bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term trends in evolution of indels in protein sequences
Authors: Wolf Yuri , Madej Thomas , Babenko Vladimir , Shoemaker Benjamin , Panchenko Anna R 
Published: February 2007

Abstract

Background
In this paper we describe an analysis of the size evolution of both protein domains and their indels, as inferred by changing sizes of whole domains or individual unaligned regions or "spacers". We studied relatively early evolutionary events and focused on protein domains which are conserved among various taxonomy groups.

Results
We found that more than one third of all domains have a statistically significant tendency to increase/decrease in size in evolution as judged from the overall domain size distribution as well as from the size distribution of individual spacers. Moreover, the fraction of domains and individual spacers increasing in size is almost twofold larger than the fraction decreasing in size.

Conclusion
We showed that the tolerance to insertion and deletion events depends on the domain's taxonomy span. Eukaryotic domains are depleted in insertions compared to the overall test set, namely, the number of spacers increasing in size is about the same as the number of spacers decreasing in size. On the other hand, ancient domain families show some bias towards insertions or spacers which grow in size in evolution. Domains from several Gene Ontology categories also demonstrate certain tendencies for insertion or deletion events as inferred from the analysis of spacer sizes.
Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli
Authors: Okuda Shujiro , Kawashima Shuichi , Kobayashi Kazuo , Ogasawara Naotake , Kanehisa Minoru , Goto Susumu 
Published: February 2007

Abstract

Background
Operon structures play an important role in transcriptional regulation in prokaryotes. However, there have been fewer studies on complicated operon structures in which the transcriptional units vary with changing environmental conditions. Information about such complicated operons is helpful for predicting and analyzing operon structures, as well as understanding gene functions and transcriptional regulation.

Results
We systematically analyzed the experimentally verified transcriptional units (TUs) in Bacillus subtilis and Escherichia coli obtained from ODB and RegulonDB. To understand the relationships between TUs and operons, we defined a new classification system for adjacent gene pairs, divided into three groups according to the level of gene co-regulation: operon pairs (OP) belong to the same TU, sub-operon pairs (SOP) that are at the transcriptional boundaries within an operon, and non-operon pairs (NOP) belonging to different operons. Consequently, we found that the levels of gene co-regulation was correlated to intergenic distances and gene expression levels. Additional analysis revealed that they were also correlated to the levels of conservation across about 200 prokaryotic genomes. Most interestingly, we found that functional associations in SOPs were more observed in the environmental and genetic information processes.

Conclusion
Complicated operon strucutures were correlated with genome organization and gene expression profiles. Such intricately regulated operons allow functional differences depending on environmental conditions. These regulatory mechanisms are helpful in accommodating the variety of changes that happen around the cell. In addition, such differences may play an important role in the evolution of gene order across genomes.
Invasive pulmonary aspergillosis in patients with decompensated cirrhosis: case series
Authors: Prodanovic Hélène , Cracco Christophe , Massard Julien , Barrault Camille , Thabut Dominique , Duguet Alexandre , Datry Annick , Derenne Jean-Philippe , Poynard Thierry , Similowski Thomas 
Published: February 2007

Abstract

Background
Opportunistic invasive fungal infections are increasingly frequent in intensive care patients. Their clinical spectrum goes beyond the patients with malignancies, and for example invasive pulmonary aspergillosis has recently been described in critically ill patients without such condition. Liver failure has been suspected to be a risk factor for aspergillosis.

Case presentation
We describe three cases of adult respiratory distress syndrome with sepsis, shock and multiple organ failure in patients with severe liver failure among whom two had positive Aspergillus antigenemia and one had a positive Aspergillus serology. In all cases bronchoalveolar lavage fluid was positive for Aspergillus fumigatus. Outcome was fatal in all cases despite treatment with voriconazole and agressive symptomatic treatment.

Conclusion
Invasive aspergillosis should be among rapidly raised hypothesis in cirrhotic patients developing acute respiratory symptoms and alveolar opacities.
E2F-1 induces melanoma cell apoptosis via PUMA up-regulation and Bax translocation
Authors: Hao Hongying , Dong Yanbin , Bowling Maria T , Gomez-Gutierrez Jorge G , Zhou H Sam , McMasters Kelly M 
Published: February 2007

Abstract

Background
PUMA is a pro-apoptotic Bcl-2 family member that has been shown to be involved in apoptosis in many cell types. We sought to ascertain whether induction of PUMA plays a crucial role in E2F-1-induced apoptosis in melanoma cells.

Methods
PUMA gene and protein expression levels were detected by real-time PCR and Western blot in SK-MEL-2 and HCT116 cell lines after Ad-E2F-1 infection. Activation of the PUMA promoter by E2F-1 overexpression was detected by dual luciferase reporter assay. E2F-1-induced Bax translocation was shown by immunocytochemistry. The induction of caspase-9 activity was measured by caspase-9 colorimetric assay kit.

Results
Up-regulation of the PUMA gene and protein by E2F-1 overexpression was detected by real-time PCR and Western blot analysis in the SK-MEL-2 melanoma cell line. In support of this finding, we found six putative E2F-1 binding sites within the PUMA promoter. Subsequent dual luciferase reporter assay showed that E2F-1 expression could increase the PUMA gene promoter activity 9.3 fold in SK-MEL-2 cells. The role of PUMA in E2F-1-induced apoptosis was further investigated in a PUMA knockout cell line. Cell viability assay showed that the HCT116 PUMA-/- cell line was more resistant to Ad-E2F-1-mediated cell death than the HCT116 PUMA+/+ cell line. Moreover, a 2.2-fold induction of the PUMA promoter was also noted in the HCT116 PUMA+/+ colon cancer cell line after Ad-E2F-1 infection. Overexpression of a truncated E2F-1 protein that lacks the transactivation domain failed to up-regulate PUMA promoter, suggesting that PUMA may be a transcriptional target of E2F-1. E2F-1-induced cancer cell apoptosis was accompanied by Bax translocation from the cytosol to mitochondria and the induction of caspase-9 activity, suggesting that E2F-1-induced apoptosis is mediated by PUMA through the cytochrome C/Apaf-1-dependent pathway.

Conclusion
Our studies strongly demonstrated that E2F-1 induces melanoma cell apoptosis via PUMA up-regulation and Bax translocation. The signaling pathways provided here will further enhance insights on the mechanisms of E2F-1-induced cancer cell apoptosis as a strategy for cancer therapy.
Breast density and polymorphisms in genes coding for CYP1A2 and COMT: the Multiethnic Cohort
Authors: Takata Yumie , Maskarinec Gertraud , Le Marchand Loïc 
Published: February 2007

Abstract

Background
Mammographic density is a strong predictor of breast cancer risk and is increased by hormone replacement therapy (HRT). Some associations with genetic polymorphisms in enzymes involved in estrogen metabolism have been described. This cross-sectional analysis examined the relation between mammographic density and the CYP1A2*1F and COMT Val
58
Met polymorphisms among 332 breast cancer cases and 254 controls in the Hawaii component of the Multiethnic Cohort.

Methods
Mammographic density, before diagnosis in cases, was quantified by using a validated computer-assisted method. Blood samples were genotyped by standard PCR/RFLP methods. Adjusted mean percent density was calculated by genotype using mixed models with the unstructured covariance option.

Results
A positive association between the C allele in the CYP1A2*1F gene and percent density, but not the dense area, was suggested (p = 0.11). The relation was limited to controls (p = 0.045), postmenopausal women not using HRT (p = 0.08), and normal weight subjects (p = 0.046). We did not observe any relation between the COMT Val
58
Met polymorphism and breast density.

Conclusion
The lack of an association between the CYP1A2 genotype and the size of the dense areas suggests an effect on the non-dense, i.e., fatty breast tissue. The discrepancies among studies may be due to differential susceptibility; changes in enzyme activity as a result of the CYP1A2*1F polymorphism may influence breast tissue differently depending on hormonal status. Larger studies with the ability to look at interactions would be useful to elucidate the influence of genetic variation in CYP1A2 and COMT on the risk of developing breast cancer.
Gene expression analysis in human osteoblasts exposed to dexamethasone identifies altered developmental pathways as putative drivers of osteoporosis
Authors: Hurson Conor J , Butler Joseph S , Keating Dominic T , Murray David W , Sadlier Denise M , O'Byrne John M , Doran Peter P 
Published: February 2007

Abstract

Background
Osteoporosis, a disease of decreased bone mineral density represents a significant and growing burden in the western world. Aging population structure and therapeutic use of glucocorticoids have contributed in no small way to the increase in the incidence of this disease. Despite substantial investigative efforts over the last number of years the exact molecular mechanism underpinning the initiation and progression of osteoporosis remain to be elucidated. This has meant that no significant advances in therapeutic strategies have emerged, with joint replacement surgery being the mainstay of treatment.

Methods
In this study we have used an integrated genomics profiling and computational biology based strategy to identify the key osteoblast genes and gene clusters whose expression is altered in response to dexamethasone exposure. Primary human osteoblasts were exposed to dexamethasone in vitro and microarray based transcriptome profiling completed.

Results
These studies identified approximately 500 osteoblast genes whose expression was altered. Functional characterization of the transcriptome identified developmental networks as being reactivated with 106 development associated genes found to be differentially regulated. Pathway reconstruction revealed coordinate alteration of members of the WNT signaling pathway, including frizzled-2, frizzled-7, DKK1 and WNT5B, whose differential expression in this setting was confirmed by real time PCR.

Conclusion
The WNT pathway is a key regulator of skeletogenesis as well as differentiation of bone cells. Reactivation of this pathway may lead to altered osteoblast activity resulting in decreased bone mineral density, the pathological hallmark of osteoporosis. The data herein lend weight to the hypothesis that alterations in developmental pathways drive the initiation and progression of osteoporosis.
Novel system uses probasin-based promoter, transcriptional silencers and amplification loop to induce high-level prostate expression
Authors: Woraratanadharm Jan , Rubinchik Semyon , Yu Hong , Dong John Y 
Published: February 2007

Abstract

Background
Despite several effective treatment options available for prostate cancer, it remains the second leading cause of cancer death in American men. Thus, there is a great need for new treatments to improve outcomes. One such strategy is to eliminate cancer through the expression of cytotoxic genes specifically in prostate cells by gene therapy vectored delivery. To prevent systemic toxicity, tissue- and/or cancer-specific gene expression is required. However, the use of tissue- or cancer-specific promoters to target transgene expression has been hampered by their weak activity.

Results
To address this issue, we have developed a regulation strategy that includes feedback amplification of gene expression along with a differentially suppressible tetracycline regulated expression system (DiSTRES). By differentially suppressing expression of the tetracycline-regulated transcriptional activator (tTA) and silencer (tTS) genes based on the cell origin, this leads to the activation and silencing of the TRE promoter, respectively. In vitro transduction of LNCaP cells with Ad/GFP
DiSTRES lead to GFP expression levels that were over 30-fold higher than Ad/CMV-GFP. Furthermore, Ad/FasL-GFPDiSTRES demonstrated cytotoxic effects in prostate cancer cells known to be resistant to Fas-mediated apoptosis.

Conclusion
Prostate-specific regulation from the DiSTRES system, therefore, serves as a promising new regulation strategy for future applications in the field of cancer gene therapy and gene therapy as a whole.
A silent H-bond can be mutationally activated for high-affinity interaction of BMP-2 and activin type IIB receptor
Authors: Weber Dionys , Kotzsch Alexander , Nickel Joachim , Harth Stefan , Seher Axel , Mueller Uwe , Sebald Walter , Mueller Thomas D 
Published: February 2007

Abstract

Background
Bone morphogenetic proteins (BMPs) are key regulators in the embryonic development and postnatal tissue homeostasis in all animals. Loss of function or dysregulation of BMPs results in severe diseases or even lethality. Like transforming growth factors β (TGF-βs), activins, growth and differentiation factors (GDFs) and other members of the TGF-β superfamily, BMPs signal by assembling two types of serine/threonine-kinase receptor chains to form a hetero-oligomeric ligand-receptor complex. BMP ligand receptor interaction is highly promiscuous, i.e. BMPs bind more than one receptor of each subtype, and a receptor bind various ligands. The activin type II receptors are of particular interest, since they bind a large number of diverse ligands. In addition they act as high-affinity receptors for activins but are also low-affinity receptors for BMPs. ActR-II and ActR-IIB therefore represent an interesting example how affinity and specificity might be generated in a promiscuous background.

Results
Here we present the high-resolution structures of the ternary complexes of wildtype and a variant BMP-2 bound to its high-affinity type I receptor BMPR-IA and its low-affinity type II receptor ActR-IIB and compare them with the known structures of binary and ternary ligand-receptor complexes of BMP-2. In contrast to activin or TGF-β3 no changes in the dimer architecture of the BMP-2 ligand occur upon complex formation. Functional analysis of the ActR-IIB binding epitope shows that hydrophobic interactions dominate in low-affinity binding of BMPs; polar interactions contribute only little to binding affinity. However, a conserved H-bond in the center of the type II ligand-receptor interface, which does not contribute to binding in the BMP-2 – ActR-IIB interaction can be mutationally activated resulting in a BMP-2 variant with high-affinity for ActR-IIB. Further mutagenesis studies were performed to elucidate the binding mechanism allowing us to construct BMP-2 variants with defined type II receptor binding properties.

Conclusion
Binding specificity of BMP-2 for its three type II receptors BMPR-II, Act-RII and ActR-IIB is encoded on single amino acid level. Exchange of only one or two residues results in BMP-2 variants with a dramatically altered type II receptor specificity profile, possibly allowing construction of BMP-2 variants that address a single type II receptor. The structure-/function studies presented here revealed a new mechanism, in which the energy contribution of a conserved H-bond is modulated by surrounding intramolecular interactions to achieve a switch between low- and high-affinity binding.
Day care cataract surgery in Central and Southern Italy: a multicentric survey
Authors: Cillino Salvatore , Casuccio Alessandra , Di Pace Francesco , Pillitteri Francesco , Cillino Giovanni , Lodato Gaetano 
Published: February 2007

Abstract
Background
Cataract day surgery has rapidly gained worldwide acceptance, because the new surgical techniques and costs are generally lower than those involved in ordinary hospitalization. Cataract surgery serves as a proxy indicator of the trend towards day surgery hospitalization in Italy and, therefore, of regional variability in health-care delivery and cost. The aim of this study was to update the diffusion of cataract day surgery through various surgical ophthalmological centers in central and southern Italy during 2005.

Methods
A two-stage stratified cluster sampling method was used to draw a sample of Cataract Surgery Unit from Ophthalmic Units of central and southern Italy. A questionnaire was sent to 25 cataract surgery centers in nine health districts that represented the range of establishments (public, private, accredited or otherwise) in which cataract surgery is performed. Data were collected on numbers of procedures performed in 2005, hospital admission type, time from the onset of cataract day surgery, surgical procedure, and presence of other surgical centers.

Results
The response rate was 42% (10 surveys), resulting in at least one completed questionnaire for each of these 9 districts. There is a positive trend towards day surgery hospitalization in all surgical centers. The percentage of patients treated as outpatients during 2005 varied from 50–60% (Avellino, Naples, Campobasso), to 80–90% (Rome, Bari), up to 90–100% (Catania, Palermo, Siracusa and Trapani), with an increasing trend in all the centers studied. Few differences were found in surgical procedures, and these were statistically insignificant.

Conclusion
Our results confirm a positive trend towards day surgery in place of hospital inpatient admission for cataract surgery. This trend is expected to close the existing regional gap in Italy. Increased efficiency is an overriding need for the National Health Service in order to improve the rationalization of resources.
Record linkage research and informed consent: who consents?
Authors: Huang Nicole , Shih Shu-Fang , Chang Hsing-Yi , Chou Yiing-Jenq 
Published: February 2007

Abstract

Background
Linking computerized health insurance records with routinely collected survey data is becoming increasingly popular in health services research. However, if consent is not universal, the requirement of written informed consent may introduce a number of research biases. The participants of a national health survey in Taiwan were asked to have their questionnaire results linked to their national health insurance records. This study compares those who consented with those who refused.

Methods
A national representative sample (n = 14,611 adults) of the general adult population aged 20 years or older who participated in the Taiwan National Health Interview Survey (NHIS) and who provided complete survey information were used in this study. At the end of the survey, the respondents were asked if they would give permission to access their National Health Insurance records. Information given by the interviewees in the survey was used to analyze who was more likely to consent to linkage and who wasn't.

Results
Of the 14,611 NHIS participants, 12,911 (88%) gave consent, and 1,700 (12%) denied consent. The elderly, the illiterate, those with a lower income, and the suburban area residents were significantly more likely to deny consent. The aborigines were significantly less likely to refuse. No discrepancy in gender and self-reported health was found between individuals who consented and those who refused.

Conclusion
This study is the first population-based study in assessing the consent pattern in a general Asian population. Consistent with people in Western societies, in Taiwan, a typical Asian society, a high percentage of adults gave consent for their health insurance records and questionnaire results to be linked. Consenters differed significantly from non-consenters in important aspects such as age, ethnicity, and educational background. Consequently, having a high consent rate (88%) may not fully eliminate the possibility of selection bias. Researchers should take this source of bias into consideration in their study design and investigate any potential impact of this source of bias on their results.
Quantum dot-induced cell death involves Fas upregulation and lipid peroxidation in human neuroblastoma cells
Authors: Choi Angela O , Cho Sung Ju , Desbarats Julie , Lovrić Jasmina , Maysinger Dusica 
Published: February 2007

Abstract

Background
Neuroblastoma, a frequently occurring solid tumour in children, remains a therapeutic challenge as existing imaging tools are inadequate for proper and accurate diagnosis, resulting in treatment failures. Nanoparticles have recently been introduced to the field of cancer research and promise remarkable improvements in diagnostics, targeting and drug delivery. Among these nanoparticles, quantum dots (QDs) are highly appealing due to their manipulatable surfaces, yielding multifunctional QDs applicable in different biological models. The biocompatibility of these QDs, however, remains questionable.

Results
We show here that QD surface modifications with N-acetylcysteine (NAC) alter QD physical and biological properties. In human neuroblastoma (SH-SY5Y) cells, NAC modified QDs were internalized to a lesser extent and were less cytotoxic than unmodified QDs. Cytotoxicity was correlated with Fas upregulation on the surface of treated cells. Alongside the increased expression of Fas, QD treated cells had increased membrane lipid peroxidation, as measured by the fluorescent BODIPY-C11 dye. Moreover, peroxidized lipids were detected at the mitochondrial level, contributing to the impairment of mitochondrial functions as shown by the MTT reduction assay and imaged with confocal microscopy using the fluorescent JC-1 dye.

Conclusion
QD core and surface compositions, as well as QD stability, all influence nanoparticle internalization and the consequent cytotoxicity. Cadmium telluride QD-induced toxicity involves the upregulation of the Fas receptor and lipid peroxidation, leading to impaired neuroblastoma cell functions. Further improvements of nanoparticles and our understanding of the underlying mechanisms of QD-toxicity are critical for the development of new nanotherapeutics or diagnostics in nano-oncology.