bluuebunny/crossref_metadata_2025_split huggingface dataset:
Smad1 and Smad5 differentially regulate embryonic hematopoiesis
Authors: McReynolds Lisa J. , Gupta Sunny , Figueroa Maria E. , Mullins Mary C. , Evans Todd 
Published: August 2007

AbstractThe bone morphogenetic protein (BMP) signaling pathway regulates multiple steps of hematopoiesis, mediated through receptor-regulated Smads, including Smad1 and Smad5. Here, we use loss-of-function approaches in zebrafish to compare the roles of Smad1 and Smad5 during embryonic hematopoiesis. We show that knockdown of Smad1 or Smad5 generates distinct and even opposite hematopoietic phenotypes. Embryos depleted for Smad1 have an increased number of primitive erythrocytes, but fail to produce mature embryonic macrophages. In contrast, Smad5-depleted embryos are defective in primitive erythropoiesis, yet have normal numbers of macrophages. Loss of either Smad1 or Smad5 causes a failure in the generation of definitive hematopoietic progenitors. To investigate the mechanism behind these phenotypes, we used rescue experiments and found that Smad5 is unable to rescue the Smad1 loss-of-function phenotype, indicating that the 2 highly related proteins have inherently distinct activities. Microarray experiments revealed that the 2 proteins redundantly regulate the key initiators of the hemato-vascular program, including scl, lmo2, and gfi1. However, each also regulates a remarkably distinct genetic program, with Smad5 uniquely regulating the BMP signaling pathway itself. Our results suggest that specificity of BMP signaling output, with respect to hematopoiesis, can be explained by differential functions of Smad1 and Smad5.
antiCODE: a natural sense-antisense transcripts database
Authors: Yin Yifei , Zhao Yi , Wang Jie , Liu Changning , Chen Shuguang , Chen Runsheng , Zhao Haitao 
Published: August 2007

AbstractBackgroundNatural antisense transcripts (NATs) are endogenous RNA molecules that exhibit partial or complete complementarity to other RNAs, and that may contribute to the regulation of molecular functions at various levels. In recent years, large-scale NAT screens in several model organisms have produced much data, but there is no database to assemble all these data. AntiCODE intends to function as an integrated NAT database for this purpose.ResultsThis release of antiCODE contains more than 30,000 non-redundant natural sense-antisense transcript pairs from 12 eukaryotic model organisms. In order to provide an integrated NAT research platform, efficient browser, search and Blast functions have been included to enable users to easily access information through parameters such as species, accession number, overlapping patterns, coding potential etc. In addition to the collected information, antiCODE also introduces a simple classification system to facilitate the study of natural antisense transcripts.ConclusionThough a few similar databases also dealing with NATs have appeared lately, antiCODE is the most comprehensive among these, comprising almost all currently detected NAT pairs.
Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation
Authors: Klee Kathrin , Ernst Rebecca , Spannagl Manuel , Mayer Klaus FX 
Published: August 2007

Abstract

Background
Apollo, a genome annotation viewer and editor, has become a widely used genome annotation and visualization tool for distributed genome annotation projects. When using Apollo for annotation, database updates are carried out by uploading intermediate annotation files into the respective database. This non-direct database upload is laborious and evokes problems of data synchronicity.

Results
To overcome these limitations we extended the Apollo data adapter with a generic, configurable web service client that is able to retrieve annotation data in a GAME-XML-formatted string and pass it on to Apollo's internal input routine.

Conclusion
This Apollo web service adapter, Apollo2Go, simplifies the data exchange in distributed projects and aims to render the annotation process more comfortable.
The Apollo2Go software is freely available from ftp://ftpmips.gsf.de/plants/apollo_webservice.
Transposable element distribution, abundance and role in genome size variation in the genus Oryza
Authors: Zuccolo Andrea , Sebastian Aswathy , Talag Jayson , Yu Yeisoo , Kim HyeRan , Collura Kristi , Kudrna Dave , Wing Rod A 
Published: August 2007

Abstract

Background
The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop – rice (Oryza sativa [AA]). Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements) in shaping these genomes and in their contributing to genome size variation.

Results
We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial.

Conclusion
Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys) account for a significant portion of the genome size variations present in the Oryza genus.
Common and specific genomic sequences of avian and human extraintestinal pathogenic Escherichia coli as determined by genomic subtractive hybridization
Authors: Kariyawasam Subhashinie , Scaccianoce Jennifer A , Nolan Lisa K 
Published: August 2007

Abstract

Background
Suppression subtractive hybridization (SSH) strategy was used with extraintestinal pathogenic Escherichia coli (EXPEC) that cause avian colibacillosis (avian pathogenic E. coli or APEC) and human urinary tract infections (uropathogenic E. coli or UPEC) to determine if they possessed genes that were host and/or niche specific. Both APEC and UPEC isolates were used as tester and driver strains in 4 different SSHs in order to obtain APEC- and UPEC-specific subtraction fragments (SFs).

Results
These procedures yielded a total of 136 tester-specific SFs of which 85 were APEC-derived and 51 were UPEC-derived. Most of the APEC-derived SFs were associated with plasmids; whereas, the majority of UPEC-derived sequences matched to the bacterial chromosome. We further determined the distribution of these tester-derived sequences in a collection of UPEC and APEC isolates using polymerase chain reaction techniques. Plasmid-borne, APEC-derived sequences (tsh, cva B, tra R, tra C and sop B) were predominantly present in APEC, as compared to UPEC. Of the UPEC-derived SFs, those encoding hemolysin D and F1C major and minor fimbrial subunits were present only in UPEC. However, two UPEC-derived SFs that showed strong similarity to the uropathgenic-specific protein gene (usp) occurred in APEC, demonstrating that usp is not specific to UPEC.

Conclusion
This study provides evidence of the genetic variability of ExPEC as well as genomic similarities between UPEC and APEC; it did not identify any single marker that would dictate host and/or niche specificity in APEC or UPEC. However, further studies on the genes that encode putative or hypothetical proteins might offer important insight into the pathogenesis of disease, as caused by these two ExPEC.
Meningitis registry of hospitalized cases in children: epidemiological patterns of acute bacterial meningitis throughout a 32-year period
Authors: Theodoridou Maria N , Vasilopoulou Vasiliki A , Atsali Erato E , Pangalis Anastasia M , Mostrou Glyceria J , Syriopoulou Vassiliki P , Hadjichristodoulou Christos S 
Published: August 2007

Abstract

Background
Bacterial meningitis remains a source of substantial morbidity and mortality in childhood. During the last decades gradual changes have been observed in the epidemiology of bacterial meningitis, related to the introduction of new polysaccharide and conjugate vaccines. The study presents an overview of the epidemiological patterns of acute bacterial meningitis in a tertiary children 's hospital during a 32-year period, using information from a disease registry. Moreover, it discusses the contribution of communicable disease registries in the study of acute infectious diseases.

Methods
In the early 1970s a Meningitis Registry (MR) was created for patients admitted with meningitis in Aghia Sofia Children's Hospital in Athens. The MR includes demographic, clinical and laboratory data as well as treatment, complications and outcome of the patients. In 2000 a database was created and the collected data were entered, analyzed and presented in three chronological periods: A (1974–1984), B (1985–1994) and C (1995–2005).

Results
Of the 2,477 cases of bacterial meningitis registered in total, 1,146 cases (46.3%) were classified as "probable" and 1,331 (53.7%) as "confirmed" bacterial meningitis. The estimated mean annual Incidence Rate (IR) was 16.9/100,000 for bacterial meningitis, 8.9/100,000 for Neisseria meningitidis, 1.3/100,000 for Streptococcus pneumoniae, 2.5/100,000 for Haemophilus influenzae type b (Hib) before vaccination and 0.4/100,000 for Hib after vaccination. Neisseria meningitis constituted the leading cause of childhood bacterial meningitis for all periods and in all age groups. Hib was the second most common cause of bacterial meningitis before the introduction of Hib conjugate vaccine, in periods A and B. The incidence of bacterial meningitis due to Streptococcus pneumoniae was stable. The long-term epidemiological pattern of Neisseria meningitidis appears in cycles of approximately 10 years, confirmed by a significant rise of IR in period C. The Case Fatality Rate (CFR) from all causes was 3.8%, while higher CFR were estimated for Streptococcus pneumoniae (7.5%, RR=2.1, 95% CI 1.2–3.7) and Neisseria meningitidis (4.8%, RR=1.7, 95% CI 1.1–2.5) compared to other pathogens. Moreover, overall CFR varied significantly among the three time periods (p = 0.0015), and was estimated to be higher in period C.

Conclusion
By using the MR we were able to delineate long-term changes in the epidemiology of bacterial meningitis. Thus the MR proved to be a useful tool in the study and the prevention of communicable diseases in correlation with prevention strategies, such as vaccinations.
The prevalance, epidemiology and risk factors for onychomycosis in hemodialysis patients
Authors: Kuvandik Güven , Çetin Meryem , Genctoy Gultekin , Horoz Mehmet , Duru Mehmet , Akcali Cenk , Satar Salim , Kiykim Ahmet A , Kaya Hasan 
Published: August 2007

AbstractBackgroundOnychomycosis has a high prevalance among immunocompromised patients such as diabetics and hemodialysis patients. In the present study, we aimed to investigate the prevalence of onychomycosis among hemodialysis patients with and without diabetes mellitus, and to find out the factors likely to be associated with the development of onychomycosis among hemodialysis patients.MethodsOne hundred and nine hemodialysis patients were enrolled. Fifty-seven of hemodialysis patients had the diagnosis of diabetes mellitus. Nail scrapings were obtained from 76 patients who had dystrophic nail changes. Samples were examined with 20% potassium hydroxide solution and all of the samples were inoculated on Saboraud's dextrose agar, potateus dextrose agar and mycobiotic agar. Diagnosis of onychomycosis was based on the presence of both positive clinical signs and positive potassium hydroxide test.ResultsOnychomycosis was diagnosed in 26.6% of hemodialysis patients. Diabetes mellitus was present in 68.9% of patients with onychomycosis. Toenail scraping cultures were reported to be positive in 19.7% of patients with dystrophic nail changes. Logistic regression analysis revealed that the presence of diabetes mellitus and the mean duration of hemodialysis were the significant predictors associated with the development of onychomycosis.ConclusionThe prevalence of dystrophic nail changes and onychomycosis is increased among hemodialysis patients. The dialysis duration and the presence of diabetes mellitus are the independent risk factors associated with the development of onychomycosis in uraemic patients.
Attitudes, understanding, and concerns regarding medical research amongst Egyptians: A qualitative pilot study
Authors: Khalil Susan S , Silverman Henry J , Raafat May , El-Kamary Samer , El-Setouhy Maged 
Published: August 2007

Abstract

Background
Medical research must involve the participation of human subjects. Knowledge of patients' perspectives and concerns with their involvement in research would enhance recruitment efforts, improve the informed consent process, and enhance the overall trust between patients and investigators. Several studies have examined the views of patients from Western countries. There is limited empirical research involving the perspectives of individuals from developing countries. The purpose of this study is to examine the attitudes of Egyptian individuals toward medical research. Such information would help clarify the type and extent of concerns regarding research participation of individuals from cultural, economic, and political backgrounds that differ from those in developed countries.

Methods
We conducted semi-structured interviews with 15 Egyptian individuals recruited from the outpatient settings (public and private) at Ain Shams University in Cairo, Egypt. Interviews were taped, transcribed, and translated. Thematic analysis followed.

Results
All individuals valued the importance of medical research; however most would not participate in research that involved more than minimal risk. Individuals were comfortable with studies involving surveys and blood sampling, but many viewed drug trials as being too risky. All participants valued the concept of informed consent, as they thought that their permission to be in a research study was paramount. Many participants had discomfort with or difficulty in the understanding several research concepts: randomization, double-blind, and clinical equipoise. Trust in the physicians performing research was important in deciding to participate in clinical research. The small sample size and the selection bias associated with obtaining information from only those who agreed to participate in a research study represent limitations in this study.

Conclusion
Overall, individuals in our sample recognize the value of medical research and have a great deal of trust regarding medical research and their participation in research. There were, however, concerns with the level of research risks associated with several types of medical research. Many also demonstrated confusion with certain research methodologies. We recommend 1) enhanced educational efforts regarding general research concepts to enhance the validity of informed consent and 2) further survey studies in other areas of Egypt to determine the generalizability of our results.
PKCepsilon and an increase in intracellular calcium concentration are necessary for PGF2alpha to inhibit LH-stimulated progesterone secretion in cultured bovine steroidogenic luteal cells
Authors: Goravanahally Madhusudan P , Sen Aritro , Inskeep Emmet K , Flores Jorge A 
Published: August 2007

Abstract
The hypotheses that PKCepsilon is necessary for: 1) PGF2alpha to inhibit LH-stimulated progesterone (P4) secretion, and 2) for the expression of key prostaglandin synthesizing/metabolizing enzymes were tested in bovine luteal cells in which PKCepsilon expression had been ablated using a validated siRNA protocol. Steroidogenic cells from Day -6 bovine corpus luteum (CL) were isolated and transfected to reduce PKCepsilon expression after 48, 72 and 96 h. A third tested hypothesis was that an increase in intracellular calcium concentration ([Ca(2+)]i) is the cellular mechanism through which PGF2alpha inhibits luteal progesterone. The hypothesis was tested with two pharmacological agents. In the first test, the dose-dependent effects on raising the [Ca(2+)]i with the ionophore, A23187, on basal and LH-stimulated P4 secretion in cells collected from early (Day -4) and mid-cycle (Day -10) bovine CL was examined. In the second test, the ability of PGF2alpha to inhibit LH-stimulated P4 secretion in Day-10 luteal cells was examined under conditions in which an elevation in [Ca(2+)]i had been buffered by means of the intracellular calcium chelator, Bapta-AM.
PKCepsilon expression was reduced 65 and 75% by 72 and 96 h after transfection, respectively. In cells in which PKCepsilon expression was ablated by 75%, the inhibitory effect of PGF2alpha on LH-stimulated P4 secretion was only 29% lower than in the LH-stimulated group. In contrast, it was reduced by 75% in the group where PKCepsilon expression had not been reduced (P < 0.05). Real time PCR analysis indicated that there were no differences in the expression of cyclooxygenase-2 (COX-2), aldoketoreductase 1B5 (AKR1B5), prostaglandin E synthase (PGES), hydroxyprostaglandin-15 dehydrogenase (PGDH) and PGE2 -9-reductase as a function of PKCepsilon down-regulation. Finally, LH stimulated secretion of P4 at each luteal stage (Day -4 and -10), and PGF2alpha inhibited this only in Day -10 cells (P < 0.05). When A23187 was used at concentrations greater than 0.1 μmol, the induced elevation in [Ca(2+)]i inhibited the effect of LH on secretion of P4 in Day -4 and -10 cells (P < 0.05, Fig. 5). The inhibitory effect of PGF2alpha on LH-stimulated P4 in Day -10 cells was reduced if an increase in [Ca(2+)]i was prevented with Bapta-AM. These results support the hypothesis that differential expression of PKCepsilon and an elevation of [Ca(2+)]i are important for acquisition of luteolytic response to PGF2alpha.
Application of Atomic Dielectric Resonance Spectroscopy for the screening of blood samples from patients with clinical variant and sporadic CJD
Authors: Fagge Timothy J , Barclay G Robin , Stove G Colin , Stove Gordon , Robinson Michael J , Head Mark W , Ironside James W , Turner Marc L 
Published: August 2007

Abstract

Background
Sub-clinical variant Creutzfeldt-Jakob disease (vCJD) infection and reports of vCJD transmission through blood transfusion emphasise the need for blood screening assays to ensure the safety of blood and transplanted tissues. Most assays aim to detect abnormal prion protein (PrPSc), although achieving required sensitivity is a challenge.

Methods
We have used innovative Atomic Dielectric Resonance Spectroscopy (ADRS), which determines dielectric properties of materials which are established by reflectivity and penetration of radio/micro waves, to analyse blood samples from patients and controls to identify characteristic ADR signatures unique to blood from vCJD and to sCJD patients. Initial sets of blood samples from vCJD, sCJD, non-CJD neurological diseases and normal healthy adults (blood donors) were screened as training samples to determine group-specific ADR characteristics, and provided a basis for classification of blinded sets of samples.

Results
Blood sample groups from vCJD, sCJD, non-CJD neurological diseases and normal healthy adults (blood donors) screened by ADRS were classified with 100% specificity and sensitivity, discriminating these by a co-variance expert analysis system.

Conclusion
ADRS appears capable of recognising and discriminating serum samples from vCJD, sCJD, non-CJD neurological diseases, and normal healthy adults, and might be developed to provide a system for primary screening or confirmatory assay complementary to other screening systems.
Targeting APOBEC3A to the viral nucleoprotein complex confers antiviral activity
Authors: Goila-Gaur Ritu , Khan Mohammad A , Miyagi Eri , Kao Sandra , Strebel Klaus 
Published: August 2007

Abstract

Background
APOBEC3 (A3) proteins constitute a family of cytidine deaminases that provide intracellular resistance to retrovirus replication and to transposition of endogenous retroelements. A3A has significant homology to the C-terminus of A3G but has only a single cytidine deaminase active site (CDA), unlike A3G, which has a second N-terminal CDA previously found to be important for Vif sensitivity and virus encapsidation. A3A is packaged into HIV-1 virions but, unlike A3G, does not have antiviral properties. Here, we investigated the reason for the lack of A3A antiviral activity.

Results
Sequence alignment of A3G and A3A revealed significant homology of A3A to the C-terminal region of A3G. However, while A3G co-purified with detergent-resistant viral nucleoprotein complexes (NPC), virus-associated A3A was highly detergent-sensitive leading us to speculate that the ability to assemble into NPC may be a property conveyed by the A3G N-terminus. To test this model, we constructed an A3G-3A chimeric protein, in which the N-terminal half of A3G was fused to A3A. Interestingly, the A3G-3A chimera was packaged into HIV-1 particles and, unlike A3A, associated with the viral NPC. Furthermore, the A3G-3A chimera displayed strong antiviral activity against HIV-1 and was sensitive to inhibition by HIV-1 Vif.

Conclusion
Our results suggest that the A3G N-terminal domain carries determinants important for targeting the protein to viral NPCs. Transfer of this domain to A3A results in A3A targeting to viral NPCs and confers antiviral activity.