bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concordance rates between parent and teacher clinical evaluation of language fundamentals observational rating scale
Authors: Massa Jacqueline , Gomes Hilary , Tartter Vivien , Wolfson Virginia , Halperin Jeffrey M. 
Published: January 2008

Background: Research has shown that early identification of children with language issues is critical for effective intervention, and yet many children are not identified until school age. The use of parent‐completed rating scales, especially in urban, minority populations, might improve early identification if parent ratings are found to be reliable and valid.Aims: To evaluate the reliability and validity of the Observational Rating Scale (ORS) in an urban setting where it may be difficult to distinguish language difficulties from cultural language differences.Methods & Procedures: The present study examined the degree to which parent and teacher ORS scores for 73 7–10‐year‐old children (47 boys) had concordance for the four ORS dimensions of Listening, Speaking, Reading, and Writing, as well as for a composite ORS score. The relationship between the ORS ratings and the children's scores on the CELF‐3, or CELF‐4 Receptive and Expressive scores, and the WIAT Reading Composite scores were also examined.Outcomes & Results: Parent and teacher concordance rates for the ORS were significant, but moderate for the Speaking, Reading, and Writing categories and for the overall ORS score. There were also significant relationships between the ORS scores and performance on standardized language and reading tests supporting the validity of the ORS.Conclusions: The reliability and validity of the ORS have been replicated and extended to a diverse, urban population. Further, parent ratings were shown to provide as least as good information about language function as teacher ratings. Finally, it was suggested that an overall ORS score may provide a better indicator of overall language function than the domain scores.
Sentence production in students with dyslexia
Authors: Altmann Lori J. P. , Lombardino Linda J. , Puranik Cynthia 
Published: January 2008

Background:While spoken language deficits have been identified in children with developmental dyslexia, microanalysis of sentence production proficiency in these children is a largely unexplored area.Aims:The current study examines proficiency of syntactic production in children and young adults with dyslexia and typically developing age‐matched controls on a constrained sentence production task targeting two advanced argument structures, theme–experiencer verbs and irregular past participles.Methods & Procedures:Participants aged between 8 and 22 years produced sentences that included three stimulus words, a proper name, an inanimate noun and a verb from one of three categories: control verbs (agent–patient verbs with regular morphology); theme–experiencer verbs, which require an inanimate subject in active sentences (e.g. The bookboredSarah); and irregular past participles, which require awareness of the syntactic requirements associated with the ‐enpast participle ending, i.e. that this verb form cannot be used as a simple past tense (e.g. *Mary ___ hidden the candy).Outcomes & Results:Students with dyslexia produced more dysfluent, ungrammatical and incomplete responses than normal readers; however, the developmental trajectories of the verb types varied between groups. Normal readers performed similarly with both experimental verb types, but those with dyslexia were particularly impaired using irregular past participles in sentences.Conclusions:The findings support a model of lexical representation in which development of grammar hinges on the acquisition of lexical knowledge. Furthermore, the data suggest that individuals with dyslexia may have difficulties with sentence formulation that persist into adulthood.
Message from the Editor
Authors: Thomas Paul 
Published: January 2008

To begin, I would like to wish our readers, authors, referees and Board of Editors a successful and happy 2008 and thank them for their contributions to Nuclear Fusion in 2007.
I took over the editorship of Nuclear Fusion in January, and the year has been one in which the community as a whole has been busier than ever with a variety of duties associated with the ITER project.
It was with pride that we published the Progress in the ITER Physics Basis in the June issue of the journal (stacks.iop.org/NF/47/i=6). The task undertaken by the coordinators, authors and referees was a daunting one but one which led to an outstandingly successful issue. The response from readers has been phenomenal and there were in the region of 10 000 downloads of papers in the first month following publication.
Looking to 2008 and beyond, the journal will endeavour to continue to support the work of the fusion community.

Refereeing

As we have done since January 2005, we would like to thank our top ten most loyal referees who have helped the journal with its double-referee peer-review procedure in the past year. At the Nuclear Fusion Editorial Office we are fully aware of the load we put on the shoulders of our referees. At the end of 2004 the Editorial Board decided that a gesture of gratitude should be made to our most loyal referees. We offer them a personal subscription to Nuclear Fusion with electronic access for one year, free of charge.
To select the top referees we have adopted the criterion that a researcher should have acted as a referee or adjudicator for at least three different manuscripts during the period from summer 2006 to the end of 2007. We have excluded our Board members and those referees who were already listed in the top ten in the last two years.
According to our records the following people met this criterion. Congratulations and many, many thanks!

H.L. Berk (Texas University, USA)

J.S. DeGrassie (GAT, USA)

C. Deutsch (Paris University, France)

N. Hayashi (JAEA, Japan)

P. Ghendrih (CEA, France)

E. Gusakov (Ioffe Institute, Russia)

T.C. Luce (GAT, USA)

N. Oyama (JAEA, Japan)

J.J. Ramos (MIT, USA)

H. Takenaga (JAEA, Japan)

In addition there is a group of several hundred referees who have helped us in the past year to maintain the high scientific standard of Nuclear Fusion. At the end of this issue we give the full list of all referees for 2007. Our thanks to them!

Peer-review process

We are pleased to report that further progress has been made in speeding up our publishing process, without any compromise of quality. Those authors who regularly submit work based on contributions to the Fusion Energy Conference (FEC) will, perhaps, have noticed the reduction in times compared to earlier years.
We believe that Nuclear Fusion maintains its position in the field because of the perceived high quality of the submissions, the refereeing and the editorial processes. This position of strength will be built upon as we endeavour to further improve the service to the journal's authors and readers.
A note on difficult structure alignment problems
Authors: Sippl Manfred J. , Wiederstein Markus 
Published: January 2008

Abstract
Summary: Progress in structural biology depends on several key technologies. In particular tools for alignment and superposition of protein structures are indispensable. Here we describe the use of the TopMatch web service, an effective computational tool for protein structure alignment, for the visualization of structural similarities, and for highlighting relationships found in protein classifications. We provide several instructive examples.
Availability: TopMatch is available as a public web service at http://services.came.sbg.ac.at
Contact: sippl@came.sbg.ac.at
NetworkBLAST: comparative analysis of protein networks
Authors: Kalaev Maxim , Smoot Mike , Ideker Trey , Sharan Roded 
Published: January 2008

Abstract
Summary: The identification of protein complexes is a fundamental challenge in interpreting protein–protein interaction data. Cross-species analysis allows coping with the high levels of noise that are typical to these data. The NetworkBLAST web-server provides a platform for identifying protein complexes in protein-protein interaction networks. It can analyze a single network or two networks from different species. In the latter case, NetworkBLAST outputs a set of putative complexes that are evolutionarily conserved across the two networks.
Availability: NetworkBLAST is available as web-server at: www.cs.tau.ac.il/~roded/networkblast.htm
Contact: kalaevma@post.tau.ac.il; roded@post.tau.ac.il
Decomp—from interpreting Mass Spectrometry peaks to solving the Money Changing Problem
Authors: Böcker Sebastian , Lipták Zsuzsanna , Martin Marcel , Pervukhin Anton , Sudek Henner 
Published: January 2008

Abstract
Summary: We introduce Decomp, a tool that computes the sum formula of all molecules whose mass equals the input mass. This problem arises frequently in biochemistry and mass spectrometry (MS), when we know the molecular mass of a protein, DNA or metabolite fragment but have no other information. A closely related problem is known as the Money Changing Problem (MCP), where all masses are positive integers. Recently, efficient algorithms have been developed for the MCP, in which Decomp applies to real-valued MS data. The excellent performance of this method on proteomic and metabolomic MS data has recently been demonstrated. Decomp has an easy-to-use graphical interface, which caters for both types of users: those interested in solving MCP instances and those submitting MS data.
Availability: Decomp is freely accessible at http://bibiserv.techfak.uni-bielefeld.de/decomp/
Contact: anton.pervukhin@minet.uni-jena.de
Decreased Potency of the
Vibrio cholerae
Sheathed Flagellum To Trigger Host Innate Immunity
Authors: Yoon Sang Sun , Mekalanos John J. 
Published: January 2008

ABSTRACT

Vibrio cholerae
is a monoflagellated gram-negative bacterium that causes the severe diarrheal disease cholera. In contrast to
Salmonella enterica
serovar Typhimurium infection, which is accompanied by both acute diarrhea and high-level inflammation,
V. cholerae
infection is largely noninflammatory in human hosts. Bacterial flagella are composed of flagellin, a highly conserved protein that is also a target of the innate immune response. Because the
V. cholerae
flagellum is covered by a sheath, we hypothesized that it might be less prone to activation of the innate immune response than nonsheathed flagella, such as those produced by
Salmonella
serovar Typhimurium. Indeed, compared with
Salmonella
serovar Typhimurium flagella,
V. cholerae
flagella demonstrated significantly reduced NF-κB activation in A549 human pulmonary epithelial cells. However,
V. cholerae
flagellin monomers, FlaD and FlaC, were almost equally potent with purified FliC, a monomer derived from
Salmonella
serovar Typhimurium flagella, in NF-κB activation. Heat- and acid-induced dissociation assays showed that
Salmonella
serovar Typhimurium flagella disassembled far more readily into monomeric flagellins than
V. cholerae
flagella, suggesting that the differential levels of NF-κB activation by
V. cholerae
and
Salmonella
serovar Typhimurium flagella are likely attributable to the difference in their flagellin shedding. Our results suggest that monomer dissociation of
V. cholerae
flagella is suppressed likely due to the presence of the sheath and that this unique structural feature of
V. cholerae
flagella may have evolved as a strategy to evade flagellin-triggered host innate immune responses in various host species.
Degradation of Complement 3 by Streptococcal Pyrogenic Exotoxin B Inhibits Complement Activation and Neutrophil Opsonophagocytosis
Authors: Kuo Chih-Feng , Lin Yee-Shin , Chuang Woei-Jer , Wu Jiunn-Jong , Tsao Nina 
Published: January 2008

ABSTRACTStreptococcal pyrogenic exotoxin B (SPE B), a cysteine protease, is an important virulence factor in group A streptococcus (GAS) infection. The inhibition of phagocytic activity by SPE B may help prevent bacteria from being ingested. In this study, we examined the mechanism SPE B uses to enable bacteria to resist opsonophagocytosis. Using an enzyme-linked immunosorbent assay, we found that SPE B-treated serum impaired the activation of the classical, the lectin, and the alternative complement pathways. In contrast, C192S, a SPE B mutant lacking protease activity, had no effect on complement activation. Further study showed that cleavage of serum C3 by SPE B, but not C192S, blocked zymosan-induced production of reactive oxygen species in neutrophils as a result of decreased deposition of C3 fragments on the zymosan surface. Reconstitution of C3 into SPE B-treated serum unblocked zymosan-mediated neutrophil activation dose dependently. SPE B-treated, but not C192S-treated, serum also impaired opsonization of C3 fragments on the surface of GAS strain A20. Moreover, the amount of C3 fragments on the A20 cell surface, a SPE B-producing strain, was less than that on its isogenic mutant strain, SW507, after opsonization with normal serum. A20 opsonized with SPE B-treated serum was more resistant to neutrophil killing than A20 opsonized with normal serum, and SPE B-mediated resistance was C3 dependent. These results suggest a novel SPE B mechanism, one which degrades serum C3 and enables GAS to resist complement damage and opsonophagocytosis.
A Chemokine-Degrading Extracellular Protease Made by Group AStreptococcusAlters Pathogenesis by Enhancing Evasion of the Innate Immune Response
Authors: Sumby Paul , Zhang Shizhen , Whitney Adeline R. , Falugi Fabiana , Grandi Guido , Graviss Edward A. , DeLeo Frank R. , Musser James M. 
Published: January 2008

ABSTRACTCircumvention of the host innate immune response is critical for bacterial pathogens to infect and cause disease. Here we demonstrate that the group AStreptococcus(GAS;Streptococcus pyogenes) protease SpyCEP (S. pyogenescell envelope protease) cleaves granulocyte chemotactic protein 2 (GCP-2) and growth-related oncogene alpha (GROα), two potent chemokines made abundantly in human tonsils. Cleavage of GCP-2 and GROα by SpyCEP abrogated their abilities to prime neutrophils for activation, detrimentally altering the innate immune response. SpyCEP expression is negatively regulated by the signal transduction system CovR/S. Purified recombinant CovR bound thespyCEPgene promoter region in vitro, indicating direct regulation. Immunoreactive SpyCEP protein was present in the culture supernatants ofcovR/Smutant GAS strains but not in supernatants from wild-type strains. However, wild-type GAS strains do express SpyCEP, where it is localized to the cell wall. Strain MGAS2221, an organism representative of the highly virulent and globally disseminated M1T1 GAS clone, differed significantly from its isogenicspyCEPmutant derivative strain in a mouse soft tissue infection model. Interestingly, and in contrast to previous studies, the isogenic mutant strain generated lesions of larger size than those formed following infection with the parent strain. The data indicate that SpyCEP contributes to GAS virulence in a strain- and disease-dependent manner.
Chemical Attenuation of
Plasmodium berghei
Sporozoites Induces Sterile Immunity in Mice
Authors: Purcell Lisa A. , Yanow Stephanie K. , Lee Moses , Spithill Terry W. , Rodriguez Ana 
Published: January 2008

ABSTRACT

Radiation and genetic attenuation of
Plasmodium
sporozoites are two approaches for whole-organism vaccines that protect against malaria. We evaluated chemical attenuation of sporozoites as an alternative vaccine strategy. Sporozoites were treated with the DNA sequence-specific alkylating agent centanamycin, a compound that significantly affects blood stage parasitemia and transmission of murine malaria and also inhibits
Plasmodium falciparum
growth in vitro. Here we show that treatment of
Plasmodium berghei
sporozoites with centanamycin impaired parasite function both in vitro and in vivo. The infection of hepatocytes by sporozoites in vitro was significantly reduced, and treated parasites showed arrested liver stage development. Inoculation of mice with sporozoites that were treated in vitro with centanamycin failed to produce blood stage infections. Furthermore, BALB/c and C57BL/6 mice vaccinated with treated sporozoites were protected against subsequent challenge with wild-type sporozoites. Our findings demonstrate that chemically attenuated sporozoites could be a viable alternative for the production of an effective liver stage vaccine for malaria.
Epidemiological Characteristics of Methicillin-Resistant
Staphylococcus aureus
Isolates from Children with Eczematous Atopic Dermatitis Lesions
Authors: Chung Hee-Jung , Jeon Hong-Seon , Sung Heungsup , Kim Mi-Na , Hong Soo-Jong 
Published: January 2008

ABSTRACT

In this study, we investigated the rate of colonization of skin of children with atopic dermatitis (AD) by methicillin-resistant
Staphylococcus aureus
(MRSA) and characterized the isolates. Active skin lesions in pediatric AD patients were cultured with Rodac Staph (Komed, Korea).
S. aureus
isolates were examined for drug susceptibilities, analyzed for the
eta
,
etb
,
tst
, and
pvl
genes, and typed using
agr
polymorphism, pulsed-field gel electrophoresis of SmaI-restricted chromosomal DNA, and staphylococcal cassette chromosome
mec
(SCC
mec
) typing. Eighty-seven (75.4%) of 115 patients had cultivable
S. aureus
isolates, 16 of which (18.3%) were MRSA. All MRSA isolates were susceptible to chloramphenicol, rifampin, cotrimoxazole, and ciprofloxacin. While methicillin-susceptible
S. aureus
(MSSA) isolates were composed of 23 isolates of singular types and nine clusters comprising 48 isolates, MRSA isolates were typed into three clones: eight isolates of pulsotype A-
agr
-
1
-SCC
mec
IV, five isolates of pulsotype B-
agr
-
3
-SCC
mec
IIb-
etb
positive, and three isolates of pulsotype C-
agr
-
3
-SCC
mec
IV. Three SCC
mec
IVA MRSA isolates were
tst
positive, but none were positive for the
pvl
or
eta
gene. Among 71 MSSA isolates, 7 isolates were
tst
positive, 6 of which were pulsotype F-
agr
-
3
, and 9 of 10
agr
-
4
isolates were
eta
positive. The average ages of patients carrying MSSA, SCC
mec
IVA MRSA, and SCC
mec
IIb MRSA were 7.7 ± 4.6, 3.1 ± 1.5, and 8.2 ± 3.1 years, respectively. Among the patients carrying MRSA, two patients had been treated with oral antimicrobials, and one had been admitted to the hospital 18 months previously. In conclusion, community-acquired MRSA isolates of a few clones colonized the skin of patients with AD without risk factors for the acquisition of hospital-acquired MRSA, which suggested that the skin of children with AD may represent a significant reservoir of MRSA colonization in the community.
Use of PCR-BasedMycobacterium tuberculosisGenotyping To Prioritize Tuberculosis Outbreak Control Activities
Authors: Ashworth Maegan , Horan Kathleen L. , Freeman Robert , Oren Eyal , Narita Masahiro , Cangelosi Gerard A. 
Published: January 2008

ABSTRACTGenotypic analysis ofMycobacterium tuberculosisisolates is increasingly applied in direct support of tuberculosis outbreak control activities. This is facilitated by PCR-based strain typing methods that enable the genotypic characterization of samples containing small numbers ofM. tuberculosiscells. By using DNA extracted directly from primary diagnostic cultures, PCR-based methods were applied to a tuberculosis outbreak investigation and to surveillance in King County, Washington. In the outbreak investigation, five epidemiologically linkedM. tuberculosisisolates had a unique pattern at mycobacterial interspersed repeating unit (MIRU) loci 10 and 23 when the pattern was compared to the patterns in a local MIRU locus database. In order to quickly identify new cases involving this strain (termed SBRI10), targeted genotyping at these two loci was performed with cultures from epidemiologically associated tuberculosis cases. Isolates with the characteristic genotypes at loci 10 and 23 were further analyzed by use of a 12-locus MIRU panel and by repetitive-unit-sequence-based PCR (rep-PCR). Between May 2004 and January 2005, 82 cases were screened, of which 14 were identified for further analysis and 13 were confirmed to be infected with SBRI10. Between September 2005 and August 2006, surveillance universal genotyping was performed by using the 12-locus MIRU panel with DNA from primary diagnostic enrichment cultures. A total of 161 samples were submitted for analysis, and 156 were successfully typed. Fifty-one cases formed 18 presumptive clusters by MIRU locus typing. Of these, 30 cases were confirmed to be members of 11 clusters by rep-PCR. Presumptive genotypic data were available rapidly, sometimes within 2 weeks of diagnosis. In this fashion, PCR-based genotyping provided data that can be used to prioritize disease control activities.
DiarrheagenicEscherichia coliandShigellaStrains Isolated from Children in a Hospital Case-Control Study in Hanoi, Vietnam
Authors: Hien Bui Thi Thu , Scheutz Flemming , Cam Phung Dac , Serichantalergs Oralak , Huong Tran Thu , Thu Tran Minh , Dalsgaard Anders 
Published: January 2008

ABSTRACTThis case-control study detected and characterizedShigellaand diarrheagenicEscherichia coli(DEC) types among Vietnamese children less than 5 years old. In 249 children with diarrhea and 124 controls,Shigellaspp. was an important cause of diarrhea (P< 0.05). We used multiplex PCR and DNA probes to detect enteroinvasiveE. coli(EIEC), enteroaggregativeE. coli(EAggEC), enteropathogenicE. coli(EPEC), attaching and effacingE. coli(A/EEC), verocytotoxin-producingE. coli(VTEC), and enterotoxigenicE. coli(ETEC). The prevalences of DEC in the diarrhea and control groups were 25.7 and 10.5%, respectively. In 62 children with diarrhea, 64 DEC strains included 22 EAggEC (8.8%), 2 EIEC (0.8%), 23 A/EEC (9.2%), 7 EPEC (2.8%), and 10 ETEC strains (4.0%). Among controls, 13 DEC strains included 5 EAggEC strains (4.0%), 7 A/EEC strains (5.6%), and 1 EPEC strain. The characterization of DEC by serotypes, antimicrobial susceptibility patterns, virulence genes, and pulsed-field gel electrophoresis showed the occurrence of many different and highly heterogenic DEC subtypes, but common serotypes were found among ETEC, EIEC and EPEC, respectively. Serotyping was used to distinguish between A/EEC and EPEC. However, A/EEC, EPEC, and EAggEC were isolated at high frequency from both cases and controls. Further in-depth studies are needed to better understand important virulence factors of DEC, especially A/EEC, EPEC, and EAggEC.
Sputum Smear Microscopy: Evaluation of Impact of Training, Microscope Distribution, and Use of External Quality Assessment Guidelines for Resource-Poor Settings
Authors: Van Rie A. , Fitzgerald D. , Kabuya G. , Van Deun A. , Tabala M. , Jarret N. , Behets F. , Bahati E. 
Published: January 2008

ABSTRACT
Sputum smear microscopy is the main and often only laboratory technique used for the diagnosis of tuberculosis in resource-poor countries, making quality assurance (QA) of smear microscopy an important activity. We evaluated the effects of a 5-day refresher training course for laboratory technicians and the distribution of new microscopes on the quality of smear microscopy in 13 primary health care laboratories in Kinshasa, Democratic Republic of Congo. The 2002 external QA guidelines for acid-fast bacillus smear microscopy were implemented, and blinded rechecking of the slides was performed before and 9 months after the training course and microscope distribution. We observed that the on-site checklist was highly time-consuming but could be tailored to capture frequent problems. Random blinded rechecking by the lot QA system method decreased the number of slides to be reviewed. Most laboratories needed further investigation for possible unacceptable performance, even according to the least-stringent interpretation. We conclude that the 2002 external QA guidelines are feasible for implementation in resource-poor settings, that the efficiency of external QA can be increased by selecting sample size parameters and interpretation criteria that take into account the local working conditions, and that greater attention should be paid to the provision of timely feedback and correction of the causes of substandard performance at poorly performing laboratories.