bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative evaluation of short-term biomarker response to treatment for growth hormone deficiency in Chinese children with growth hormone deficiency born small for or appropriate for gestational age: a randomized phase IV open-label study
Authors: Lu Wenli , Shen Shuixian , Luo Xiaoping , Gong Chunxiu , Gu Xuefan , Li Yun , Du Minlian , Jin Runming , Zhou Queena , Wang Wei 
Published: April 2013

Objectives: To compare the response between Chinese children with growth hormone deficiency (GHD) born either small for gestational age (SGA) or appropriate for gestational age (AGA) after 4 weeks of recombinant human growth hormone (r-hGH) therapy. Methods: This was a phase IV, open-label, multicenter, interventional study (NCT01187550). Prepubertal children with GHD received open-label treatment with daily r-hGH (0.033 mg/kg) for 4 weeks. Serum levels of insulin-like growth factor I (IGF-I) and insulin-like growth factor-binding protein 3 (IGFBP3), and metabolic markers (including fasting glucose, insulin, total cholesterol, and homeostasis model assessment of insulin resistance) were assessed at baseline and after 4 weeks of treatment, and were analyzed according to patient subgroup (SGA or AGA). Results: A total of 205 children with GHD (mean age 10.4 years; 175 AGA, 30 SGA) were included in the analysis. Mean baseline serum IGF-I and IGFBP3 standard deviation scores (SDS) across the whole patient population were lower than the population norms (mean values: -2.1 SDS for IGF-I and -1.2 SDS for IGFBP3), with no significant differences between the two patient subgroups. After 4 weeks, IGF-I and IGFBP3 levels increased by 1.0 SDS ( p < 0.001) and 0.34 SDS ( p < 0.001), respectively, but no significant differences were found between the two patient subgroups for growth-related or metabolic markers. Conclusions: For children with GHD born SGA, IGF-I and IGFBP3 are short-term biomarkers of responsiveness to treatment with growth hormone, as for children with GHD born AGA.
Logic Learning Machine creates explicit and stable rules stratifying neuroblastoma patients
Authors: Cangelosi Davide , Blengio Fabiola , Versteeg Rogier , Eggert Angelika , Garaventa Alberto , Gambini Claudio , Conte Massimo , Eva Alessandra , Muselli Marco , Varesio Luigi 
Published: April 2013

Abstract

Background
Neuroblastoma is the most common pediatric solid tumor. About fifty percent of high risk patients die despite treatment making the exploration of new and more effective strategies for improving stratification mandatory. Hypoxia is a condition of low oxygen tension occurring in poorly vascularized areas of the tumor associated with poor prognosis. We had previously defined a robust gene expression signature measuring the hypoxic component of neuroblastoma tumors (NB-hypo) which is a molecular risk factor. We wanted to develop a prognostic classifier of neuroblastoma patients' outcome blending existing knowledge on clinical and molecular risk factors with the prognostic NB-hypo signature. Furthermore, we were interested in classifiers outputting explicit rules that could be easily translated into the clinical setting.

Results
Shadow Clustering (SC) technique, which leads to final models called Logic Learning Machine (LLM), exhibits a good accuracy and promises to fulfill the aims of the work. We utilized this algorithm to classify NB-patients on the bases of the following risk factors: Age at diagnosis, INSS stage, MYCN amplification and NB-hypo. The algorithm generated explicit classification rules in good agreement with existing clinical knowledge. Through an iterative procedure we identified and removed from the dataset those examples which caused instability in the rules. This workflow generated a stable classifier very accurate in predicting good and poor outcome patients. The good performance of the classifier was validated in an independent dataset. NB-hypo was an important component of the rules with a strength similar to that of tumor staging.

Conclusions
The novelty of our work is to identify stability, explicit rules and blending of molecular and clinical risk factors as the key features to generate classification rules for NB patients to be conveyed to the clinic and to be used to design new therapies. We derived, through LLM, a set of four stable rules identifying a new class of poor outcome patients that could benefit from new therapies potentially targeting tumor hypoxia or its consequences.
Analysis and consensus of currently available intrinsic protein disorder annotation sources in the MobiDB database
Authors: Di Domenico Tomás , Walsh Ian , Tosatto Silvio CE 
Published: April 2013

Abstract

Background
Intrinsic protein disorder is becoming an increasingly important topic in protein science. During the last few years, intrinsically disordered proteins (IDPs) have been shown to play a role in many important biological processes, e.g. protein signalling and regulation. This has sparked a need to better understand and characterize different types of IDPs, their functions and roles. Our recently published database, MobiDB, provides a centralized resource for accessing and analysing intrinsic protein disorder annotations.

Results
Here, we present a thorough description and analysis of the data made available by MobiDB, providing descriptive statistics on the various available annotation sources. Version 1.2.1 of the database contains annotations for ca. 4,500,000 UniProt sequences, covering all eukaryotic proteomes. In addition, we describe a novel consensus annotation calculation and its related weighting scheme. The comparison between disorder information sources highlights how the MobiDB consensus captures the main features of intrinsic disorder and correlates well with manually curated datasets. Finally, we demonstrate the annotation of 13 eukaryotic model organisms through MobiDB's datasets, and of an example protein through the interactive user interface.

Conclusions
MobiDB is a central resource for intrinsic disorder research, containing both experimental data and predictions. In the future it will be expanded to include additional information for all known proteins.
VIRGO: visualization of A-to-I RNA editing sites in genomic sequences
Authors: Distefano Rosario , Nigita Giovanni , Macca Valentina , Laganà Alessandro , Giugno Rosalba , Pulvirenti Alfredo , Ferro Alfredo 
Published: April 2013

Abstract

Background
RNA Editing is a type of post-transcriptional modification that takes place in the eukaryotes. It alters the sequence of primary RNA transcripts by deleting, inserting or modifying residues. Several forms of RNA editing have been discovered including A-to-I, C-to-U, U-to-C and G-to-A. In recent years, the application of global approaches to the study of A-to-I editing, including high throughput sequencing, has led to important advances. However, in spite of enormous efforts, the real biological mechanism underlying this phenomenon remains unknown.

Description
In this work, we present VIRGO (http://atlas.dmi.unict.it/virgo/), a web-based tool that maps Ato-G mismatches between genomic and EST sequences as candidate A-to-I editing sites. VIRGO is built on top of a knowledge-base integrating information of genes from UCSC, EST of NCBI, SNPs, DARNED, and Next Generations Sequencing data. The tool is equipped with a user-friendly interface allowing users to analyze genomic sequences in order to identify candidate A-to-I editing sites.

Conclusions
VIRGO is a powerful tool allowing a systematic identification of putative A-to-I editing sites in genomic sequences. The integration of NGS data allows the computation of p-values and adjusted p-values to measure the mapped editing sites confidence. The whole knowledge base is available for download and will be continuously updated as new NGS data becomes available.
Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. triticireveal polymorphic and haustorial expressed secreted proteins as candidate effectors
Authors: Cantu Dario , Segovia Vanesa , MacLean Daniel , Bayles Rosemary , Chen Xianming , Kamoun Sophien , Dubcovsky Jorge , Saunders Diane GO , Uauy Cristobal 
Published: April 2013

Abstract

Background
Wheat yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici (PST) is one of the most devastating diseases of wheat worldwide. To design effective breeding strategies that maximize the potential for durable disease resistance it is important to understand the molecular basis of PST pathogenicity. In particular, the characterisation of the structure, function and evolutionary dynamics of secreted effector proteins that are detected by host immune receptors can help guide and prioritize breeding efforts. However, to date, our knowledge of the effector repertoire of cereal rust pathogens is limited.

Results
We re-sequenced genomes of four PST isolates from the US and UK to identify effector candidates and relate them to their distinct virulence profiles. First, we assessed SNP frequencies between all isolates, with heterokaryotic SNPs being over tenfold more frequent (5.29 ± 2.23 SNPs/kb) than homokaryotic SNPs (0.41 ± 0.28 SNPs/kb). Next, we implemented a bioinformatics pipeline to integrate genomics, transcriptomics, and effector-focused annotations to identify and classify effector candidates in PST. RNAseq analysis highlighted transcripts encoding secreted proteins that were significantly enriched in haustoria compared to infected tissue. The expression of 22 candidate effector genes was characterised using qRT-PCR, revealing distinct temporal expression patterns during infection in wheat. Lastly, we identified proteins that displayed non-synonymous substitutions specifically between the two UK isolates PST-87/7 and PST-08/21, which differ in virulence to two wheat varieties. By focusing on polymorphic variants enriched in haustoria, we identified five polymorphic effector candidates between PST-87/7 and PST-08/21 among 2,999 secreted proteins. These allelic variants are now a priority for functional validation as virulence/avirulence effectors in the corresponding wheat varieties.

Conclusions
Integration of genomics, transcriptomics, and effector-directed annotation of PST isolates has enabled us to move beyond the single isolate-directed catalogues of effector proteins and develop a framework for mining effector proteins in closely related isolates and relate these back to their defined virulence profiles. This should ultimately lead to more comprehensive understanding of the PST pathogenesis system, an important first step towards developing more effective surveillance and management strategies for one of the most devastating pathogens of wheat.
Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas
Authors: Shen Xuemei , Hu Hongbo , Peng Huasong , Wang Wei , Zhang Xuehong 
Published: April 2013

AbstractBackgroundSomePseudomonasstrains function as predominant plant growth-promoting rhizobacteria (PGPR). Within this group,Pseudomonas chlororaphisandPseudomonas fluorescensare non-pathogenic biocontrol agents, and somePseudomonas aeruginosaandPseudomonas stutzeristrains are PGPR.P.chlororaphisGP72 is a plant growth-promoting rhizobacterium with a fully sequenced genome. We conducted a genomic analysis comparing GP72 with three other pseudomonad PGPR:P.fluorescensPf-5,P.aeruginosaM18, and the nitrogen-fixing strainP.stutzeriA1501. Our aim was to identify the similarities and differences among these strains using a comparative genomic approach to clarify the mechanisms of plant growth-promoting activity.ResultsThe genome sizes of GP72, Pf-5, M18, and A1501 ranged from 4.6 to 7.1 M, and the number of protein-coding genes varied among the four species. Clusters of Orthologous Groups (COGs) analysis assigned functions to predicted proteins. The COGs distributions were similar among the four species. However, the percentage of genes encoding transposases and their inactivated derivatives (COG L) was 1.33% of the total genes with COGs classifications in A1501, 0.21% in GP72, 0.02% in Pf-5, and 0.11% in M18. A phylogenetic analysis indicated that GP72 and Pf-5 were the most closely related strains, consistent with the genome alignment results. Comparisons of predicted coding sequences (CDSs) between GP72 and Pf-5 revealed 3544 conserved genes. There were fewer conserved genes when GP72 CDSs were compared with those of A1501 and M18. Comparisons among the fourPseudomonasspecies revealed 603 conserved genes in GP72, illustrating common plant growth-promoting traits shared among these PGPR. Conserved genes were related to catabolism, transport of plant-derived compounds, stress resistance, and rhizosphere colonization. Some strain-specific CDSs were related to different kinds of biocontrol activities or plant growth promotion. The GP72 genome contained thecusoperon (related to heavy metal resistance) and a gene cluster involved in type IV pilus biosynthesis, which confers adhesion ability.ConclusionsComparative genomic analysis of four representative PGPR revealed some conserved regions, indicating common characteristics (metabolism of plant-derived compounds, heavy metal resistance, and rhizosphere colonization) among these pseudomonad PGPR. Genomic regions specific to each strain provide clues to its lifestyle, ecological adaptation, and physiological role in the rhizosphere.
Enhanced biocidal activity of Au nanoparticles synthesized in one pot using 2, 4-dihydroxybenzene carbodithioic acid as a reducing and stabilizing agent
Authors: Naz Syeda Sohaila , Islam Nazar Ul , Shah Muhammad Raza , Alam Syed Sartaj , Iqbal Zafar , Bertino Massimo , Franzel Louis , Ahmed Afifa 
Published: April 2013

Abstract

Background
The conjugation of gold nanoparticles with biocides such as natural products, oligosaccharides, DNA, proteins has attracted great attention of scientists recently. Gold NPs covered with biologically important molecules showed significant enhancement in biological activity in comparison with the activity of the free biocides. However, these reports are not very systematic and do not allow to draw definitive conclusions. We therefore embarked in a systematic study related to the synthesis and characterization of biocidal activities of Au nanoparticles conjugated to a wide variety of synthetic and natural biomolecules. In this specific report, we investigated the activity of a synthetic biocide, 2-4, Dihydroxybenzene carbodithioic acid (DHT).

Results
Au nanoparticles (NP) with a mean size of about 20 nm were synthesized and functionalized in one pot with the help of biocide 2,4-Dihydroxybenzene carbodithioic acid (DHT) to reduce HAuCl4 in aqueous solution. Conjugation of DHT with gold was confirmed by FT-IR and the amount of DHT conjugated to the Au nanoparticles was found to be 7% by weight by measuring the concentration of DHT in the supernatant after centrifugation of the Au NPs. To ascertain the potential for in vivo applications, the stability of the suspensions was investigated as a function of pH, temperature and salt concentration. Antibacterial, antifungal, insecticidal and cytotoxic activities of the Au-DHT conjugates were compared with those of pure DHT and of commercially available biocides. In all cases, the biocidal activity of the Au-DHT conjugates was comparable to that of commercial products and of DHT.

Conclusions
Since the DHT concentration in the Au-DHT conjugates was only about 7%, our results indicate that conjugation to the Au NPs boosts the biocidal activity of DHT by about 14 times. The suspensions were found to be stable for several days at temperatures of up to 100°C, salt concentrations up to 4 mol/L and a pH range of 2-13.
The socio-cultural importance of Mauritia flexuosa palm swamps (aguajales) and implications for multi-use management in two Maijuna communities of the Peruvian Amazon
Authors: Gilmore Michael P , Endress Bryan A , Horn Christa M 
Published: April 2013

Abstract
Background
Fruit from the palm Mauritia flexuosa (aguaje) is harvested throughout the Peruvian Amazon for subsistence and commercial purposes. Recent estimates suggest that residents of Iquitos, the largest city in the region, consume approximately 148.8 metric tons of aguaje fruit per month, the vast majority of which is harvested by felling and killing adult female trees. In this study, we sought to better understand and document the importance of M. flexuosa palm swamps (aguajales) in two Maijuna indigenous communities to inform the sustainable management of this habitat and species.

Methods
Semi-structured interviews, focus groups, and household surveys were carried out to assess the significance of aguajales and their associated plant and animal resources as well as to determine how the relationship that the Maijuna have with aguajales has changed over time.

Results
Aguajales and their associated resources are culturally significant and useful to the Maijuna in a wide variety of ways. In addition to M. flexuosa, the Maijuna use over 60 different species of plants from aguajales. When M. flexuosa is in fruit, aguajales are important hunting areas with a total of 20 different animal species hunted. The Maijuna also have traditional beliefs about aguajales, believing that malevolent supernatural beings reside in them. Notably, the relationship that the Maijuna have with aguajales has changed considerably over the years as aguaje fruit went from a subsistence item collected opportunistically from the ground to a market good destructively harvested beginning in the early 1990s. The Maijuna are concerned not only about how this has affected the future commercial harvest of aguaje but also about its effects on game animals given the importance of hunting to Maijuna cultural identity, subsistence, and income generation.

Conclusions
In order to meet the multiple socio-cultural and economic needs of the Maijuna, sustainable management efforts must be expanded to not only focus on the commercial harvest of aguaje but also other facets of their relationship with this habitat. Our study suggests that the research and development of multi-use forest management plans must not be restricted to commercial forest products and ecosystem services given that many communities rely on tropical forests for a wide range of non-market cultural, economic, and subsistence goods and services.
Proteolysis of Xenopus Cip-type CDK inhibitor, p16Xic2, is regulated by PCNA binding and CDK2 phosphorylation
Authors: Zhu Xi-Ning , Kim Dong Hyun , Lin Horng-Ru , Budhavarapu Varija N , Rosenbaum Herbert B , Mueller Paul R , Yew P Renee 
Published: April 2013

Abstract

Background
Cell division is positively regulated by cyclin-dependent kinases (CDKs) partnered with cyclins and negatively regulated by CDK inhibitors. In the frog, Xenopus laevis, three types of CDK inhibitors have been described: p27Xic1 (Xic1) which shares sequence homology with both p21Cip1 and p27Kip1 from mammals, p16Xic2 (Xic2) which shares sequence homology with p21Cip1, and p17Xic3 (Xic3) which shares sequence homology with p27Kip1. While past studies have demonstrated that during DNA polymerase switching, Xic1 is targeted for protein turnover dependent upon DNA, Proliferating Cell Nuclear Antigen (PCNA), and the ubiquitin ligase CRL4Cdt2, little is known about the processes that regulate Xic2 or Xic3.

Methods
We used the Xenopus interphase egg extract as a model system to examine the regulation of Xic2 by proteolysis and phosphorylation.

Results
Our studies indicated that following primer synthesis during the initiation of DNA replication, Xic2 is targeted for DNA- and PCNA-dependent ubiquitin-mediated proteolysis and that Cdt2 can promote Xic2 turnover. Additionally, during interphase, Xic2 is phosphorylated by CDK2 at Ser-98 and Ser-131 in a DNA-independent manner, inhibiting Xic2 turnover. In the presence of double-stranded DNA ends, Xic2 is also phosphorylated at Ser-78 and Ser-81 by a caffeine-sensitive kinase, but this phosphorylation does not alter Xic2 turnover. Conversely, in the presence or absence of DNA, Xic3 was stable in the Xenopus interphase egg extract and did not exhibit a shift indicative of phosphorylation.

Conclusions
During interphase, Xic2 is targeted for DNA- and PCNA-dependent proteolysis that is negatively regulated by CDK2 phosphorylation. During a response to DNA damage, Xic2 may be alternatively regulated by phosphorylation by a caffeine-sensitive kinase. Our studies suggest that the three types of Xenopus CDK inhibitors, Xic1, Xic2, and Xic3 appear to be uniquely regulated which may reflect their specialized roles during cell division or early development in the frog.
SOCIOLOGICAL DESIGN OF NEW PROFESSION
Authors: Зарубин  
Published: April 2013

A new profession design technology is reveled in this article. A tool of this design is operational sociology. The main directions related to
innovative program of training of higher education specialists in the area of humanitarian technologies are discovered. The sociological construction process consists of several stages. The fi rst one is theoretical basis for the professional fi eld of humanitarian technology. Human technologies have non-material elements as their components which includes knowledge, ideas, sign environment. The second stage of design is building of model of professional competences. The third stage is interaction of high education institution with competent expert community. It has been found that a new type of relationship, the priority of which is involvement of employers in development and implementation of high education institution’s educational policy appears in the modern conditions. The fi nal stage is creation of innovative educational program for new profession staff training — “specialists in the area of humanitarian technologies”.
Co-extraction and stripping behavior of trivalent actinides and fission products in N,N-di-2-ethylhexyl-N´,N´-dioctyl-diglycolamide
Authors: Ravi Jammu , Venkatesan K. A. , Antony M. P. , Srinivasan T. G. , Vasudeva Rao P. R. 
Published: April 2013

Abstract
A solution of 0.1 M N,N-di-2-ethylhexyl-N´,N´-di-octyl-3-oxa-1,5-diamide (DEHDODGA)-0.5 M N,N-dihexyloctanamide (DHOA) in n-dodecane has been evaluated for the separation of trivalent actinides from high-level liquid waste (HLLW). The extraction and stripping behaviour of Am(III) and other metal ions present in HLLW was studied. The distribution ratio of various metal ions was measured as a function of concentration of nitric acid and interfering ion. The extraction of metal ions decreased in the order M4+ ≥ M3+ ≫ M2+ ∼ MO2
2+ ≫ M+. The extraction of Am(III), Eu(III), Y(III), and Zr(IV) was quantitative. However, the distribution ratio of unwanted metal ions such as Fe(III), Co(II), Sb(III), Mn(II), and Cs(I) was negligible. The distribution ratios of Cd(II), Ru(III), Pd(II), Mo(VI), Cr(VI), Ba(II), Ni(II), and Sr(II) were not insignificant, but were quite low. The conditions needed for the quantitative recovery of trivalents from the loaded organic phase were optimized with the use of diethylenetriaminepentaacetic acid (DTPA)-citric acid at pH 3 to facilitate the mutual separation of lanthanides-actinides in the subsequent step.