bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures
Authors: Popenda Mariusz , Szachniuk Marta , Blazewicz Marek , Wasik Szymon , Burke Edmund K , Blazewicz Jacek , Adamiak Ryszard W 
Published: May 2010

AbstractBackgroundRecent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization.DescriptionRNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available athttp://rnafrabase.cs.put.poznan.pl.ConclusionsRNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field.
Bootstrap-based Support of HGT Inferred by Maximum Parsimony
Authors: Park Hyun Jung , Jin Guohua , Nakhleh Luay 
Published: May 2010

AbstractBackgroundMaximum parsimony is one of the most commonly used criteria for reconstructing phylogenetic trees. Recently, Nakhleh and co-workers extended this criterion to enable reconstruction ofphylogenetic networks, and demonstrated its application to detecting reticulate evolutionary relationships. However, one of the major problems with this extension has been that it favors more complex evolutionary relationships over simpler ones, thus having the potential for overestimating the amount of reticulation in the data. Anad hocsolution to this problem that has been used entails inspecting the improvement in the parsimony length as more reticulation events are added to the model, and stopping when the improvement is below a certain threshold.ResultsIn this paper, we address this problem in a more systematic way, by proposing a nonparametric bootstrap-based measure of support of inferred reticulation events, and using it to determine the number of those events, as well as their placements. A number of samples is generated from the given sequence alignment, and reticulation events are inferred based on each sample. Finally, the support of each reticulation event is quantified based on the inferences made over all samples.ConclusionsWe have implemented our method in the NEPAL software tool (available publicly athttp://bioinfo.cs.rice.edu/), and studied its performance on both biological and simulated data sets. While our studies show very promising results, they also highlight issues that are inherently challenging when applying the maximum parsimony criterion to detect reticulate evolution.
A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae
Authors: Shen Yong-Yi , Liang Lu , Sun Yan-Bo , Yue Bi-Song , Yang Xiao-Jun , Murphy Robert W , Zhang Ya-Ping 
Published: May 2010

AbstractBackgroundThe Galliformes is a well-known and widely distributed Order in Aves. The phylogenetic relationships of galliform birds, especially the turkeys, grouse, chickens, quails, and pheasants, have been studied intensively, likely because of their close association with humans. Despite extensive studies, convergent morphological evolution and rapid radiation have resulted in conflicting hypotheses of phylogenetic relationships. Many internal nodes have remained ambiguous.ResultsWe analyzed the complete mitochondrial (mt) genomes from 34 galliform species, including 14 new mt genomes and 20 published mt genomes, and obtained a single, robust tree. Most of the internal branches were relatively short and the terminal branches long suggesting an ancient, rapid radiation. The Megapodiidae formed the sister group to all other galliforms, followed in sequence by the Cracidae, Odontophoridae and Numididae. The remaining clade included the Phasianidae, Tetraonidae and Meleagrididae. The genusArborophilawas the sister group of the remaining taxa followed byPolyplectron. This was followed by two major clades: ((((Gallus,Bambusicola)Francolinus) (Coturnix,Alectoris))Pavo) and (((((((Chrysolophus,Phasianus)Lophura)Syrmaticus)Perdix)Pucrasia) (Meleagris,Bonasa)) ((Lophophorus,Tetraophasis)Tragopan))).ConclusionsThe traditional hypothesis of monophyletic lineages of pheasants, partridges, peafowls and tragopans was not supported in this study. Mitogenomic analyses recovered robust phylogenetic relationships and suggested that the Galliformes formed a model group for the study of morphological and behavioral evolution.
Frequent and recent retrotransposition of orthologous genes plays a role in the evolution of sperm glycolytic enzymes
Authors: Vemuganti Soumya A , de Villena Fernando Pardo-Manuel , O'Brien Deborah A 
Published: May 2010

AbstractBackgroundThe central metabolic pathway of glycolysis converts glucose to pyruvate, with the net production of 2 ATP and 2 NADH per glucose molecule. Each of the ten reactions in this pathway is typically catalyzed by multiple isozymes encoded by a multigene family. Several isozymes in this pathway are expressed only during spermatogenesis, and gene targeting studies indicate that they are essential for sperm function and male fertility in mouse. At least three of the novel glycolytic isozymes are encoded by retrogenes (Pgk2,Aldoart1, andAldoart2). Their restricted expression profile suggests that retrotransposition may play a significant role in the evolution of sperm glycolytic enzymes.ResultsWe conducted a comprehensive genomic analysis of glycolytic enzymes in the human and mouse genomes and identified several intronless copies for all enzymes in the pathway, exceptPfk. Within each gene family, a single orthologous gene was typically retrotransposed frequently and independently in both species. Several retroposed sequences maintained open reading frames (ORFs) and/or provided evidence of alternatively spliced exons. We analyzed expression of sequences with ORFs and <99% sequence identity in the coding region and obtained evidence for the expression of an alternativeGpi1transcript in mouse spermatogenic cells.ConclusionsOur analysis detected frequent, recent, and lineage-specific retrotransposition of orthologous glycolytic enzymes in the human and mouse genomes. Retrotransposition events are associated with LINE/LTR and genomic integration is random. We found evidence for the alternative splicing of parent genes. Many retroposed sequences have maintained ORFs, suggesting a functional role for these genes.
Epidemiology of Herpes Zoster Infection among Patients Treated in Primary Care Centres in the Valencian Community (Spain)
Authors: Cebrián-Cuenca Ana M , Díez-Domingo Javier , Rodríguez María San-Martín , Puig-Barberá Joan , Navarro-Pérez Jorge ,   the 'Herpes Zoster Research Group of the Valencian Community'
Published: May 2010

Abstract

Background
There is little available data regarding the epidemiology of herpes zoster (HZ) in Spain. This study's main goal was to estimate the annual incidence of HZ in the Autonomous Community of Valencia.

Methods
From December 1st 2006 to December 1st 2007, a prospective study was carried out in 24 primary health care centres that together provide care for a population of 36,030 persons aged >14 years. We included all adult patients with a clinical diagnosis of HZ who were seen at these centres during the one-year study period. Demographic (i.e., age, gender, and area of residence) and clinical data were also collected from these patients.

Results
A total of 146 cases of HZ were identified during the study period. The annual incidence of HZ was 4.1/1,000 individuals >14 years of age (95% confidence interval [CI]: 3.4-4.7). Cases of HZ were predominantly unilateral and most commonly affected women and people living in rural areas. The most frequently reported symptoms were pain, dysesthesia and itching. A total of 46% of patients also had underlying illnesses (e.g., chronic diseases and/or malignancy) and 24% of patients experienced complications, which were mostly ocular in nature. A total of 91% of patients were treated with antiviral drugs. The median time from symptoms onset to diagnosis was 6.3 days (range: 2.0-8.3).

Conclusions
HZ is a common illness in our region (especially in the older population) that causes a significant clinical burden on primary care providers.
Exploitation of the interaction of measles virus fusogenic envelope proteins with the surface receptor CD46 on human cells for microcell-mediated chromosome transfer
Authors: Katoh Motonobu , Kazuki Yasuhiro , Kazuki Kanako , Kajitani Naoyo , Takiguchi Masato , Nakayama Yuji , Nakamura Takafumi , Oshimura Mitsuo 
Published: May 2010

Abstract

Background
Microcell-mediated chromosome transfer (MMCT) is a technique by which a chromosome(s) is moved from donor to recipient cells by microcell fusion. Polyethylene glycol (PEG) has conventionally been used as a fusogen, and has been very successful in various genetic studies. However, PEG is not applicable for all types of recipient cells, because of its cell type-dependent toxicity. The cytotoxicity of PEG limits the yield of microcell hybrids to low level (10-6 to 10-5 per recipient cells). To harness the full potential of MMCT, a less toxic and more efficient fusion protocol that can be easily manipulated needs to be developed.

Results
Microcell donor CHO cells carrying a human artificial chromosome (HAC) were transfected with genes encoding hemagglutinin (H) and fusion (F) proteins of an attenuated Measles Virus (MV) Edmonston strain. Mixed culture of the CHO transfectants and MV infection-competent human fibrosarcoma cells (HT1080) formed multinucleated syncytia, suggesting the functional expression of the MV-H/F in the CHO cells. Microcells were prepared and applied to HT1080 cells, human immortalized mesenchymal stem cells (hiMSC), and primary fibroblasts. Drug-resistant cells appeared after selection in culture with Blasticidin targeted against the tagged selection marker gene on the HAC. The fusion efficiency was determined by counting the total number of stable clones obtained in each experiment. Retention of the HAC in the microcell hybrids was confirmed by FISH analyses. The three recipient cell lines displayed distinct fusion efficiencies that depended on the cell-surface expression level of CD46, which acts as a receptor for MV. In HT1080 and hiMSC, the maximum efficiency observed was 50 and 100 times greater than that using conventional PEG fusion, respectively. However, the low efficiency of PEG-induced fusion with HFL1 was not improved by the MV fusogen.

Conclusions
Ectopic expression of MV envelope proteins provides an efficient recipient cell-oriented MMCT protocol, facilitating extensive applications for studies of gene function and genetic corrections.
Novel protein kinase D inhibitors cause potent arrest in prostate cancer cell growth and motility
Authors: LaValle Courtney R , Bravo-Altamirano Karla , Giridhar Karthik V , Chen Jun , Sharlow Elizabeth , Lazo John S , Wipf Peter , Wang Q Jane 
Published: May 2010

AbstractBackgroundProtein kinase D (PKD) has been implicated in a wide range of cellular processes and pathological conditions including cancer. However, targeting PKD therapeutically and dissecting PKD-mediated cellular responses remains difficult due to lack of a potent and selective inhibitor. Previously, we identified a novel pan-PKD inhibitor, CID755673, with potency in the upper nanomolar range and high selectivity for PKD. In an effort to further enhance its selectivity and potency for potentialin vivoapplication, small molecule analogs of CID755673 were generated by modifying both the core structure and side-chains.ResultsAfter initial activity screening, five analogs with equal or greater potencies as CID755673 were chosen for further analysis: kb-NB142-70, kb-NB165-09, kb-NB165-31, kb-NB165-92, and kb-NB184-02. Our data showed that modifications to the aromatic core structure in particular significantly increased potency while retaining high specificity for PKD. When tested in prostate cancer cells, all compounds inhibited PMA-induced autophosphorylation of PKD1, with kb-NB142-70 being most active. Importantly, these analogs caused a dramatic arrest in cell proliferation accompanying elevated cytotoxicity when applied to prostate cancer cells. Cell migration and invasion were also inhibited by these analogs with varying potencies that correlated to their cellular activity.ConclusionsThroughout the battery of experiments, the compounds kb-NB142-70 and kb-NB165-09 emerged as the most potent and specific analogsin vitroand in cells. These compounds are undergoing further testing for their effectiveness as pharmacological tools for dissecting PKD function and as potential anti-cancer agents in the treatment of prostate cancer.
Towards a precise test for malaria diagnosis in the Brazilian Amazon: comparison among field microscopy, a rapid diagnostic test, nested PCR, and a computational expert system based on artificial neural networks
Authors: Andrade Bruno B , Reis-Filho Antonio , Barros Austeclino M , Souza-Neto Sebastião M , Nogueira Lucas L , Fukutani Kiyoshi F , Camargo Erney P , Camargo Luís MA , Barral Aldina , Duarte Ângelo , Barral-Netto Manoel 
Published: May 2010

Abstract

Background
Accurate malaria diagnosis is mandatory for the treatment and management of severe cases. Moreover, individuals with asymptomatic malaria are not usually screened by health care facilities, which further complicates disease control efforts. The present study compared the performances of a malaria rapid diagnosis test (RDT), the thick blood smear method and nested PCR for the diagnosis of symptomatic malaria in the Brazilian Amazon. In addition, an innovative computational approach was tested for the diagnosis of asymptomatic malaria.

Methods
The study was divided in two parts. For the first part, passive case detection was performed in 311 individuals with malaria-related symptoms from a recently urbanized community in the Brazilian Amazon. A cross-sectional investigation compared the diagnostic performance of the RDT Optimal-IT, nested PCR and light microscopy. The second part of the study involved active case detection of asymptomatic malaria in 380 individuals from riverine communities in Rondônia, Brazil. The performances of microscopy, nested PCR and an expert computational system based on artificial neural networks (MalDANN) using epidemiological data were compared.

Results
Nested PCR was shown to be the gold standard for diagnosis of both symptomatic and asymptomatic malaria because it detected the major number of cases and presented the maximum specificity. Surprisingly, the RDT was superior to microscopy in the diagnosis of cases with low parasitaemia. Nevertheless, RDT could not discriminate the Plasmodium species in 12 cases of mixed infections (Plasmodium vivax + Plasmodium falciparum). Moreover, the microscopy presented low performance in the detection of asymptomatic cases (61.25% of correct diagnoses). The MalDANN system using epidemiological data was worse that the light microscopy (56% of correct diagnoses). However, when information regarding plasma levels of interleukin-10 and interferon-gamma were inputted, the MalDANN performance sensibly increased (80% correct diagnoses).

Conclusions
An RDT for malaria diagnosis may find a promising use in the Brazilian Amazon integrating a rational diagnostic approach. Despite the low performance of the MalDANN test using solely epidemiological data, an approach based on neural networks may be feasible in cases where simpler methods for discriminating individuals below and above threshold cytokine levels are available.
Low titers of measles antibody in mothers whose infants suffered from measles before eligible age for measles vaccination
Authors: Zhao Hong , Lu Pei-Shan , Hu Yali , Wu Qiaozhen , Yao Wenhu , Zhou Yi-Hua 
Published: May 2010

Abstract

Background
Resurgence or outbreak of measles recently occurred in both developed and developing countries despite long-standing widespread use of measles vaccine. Measles incidence in China has increased since 2002, particularly in infants and in persons ≥ 15 years of age. It is speculated that infants may acquire fewer measles IgG from their mothers, resulting in the reduced duration of protection during their early months of life. This study aimed to clarify the reason of increased susceptibility to measles in young infants in China. Measles IgG in 24 measles infants ≤ 9 months of age and their vaccinated mothers was quantitatively measured. The mean measles neutralizing titer in the vaccinated mothers and in 13 age-match women with the histories of clinical measles were compared.

Results
All the mothers were confirmed to be vaccinated successfully by the presence of measles IgG. Six vaccinated mothers were positive for measles IgM and had high concentrations of measles IgG and the neutralizing antibody, indicating underwent natural boosting. The mean measles neutralizing titer in 18 vaccinated mothers without natural boosting were significantly lower than that in 13 age-match women with the histories of clinical measles (1:37 vs 1:182, P < 0.05).

Conclusions
Our results suggest that infants born to mothers who acquired immunity to measles by vaccination may get a relatively small amount of measles antibody, resulting in loss of the immunity to measles before the vaccination age. Measures to improve the immunity in young infants not eligible for measles vaccination would be critical to interrupt the measles transmission in China.
Challenges in experimental data integration within genome-scale metabolic models
Authors: Bourguignon Pierre-Yves , Samal Areejit , Képès François , Jost Jürgen , Martin Olivier C 
Published: May 2010

Abstract
A report of the meeting "Challenges in experimental data integration within genome-scale metabolic models", Institut Henri Poincaré, Paris, October 10-11 2009, organized by the CNRS-MPG joint program in Systems Biology.
Fluid accumulation, recognition and staging of acute kidney injury in critically-ill patients
Authors: Macedo Etienne , Bouchard Josée , Soroko Sharon H , Chertow Glenn M , Himmelfarb Jonathan , Ikizler T Alp , Paganini Emil P , Mehta Ravindra L ,   for the Program to Improve Care in Acute Renal Disease (PICARD) study
Published: May 2010

Abstract
Introduction
Serum creatinine concentration (sCr) is the marker used for diagnosing and staging acute kidney injury (AKI) in the RIFLE and AKIN classification systems, but is influenced by several factors including its volume of distribution. We evaluated the effect of fluid accumulation on sCr to estimate severity of AKI.

Methods
In 253 patients recruited from a prospective observational study of critically-ill patients with AKI, we calculated cumulative fluid balance and computed a fluid-adjusted sCr concentration reflecting the effect of volume of distribution during the development phase of AKI. The time to reach a relative 50% increase from the reference sCr using the crude and adjusted sCr was compared. We defined late recognition to estimate severity of AKI when this time interval to reach 50% relative increase between the crude and adjusted sCr exceeded 24 hours.

Results
The median cumulative fluid balance increased from 2.7 liters on day 2 to 6.5 liters on day 7. The difference between adjusted and crude sCr was significantly higher at each time point and progressively increased from a median difference of 0.09 mg/dL to 0.65 mg/dL after six days. Sixty-four (25%) patients met criteria for a late recognition to estimate severity progression of AKI. This group of patients had a lower urine output and a higher daily and cumulative fluid balance during the development phase of AKI. They were more likely to need dialysis but showed no difference in mortality compared to patients who did not meet the criteria for late recognition of severity progression.

Conclusions
In critically-ill patients, the dilution of sCr by fluid accumulation may lead to underestimation of the severity of AKI and increases the time required to identify a 50% relative increase in sCr. A simple formula to correct sCr for fluid balance can improve staging of AKI and provide a better parameter for earlier recognition of severity progression.
Molecular chaperones and protein-folding catalysts as intercellular signaling regulators in immunity and inflammation
Authors: Henderson Brian , Pockley A Graham 
Published: May 2010

AbstractReview critically examines the hypothesis that molecular chaperones from prokaryotic and eukaryotic sources can be secreted by cells and function as intercellular signaling molecules.This review critically examines the hypothesis that molecular chaperones and protein-folding catalysts from prokaryotes and eukaryotes can be secreted by cells and function as intercellular signals, principally but not exclusively, for leukocytes. A growing number of molecular chaperones have been reported to function as ligands for selected receptors and/or receptors for specific ligands. Molecular chaperones initially appeared to act primarily as stimulatory signals for leukocytes and thus, were seen as proinflammatory mediators. However, evidence is now emerging that molecular chaperones can have anti-inflammatory actions or, depending on the protein and concentration, anti- and proinflammatory functions. Recasting the original hypothesis, we propose that molecular chaperones and protein-folding catalysts are “moonlighting” proteins that function as homeostatic immune regulators but may also under certain circumstances, contribute to tissue pathology. One of the key issues in the field of molecular chaperone biology relates to the role of microbial contaminants in their signaling activity; this too will be evaluated critically. The most fascinating aspect of molecular chaperones probably relates to evidence for their therapeutic potential in human disease, and ongoing studies are evaluating this potential in a range of clinical settings.