bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dependence of tar, nicotine and carbon monoxide yields on physical parameters: implications for exposure, emissions control and monitoring
Authors: Stephens W E 
Published: June 2007

Objective:To estimate the extent to which tar, nicotine and carbon monoxide (TNCO) yields are dependent on cigarette design features such as burn rate, filter ventilation and paper porosity, and to consider the implications for human exposure and the regulation of TNCO emissions. A related aim is to determine whether accurate prediction of TNCO yields is possible using only simple physical parameters.Design and methods:Datasets that include quantitative design parameters as well as measurements of TNCO yields collected under standard conditions with vents unblocked (International Organization for Standardization) and under intense conditions with vents fully blocked (Health Canada) were compiled from the literature (primarily US and UK brands). Forward stepwise multiple regression analysis is used to assess the relative importance of each design feature in explaining variability in the observed emissions. Using randomly split data subsets, multiple linear regression is used to model the dependence of TNCO yields on design features in the training subset and validated against the test subset. Tar and carbon monoxide correlate with many of the particulate- and volatile-phase toxins in smoke, and brand values normalised to nicotine yield are used as surrogate measures of exposure within the bounds defined by non-intense and intense smoking protocols.Results and conclusions:Filter ventilation is the dominant control on measured TNCO emissions, but other factors including burn rate, amount of tobacco and paper porosity also contribute. Yields are predictable with reasonable accuracy and precision using only measured physical parameters. Surrogate exposure indicators suggest that filter ventilation does not lead to any reduction in exposure and that highly ventilated (low-yield) brands may actually increase exposure to the more volatile toxins.
Reconsidering stress and smoking: a qualitative study among college students
Authors: Nichter Mark , Nichter Mimi , Carkoglu Asli ,   the Tobacco Etiology Research Network
Published: June 2007

Background:Although it is widely acknowledged among adult smokers that increases in smoking are often precipitated by stressful events, far less attention has been given to smoking during times of stress among youth.Aims:To address this gap by drawing attention to the social utility of smoking in contexts associated with stress among college students.Design:Face-to-face semistructured interviews with college freshmen at a large midwestern university in the US.Participants:Male and female low-level smokers (n = 24), defined as those who reported regular weekday smoking (typically 3–4 cigarettes a day) and smoking at parties on weekends, were interviewed once in person. In addition, 40 brief interviews with smokers were conducted during final examination.Measurements:Interviews focused on a range of issues including current smoking behaviour and reasons for smoking. As part of the interview, students were given a deck of cards that listed a range of reasons for smoking. Participants were asked to select cards that described their smoking experience in the past 2 weeks. Those who selected cards that indicated smoking when stressed were asked to explain the reasons why they did so.Results:A review of qualitative responses reveals that smoking served multiple functions during times of stress for college students. Cigarettes are a consumption event that facilitates a brief social interaction during study times when students feel isolated from their friends. Cigarettes also serve as an idiom of distress, signalling non-verbally to others that they were stressed. Students described smoking to manage their own stress and also to help manage “second-hand stress” from their friends and classmates.Conclusions:Moving away from an individual-focused analysis of stress to a broader assessment of the social contexts of smoking provides a more nuanced account of the multifunctionalilty of cigarettes in students’ lives. Qualitative research draws attention to issues including the need for smoking and socialising during examination time, smoking as a way to take a break and refocus, notions of second-hand stress and smoking to manage social relationships.
Nuclear CD40 interacts with c-Rel and enhances proliferation in aggressive B-cell lymphoma
Authors: Zhou Hai-Jun , Pham Lan V. , Tamayo Archito T. , Lin-Lee Yen-Chiu , Fu Lingchen , Yoshimura Linda C. , Ford Richard J. 
Published: June 2007

AbstractCD40 is an integral plasma membrane–associated member of the TNF receptor family that has recently been shown to also reside in the nucleus of both normal B cells and large B-cell lymphoma (LBCL) cells. However, the physiological function of CD40 in the B-cell nucleus has not been examined. In this study, we demonstrate that nuclear CD40 interacts with the NF-κB protein c-Rel, but not p65, in LBCL cells. Nuclear CD40 forms complexes with c-Rel on the promoters of NF-κB target genes, CD154, BLyS/BAFF, and Bfl-1/A1, in various LBCL cell lines. Wild-type CD40, but not NLS-mutated CD40, further enhances c-Rel–mediated Blys promoter activation as well as proliferation in LBCL cells. Studies in normal B cells and LBCL patient cells further support a nuclear transcriptional function for CD40 and c-Rel. Cooperation between nuclear CD40 and c-Rel appears to be important in regulating cell growth and survival genes involved in lymphoma cell proliferation and survival mechanisms. Modulating the nuclear function of CD40 and c-Rel could reveal new mechanisms in LBCL pathophysiology and provide potential new targets for lymphoma therapy.
Genomic analysis of the secretion stress response in the enzyme-producing cell factory Aspergillus niger
Authors: Guillemette Thomas , van Peij Noël NME , Goosen Theo , Lanthaler Karin , Robson Geoffrey D , van den Hondel Cees AMJJ , Stam Hein , Archer David B 
Published: June 2007

Abstract

Background
Filamentous fungi such as Aspergillus niger have a high capacity secretory system and are therefore widely exploited for the industrial production of native and heterologous proteins. However, in most cases the yields of non-fungal proteins are significantly lower than those obtained for fungal proteins. One well-studied bottleneck appears to be the result of mis-folding of heterologous proteins in the ER during early stages of secretion, with related stress responses in the host, including the unfolded protein response (UPR). This study aims at uncovering transcriptional and translational responses occurring in A. niger exposed to secretion stress.

Results
A genome-wide transcriptional analysis of protein secretion-related stress responses was determined using Affymetrix DNA GeneChips and independent verification for selected genes. Endoplasmic reticulum (ER)-associated stress was induced either by chemical treatment of the wild-type cells with dithiothreitol (DTT) or tunicamycin, or by expressing a human protein, tissue plasminogen activator (t-PA). All of these treatments triggered the UPR, as shown by the expression levels of several well-known UPR target genes. The predicted proteins encoded by most of the up-regulated genes function as part of the secretory system including chaperones, foldases, glycosylation enzymes, vesicle transport proteins, and ER-associated degradation proteins. Several genes were down-regulated under stress conditions and these included several genes that encode secreted enzymes. Moreover, translational regulation under ER stress was investigated by polysomal fractionation. This analysis confirmed the post-transcriptional control of hacA expression and highlighted that differential translation also occurs during ER stress, in particular for some genes encoding secreted proteins or proteins involved in ribosomal biogenesis and assembly.

Conclusion
This is first genome-wide analysis of both transcriptional and translational events following protein secretion stress. Insight has been gained into the molecular basis of protein secretion and secretion-related stress in an effective protein-secreting fungus, and provides an opportunity to identify target genes for manipulation in strain improvement strategies.
Comprehensive analysis of co-occurring domain sets in yeast proteins
Authors: Cohen-Gihon Inbar , Nussinov Ruth , Sharan Roded 
Published: June 2007

AbstractBackgroundProtein domains are fundamental evolutionary units of protein architecture, composing proteins in a modular manner. Combinations of two or more, possibly non-adjacent, domains are thought to play specific functional roles within proteins. Indeed, while the number of potential co-occurring domain sets (CDSs) is very large, only a few of these occur in nature. Here we study the principles governing domain content of proteins, using yeast as a model species.ResultsWe design a novel representation of proteins and their constituent domains as a protein-domain network. An analysis of this network reveals 99 CDSs that occur in proteins more than expected by chance. The identified CDSs are shown to preferentially include ancient domains that are conserved from bacteria or archaea. Moreover, the protein sets spanned by these combinations were found to be highly functionally coherent, significantly match known protein complexes, and enriched with protein-protein interactions. These observations serve to validate the biological significance of the identified CDSs.ConclusionOur work provides a comprehensive list of co-occurring domain sets in yeast, and sheds light on their function and evolution.
The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms
Authors: Kiraga Joanna , Mackiewicz Pawel , Mackiewicz Dorota , Kowalczuk Maria , Biecek Przemysław , Polak Natalia , Smolarczyk Kamila , Dudek Miroslaw R , Cebrat Stanislaw 
Published: June 2007

AbstractBackgroundThe distribution of isoelectric point (pI) of proteins in a proteome is universal for all organisms. It is bimodal dividing the proteome into two sets of acidic and basic proteins. Different species however have different abundance of acidic and basic proteins that may be correlated with taxonomy, subcellular localization, ecological niche of organisms and proteome size.ResultsWe have analysed 1784 proteomes encoded by chromosomes of Archaea, Bacteria, Eukaryota, and also mitochondria, plastids, prokaryotic plasmids, phages and viruses. We have found significant correlation in more than 95% of proteomes between the protein length and pI in proteomes – positive for acidic proteins and negative for the basic ones. Plastids, viruses and plasmids encode more basic proteomes while chromosomes of Archaea, Bacteria, Eukaryota, mitochondria and phages more acidic ones. Mitochondrial proteomes of Viridiplantae, Protista and Fungi are more basic than Metazoa. It results from the presence of basic proteins in the former proteomes and their absence from the latter ones and is related with reduction of metazoan genomes. Significant correlation was found between the pI bias of proteomes encoded by prokaryotic chromosomes and proteomes encoded by plasmids but there is no correlation between eukaryotic nuclear-coded proteomes and proteomes encoded by organelles. Detailed analyses of prokaryotic proteomes showed significant relationships between pI distribution and habitat, relation to the host cell and salinity of the environment, but no significant correlation with oxygen and temperature requirements. The salinity is positively correlated with acidicity of proteomes. Host-associated organisms and especially intracellular species have more basic proteomes than free-living ones. The higher rate of mutations accumulation in the intracellular parasites and endosymbionts is responsible for the basicity of their tiny proteomes that explains the observed positive correlation between the decrease of genome size and the increase of basicity of proteomes. The results indicate that even conserved proteins subjected to strong selectional constraints follow the global trend in the pI distribution.ConclusionThe distribution of pI of proteins in proteomes shows clear relationships with length of proteins, subcellular localization, taxonomy and ecology of organisms. The distribution is also strongly affected by mutational pressure especially in intracellular organisms.
Lack of association between the chemokine receptor 5 polymorphism CCR5delta32 in rheumatoid arthritis and juvenile idiopathic arthritis
Authors: Lindner Ewald , Nordang Gry BN , Melum Espen , Flatø Berit , Selvaag Anne Marit , Thorsby Erik , Kvien Tore K , Førre Øystein T , Lie Benedicte A 
Published: June 2007

Abstract

Background
The chemokine receptor CCR5 has been detected at elevated levels on synovial T cells, and a 32 bp deletion in the CCR5 gene leads to a non-functional receptor. A negative association between the CCR5Δ32 and rheumatoid arthritis (RA) has been reported, although with conflicting results. In juvenile idiopathic arthritis (JIA), an association with CCR5 was recently reported. The purpose of this study was to investigate if the CCR5Δ32 polymorphism is associated with RA or JIA in Norwegian cohorts.

Methods
853 RA patients, 524 JIA patients and 658 controls were genotyped for the CCR5Δ32 polymorphism.

Results
The CCR5Δ32 allele frequency was 11.5% in the controls vs. 10.4% in RA patients (OR = 0.90; P = 0.36) and 9.7% in JIA patients (OR = 0.85; P = 0.20). No decreased homozygosity was observed for CCR5Δ32, as previously suggested.

Conclusion
Our data do not support an association between the CCR5Δ32 allele and Norwegian RA or JIA patients. Combining our results with those from a recently published meta-analysis still provide evidence for a role for CCR5Δ32 in RA, albeit substantially weaker than the effect first reported.
Production of in vitro amplified DNA pseudolibraries and high-throughput cDNA target amplification
Authors: Frey Daniel , Kambach Christian , Steinmetz Michel O , Jaussi Rolf 
Published: June 2007

Abstract

Background
Many structural biology- and high-throughput laboratories experience the acquisition of multiple cDNAs from different sources as a rather time- and resource-consuming procedure. The techniques presented here solve these problems.

Results
An advanced target cDNA amplification procedure employing RNA- or cDNA-derived pseudolibraries circumvents the usual DNA transfection during library establishment. A small sample of reverse transcribed ss- or ds-cDNA or DNA from a pre-existing library is multiplied by in vitro rolling circle ramification amplification. The resulting cDNA pseudolibrary serves as a template for numerous highly efficient PCR amplifications and permits production and analysis of target cDNAs on an automated liquid handling workstation.

Conclusion
The overall efficiency of the simple protocol collection approaches 100% for targets from libraries with low complexity such as Drosophila and yields >80% of amplicons up to 3 kb size in the case of human cDNA.
Chaperone-based procedure to increase yields of soluble recombinant proteins produced in E. coli
Authors: de Marco Ario , Deuerling Elke , Mogk Axel , Tomoyasu Toshifumi , Bukau Bernd 
Published: June 2007

Abstract

Background
The overproduction of recombinant proteins in host cells often leads to their misfolding and aggregation. Previous attempts to increase the solubility of recombinant proteins by co-overproduction of individual chaperones were only partially successful. We now assessed the effects of combined overproduction of the functionally cooperating chaperone network of the E. coli cytosol on the solubility of recombinant proteins.

Results
A two-step procedure was found to show the strongest enhancement of solubility. In a first step, the four chaperone systems GroEL/GroES, DnaK/DnaJ/GrpE, ClpB and the small HSPs IbpA/IbpB, were coordinately co-overproduced with recombinant proteins to optimize de novo folding. In a second step, protein biosynthesis was inhibited to permit chaperone mediated refolding of misfolded and aggregated proteins in vivo. This novel strategy increased the solubility of 70% of 64 different heterologous proteins tested up to 42-fold.

Conclusion
The engineered E. coli strains and the two-step procedure presented here led to a remarkable increase in the solubility of a various recombinant proteins and should be applicable to a wide range of target proteins produced in biotechnology.
Validation and cultural adaptation of a German version of the Physicians' Reactions to Uncertainty scales
Authors: Schneider Antonius , Szecsenyi Joachim , Barie Stefan , Joest Katharina , Rosemann Thomas 
Published: June 2007

Abstract
Background
The aim of the study was to examine the validity of a translated and culturally adapted version of the Physicians' Reaction to Uncertainty scales (PRU) in primary care physicians.

Methods
In a structured process, the original questionnaire was translated, culturally adapted and assessed after administering it to 93 GPs. Test-retest reliability was tested by sending the questionnaire to the GPs again after two weeks.

Results
The principal factor analysis confirmed the postulated four-factor structure underlying the 15 items. In contrast to the original version, item 5 achieved a higher loading on the 'concern about bad outcomes' scale. Consequently, we rearranged the scales. Good item-scale correlations were obtained, with Pearson's correlation coefficient ranging from 0.56–0.84. As regards the item-discriminant validity between the scales 'anxiety due to uncertainty' and 'concern about bad outcomes', partially high correlations (Pearson's correlation coefficient 0.02–0.69; p < 0.001) were found, indicating an overlap between both constructs. The assessment of internal consistency revealed satisfactory values; Cronbach's alpha of the rearranged version was 0.86 or higher for all scales. Test-retest-reliability, assessed by means of the intraclass-correlation-coefficient (ICC), exceeded 0.84, except for the 'reluctance to disclose mistakes to physicians' scale (ICC = 0.66). In this scale, some substantial floor effects occurred, with 29.3% of answers showing the lowest possible value.

Conclusion
Dealing with uncertainty is an important issue in daily practice. The psychometric properties of the rearranged German version of the PRU are satisfying. The revealed floor effects do not limit the significance of the questionnaire. Thus, the German version of the PRU could contribute to the further evaluation of the impact of uncertainty in primary care physicians.
In vivo optical imaging of integrin αV-β3 in mice using multivalent or monovalent cRGD targeting vectors
Authors: Jin Zhao-Hui , Josserand Véronique , Foillard Stéphanie , Boturyn Didier , Dumy Pascal , Favrot Marie-Christine , Coll Jean-Luc 
Published: June 2007

Abstract

Background
The cRGD peptide is a promising probe for early non-invasive detection of tumors. This study aimed to demonstrate how RAFT-c(-RGDfK-)4, a molecule allowing a tetrameric presentation of cRGD, improved cRGD-targeting potential using in vivo models of αVβ3-positive or negative tumors.

Results
We chose the human embryonic kidney cells HEK293(β3) (high levels of αVβ3) or HEK293(β1) (αVβ3-negative but expressing αV and β1) engrafted subcutaneously (s.c.) in mice. Non-invasive in vivo optical imaging demonstrated that as compared to its monomeric cRGD analogue, Cy5-RAFT-c(-RGDfK-)4 injected intravenously had higher uptake, prolonged retention and markedly enhanced contrast in HEK293(β3) than in the HEK293(β1) tumors. Blocking studies further demonstrated the targeting specificity and competitive binding ability of the tetramer.

Conclusion
In conclusion, we demonstrated that Cy5-RAFT-c(-RGDfK-)4 was indeed binding to the αVβ3 receptor and with an improved activity as compared to its monomeric analog, confirming the interest of using multivalent ligands. Intravenous injection of Cy5-RAFT-c(-RGDfK-)4 in this novel pair of HEK293(β3) and HEK293(β1) tumors, provided tumor/skin ratio above 15. Such an important contrast plus the opportunity to use the HEK293(β1) negative control cell line are major assets for the community of researchers working on the design and amelioration of RGD-targeted vectors or on RGD-antagonists.
Clearance of low levels of HCV viremia in the absence of a strong adaptive immune response
Authors: Meyer Manuela F , Lehmann Marc , Cornberg Markus , Wiegand Johannes , Manns Michael P , Klade Christoph , Wedemeyer Heiner 
Published: June 2007

AbstractSpontaneous clearance of hepatitis C virus (HCV) has frequently been associated with the presence of HCV-specific cellular immunity. However, there had been also reports in chimpanzees demonstrating clearance of HCV-viremia in the absence of significant levels of detectable HCV-specific cellular immune responses. We here report seven asymptomatic acute hepatitis C cases with peak HCV-RNA levels between 300 and 100.000 copies/ml who all cleared HCV-RNA spontaneously. Patients were identified by a systematic screening of 1176 consecutive new incoming offenders in a German young offender institution. Four of the seven patients never developed anti-HCV antibodies and had normal ALT levels throughout follow-up. Transient weak HCV-specific CD4+ T cell responses were detectable in five individuals which did not differ in strength and breadth from age- and sex-matched patients with chronic hepatitis C and long-term recovered patients. In contrast, HCV-specific MHC-class-I-tetramer-positive cells were found in 3 of 4 HLA-A2-positive patients. Thus, these cases highlight that clearance of low levels of HCV viremia is possible in the absence of a strong adaptive immune response which might explain the low seroconversion rate after occupational exposure to HCV.
Porcine adenovirus type 3 E1Blarge protein downregulates the induction of IL-8
Authors: Zhou Yan , Ficzycz Andrew , Tikoo Suresh Kumar 
Published: June 2007

AbstractReplication-defective (E1-E3 deleted) adenovirus vector based gene delivery results in the induction of cytokines including IL-8, which may contribute to the development of inflammatory immune responses. Like other adenoviruses, E1 + E3 deleted porcine adenovirus (PAdV) 3 induces the production of IL-8 in infected cells. In contrast, no IL-8 production could be detected in cells infected with wild-type or mutant PAdV-3s containing deletion in E1A + E3 (PAV211) or E1Bsmall+ E3 (PAV212). Expression of PAdV-3 E1Blargeinhibited the NF-κB dependent transcription of luciferase from IL-8 promoter. Imunofluorescence and electrophoretic mobility shift assays suggested that constitutive expression of PAdV-3 E1Blargeinhibited the nuclear translocation of NF-κB and its subsequent binding to DNA. These results suggest that E1Blargeinteracts with NF-κB to prevent transcription and down regulate proinflammatory cytokine IL-8 production.