bluuebunny/crossref_metadata_2025_split huggingface dataset:
Liver Transduction with Recombinant Adeno-Associated Virus Is Primarily Restricted by Capsid Serotype Not Vector Genotype
Authors: Grimm Dirk , Pandey Kusum , Nakai Hiroyuki , Storm Theresa A. , Kay Mark A. 
Published: December 2005

ABSTRACT

We and others have recently reported highly efficient liver gene transfer with adeno-associated virus 8 (AAV-8) pseudotypes, i.e., AAV-2 genomes packaged into AAV-8 capsids. Here we studied whether liver transduction could be further enhanced by using viral DNA packaging sequences (inverted terminal repeats [ITRs]) derived from AAV genotypes other than 2. To this end, we generated two sets of vector constructs carrying expression cassettes embedding a
gfp
gene or the human factor IX (
hfIX
) gene flanked by ITRs from AAV genotypes 1 through 6. Initial in vitro analyses of
gfp
vector DNA replication, encapsidation, and cell transduction revealed a surprisingly high degree of interchangeability among the six genotypes. For subsequent in vivo studies, we cross-packaged the six
hfIX
variants into AAV-8 and infused mice via the portal vein with doses of 5 × 10
10
to 1.8 × 10
12
particles. Notably, all vectors expressed comparably high plasma hFIX levels within a dose cohort over the following 6 months, concurrent with the finding of equivalent vector DNA copy numbers per cell. Partial hepatectomies resulted in ∼80% drops of hFIX levels and vector DNA copy numbers in all groups, indicating genotype-independent persistence of predominantly episomal vector DNA. Southern blot analyses of total liver DNA in fact confirmed the presence of identical and mostly nonintegrated molecular vector forms for all genotypes. We conclude that, unlike serotypes, AAV genotypes are not critical for efficient hepatocyte transduction and can be freely substituted. This corroborates our current model for AAV vector persistence in the liver and provides useful information for the future design and application of recombinant AAV.
Nonstructural Protein 3 of Bluetongue Virus Assists Virus Release by Recruiting ESCRT-I Protein Tsg101
Authors: Wirblich Christoph , Bhattacharya Bishnupriya , Roy Polly 
Published: December 2005

ABSTRACTThe release ofBluetongue virus(BTV) and other members of theOrbivirusgenus from infected host cells occurs predominantly by cell lysis, and in some cases, by budding from the plasma membrane. Two nonstructural proteins, NS3 and NS3A, have been implicated in this process. Here we show that both proteins bind to human Tsg101 and its ortholog fromDrosophila melanogasterwith similar strengths in vitro. This interaction is mediated by a conserved PSAP motif in NS3 and appears to play a role in virus release. The depletion of Tsg101 with small interfering RNA inhibits the release of BTV and African horse sickness virus, a related orbivirus, from HeLa cells up to fivefold and threefold, respectively. Like most other viral proteins which recruit Tsg101, NS3 also harbors a PPXY late-domain motif that allows NS3 to bind NEDD4-like ubiquitin ligases in vitro. However, the late-domain motifs in NS3 do not function as effectively in facilitating the release of mini Gag virus-like particles from 293T cells as the late domains from human immunodeficiency virus type 1, human T-cell leukemia virus, and Ebola virus. A mutagenesis study showed that the arginine residue in the PPRY motif is responsible for the low activity of the NS3 late-domain motifs. Our data suggest that the BTV late-domain motifs either recruit an antagonist that interferes with budding or fail to recruit an agonist which is different from NEDD4.
The Herpes Simplex Virus Type 1 vhs-UL41 Gene Secures Viral Replication by Temporarily Evading Apoptotic Cellular Response to Infection: Vhs-UL41 Activity Might Require Interactions with Elements of Cellular mRNA Degradation Machinery
Authors: Barzilai Ari , Zivony-Elbom Ifaat , Sarid Ronit , Noah Eran , Frenkel Niza 
Published: December 2005

ABSTRACTWe have previously shown that herpes simplex virus type 1 (HSV-1) infection is associated with early destabilization/degradation of infected cell mRNAs and consequent shutoff of host protein synthesis by the activity of the virion-associated host shutoff (vhs) UL41 protein. Wild-type (wt) virus destabilized/degraded the housekeeping β-actin and α-tubulin mRNAs as well host stress functions, like the heat shock 70 protein induced postinfection. vhs mutants did not degrade the mRNAs. Elaborate studies by others have been concerned with the mode of mRNA degradation and the mRNAs affected. We now describe vhs activity in primary cultures of mouse cerebellar granule neurons (CGNs). Specifically, (i) upon infection in the presence of actinomycin D to test activity of input viral particles, there was a generalized inhibition of protein synthesis, which depended on the input multiplicity of infection (MOI). (ii) Low-MOI infection with vhs-1 mutant virus was associated with increased synthesis of all apparent proteins. Higher MOIs caused some shutoff, albeit significantly lower than that of wt virus. This pattern could reflect an interaction(s) of vhs-1 protein with host machinery involved in cellular mRNA destabilization/degradation, sequestering this activity. (iii) wt virus infection was associated with cell survival, at least for a while, whereas mutant virus induced apoptotic cell death at earlier times. (iv) wt virus replicated well in the CGNs, whereas there was no apparent replication of the vhs-1 mutant virus. (v) The vhs-1 mutant could serve as helper virus for composite amplicon vectors carrying marker genes and the human p53 gene. Ongoing studies test the use of vhs-1-based composite oncolytic vectors towards cancer gene therapy.
Respiratory Syncytial Virus (RSV) Infects Neuronal Cells and Processes That Innervate the Lung by a Process Involving RSV G Protein
Authors: Li Xia-qing , Fu Zhen F. , Alvarez Rene , Henderson Christine , Tripp Ralph A. 
Published: December 2005

ABSTRACT
Respiratory syncytial virus (RSV) is a primary cause of morbidity and life-threatening lower respiratory tract disease in infants and young children. Children with acute RSV bronchiolitis often develop respiratory sequelae, but the disease mechanisms are poorly understood. Mounting evidence suggests that RSV may mediate persistent infection. Using immunohistochemistry to identify RSV and RSV-infected cell types, we show that RSV infects primary neurons and neuronal processes that innervate the lungs through a process that involves RSV G protein and the G protein CX3C motif. These findings suggest a mechanism for disease chronicity and have important implications for RSV disease intervention strategies.
THE IMPACT OF ENVIRONMENTAL STRINGENCY ON THE FOREIGN DIRECT INVESTMENTS OF THE OECD COUNTRIES
Authors: MIHCI HAKAN , CAGATAY SELIM , KOSKA ONUR 
Published: December 2005

The main objective of this paper is to evaluate the impact of the environmental stringency on trade and the foreign direct investments (FDI) in particular. To do so, both theoretical and empirical investigations are performed. During the empirical investigation, an index of environmental sensitivity performance (IESP) is constructed for the OECD countries. Additionally, the main determinants of the OECD countries' FDI outflows are also analysed alongside with the environmental sensitivity variable for the countries in the sample. The empirical analysis in this paper finds some evidence to suggest that environmental stringency has an important impact on the FDI outflows of the OECD countries. The impact of the degree of environmental stringency on the FDI is significantly positive implying a direct relationship between FDI outflows and relative environmental sensitivity performance of the OECD countries.
InterferenceAnalyzer: Tools for the analysis and simulation of multi-locus genetic data
Authors: Viswanath Lalitha , Housworth Elizabeth A 
Published: December 2005

Abstract
Background
Good statistical models for analyzing and simulating multilocus recombination data exist but are not accessible to many biologists because their use requires reasonably sophisticated mathematical and computational implementation. While some labs have direct access to statisticians or programmers competent to carry out such analyses, many labs do not. We have created a platform independent application with an easy-to-use graphical user interface that will carry out such analyses including the simulations needed to bootstrap confidence intervals for the parameters of interest. This software should make multi-locus techniques accessible to labs that previously relied on less powerful and potentially statistically confounded single interval or double interval techniques.

Results
We introduce InterferenceAnalyzer, an implementation with a user-friendly graphical interface incorporating previously developed algorithms for the analysis and simulation of multilocus recombination data. We demonstrate the use and features of the program with an example of multilocus tetrad data from the mustard plant, Arabidopsis thaliana, and the yeast, Saccharomyces cerevisiae.

Conclusion
InterferenceAnalyzer provides easy access to the powerful and appropriate statistical tools for the multi-locus analysis of genetic data.
Kalign – an accurate and fast multiple sequence alignment algorithm
Authors: Lassmann Timo , Sonnhammer Erik LL 
Published: December 2005

Abstract
Background
The alignment of multiple protein sequences is a fundamental step in the analysis of biological data. It has traditionally been applied to analyzing protein families for conserved motifs, phylogeny, structural properties, and to improve sensitivity in homology searching. The availability of complete genome sequences has increased the demands on multiple sequence alignment (MSA) programs. Current MSA methods suffer from being either too inaccurate or too computationally expensive to be applied effectively in large-scale comparative genomics.

Results
We developed Kalign, a method employing the Wu-Manber string-matching algorithm, to improve both the accuracy and speed of multiple sequence alignment. We compared the speed and accuracy of Kalign to other popular methods using Balibase, Prefab, and a new large test set. Kalign was as accurate as the best other methods on small alignments, but significantly more accurate when aligning large and distantly related sets of sequences. In our comparisons, Kalign was about 10 times faster than ClustalW and, depending on the alignment size, up to 50 times faster than popular iterative methods.

Conclusion
Kalign is a fast and robust alignment method. It is especially well suited for the increasingly important task of aligning large numbers of sequences.
The role and performance of chest X-ray for the diagnosis of tuberculosis: A cost-effectiveness analysis in Nairobi, Kenya
Authors: van Cleeff MRA , Kivihya-Ndugga LE , Meme H , Odhiambo JA , Klatser PR 
Published: December 2005

Abstract

Background
The objective of this study was to establish 1) the performance of chest X-ray (CXR) in all suspects of tuberculosis (TB), as well as smear-negative TB suspects and 2) to compare the cost-effectiveness of the routine diagnostic pathway using Ziehl-Neelsen (ZN) sputum microscopy followed by CXR if case of negative sputum result (ZN followed by CXR) with an alternative pathway using CXR as a screening tool (CXR followed by ZN).

Methods
From TB suspects attending a chest clinic in Nairobi, Kenya, three sputum specimens were examined for ZN and culture (Lowenstein Jensen). Culture was used as gold standard. From each suspect a CXR was made using a four point scoring system: i: no pathology, ii: pathology not consistent for TB, iii: pathology consistent for TB and iv: pathology highly consistent for TB. The combined score i + ii was labeled as "no TB" and the combined score iii + iv was labeled as "TB". Films were re-read by a reference radiologist. HIV test was performed on those who consented. Laboratory and CXR costs were used to compare for cost-effectiveness.

Results
Of the 1,389 suspects enrolled, for 998 (72%) data on smear, culture and CXR was complete. 714 films were re-read, showing a 89% agreement (kappa value = 0.75 s.e.0.037) for the combined scores "TB" or "no-TB". The sensitivity/specificity of the CXR score "TB" among smear-negative suspects was 80%/67%. Using chest CXR as a screening tool in all suspects, sensitivity/specificity of the score "any pathology" was 92%, respectively 63%. The cost per correctly diagnosed case was for the routine process $8.72, compared to $9.27 using CXR as screening tool. When costs of treatment were included, CXR followed by ZN became more cost-effective.

Conclusion
The diagnostic pathway ZN followed by CXR was more cost-effective as compared to CXR followed by ZN. When cost of treatment was also considered CXR followed by ZN became more cost-effective. The low specificity of chest X-ray remains a subject of concern. Depending whether CXR was performed on all suspects or on smear-negative suspects only, 22%–45% of patients labeled as "TB" had a negative culture. The introduction of a well-defined scoring system, clinical conferences and a system of CXR quality control can contribute to improved diagnostic performance.
Association between frequent use of nonsteroidal anti-inflammatory drugs and breast cancer
Authors: Rahme Elham , Ghosn Joumana , Dasgupta Kaberi , Rajan Raghu , Hudson Marie 
Published: December 2005

Abstract

Background
Eighty percent of all breast cancers and almost 90% of breast cancer deaths occur among post-menopausal women. We used a nested case control design to examine the association between nonsteroidal anti-inflammatory drug (NSAID) use and breast cancer occurrence among women over 65 years of age. The cyclooxygenase (COX)-2 enzyme is expressed more in breast cancers than in normal breast tissue. COX-2 inhibition may have a role in breast cancer prevention.

Methods
In the Canadian province of Quebec, physician services are covered through a governmental insurance plan. Medication costs are covered for those ≥ 65 years of age and a publicly funded screening program for breast cancer targets all women 50 years of age or older. We obtained encrypted data from these insurance databases on all women ≥ 65 years of age who filled a prescription for COX-2 inhibitors, non-selective NSAIDs (ns-NSAIDs), aspirin, or acetaminophen between January 1998 and December 2002. Cases were defined as those women who have undergone mammography between April 2001 and June 2002 and had a diagnosis of breast cancer within six months following mammography. Controls included those who have undergone mammography between April 2001 and June 2002 without a diagnosis of any cancer during the six months following mammography. The exposure of interest, frequent NSAID use, was defined as use of ns-NSAIDs and/or COX-2 inhibitors for ≥ 90 days during the year prior to mammography. Frequent use served as a convenient proxy for long term chronic use.

Results
We identified 1,090 cases and 44,990 controls. Cases were older and more likely to have breast cancer risk factors. Logistic regression models adjusting for potential confounders showed that frequent use of ns-NSAIDs and/or COX-2 inhibitors was associated with a lower risk of breast cancer (OR: 0.75, 95% confidence interval 0.64–0.89). Results were similar for COX-2 inhibitors (0.81, 0.68–0.97) and ns-NSAIDs (0.65, 0.43–0.99), when assessed separately. Frequent use of aspirin at doses > 100 mg/day in the year prior to mammography was also associated with a lower risk of breast cancer (0.75, 0.64–0.89). However, use of aspirin at doses ≤ 100 mg/day did not have any association with breast cancer (0.91, 0.71–1.16).

Conclusion
Women who use NSAIDs or doses of aspirin > 100 mg frequently may have a lower risk of breast cancer.
National estimates for maternal mortality: an analysis based on the WHO systematic review of maternal mortality and morbidity
Authors: Betrán Ana P , Wojdyla Daniel , Posner Samuel F , Gülmezoglu A Metin 
Published: December 2005

Abstract

Background
Despite the worldwide commitment to improving maternal health, measuring, monitoring and comparing maternal mortality estimates remain a challenge. Due to lack of data, international agencies have to rely on mathematical models to assess its global burden. In order to assist in mapping the burden of reproductive ill-health, we conducted a systematic review of incidence/prevalence of maternal mortality and morbidity.

Methods
We followed the standard methodology for systematic reviews. This manuscript presents nationally representative estimates of maternal mortality derived from the systematic review. Using regression models, relationships between study-specific and country-specific variables with the maternal mortality estimates are explored in order to assist further modelling to predict maternal mortality.

Results
Maternal mortality estimates included 141 countries and represent 78.1% of the live births worldwide. As expected, large variability between countries, and within regions and subregions, is identified. Analysis of variability according to study characteristics did not yield useful results given the high correlation with each other, with development status and region. A regression model including selected country-specific variables was able to explain 90% of the variability of the maternal mortality estimates. Among all country-specific variables selected for the analysis, three had the strongest relationships with maternal mortality: proportion of deliveries assisted by a skilled birth attendant, infant mortality rate and health expenditure per capita.

Conclusion
With the exception of developed countries, variability of national maternal mortality estimates is large even within subregions. It seems more appropriate to study such variation through differentials in other national and subnational characteristics. Other than region, study of country-specific variables suggests infant mortality rate, skilled birth attendant at delivery and health expenditure per capita are key variables to predict maternal mortality at national level.
Stromal mesenchyme cell genes of the human prostate and bladder
Authors: Goo Young Ah , Goodlett David R , Pascal Laura E , Worthington Kelsey D , Vessella Robert L , True Lawrence D , Liu Alvin Y 
Published: December 2005

AbstractBackgroundStromal mesenchyme cells play an important role in epithelial differentiation and likely in cancer as well. Induction of epithelial differentiation is organ-specific, and the genes responsible could be identified through a comparative genomic analysis of the stromal cells from two different organs. These genes might be aberrantly expressed in cancer since cancer could be viewed as due to a defect in stromal signaling. We propose to identify the prostate stromal genes by analysis of differentially expressed genes between prostate and bladder stromal cells, and to examine their expression in prostate cancer.MethodsImmunohistochemistry using antibodies to cluster designation (CD) cell surface antigens was first used to characterize the stromas of the prostate and bladder. Stromal cells were prepared from either prostate or bladder tissue for cell culture. RNA was isolated from the cultured cells and analyzed by DNA microarrays. Expression of candidate genes in normal prostate and prostate cancer was examined by RT-PCR.ResultsThe bladder stroma was phenotypically different from that of the prostate. Most notable was the presence of a layer of CD13+cells adjacent to the urothelium. This structural feature was also seen in the mouse bladder. The prostate stroma was uniformly CD13-. A number of differentially expressed genes between prostate and bladder stromal cells were identified. One prostate gene, proenkephalin (PENK), was of interest because it encodes a hormone. Secreted proteins such as hormones and bioactive peptides are known to mediate cell-cell signaling. Prostate stromal expression of PENK was verified by an antibody raised against a PENK peptide, by RT-PCR analysis of laser-capture microdissected stromal cells, and by database analysis. Gene expression analysis showed that PENK expression was down-regulated in prostate cancer.ConclusionOur findings show that the histologically similar stromas of the prostate and bladder are phenotypically different, and express organ-specific genes. The importance of these genes in epithelial development is suggested by their abnormal expression in cancer. Among the candidates is the hormone PENK and the down-regulation of PENK expression in cancer suggests a possible association with cancer development.
Lymph node infarction – a rare complication associated with disseminated intra vascular coagulation in a case of dengue fever
Authors: Rao I Satish , Loya Anand C , Ratnakar KS , Srinivasan VR 
Published: December 2005

Abstract

Background
Lymph node infarction is known to occur in association with many non-neoplastic and neoplastic conditions however its occurrence in association with DIC is not reported hitherto in the literature.

Case presentation
We describe an unusual case of lymph node infarction in a twenty seven year old male following disseminated intravascular coagulation (DIC) in a case of dengue fever. Multiple sections of the infarcted and the surrounding non-infarcted lymph nodes failed to reveal any predisposing condition. How ever the parahilar vessels showed thrombotic occlusion, which must have been responsible for the infarction.

Conclusion
Global infarction of the lymph node may mask the underlying pathology. Any malignancy especially lymphoma may coexist or follow lymph node infarction, therefore the patient needs constant surveillance.
Dual-modality impairment of implicit learning of letter-strings versus color-patterns in patients with schizophrenia
Authors: Chiu Ming-Jang , Liu Kristina , Hsieh Ming H , Hwu Hai-Gwo 
Published: December 2005

Abstract

Background
Implicit learning was reported to be intact in schizophrenia using artificial grammar learning. However, emerging evidence indicates that artificial grammar learning is not a unitary process. The authors used dual coding stimuli and schizophrenia clinical symptom dimensions to re-evaluate the effect of schizophrenia on various components of artificial grammar learning.

Methods
Letter string and color pattern artificial grammar learning performances were compared between 63 schizophrenic patients and 27 comparison subjects. Four symptom dimensions derived from a Chinese Positive and Negative Symptom Scale ratings were correlated with patients' artificial grammar implicit learning performances along the two stimulus dimensions. Patients' explicit memory performances were assessed by verbal paired associates and visual reproduction subtests of the Wechsler Memory Scales Revised Version to provide a contrast to their implicit memory function.

Results
Schizophrenia severely hindered color pattern artificial grammar learning while the disease affected lexical string artificial grammar learning to a lesser degree after correcting the influences from age, education and the performance of explicit memory function of both verbal and visual modalities. Both learning performances correlated significantly with the severity of patients' schizophrenic clinical symptom dimensions that reflect poor abstract thinking, disorganized thinking, and stereotyped thinking.

Conclusion
The results of this study suggested that schizophrenia affects various mechanisms of artificial grammar learning differently. Implicit learning, knowledge acquisition in the absence of conscious awareness, is not entirely intact in patients with schizophrenia. Schizophrenia affects implicit learning through an impairment of the ability of making abstractions from rules and at least in part decreasing the capacity for perceptual learning.