bluuebunny/crossref_metadata_2025_split huggingface dataset:
Safe Functional Inference for Uncharacterized Viral Proteins
Authors: Loewenstein Yaniv , Linial Michal 
Published: August 2008

AbstractThe explosive growth in the number of sequenced genomes has created a flood of protein sequences with unknown structure and function. A routine protocol for functional inference on an input query sequence is based on a database search for homologues. Searching a query against a non-redundant database using BLAST (or more advanced methods, e.g. PSI-BLAST) suffers from several drawbacks: (i) a local alignment often dominates the results; (ii) the reported statistical score (i.e. E-value) is often misleading; (iii) incorrect annotations may be falsely propagated. Several systematic methods are commonly used to assign sequences with functions on a genomic scale. In Pfam (1) and resources alike, statistical profiles (HMMs) are built from semi-manual multiple alignments of seed homologous sequences. The profiles are then used to scan genomic sequences for additional family members. The drawbacks of this scheme are: (i) only families with a predetermined seed are considered; (ii) the query must have a detectable sequence similarity to seed sequences; (iii) attention to internal relationships among the family members or the relations to other families is lacking; (iv) family membership is often set by pre-determined thresholds.An alternative to profile or model based methods for functional inference relies on a hierarchical clustering of the protein space, as implemented in the ProtoNet approach (2). The fundamental principle is the creation of a tree that captures evolutionary relatedness among protein families. The tree construction is fully automatic, and is based only on reported BLAST similarities among clustered sequences. The tree provides protein groupings in continuous evolutionary granularities, from closely related to distant superfamilies. Clusters in the ProtoNet tree show high correspondence with homologous sequence (i.e. Pfam and InterPro), functional (i.e. E.C. classification) and structural (i.e., SCOP) families (3). A new clustering scheme (4) has provided an extensive update to the ProtoNet process, which is now based on direct clustering of all detectable sequence similarities. Herein, we use the ProtoNet resource to develop a methodology for a consistent and safe functional inference for remote families. We illustrate the success of our approach towards clusters of poorly characterized viral proteins. Viral sequences are characterized by a rapid evolutionary rate which drives viral families to be even more remote (sequence-similarity-wise). Thus, functional inference for viral families is apparently an unsolved task. Despite this inherent difficulty, the new ProtoNet tree scaffold reliably captures weak evolutionary connections for viral families, which were previously overlooked. We take advantage of this, and propose new functional assignments for viral protein families.
BAG‐1 expression in normal endometrium, endometrial hyperplasia and endometrial cancer
Authors: SONG JAE YUN , KIM JI WON , LEE JAE KWAN , LEE NAK WOO , YEOM BOM WOO , KIM SUN HAENG , LEE KYU WAN 
Published: August 2008

AbstractBackground. BAG‐1 (Bcl‐2‐associated athanogene 1) is a BCL‐2 binding anti‐apoptotic protein that may play a role in carcinogenesis. The purpose of this study is to compare the expression rate of BAG‐1 in normal endometrium, endometrial hyperplasia and endometrial cancer, and further to determine a correlation between BAG‐1 expression and clinicopathological parameters, and overall survival. Methods. Tissue samples from 43 patients who were diagnosed with endometrial cancer, tissue samples from 20 patients with endometrial hyperplasia and tissue samples from 20 normal patients were included in the study. Immunohistochemical analyses were performed using a polyclonal anti‐BAG‐1 antibody from paraffin‐embedded blocks. Results. Cytoplasmic BAG‐1 expression of the normal endometrium, endometrial hyperplasia and endometrial cancer samples was 4/20 (20%), 3/20 (15%) and 27/43 (62%), respectively. Nuclear BAG‐1 expression was 17/20 (85%), 12/20 (60%) and 16/43 (37%), respectively. Cytoplasmic BAG‐1 expression correlated with cancer grade (p = 0.02). The mean survival of patients with positive/negative cytoplasmic BAG‐1 expression and nuclear BAG‐1 expression was 49.4/45.4 and 54.0/41.1 months, respectively, but there was no statistical difference for survival (log‐rank p = 0.31, p = 0.55). Conclusion. Cytoplasmic BAG‐1 is more frequently expressed in endometrial cancer tissues than in normal and endometrial hyperplasia tissues (p = 0.0007), and its expression correlates with cancer grade. Nuclear BAG‐1 is more frequently expressed in the normal endometrium and hyperplasia tissues than in endometrial cancer tissues (p = 0.002). Neither cytoplasmic nor nuclear BAG‐1 expression is associated with survival.
Humor, Abstraction, and Disbelief
Authors: Hoicka Elena , Jutsum Sarah , Gattis Merideth 
Published: August 2008

AbstractWe investigated humor as a context for learning about abstraction and disbelief. More specifically, we investigated how parents support humor understanding during book sharing with their toddlers. In Study 1, a corpus analysis revealed that in books aimed at 1‐to 2‐year‐olds, humor is found more often than other forms of doing the wrong thing including mistakes, pretense, lying, false beliefs, and metaphors. In Study 2, 20 parents read a book containing humorous and non‐humorous pages to their 19‐to 26‐month‐olds. Parents used a significantly higher percentage of high abstraction extra‐textual utterances (ETUs) when reading the humorous pages. In Study 3, 41 parents read either a humorous or non‐humorous book to their 18‐to 24‐month‐olds. Parents reading the humorous book made significantly more ETUs coded for a specific form of high abstraction: those encouraging disbelief of prior utterances. Sharing humorous books thus increases toddlers' exposure to high abstraction and belief‐based language.
The Wisdom of Collaborative Network Organizations: Capturing the Value of Networked Individuals
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Authors: Dutton William H. 
Published: August 2008

Abstract
Digital networks, particularly the Internet, are used widely to search for information and to share expertise and knowledge between peers. Such collaborative problem solving and co‐creation of services and products go beyond traditional organizational boundaries and geographical constraints, raising major questions about how to manage networked individuals and capture the value of their activities. This paper conveys the findings of a series of case studies designed to explore these questions. This led to a framework for categorizing the networks which suggests the management and performance of ‘collaborative network organizations’ will be contingent on the ways in which they are used to reconfigure information and communication flows for the distributed sharing, generation or co‐creation of content.
Drugs, alcohol and pregnant women—changing characteristics of women engaging with a specialist perinatal outreach addictions service
Authors: MAYET SORAYA , GROSHKOVA TEODORA , MORGAN LOUISE , MacCORMACK TRACEY , STRANG JOHN 
Published: August 2008

AbstractPregnant substance misusers present an increased risk to themselves and the unborn child. The aim of this study was to investigate changes in the characteristics of women referred to a specialist perinatal addictions outreach service (1989–1991 versus 2002–2005). A cross‐sectional audit of health records was conducted. Information was gathered for each woman who contacted the service (2002–2005). Data were compared to an earlier study in the same locality (1989–1991). A total of 167 pregnant substance‐using women were referred between 2002 and 2005, of whom 126 made contact. The mean age was 30.2 years at 20.8 weeks' fetal gestation, with 76% not in addictions treatment, 32% from black or minority ethnic (BME) communities, 49% polysubstance users and 29% homeless. The primary substance used was illicit heroin (38%), followed by cocaine (24%). Compared to 1989–1991, there were significantly more pregnant women presenting at an older age, later gestation, with increased polysubstance use and a higher percentage of women from BME communities. This service was able to access vulnerable substance‐abusing women with an altered pattern of substance use compared to over 10 years previously. However, improvements are needed for engaging all referred women and accessing women at an earlier gestation.
A COMPARATIVE PERSPECTIVE ON INTERGENERATIONAL SUPPORT
Authors: Kalmijn Matthijs , Saraceno Chiara 
Published: August 2008

ABSTRACT
It has often been argued that Southern European countries are more familialistic in their culture than Western and Northern European countries. In this paper, we examine this notion by testing the hypothesis that adult children are more responsive to the needs of their elderly parents in countries with more familialistic attitudes. To test this hypothesis, we analyse the Survey of Health, Ageing and Retirement in Europe (SHARE). We focus on three indicators of need: (a) the partner status of the parent, (b) the health status of the parent, and (c) the education of the parent. Using Heckman probit models, we examine the effects of these variables on whether or not the parent receives instrumental support from children, thereby controlling for whether or not children live independently from their parents. We estimate effects of need on support and we compare these effects across 10 European countries, using both graphic devices and a multilevel probit model where individuals are nested in countries. We find significant cross-level interactions of need variables and the degree of familialism in a country. Our analyses, thereby provide more positive evidence for the hypothesis than earlier studies, which have focused largely on comparing aggregate levels of support among countries.
The structure of SgrAI bound to DNA; recognition of an 8 base pair target
Authors: Dunten Pete W. , Little Elizabeth J. , Gregory Mark T. , Manohar Veena M. , Dalton Michael , Hough David , Bitinaite Jurate , Horton Nancy C. 
Published: August 2008

Abstract
The three-dimensional X-ray crystal structure of the ‘rare cutting’ type II restriction endonuclease SgrAI bound to cognate DNA is presented. SgrAI forms a dimer bound to one duplex of DNA. Two Ca2+ bind in the enzyme active site, with one ion at the interface between the protein and DNA, and the second bound distal from the DNA. These sites are differentially occupied by Mn2+, with strong binding at the protein–DNA interface, but only partial occupancy of the distal site. The DNA remains uncleaved in the structures from crystals grown in the presence of either divalent cation. The structure of the dimer of SgrAI is similar to those of Cfr10I, Bse634I and NgoMIV, however no tetrameric structure of SgrAI is observed. DNA contacts to the central CCGG base pairs of the SgrAI canonical target sequence (CR|CCGGYG, | marks the site of cleavage) are found to be very similar to those in the NgoMIV/DNA structure (target sequence G|CCGGC). Specificity at the degenerate YR base pairs of the SgrAI sequence may occur via indirect readout using DNA distortion. Recognition of the outer GC base pairs occurs through a single contact to the G from an arginine side chain located in a region unique to SgrAI.
The cis-regulatory map of Shewanella genomes
Authors: Liu Jiajian , Xu Xing , Stormo Gary D. 
Published: August 2008

Abstract
While hundreds of microbial genomes are sequenced, the challenge remains to define their cis-regulatory maps. Here, we present a comparative genomic analysis of the cis-regulatory map of Shewanella oneidensis, an important model organism for bioremediation because of its extraordinary abilities to use a wide variety of metals and organic molecules as electron acceptors in respiration. First, from the experimentally verified transcriptional regulatory networks of Escherichia coli, we inferred 24 DNA motifs that are conserved in S. oneidensis. We then applied a new comparative approach on five Shewanella genomes that allowed us to systematically identify 194 nonredundant palindromic DNA motifs and corresponding regulons in S. oneidensis. Sixty-four percent of the predicted motifs are conserved in at least three of the seven newly sequenced and distantly related Shewanella genomes. In total, we obtained 209 unique DNA motifs in S. oneidensis that cover 849 unique transcription units. Besides conservation in other genomes, 77 of these motifs are supported by at least one additional type of evidence, including matching to known transcription factor binding motifs and significant functional enrichment or expression coherence of the corresponding target genes. Using the same approach on a more focused gene set, 990 differentially expressed genes derived from published microarray data of S. oneidensis during exposure to metal ions, we identified 31 putative cis-regulatory motifs (16 with at least one type of additional supporting evidence) that are potentially involved in the process of metal reduction. The majority (18/31) of those motifs had been found in our whole-genome comparative approach, further demonstrating that such an approach is capable of uncovering a large fraction of the regulatory map of a genome even in the absence of experimental data. The integrated computational approach developed in this study provides a useful strategy to identify genome-wide cis-regulatory maps and a novel avenue to explore the regulatory pathways for particular biological processes in bacterial systems.
miR-16 family induces cell cycle arrest by regulating multiple cell cycle genes
Authors: Liu Qin , Fu Hanjiang , Sun Fang , Zhang Haoming , Tie Yi , Zhu Jie , Xing Ruiyun , Sun Zhixian , Zheng Xiaofei 
Published: August 2008

Abstract
MicroRNAs (miRNAs) are a class of small regulatory RNAs that are thought to be involved in diverse biological processes by regulating gene expression. Numerous miRNAs have been identified in various species, and many more miRNAs remain to be detected. Generally, hundreds of mRNAs have been predicted to be potential targets of one miRNA, so it is a great challenge to identify the genuine miRNA targets. Here, we generated the cell lines depleted of Drosha protein and screened dozens of transcripts (including Cyclin D1) regulated potentially by miRNA-mediated RNA silencing pathway. On the basis of miRNA expressing library, we established a miRNA targets reverse screening method by using luciferase reporter assay. By this method, we found that the expression of Cyclin D1 (CCND1) was regulated by miR-16 family directly, and miR-16 induced G1 arrest in A549 cells partially by CCND1. Furthermore, several other cell cycle genes were revealed to be regulated by miR-16 family, including Cyclin D3 (CCND3), Cyclin E1 (CCNE1) and CDK6. Taken together, our data suggests that miR-16 family triggers an accumulation of cells in G0/G1 by silencing multiple cell cycle genes simultaneously, rather than the individual target.
First Report of Wheat streak mosaic virus in Slovakia
Authors: Kúdela O. , Kúdelová M. , Nováková S. , Glasa M. 
Published: August 2008

The occurrence of Wheat streak mosaic virus (WSMV; genus Tritimovirus) was monitored by testing 91 wheat and barley samples collected from various localities of Slovakia from March to June 2007. Samples were screened by a commercial double-antibody sandwich-ELISA kit (Loewe Biochemica, Sauerlach, Germany). Positive results were obtained from two wheat (Triticum aestivum L.) samples from the same locality of western Slovakia. Molecular analysis of both samples was performed by reverse transcription-PCR with WSMV-specific primers (WS-8166F 5′ GAGAGCAATACTGCGTGTACG 3′ and WS-8909R 5′ GCATAATGGCTCGAAGTGATG 3′) designed according to available sequences. The expected 750-bp PCR fragment containing the N-terminal and core region of the coat protein gene (from 8166 to 8909 nt based on the Sidney81 isolate, GenBank Accession No AF057533) was obtained from both Slovak isolates. Direct sequencing (GenBank Accession Nos. EU723085 and EU723086) revealed that the two isolates have nucleotide and amino acid sequence identities of 98.3 and 100%, respectively. Except for the highly divergent Mexican isolate (Accession No. AF285170), pairwise comparisons of the Slovak isolates with sequences of other WSMV isolates (1) available in GenBank indicated respective nucleotide and amino acid sequence identities ranging from 87.6 to 98.7% and 95.2 to 100%. The Slovak isolates were most closely related to isolates from Czech Republic, Hungary, and Russia (GenBank Accession Nos. AF454454, AF454456, and AF454459). To our knowledge, this is the first report of the natural occurrence of WSMV in Slovakia. Reference: (1) D. C. Stenger et al. Virology 302:58. 2002.
First Report of Little cherry virus 2 from Sweet Cherry in Poland
Authors: Komorowska B. , Cieślińska M. 
Published: August 2008

Little cherry disease (LChD) is a serious viral disease of sweet (Prunus avium) and sour (P. cerasus) cherry trees. Infection of sensitive cultivars results in small, angular, and pointed fruits with reduced sweetness. In late summer, leaves show a characteristic red coloration or bronzing of the surfaces. One Ampelovirus species, Little cherry virus 2 (LChV-2) (2), and one unassigned species in the Closteroviridae, Little cherry virus 1 (LChV-1) (3), have been associated with LChD. Twenty-seven sour and sweet cherry trees of six varieties from orchards located in several regions of Poland were tested for LChV-1 and LChV-2. Leaf samples were taken either from trees showing fruit symptoms or from asymptomatic trees during the summer of the 2006 growing season. RNA was isolated from the leaves with an RNeasy Kit (Qiagen, Hilden, CA), and reverse transcription (RT)-PCR was performed using primer pairs LCV1U/LCV1L and LCV2UP2/LCV2LO2, which are specific for a 419-bp fragment of the LChV-1 3′ nontranslated region and a 438-bp fragment of the LChV-2 methyltransferase gene, respectively (1). The primer pair L2CPF (5′-GTTCGAAAGTGTTTCTTGAT-3′) and L2CPR (5′-GCAACAGAAAAACATATGACTCA-3′) was designed from existing LChV-2 sequences (GenBank Accession Nos. AF416335 and NC_005065) to amplify the entire LChV-2 coat protein (CP) gene (nucleotides 13,007 to 14,134). The amplified cDNA fragments of LChV-2 genome were ligated to the bacterial vector pCR2.1-TOPO (Invitrogen, Carlsbad, CA), which was used to transform Escherichia coli TOP10 competent cells following the manufacturer's protocol. Both strands of three clones for each amplified LChV-2 genome fragment were sequenced with an automated nucleotide sequencer at the Institute of Biochemistry and Biophysics in Warsaw. RT-PCR results showed that 6 of 27 trees were infected, with LChV-1 detected in five sweet cherry trees and LChV-2 singly infecting one sweet cherry tree cv Elton (isolate C4/14). The nucleotide sequence of the 438-bp methyltransferase gene fragment of isolate C4/14 showed 86, 85, and 84% identity to GenBank Accession Nos. AF333237, AF531505, and AJ430056, respectively, all previously reported LChV-2 sequences from cherry trees. Sequence analysis of the 1,088-bp coat protein gene showed 89 to 91% and 92 to 93% nucleotide and amino acid identity, respectively, with the aforementioned three LChV-2 isolates. The tree infected with LChV-2 was indexed by graft transmission to the woody indicator, Prunus avium cv. Canindex, which showed reddening of the leaves characteristic of LChD 3 months after inoculation. Since cherry production in Poland is 230,000 t per year, the disease may have a significant economic impact because the affected fruits are unsuitable either for consumption or sale. To our knowledge, this is the first report of LChV-2 in Poland. References: (1) M. E. Rott and W. Jelkmann. Phytopathology 91:261, 2001. (2) M. E. Rott and W. Jelkmann. Arch. Virol. 150:107, 2005. (3) M. Vitushkina et al. Eur. J. Plant Pathol. 103:803, 1997.
Occurrence of Hibiscus chlorotic ringspot virus in Hibiscus spp. in New Zealand
Authors: Tang J. , Elliott D. R. , Quinn B. D. , Clover G. R. G. , Alexander B. J. R. 
Published: August 2008

Hibiscus spp. are popular ornamental plants in New Zealand. The genus is susceptible to Hibiscus chlorotic ringspot virus (HCRSV), a member of the genus Carmovirus, which has been reported in Australia, El Salvador, Singapore, the South Pacific Islands, Taiwan, Thailand, and the United States (1–4). In May of 2004, chlorotic spotting and ringspots were observed on the leaves of two H. rosa-sinensis plants in a home garden in Auckland, New Zealand. When inoculated with sap from symptomatic leaves, Chenopodium quinoa and C. amaranticolor developed faint chlorotic local lesions 12 to 15 days later. Phaseolus vulgaris exhibited small necrotic local spots 10 days postinoculation. No symptoms were observed on inoculated plants of Cucumis sativus, Gomphrena globosa, Nicotiana Clevelandii, N. tabacum, or N. sylvestris. Plants of H. rosa-sinensis and the three symptomatic indicator species tested positive for HCRSV using polyclonal antiserum (Agdia Inc., Elkhart, IN) in a double antibody sandwich (DAS)-ELISA. Forward (5′-GGAACCCGTCCTGTTACTTC-3′) and reverse (5′-ATCACATCCACATCCCCTTC-3′) primers were designed on the basis of a conserved region in the coat protein gene (nt 2722–3278) of HCRSV isolates in GenBank (Accession Nos. X86448 and DQ392986). A product of the expected size (557 bp) was amplified by reverse transcription (RT)-PCR with total RNA extracted from the four infected species. Comparison of the sequence of the amplicon from H. rosa-sinensis (GenBank Accession No. EU554660) with HCRSV isolates from Singapore and Taiwan (GenBank Accession Nos. X86448 and DQ392986) showed 99 and 94% nucleotide identity, respectively. From 2006 to 2008, samples from a further 25 symptomatic hibiscus plants were collected from different locations in the Auckland region. Nineteen, including plants of H. diversifolius, H. rosa-sinensis, and H. syriacus, tested positive for HCRSV by RT-PCR. To our knowledge, this is the first report of HCRSV in New Zealand and of the virus in H. diversifolius and H. syriacus. HCRSV is considered to be widespread in New Zealand. References: (1) A. A. Brunt et al. Plant Pathol. 49:798, 2000. (2) S. C. Li et al. Plant Pathol. 51:803, 2002. (3) H. Waterworth. No.227 in: Descriptions of Plant Viruses. CMI/AAB, Surrey, UK, 1980. (4) S. M. Wong et al. Acta Hortic. 432:76, 1996.