bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trachea Epithelium as a “Canary” for Cigarette Smoking‐Induced Biologic Phenotype of the Small Airway Epithelium
Authors: Turetz Meredith L. , O’Connor Timothy P. , Tilley Ann E. , Strulovici‐Barel Yael , Salit Jacqueline , Dang David , Teater Matthew , Mezey Jason , Clark Andrew G. , Crystal Ronald G. 
Published: July 2009

AbstractThe initial site of smoking‐induced lung disease is the small airway epithelium, which is difficult and time consuming to sample by fiberoptic bronchoscopy. We developed a rapid, office‐based procedure to obtain trachea epithelium without conscious sedation from healthy nonsmokers (n= 26) and healthy smokers (n= 19, 27 ± 15 pack‐year). Gene expression differences (fold change >1.5,p< 0.01, Benjamini–Hochberg correction) were assessed with Affymetrix microarrays. A total of 1,057 probe sets were differentially expressed in healthy smokers versus nonsmokers, representing >500 genes. Trachea gene expression was compared to an independent group of small airway epithelial samples (n= 23 healthy nonsmokers,n= 19 healthy smokers, 25 ± 12 pack‐year). The trachea epithelium is more sensitive to smoking, responding with threefold more differentially expressed genes than small airway epithelium. The trachea transcriptome paralleled the small airway epithelium, with 156 of 167 (93%) genes that are significantly up‐ and downregulated by smoking in the small airway epithelium showing similar direction and magnitude of response to smoking in the trachea. Trachea epithelium can be obtained without conscious sedation, representing a less invasive surrogate “canary” for smoking‐induced changes in the small airway epithelium. This should prove useful in epidemiologic studies correlating gene expression with clinical outcome in assessing smoking‐induced lung disease.
Primary hepatic lymphoma: Imaging findings
Authors: Elsayes KM , Menias CO , Willatt JM , Pandya A , Wiggins M 
Published: July 2009

SummaryPrimary hepatic lymphoma (PHL) is rare, accounting for less than 1% of all extranodal lymphomas. In this article, we retrospectively reviewed the imaging features of 12 pathologically proven cases of primary hepatic lymphoma.
NRG1 / ERBB3 signaling in melanocyte development and melanoma: inhibition of differentiation and promotion of proliferation
Authors: Buac Kristina , Xu Mai , Cronin Julie , Weeraratna Ashani T. , Hewitt Stephen M. , Pavan William J. 
Published: July 2009

SummaryNeuregulin (NRG) signaling through the receptor tyrosine kinase, ERBB3, is required for embryonic development, and dysregulated signaling has been associated with cancer progression. Here, we show that NRG1/ERBB3 signaling inhibits melanocyte (MC) maturation and promotes undifferentiated, migratory and proliferative cellular characteristics. Embryonic analyses demonstrated that initial MC specification and distribution were not dependent on ERBB3 signaling. However NRG1/ERBB3 signaling was both necessary and sufficient to inhibit differentiation of later stages of MC development in culture. Analysis of tissue arrays of human melanoma samples suggests that ERBB3 signaling may also contribute to metastatic progression of melanoma as ERBB3 was phosphorylated in primary tumors compared with nevi or metastatic lesions. Neuregulin 1‐treated MCs demonstrated increased proliferation and invasion and altered morphology concomitant with decreased levels of differentiation genes, increased levels of proliferation genes and altered levels of melanoma progression and metastases genes. ERBB3 activation in primary melanomas suggests that NRG1/ERBB3 signaling may contribute to the progression of melanoma from benign nevi to malignancies. We propose that targeting ERBB3 activation and downstream genes identified in this study may provide novel therapeutic interventions for malignant melanoma.
Establishment of Reference Values of CD4 and CD8 Lymphocyte Subsets in Healthy Nigerian Adults
Authors: Oladepo D. K. , Idigbe E. O. , Audu R. A. , Inyang U. S. , Imade G. E. , Philip A. O. , Okafor G. O. , Olaleye D. , Mohammed S. B. , Odunukwe N. N. , Harry T. O. , Edyong-Ekpa M. , Idoko J. , Musa A. Z. , Adedeji A. , Nasidi A. , Ya'aba Y. , Ibrahim K. 
Published: July 2009

ABSTRACT
A total of 2,570 apparently healthy human immunodeficiency virus-negative adults from the six geopolitical zones in the country were enrolled in our study in 2006. The samples were assayed using the Cyflow technique. Data were analyzed using the Statistical Package for Social Scientists (SPSS). The majority (64%) of the participants had CD4 counts within the range of 501 to 1,000 cells/μl. The reference range for CD4 was 365 to 1,571 cells/μl, while the reference range for CD8 was 145 to 884 cells/μl.
First Description of
NOD2
Variant Associated with Defective Neutrophil Responses in a Woman with Granulomatous Mastitis Related to Corynebacteria
Authors: Bercot Béatrice , Kannengiesser Caroline , Oudin Claire , Grandchamp Bernard , Sanson-le Pors Marie-José , Mouly Stéphane , Elbim Carole 
Published: July 2009

ABSTRACT

We report the first case of granulomatous mastitis due to
Corynebacterium kroppenstedtii
linked to strongly impaired neutrophil responses to Nod2 agonist and a single nucleotide polymorphism within the
NOD2
gene (SNP13 [Leu1007fsinsC]) in a heterozygous state. These findings provided the first demonstration of impaired Nod2 function associated with corynebacterial infection.
Development of a Multiplex PCR-Based Rapid Typing Method for EnterohemorrhagicEscherichia coliO157 Strains
Authors: Ooka Tadasuke , Terajima Jun , Kusumoto Masahiro , Iguchi Atsushi , Kurokawa Ken , Ogura Yoshitoshi , Asadulghani Md , Nakayama Keisuke , Murase Kazunori , Ohnishi Makoto , Iyoda Sunao , Watanabe Haruo , Hayashi Tetsuya 
Published: July 2009

ABSTRACTEnterohemorrhagicEscherichia coliO157 (EHEC O157) is a food-borne pathogen that has raised worldwide public health concern. The development of simple and rapid strain-typing methods is crucial for the rapid detection and surveillance of EHEC O157 outbreaks. In the present study, we developed a multiplex PCR-based strain-typing method for EHEC O157, which is based on the variability in genomic location of IS629among EHEC O157 strains. This method is very simple, in that the procedures are completed within 2 h, the analysis can be performed without the need for special equipment or techniques (requiring only conventional PCR and agarose gel electrophoresis systems), the results can easily be transformed into digital data, and the genes for the major virulence markers of EHEC O157 (thestx1,stx2, andeaegenes) can be detected simultaneously. Using this method, 201 EHEC O157 strains showing different XbaI digestion patterns in pulsed-field gel electrophoresis (PFGE) analysis were classified into 127 types, and outbreak-related strains showed identical or highly similar banding patterns. Although this method is less discriminatory than PFGE, it may be useful as a primary screening tool for EHEC O157 outbreaks.
Outbreak of Intestinal Infection Due toRhizopus microsporus
Authors: Cheng Vincent C. C. , Chan Jasper F. W. , Ngan Antonio H. Y. , To Kelvin K. W. , Leung S. Y. , Tsoi H. W. , Yam W. C. , Tai Josepha W. M. , Wong Samson S. Y. , Tse Herman , Li Iris W. S. , Lau Susanna K. P. , Woo Patrick C. Y. , Leung Anskar Y. H. , Lie Albert K. W. , Liang Raymond H. S. , Que T. L. , Ho P. L. , Yuen K. Y. 
Published: July 2009

ABSTRACTSinopulmonary and rhinocerebral zygomycosis has been increasingly found in patients with hematological malignancies and bone marrow transplantation, but intestinal zygomycosis remains very rare in the literature. We investigated an outbreak of intestinal infection due toRhizopus microsporusin 12 patients on treatment for hematological malignancies over a period of 6 months in a teaching hospital. The intake of allopurinol during hospitalization (P< 0.001) and that of commercially packaged ready-to-eat food items in the preceding 2 weeks (P< 0.001) were found to be independently significant risk factors for the development of intestinal zygomycosis. A total of 709 specimens, including 378 environmental and air samples, 181 food samples, and 150 drug samples, were taken for fungal culture. Among them, 16 samples of allopurinol tablets, 3 prepackaged ready-to-eat food items, and 1 pair of wooden chopsticks were positive forRhizopus microsporus, which was confirmed by ITS1-5.8S-ITS2 rRNA gene cluster (internal transcribed spacer [ITS]) sequencing. The mean viable fungal counts of allopurinol obtained from wards and pharmacy were 4.22 × 103CFU/g of tablet (range, 3.07 × 103to 5.48 × 103) and 3.24 × 103CFU/g of tablet (range, 2.68 × 103to 3.72 × 103), respectively, which were much higher than the mean count of 2 × 102CFU/g of food. Phylogenetic analysis by ITS sequencing showed multiple clones from isolates of contaminated allopurinol tablets and ready-to-eat food, of which some were identical to patients' isolates, and with one isolate in the cornstarch used as an excipient for manufacture of this drug. We attempted to type the isolates by random amplification of polymorphic DNA analysis, with limited evidence of clonal distribution. The primary source of the contaminating fungus was likely to be the cornstarch used in the manufacturing of allopurinol tablets or ready-to-eat food.Rhizopus microsporusis thermotolerant and can multiply even at 50°C. The long holding time of the intermediates during the manufacturing process of allopurinol amplified the fungal load. Microbiological monitoring of drugs manufactured for highly immunosuppressed patients should be considered.
Failure of the MicroScan WalkAway System To Detect Heteroresistance to Carbapenems in a Patient with
Enterobacter aerogenes
Bacteremia
Authors: Gordon N. C. , Wareham D. W. 
Published: July 2009

ABSTRACT

We report the failure of the automated MicroScan WalkAway system to detect carbapenem heteroresistance in
Enterobacter aerogenes
. Carbapenem resistance has become an increasing concern in recent years, and robust surveillance is required to prevent dissemination of resistant strains. Reliance on automated systems may delay the detection of emerging resistance.
Determining Seminal Plasma Human Immunodeficiency Virus Type 1 Load in the Context of Efficient Highly Active Antiretroviral Therapy
Authors: Pasquier Christophe , Sauné Karine , Raymond Stéphanie , Moinard Nathalie , Daudin Myriam , Bujan Louis , Izopet Jacques 
Published: July 2009

ABSTRACTThe semen plasma virus load is measured to ensure the safety of sperm processing during medically assisted procreation (MAP) for couples with a human immunodeficiency virus type 1 (HIV-1)-infected man. A practical, automated protocol using the COBAS Ampliprep CAP/CTM kit in the COBAS TaqMan96 system was developed to measure the HIV-1 load in semen plasma samples. HIV-1 was detected in 13.4% of the semen samples processed at our MAP center. Of the eight patients having a detectable semen HIV-1 load, five had no detectable virus in their blood plasma. This highlights the residual risk of HIV-1 transmission during unprotected intercourse and raises the question of the possible consequences of ineffective highly active antiretroviral therapy in the genital tract.
A Genetic Variant of Hepatitis B Virus Divergent from Known Human and Ape Genotypes Isolated from a Japanese Patient and Provisionally Assigned to New Genotype J
Authors: Tatematsu Kanako , Tanaka Yasuhito , Kurbanov Fuat , Sugauchi Fuminaka , Mano Shuhei , Maeshiro Tatsuji , Nakayoshi Tomokuni , Wakuta Moriaki , Miyakawa Yuzo , Mizokami Masashi 
Published: July 2009

ABSTRACTHepatitis B virus (HBV) of a novel genotype (J) was recovered from an 88-year-old Japanese patient with hepatocellular carcinoma who had a history of residing in Borneo during the World War II. It was divergent from eight human (A to H) and four ape (chimpanzee, gorilla, gibbon, and orangutan) HBV genotypes, as well as from a recently proposed ninth human genotype I, by 9.9 to 16.5% of the entire genomic sequence and did not have evidence of recombination with any of the nine human genotypes and four nonhuman genotypes. Based on a comparison of the entire nucleotide sequence against 1,440 HBV isolates reported, HBV/J was nearest to the gibbon and orangutan genotypes (mean divergences of 10.9 and 10.7%, respectively). Based on a comparison of four open reading frames, HBV/J was closer to gibbon/orangutan genotypes than to human genotypes in the P and large S genes and closest to Australian aboriginal strains (HBV/C4) and orangutan-derived strains in the S gene, whereas it was closer to human than ape genotypes in the C gene. HBV/J shared a deletion of 33 nucleotides at the start of preS1 region with C4 and gibbon genotypes, had an S-gene sequence similar to that of C4, and expressed theaywsubtype. Efficient infection, replication, and antigen expression by HBV/J were experimentally established in two chimeric mice with the liver repopulated for human hepatocytes. The HBV DNA sequence recovered from infected mice was identical to that in the inoculum. Since HBV/J is positioned phylogenetically in between human and ape genotypes, it may help to trace the origin of HBV and merits further epidemiological surveys.
Regulation of Gene Expression in Primate Polyomaviruses
Authors: White Martyn K. , Safak Mahmut , Khalili Kamel 
Published: July 2009

ABSTRACT

Polyomaviruses are a growing family of small DNA viruses with a narrow tropism for both the host species and the cell type in which they productively replicate. Species host range may be constrained by requirements for precise molecular interactions between the viral T antigen, host replication proteins, including DNA polymerase, and the viral origin of replication, which are required for viral DNA replication. Cell type specificity involves, at least in part, transcription factors that are necessary for viral gene expression and restricted in their tissue distribution. In the case of the human polyomaviruses, BK virus (BKV) replication occurs in the tubular epithelial cells of the kidney, causing nephropathy in kidney allograft recipients, while JC virus (JCV) replication occurs in the glial cells of the central nervous system, where it causes progressive multifocal leukoencephalopathy. Three new human polyomaviruses have recently been discovered: MCV was found in Merkel cell carcinoma samples, while Karolinska Institute Virus and Washington University Virus were isolated from the respiratory tract. We discuss control mechanisms for gene expression in primate polyomaviruses, including simian vacuolating virus 40, BKV, and JCV. These mechanisms include not only modulation of promoter activities by transcription factor binding but also enhancer rearrangements, restriction of DNA methylation, alternate early mRNA splicing,
cis
-acting elements in the late mRNA leader sequence, and the production of viral microRNA.
The Expression of N-Terminal Deletion DNA Pilot Proteins Inhibits the Early Stages of φX174 Replication
Authors: Ruboyianes Mark V. , Chen Min , Dubrava Mathew S. , Cherwa James E. , Fane Bentley A. 
Published: July 2009

ABSTRACT
The φX174 DNA pilot protein H contains four predicted C-terminal coiled-coil domains. The region of the gene encoding these structures was cloned, expressed in vivo, and found to strongly inhibit wild-type replication. DNA and protein synthesis was investigated in the absence of de novo H protein synthesis and in wild-type-infected cells expressing the inhibitory proteins (ΔH). The expression of the ΔH proteins interfered with early stages of DNA replication, which did not require de novo H protein synthesis, suggesting that the inhibitory proteins interfere with the wild-type H protein that enters the cell with the penetrating DNA. As transcription and protein synthesis are dependent on DNA replication in positive single-stranded DNA life cycles, viral protein synthesis was also reduced. However, unlike DNA synthesis, efficient viral protein synthesis required de novo H protein synthesis, a novel function for this protein. A single amino acid change in the C terminus of protein H was both necessary and sufficient to confer resistance to the inhibitory ΔH proteins, restoring both DNA and protein synthesis to wild-type levels. ΔH proteins derived from the resistant mutant did not inhibit wild-type or resistant mutant replication. The inhibitory effects of the ΔH proteins were lessened by the coexpression of the internal scaffolding protein, which may suppress H-H protein interactions. While coexpression relieved the block in DNA biosynthesis, viral protein synthesis remained suppressed. These data indicate that protein H's role in DNA replication and stimulating viral protein synthesis can be uncoupled.
Avian Reovirus SigmaA Localizes to the Nucleolus and Enters the Nucleus by a Nonclassical Energy- and Carrier-Independent Pathway
Authors: Vázquez-Iglesias Lorena , Lostalé-Seijo Irene , Martínez-Costas José , Benavente Javier 
Published: July 2009

ABSTRACT
Avian reovirus sigmaA is a double-stranded RNA (dsRNA)-binding protein that has been shown to stabilize viral core particles and to protect the virus against the antiviral action of interferon. To continue with the characterization of this viral protein, we have investigated its intracellular distribution in avian cells. Most sigmaA accumulates into cytoplasmic viral factories of infected cells, and yet a significant fraction was detected in the nucleolus. The protein also localizes in the nucleolus of transfected cells, suggesting that nucleolar targeting is not facilitated by the viral infection or by viral factors. Assays performed in both intact cells and digitonin-permeabilized cells demonstrate that sigmaA is able to enter the nucleus via a nucleoporin-dependent nondiffusional mechanism that does not require added cytosolic factors or energy input. These results indicate that sigmaA by itself is able to penetrate into the nucleus using a process that is mechanistically different from the classical nuclear localization signal/importin pathway. On the other hand, two sigmaA arginines that are necessary for dsRNA binding are also required for nucleolar localization, suggesting that dsRNA-binding and nucleolar targeting are intimately linked properties of the viral protein.
Breadth of Neutralizing Antibody Response to Human Immunodeficiency Virus Type 1 Is Affected by Factors Early in Infection but Does Not Influence Disease Progression
Authors: Piantadosi Anne , Panteleeff Dana , Blish Catherine A. , Baeten Jared M. , Jaoko Walter , McClelland R. Scott , Overbaugh Julie 
Published: July 2009

ABSTRACT

The determinants of a broad neutralizing antibody (NAb) response and its effect on human immunodeficiency virus type 1 (HIV-1) disease progression are not well defined, partly because most prior studies of a broad NAb response were cross-sectional. We examined correlates of NAb response breadth among 70 HIV-infected, antiretroviral-naïve Kenyan women from a longitudinal seroincident cohort. NAb response breadth was measured 5 years after infection against five subtype A viruses and one subtype B virus. Greater NAb response breadth was associated with a higher viral load set point and greater HIV-1
env
diversity early in infection. However, greater NAb response breadth was not associated with a delayed time to a CD4
+
T-cell count of <200, antiretroviral therapy, or death. Thus, a broad NAb response results from a high level of antigenic stimulation early in infection, which likely accounts for prior observations that greater NAb response breadth is associated with a higher viral load later in infection.
Detection of EGFR and KRAS mutations on trans-thoracic needle aspiration of lung nodules by high resolution melting analysis
Authors: Fassina A , Gazziero A , Zardo D , Corradin M , Aldighieri E , Rossi G P 
Published: July 2009

Background:EGFRandKRASare the target genes for tumour response to epidermal growth factor receptor (EGFR) inhibitors.Aims:To investigateEGFRandKRASmutational status with high resolution melting (HRM) analysis applied to cytological material obtained from trans-thoracic needle aspiration (TTNA) in order to better select patients for targeted therapy.Methods:DNA was extracted from fixed material of 108 TTNAs under CT guidance, from 108 consecutive patients. In 77 TTNAs (71.3.%) that were positive for non-small cell lung cancer, the variant in exon 21 (the missense mutation at codon 858, L858R) and the deletion in exon 19 (in frame deletion at codons 747–749) of theEGFRgene, and the point mutation in exon 2 ofKRASwere investigated with HRM assay using sequencing as the reference “gold standard”.Results:Nine (11.7%) samples were positive forKRASexon 2 mutations, and two (2.6%) samples were positive for theEGFRexon 21 missense mutation by HRM assay. No deletion at exon 19 forEGFRwas detected by HRM analysis. All HRM results were confirmed by direct DNA sequencing.Conclusions:HRM analysis of cytological material was accurate for the detection of two majorEGFRmutations andKRASmutations in exon 2. HRM analysis was fast, easy to apply, cheap, highly reproducible, and could be used with small amounts of material, such as is obtainable with needle lavage. Therefore, it may be useful as an adjunct to the cytological report that yields valuable molecular information.
The principle of justice in patient priorities in the intensive care unit: the role of significant others: Table 1
Authors: Halvorsen K , Førde R , Nortvedt P 
Published: July 2009

Background:Theoretically, the principle of justice is strong in healthcare priorities both nationally and internationally. Research, however, has indicated that questions can be raised as to how this principle is dealt with in clinical intensive care.Objective:The objective of this article is to examine how significant others may affect the principle of justice in the medical treatment and nursing care of intensive care patients.Method:Field observations and in-depth interviews with physicians and nurses in intensive care units (ICU). Emphasis was placed on eliciting the underlying rationale for prioritisations in clinical intensive care with particular focus on clinicians’ considerations when limiting ICU treatment.Results:Significant others could induce an unintentional discrimination of ICU patients. Family members who were demanding received more time and attention for both the patient and themselves. Patients’ and families’ status and position and/or an interesting medical diagnosis seemed to govern the clinicians’ priorities of patients and families—consciously as well as unconsciously. The clinicians emphasised that patient information given through families was important. However, patients’ preferences and values conveyed to clinicians through their families were not always taken seriously. This even applied in cases with very serious prognoses and an explicit patient wish to forego life-prolonging treatment.Conclusion:The principle of justice was violated when qualified attention was given to significant others, and through this also to patients. Attention given to significant others was influenced by the healthcare workers’ professional and personal values, attitudes and interests.