. Our data thus identify LruA as a surface-exposed leptospiral virulence factor that contributes to leptospiral pathogenesis, possibly by modulating cellular interactions with serum protein ApoA-I.
Behavioural interventions to reduce sexual risk for HIV in heterosexual couples: a meta-analysis
Authors: LaCroix Jessica M , Pellowski Jennifer A , Lennon Carter A , Johnson Blair T 
Published: August 2013

ObjectivesThe current study was conducted to synthesise evaluations of couple-based HIV prevention interventions, assess the efficacy of these interventions in reducing sexual risk, and identify moderators of intervention efficacy.MethodsA comprehensive literature search identified 29 interventions (22 reports; N=5168 couples) that met the inclusion criteria, including enrolment of both members of a heterosexual couple, measurement of condom use at baseline and follow-up, and sufficient statistical information to calculate effect sizes. Effect sizes were analysed using fixed-effects and random-effects assumptions; factors related to intervention efficacy were identified using metaregression.ResultsOverall, there were significant increases in condom use from baseline to follow-up (d+=0.78, 95% CI 0.48 to 1.09) and significant decreases in partner concurrency (d+=0.37, 95% CI 0.13 to 0.60). Condom use increased to a greater extent when studies were conducted toward the beginning of the epidemic, were located in countries scoring lower on the Human Development Index, enrolled serodiscordant couples, and delivered intervention content in multiple contexts. Couples who had been together longer, reported higher incidence of sexually transmitted infection, were provided voluntary counselling and testing, and provided outcome measures during face-to-face interviews also reported larger increases in condom use.ConclusionsCouple-based interventions are efficacious in reducing unprotected sex within the context of romantic relationships. Future research should continue to improve risk reduction for couples.
Molecular Signatures of Epithelial Ovarian Cancer: Analysis of Associations with Tumor Characteristics and Epidemiologic Risk Factors
Authors: Schildkraut Joellen M. , Iversen Edwin S. , Akushevich Lucy , Whitaker Regina , Bentley Rex C. , Berchuck Andrew , Marks Jeffrey R. 
Published: August 2013

Abstract
Background: Six gene expression subtypes of invasive epithelial ovarian cancer were recently defined using microarrays by Tothill and colleagues. The Cancer Genome Atlas (TCGA) project subsequently replicated these subtypes and identified a signature predictive of survival in high-grade serous (HGS) cancers. We previously validated these signatures for use in formalin-fixed paraffin-embedded tissues. The aim of the present study was to determine whether these signatures are associated with specific ovarian cancer risk factors, which would add to the evidence that they reflect the heterogeneous etiology of this disease.
Methods: We modeled signature-specific tumor characteristics and epidemiologic risk factor relationships using multiple regression and multivariate response multiple regression models in 193 patients from a case–control study of epithelial ovarian cancer.
Results: We observed associations between the Tothill gene expression subtype signatures and both age at diagnosis (P = 0.0008) and race (P = 0.008). Although most established epidemiologic risk factors were not associated with molecular signatures, there was an association between breast feeding (P = 0.024) and first-degree family history of breast or ovarian cancer (P = 0.034) among the 106 HGS cases. Some of the above associations were validated using gene expression microarray data from the TCGA project. Weak associations were seen with age at menarche and duration of oral contraceptive use and the TCGA survival signature.
Conclusions: These data support the potential for genomic characterization to elucidate the etiologic heterogeneity of epithelial ovarian cancer.
Impact: This study suggests that molecular signatures may augment the ability to define etiologic subtypes of epithelial ovarian cancer. Cancer Epidemiol Biomarkers Prev; 22(10); 1709–21. ©2013 AACR.
Relationship of Mammographic Density and Gene Expression: Analysis of Normal Breast Tissue Surrounding Breast Cancer
Authors: Sun Xuezheng , Gierach Gretchen L. , Sandhu Rupninder , Williams Tyisha , Midkiff Bentley R. , Lissowska Jolanta , Wesolowska Ewa , Boyd Norman F. , Johnson Nicole B. , Figueroa Jonine D. , Sherman Mark E. , Troester Melissa A. 
Published: August 2013

Abstract
Purpose: Previous studies of breast tissue gene expression have shown that the extratumoral microenvironment has substantial variability across individuals, some of which can be attributed to epidemiologic factors. To evaluate how mammographic density and breast tissue composition relate to extratumoral microenvironment gene expression, we used data on 121 patients with breast cancer from the population-based Polish Women's Breast Cancer Study.
Experimental Design: Breast cancer cases were classified on the basis of a previously reported, biologically defined extratumoral gene expression signature with two subtypes: an Active subtype, which is associated with high expression of genes related to fibrosis and wound response, and an Inactive subtype, which has high expression of cellular adhesion genes. Mammographic density of the contralateral breast was assessed using pretreatment mammograms and a quantitative, reliable computer-assisted thresholding method. Breast tissue composition was evaluated on the basis of digital image analysis of tissue sections.
Results: The Inactive extratumoral subtype was associated with significantly higher percentage mammographic density (PD) and dense area (DA) in univariate analysis (PD: P = 0.001; DA: P = 0.049) and in multivariable analyses adjusted for age and body mass index (PD: P = 0.004; DA: P = 0.049). Inactive/higher mammographic density tissue was characterized by a significantly higher percentage of stroma and a significantly lower percentage of adipose tissue, with no significant change in epithelial content. Analysis of published gene expression signatures suggested that Inactive/higher mammographic density tissue expressed increased estrogen response and decreased TGF-β signaling.
Conclusions: By linking novel molecular phenotypes with mammographic density, our results indicate that mammographic density reflects broad transcriptional changes, including changes in both epithelia- and stroma-derived signaling. Clin Cancer Res; 19(18); 4972–82. ©2013 AACR.