bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competitive Inhibition Flow Analysis Assay for the Non-Culture-Based Detection and Serotyping of Pneumococcal Capsular Polysaccharide
Authors: Findlow H. , Laher G. , Balmer P. , Broughton C. , Carrol E. D. , Borrow R. 
Published: December 2008

ABSTRACTTraditional confirmation procedures for the identification of a pneumococcal serotype require an isolate. Non-culture-based confirmation protocols are available. Some of these confirm only the presence of pneumococci, and others are capable of identifying a limited number of serotypes. The increased use of pneumococcal polysaccharide and conjugate vaccines, especially in high-risk patient groups, and the likely increase in the number of serotypes included in future versions of the conjugate vaccines have necessitated the need for improved enhanced surveillance in order to assess their impact on public health. Since 2006, a multiplexed assay has been used at the Health Protection Agency of the United Kingdom for the detection of 14 pneumococcal serotypes which requires pneumococcal serotype-specific monoclonal antibodies (MAbs). We have developed a microsphere competitive inhibition method capable of detecting 23 pneumococcal capsular polysaccharide serotypes in cerebrospinal fluid (CSF) and urine and serotyping pneumococcal suspensions, utilizing an international reference serum, 89-SF. The assay was shown to be reproducible and specific for homologous polysaccharide. Validation of the assay was performed with a selection of MAbs specific for pneumococcal capsular polysaccharide serotypes, which confirmed the specificity of the assay. Analysis of pneumolysin PCR-positive CSF samples in the competitive inhibition assay determined a serotype for 89% of the samples. The assay developed here is well suited to large-scale epidemiologic studies because the assay is simple, robust, and rapid and utilizes readily available resources.
In Vivo and In Vitro Alterations in Influenza A/H3N2 Virus M2 and Hemagglutinin Genes: Effect of Passage in MDCK-SIAT1 Cells and Conventional MDCK Cells
Authors: Li Danjuan , Saito Reiko , Suzuki Yasushi , Sato Isamu , Zaraket Hassan , Dapat Clyde , Caperig-Dapat Isolde Ma , Suzuki Hiroshi 
Published: December 2008

ABSTRACT
No mutations were detected in the hemagglutinin gene of influenza A/H3N2 virus isolates from patients undergoing short-term amantadine treatment. However, genetic changes occurred after serial passage in either MDCK or MDCK-SIAT1 cells. Our results showed that only a few mutations were observed in MDCK-SIAT1-passaged isolates in the presence of amantadine.
Evaluation and Implementation of a Chromogenic Agar Medium for
Salmonella
Detection in Stool in Routine Laboratory Diagnostics
Authors: van Dijk Saskia , Bruins Marjan J. , Ruijs Gijs J. H. M. 
Published: December 2008

ABSTRACT

We evaluated which chromogenic agar medium for
Salmonella
detection in stool would be most sensitive and specific in our culture protocol. The use of BBL CHROMagar
Salmonella
chromogenic medium combined with xylose-lysine-deoxycholate agar yielded a sensitivity of 100% and also reduced workload and costs.
Molecular Diagnostic Identification of
Staphylococcus pseudintermedius
Authors: Bannoehr Jeanette , Franco Alessia , Iurescia Manuela , Battisti Antonio , Fitzgerald J. Ross 
Published: December 2008

ABSTRACT

We report the first diagnostic test for the identification of
Staphylococcus pseudintermedius
involving a simple PCR-restriction fragment length polymorphism approach. The method allows discrimination of
S. pseudintermedius
from the closely related members of the
Staphylococcus intermedius
group and other important staphylococcal pathogens of humans and dogs.
Interaction of Human Cytomegalovirus pUL84 with Casein Kinase 2 Is Required for oriLyt-Dependent DNA Replication
Authors: Gao Yang , Pari Gregory S. 
Published: December 2008

ABSTRACT
Human cytomegalovirus pUL84 is a phosphorylated protein that is required for lytic DNA replication and participates in regulation of virus gene expression. We previously used a proteomics assay to show that human cytomegalovirus pUL84 interacts with casein kinase 2 (CK2). We now have demonstrated that pUL84 is a substrate for CK2 in vitro, and we have determined that two putative CK2 phosphorylation sites within pUL84 mediate binding to CK2. Mutation of a threonine residue at amino acid (aa) 148 and a serine residue at aa 157 within the pUL84 protein resulted in the inability of the protein to interact with the CK2α subunit in transfected cells. Interaction of pUL84 with CK2 was essential for complementation of oriLyt-dependent DNA replication, suggesting that phosphorylation is an essential modification.
Innate immunity prevents tissue invasion byEntamoeba histolytica
Authors: Shibayama Mineko , Rivera-Aguilar Víctor , Barbosa-Cabrera Elizabeth , Rojas-Hernández Saúl , Jarillo-Luna Adriana , Tsutsumi Víctor , Pacheco-Yepez Judith , Campos-Rodríguez Rafael 
Published: December 2008

Although innate and adaptive immunity both play a role in amoebiasis, the mechanisms involved in the elimination of Entamoeba histolytica are poorly understood. To provide more information about the innate immune mechanisms that may confer protection against invasive amoebiasis, we administered inflammatory substances (bacillus Calmette-Guérin, lipopolysaccharide, complete Freund’s adjuvant, or mineral oil) into the peritoneum of hamsters. The animals were then challenged with pathogenic trophozoites of E. histolytica and, after 7 days, the protective host response was analysed. We found that the nonspecific inflammatory response induced in the peritoneum was sufficient to prevent liver invasion by E. histolytica. In vitro experiments showed that the killing of trophozoites was mediated by peritoneal macrophages and a protein of 68 kDa with peroxidase activity.
Moose–habitat relationships: integrating local Cree native knowledge and scientific findings in northern Quebec
Authors: Jacqmain Hugo , Dussault Christian , Courtois Réhaume , Bélanger Louis 
Published: December 2008

Participation of aboriginal people in Canadian forestry is a requirement of sustainable management. We proposed a culturally adapted process to integrate Cree and scientific knowledge in Eeyou Istchee (northern Quebec) that could contribute to a better mutual understanding between Cree and non-Cree, and eventually favour the social acceptability of forest management strategies. We studied moose ( Alces alces L.), the Cree featured species and the main forestry issue for the past 40 years. Cree and non-Cree have culturally differing visions for the management of moose habitat. In a previous article, we documented Cree knowledge about moose–habitat relationships. Here, we evaluated some hypotheses built from Cree knowledge by studying the behaviour of moose equipped with GPS collars. In general, results from our habitat use and selection analyses agreed with Cree observations and improved our understanding of moose–habitat relationships in northern Quebec. We jointly demonstrated the importance of mature mixedwoods, balsam fir ( Abies balsamea (L.) Mill.) stands, and riparian areas for moose in the northern black spruce ( Picea mariana (Mill.) BSP) forest. In these specific areas, management approaches other than clear-cutting should be developed to preserve moose habitat quality. Such an alternative would potentially be more acceptable for the Cree people.
Predicting the age of ancient Thuja occidentalis on cliffs
Authors: Matthes Uta , Kelly Peter E. , Larson Douglas W. 
Published: December 2008

In rocky, heterogeneous environments that support old-growth forests, the relationship between tree size and age is weaker than it is for trees growing in productive and homogeneous habitats. To assist in the management and conservation of ancient forests on rocky land of low productivity, it would be useful if the relationships among age, environmental heterogeneity, and morphological variability could be understood and used to develop predictive models of longevity so that extensive core sampling of trees would not be required. Here we sampled 296 mature Thuja occidentalis L. growing on limestone cliffs along the Niagara Escarpment, southern Ontario, Canada. We measured a variety of site conditions and morphological traits, including age, which varied from 51 to 1316 years. We then used redundancy analysis and multiple regression to model the relationships among age, morphology, growth rate, and environment, resulting in quantitative models predicting tree age from four subsets of variables. We subsequently tested the models on 60 additional trees not used to build the models and found that they predicted up to 78% of the variation in actual tree age. This approach could be adopted for use in other forest types to predict the age of trees without using tree-ring analysis.
Lake-Effect Thunderstorms in the Lower Great Lakes
Authors: Steiger Scott M. , Hamilton Robert , Keeler Jason , Orville Richard E. 
Published: December 2008

Abstract
Cloud-to-ground (CG) lightning, radar, and radiosonde data were examined to determine how frequently lake-effect storms (rain/snow) with lightning occurred over and near the lower Great Lakes region (Lakes Erie and Ontario) from September 1995 through March 2007. On average, lake-effect lightning occurred on 7.9 days and with 5.8 storm events during a particular cool season (September–March). The CG lightning with these storms had little inland extent and was usually limited to a few flashes per storm. Some storms had considerably more, with the most intense storm (based on National Lightning Detection Network observations) producing 1551 CG flashes over a 4-day period. Thundersnow events were examined in more detail because of the rarity of this phenomenon across the United States. Most lake-effect thundersnow events (75%) occurred in November and December. An analysis of model sounding data using the Buffalo Toolkit for Lake Effect Snow (BUFKIT) software package in which lower boundary conditions can be modified by lake surfaces showed that thundersnow events had an 82% increase in the mean height of the −10°C level when compared with nonelectrified lake-effect snowstorms (1.2 vs 0.7 km AGL), had higher lake-induced equilibrium levels (EL; above 3.6 km AGL) and convective available potential energy (CAPE; &gt;500 J kg−1), had low wind shear environments, and were intense, single-band storms. A nomogram of the altitude of the −10°C isotherm and EL proved to be useful in predicting lake-effect thundersnowstorms.
An Empirical Model for Surface Wind Stress Response to SST Forcing Induced by Tropical Instability Waves (TIWs) in the Eastern Equatorial Pacific
Authors: Zhang Rong-Hua , Busalacchi Antonio J. 
Published: December 2008

Abstract
High-resolution space-based observations reveal significant two-way air–sea interactions associated with tropical instability waves (TIWs); their roles in budgets of heat, salt, momentum, and biogeochemical fields in the tropical oceans have been recently demonstrated. However, dynamical model-based simulations of the atmospheric response to TIW-induced sea surface temperature (SSTTIW) perturbations remain a great challenge because of the limitation in spatial resolution and realistic representations of the related processes in the atmospheric planetary boundary layer (PBL) and their interactions with the overlying free troposphere. Using microwave remote sensing data, an empirical model is derived to depict wind stress perturbations induced by TIW-related SST forcing in the eastern tropical Pacific Ocean. Wind data are based on space–time blending of Quick Scatterometer (QuikSCAT) Direction Interval Retrieval with Thresholded Nudging (DIRTH) satellite observations and NCEP analysis fields; SST data are from the Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI). These daily data are first subject to a spatial filter of 12° moving average in the zonal direction to extract TIW-related wind stress (τTIW) and SSTTIW perturbations. A combined singular value decomposition (SVD) analysis is then applied to these zonal high-pass-filtered τTIW and SSTTIW fields. It is demonstrated that the SVD-based analysis technique can effectively extract TIW-induced covariability patterns in the atmosphere and ocean, acting as a filter by passing wind signals that are directly related with the SSTTIW forcing over the TIW active regions. As a result, the empirical model can well represent TIW-induced wind stress responses as revealed directly from satellite measurements (e.g., the structure and phase), but the amplitude can be underestimated significantly. Validation and sensitivity experiments are performed to illustrate the robustness of the empirical τTIW model. Further applications are discussed for taking into account the TIW-induced wind responses and feedback effects that are missing in large-scale climate models and atmospheric reanalysis data, as well as for uncoupled ocean and coupled mesoscale and large-scale air–sea modeling studies.
A Probabilistic Multimodel Ensemble Approach to Seasonal Prediction
Authors: Min Young-Mi , Kryjov Vladimir N. , Park Chung-Kyu 
Published: December 2008

Abstract
A probabilistic multimodel ensemble prediction system (PMME) has been developed to provide operational seasonal forecasts at the Asia–Pacific Economic Cooperation (APEC) Climate Center (APCC). This system is based on an uncalibrated multimodel ensemble, with model weights inversely proportional to the errors in forecast probability associated with the model sampling errors, and a parametric Gaussian fitting method for the estimate of tercile-based categorical probabilities.
It is shown that the suggested method is the most appropriate for use in an operational global prediction system that combines a large number of models, with individual model ensembles essentially differing in size and model weights in the forecast and hindcast datasets being inconsistent. Justification for the use of a Gaussian approximation of the precipitation probability distribution function for global forecasts is also provided.
PMME retrospective and real-time forecasts are assessed. For above normal and below normal categories, temperature forecasts outperform climatology for a large part of the globe. Precipitation forecasts are definitely more skillful than random guessing for the extratropics and climatological forecasts for the tropics. The skill of real-time forecasts lies within the range of the interannual variability of the historical forecasts.
The Smooth Signal Redundancy Hypothesis: A Functional Explanation for Relationships between Redundancy, Prosodic Prominence, and Duration in Spontaneous Speech
Authors: Aylett Matthew , Turk Alice 
Published: December 2008

This paper explores two related factors which influence variation in duration, prosodic structure and redundancy in spontaneous speech. We argue that the constraint of producing robust communication while efficiently expending articulatory effort leads to an inverse relationship between language redundancy and duration. The inverse relationship improves communication robustness by spreading information more evenly across the speech signal, yielding a smoother signal redundancy profile. We argue that prosodic prominence is a linguistic means of achieving smooth signal redundancy. Prosodic prominence increases syllable duration and coincides to a large extent with unpredictable sections of speech, and thus leads to a smoother signal redundancy. The results of linear regressions carried out between measures of redundancy, syllable duration and prosodic structure in a large corpus of spontaneous speech confirm: (1) an inverse relationship between language redundancy and duration, and (2) a strong relationship between prosodic prominence and duration. The fact that a large proportion of the variance predicted by language redundancy and prosodic prominence is nonunique suggests that, in English, prosodic prominence structure is the means with which constraints caused by a robust signal requirement are expressed in spontaneous speech.
Child codeswitching and adult content contrasts
Authors: Ervin-Tripp Susan , Reyes Iliana 
Published: December 2008

This paper discusses links between the conditions of developing child bilingualism and the adult outcomes in semiotic contrast in elicited speech and codeswitching. Analysis of interaction of children raised as bilinguals shows that from the beginning they can recognize the appropriate language for addressees. When the lexical repertoire is inadequate, borrowing occurs, and codeswitching of longer segments appears before age two. Throughout childhood and adolescence, codeswitching has increasing interactional functions as children's pragmatic skills grow. Some adult codeswitching relies on semiotic differences implied by language. It is likely that both such codeswitching and the dual selves shown in elicited discourse in different languages are limited to specific sociolinguistic situations and personal histories. These include education in a second language, adult immigration, and frequent contact with a monolingual community.
The multilingual potential in emerging grammars
Authors: Gawlitzek-Maiwald Ira , Tracy Rosemarie 
Published: December 2008

Our contribution deals with the nature of children's earliest word combinations. Based on data from monolingual (German) and bilingual (German/English) children we argue that there is no pregrammatical stage once children move beyond single-word utterances. As soon as words combine, basic organizational principles, such as the binary distinction between head and non-head, are activated and enter into coalitions with other (semantic, pragmatic) levels of representation. In addition we claim that monolinguals behave very much like bilinguals in that initially all children create coexisting grammars. Various types of evidence in favor of this proposal are considered. Convergence comes about when children (assisted by universal grammar) reconstruct derivational relationships linking hitherto independent systems. The overall process is slow, making it possible for us to detect transitional problems. Bilingual language mixing yields important insights into children's early awareness of cross-linguistic equivalence and contrasts and can be related to specific properties of a child's grammars at different developmental stages.
The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?
Authors: Douard Véronique , Brunet Frédéric , Boussau Bastien , Ahrens-Fath Isabelle , Vlaeminck-Guillem Virginie , Haendler Bernard , Laudet Vincent , Guiguen Yann 
Published: December 2008

Abstract

Background
Based on the observation of an increased number of paralogous genes in teleost fishes compared with other vertebrates and on the conserved synteny between duplicated copies, it has been shown that a whole genome duplication (WGD) occurred during the evolution of Actinopterygian fish. Comparative phylogenetic dating of this duplication event suggests that it occurred early on, specifically in teleosts. It has been proposed that this event might have facilitated the evolutionary radiation and the phenotypic diversification of the teleost fish, notably by allowing the sub- or neo-functionalization of many duplicated genes.

Results
In this paper, we studied in a wide range of Actinopterygians the duplication and fate of the androgen receptor (AR, NR3C4), a nuclear receptor known to play a key role in sex-determination in vertebrates. The pattern of AR gene duplication is consistent with an early WGD event: it has been duplicated into two genes AR-A and AR-B after the split of the Acipenseriformes from the lineage leading to teleost fish but before the divergence of Osteoglossiformes. Genomic and syntenic analyses in addition to lack of PCR amplification show that one of the duplicated copies, AR-B, was lost in several basal Clupeocephala such as Cypriniformes (including the model species zebrafish), Siluriformes, Characiformes and Salmoniformes. Interestingly, we also found that, in basal teleost fish (Osteoglossiformes and Anguilliformes), the two copies remain very similar, whereas, specifically in Percomorphs, one of the copies, AR-B, has accumulated substitutions in both the ligand binding domain (LBD) and the DNA binding domain (DBD).

Conclusion
The comparison of the mutations present in these divergent AR-B with those known in human to be implicated in complete, partial or mild androgen insensitivity syndrome suggests that the existence of two distinct AR duplicates may be correlated to specific functional differences that may be connected to the well-known plasticity of sex determination in fish. This suggests that three specific events have shaped the present diversity of ARs in Actinopterygians: (i) early WGD, (ii) parallel loss of one duplicate in several lineages and (iii) putative neofunctionalization of the same duplicate in percomorphs, which occurred a long time after the WGD.
Outcome of retinopathy of prematurity patients following adoption of revised indications for treatment
Authors: Alme Aaron M , Mulhern Michael L , Hejkal Thomas W , Meza Jane L , Qiu Fang , Ingvoldstad David D , Margalit Eyal 
Published: December 2008

Abstract

Background
The Early Treatment for Retinopathy of Prematurity study (ETROP), published in 2003, established new guidelines for treatment of retinopathy of prematurity (ROP) and demonstrated improved outcomes compared to previous guidelines. We examined outcomes before and after implementing the ETROP recommendations.

Methods
A retrospective chart review was performed using records of infants who had laser ablations for ROP performed from January, 2000 through December, 2005. Data collected included date of birth; birth weight; estimated gestational age (EGA); grading of ROP; date of laser ablation; and outcome of laser surgery. Univariate association with threshold or prethreshold treatment (Pre-ETROP and Post-ETROP, respectively) were assessed using t-tests or Wilcoxon tests. Additional comparison between groups was performed using Fisher's exact tests.

Results
581 patients were examined before and 464 after December 2003. Of these, 29/581 (5% – Pre-ETROP Group) and 53/464 (11% – Post-ETROP Group) patients advanced to criteria requiring laser treatment respectively (P = 0.0001). The average estimated gestational age (EGA) at birth was 26.3 and 25.2 weeks, with an average birth weight of 888 and 707 grams for Pre and Post-ETROP Groups, respectively. Stage 5 retinal detachment (RD) developed in 10.3% of eyes in the Pre-ETROP Group and 1.9% of eyes in the Post-ETROP Group (P = 0.02).

Conclusion
After the ETROP guidelines were implemented, there was a decrease from 10.3% to 1.9% of eyes developing Stage 5 retinal detachment, despite this group having a lower average EGA and lower average birth weight. These results underscore the importance of adoption of the Revised Indications.