bluuebunny/crossref_metadata_2025_split huggingface dataset:
Examining Relationships Among Dialect Variation, Literacy Skills, and School Context in First Grade
Authors: Terry Nicole Patton , Connor Carol McDonald , Thomas-Tate Shurita , Love Michael 
Published: February 2010

PurposeThis study examined relationships between the use of nonmainstream American English dialects, literacy skills, and school environment among typically developing first graders (n= 617), of whom 48% were African American and 52% were White, in order to describe and better understand the difficulties many children from linguistically diverse backgrounds experience while learning to read.MethodUsing hierarchical linear modeling, the authors examined the linear and quadratic relationships between students' dialect variation (DVAR) and their vocabulary, phonological awareness, and word reading skills, taking into account school environment, specifically schoolwide socioeconomic status (SES).ResultsThe relationships between DVAR and literacy outcomes depended on the outcome of interest and school SES. However, children’s race did not generally affect the trajectory or strength of the relationships between outcomes and dialect variation. For vocabulary and word reading, the association was nonlinear, that is, U-shaped, but this depended on school SES. For phonological awareness, a negative linear relationship was observed that did not depend on school SES.ConclusionsThe results inform theories on the relationship between DVAR and literacy achievement and suggest a more complex explanation of how nonmainstream American English dialect use might influence how young children learn to read.
Lexical–Semantic Organization in Children With Specific Language Impairment
Authors: Sheng Li , McGregor Karla K. 
Published: February 2010

Purpose
To determine whether children with specific language impairment (SLI) show deficits in lexical–semantic organization and, if so, whether these deficits are commensurate with their delay in vocabulary size and whether the deficits affect all children with SLI.

Method

Fourteen children with SLI, 14 age matches (AM), and 14 expressive vocabulary matches (VM) generated 3 associations to each of 48 words. Associations were coded as semantic (e.g.,
dog
–
pet
), clang (e.g.,
cow
–
how
), or erroneous (e.g.,
spoon
–
Disney
).

Results
Relative to the AM children, children with SLI produced fewer semantic responses, more clangs, and more errors. Relative to the VM children, fewer semantic responses and more errors in the children with SLI were found in by-item analyses. Across elicitation trials, semantic responses decreased in the AM and VM children but remained stable in the SLI children. Examination of individual performance in the SLI group revealed that poor semantic performance was associated with a deficit in expressive vocabulary and a gap between receptive and expressive vocabularies.

Conclusions
Significant variability in lexical–semantic organization skills exists among children with SLI. Deficits in lexical–semantic organization were demonstrated by a subgroup of children with SLI who likely had concomitant word-finding difficulties.
A model for the CO-inhibited form of [NiFe] hydrogenase: synthesis of (CO)
3
Fe(
μ
-S

t

Bu)
3
Ni{SC
6
H
3
-2,6-(mesityl)
2
} and reversible CO addition at the Ni site
Authors: Ohki Yasuhiro , Yasumura Kazunari , Ando Masaru , Shimokata Satoko , Tatsumi Kazuyuki 
Published: February 2010

A [NiFe] hydrogenase model compound having a distorted trigonal-pyramidal nickel center, (CO)
3
Fe(
μ
-S

t

Bu)
3
Ni(SDmp), 1 (Dmp = C
6
H
3
-2,6-(mesityl)
2
), was synthesized from the reaction of the tetranuclear Fe-Ni-Ni-Fe complex [(CO)
3
Fe(
μ
-S

t

Bu)
3
Ni]
2
(
μ
-Br)
2
, 2 with NaSDmp at -40 °C. The nickel site of complex 1 was found to add CO or CN

t

Bu at -40 °C to give (CO)
3
Fe(S

t

Bu)(
μ
-S

t

Bu)
2
Ni(CO)(SDmp), 3, or (CO)
3
Fe(S

t

Bu)(
μ
-S

t

Bu)
2
Ni(CN

t

Bu)(SDmp), 4, respectively. One of the CO bands of 3, appearing at 2055 cm
-1
in the infrared spectrum, was assigned as the Ni-CO band, and this frequency is comparable to those observed for the CO-inhibited forms of [NiFe] hydrogenase. Like the CO-inhibited forms of [NiFe] hydrogenase, the coordination of CO at the nickel site of 1 is reversible, while the CN

t

Bu adduct 4 is more robust.
A link between H3K27me3 mark and exon length in the gene promoters of pluripotent and differentiated cells
Authors: Chen Liang 
Published: February 2010

Abstract
We conducted a reanalysis of genome-wide histone H3 tail methylation data in mammalian pluripotent and differentiated cells. We show that the promoters marked with histone H3 lysine 27 trimethylation (H3K27me3) tend to have more exonic positions in the promoter regions. However, this is not due to any preferential marking on exons over introns by H3K27me3. The relationship is also independent the status of histone H3 lysine 4 trimethylation (H3K4me3) mark, CpG content and the platforms used in the high-throughput profiling of histone modifications. It provides evidence for the link between histone modifications and transcribed exons in promoter regions.
Contact: liang.chen@usc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Transferring vertically aligned carbon nanotubes onto a polymeric substrate using a hot embossing technique for microfluidic applications
Authors: Mathur A. , Roy S. S. , McLaughlin J. A. 
Published: February 2010

We explored the hot embossing method for transferring vertically aligned carbon nanotubes (CNTs) into microfluidic channels, fabricated on poly-methyl-methacrylate (PMMA). Patterned and unpatterned CNTs were synthesized by microwave plasma-enhanced chemical vapour deposition on silicon to work as a stamp. For hot embossing, 115°C and 1 kN force for 2 min were found to be the most suitable parameters for the complete transfer of aligned CNTs on the PMMA microchannel. Raman and SEM studies were used to analyse the microstructure of CNTs before and after hot embossing. The PMMA microparticles with dimensions (approx. 10 µm in diameter) similar to red blood cells were successfully filtered using laminar flow through these microfluidic channels. Finally, a microfluidic-based point-of-care device for blood filtration and detection of bio-molecules is drawn schematically.
Expression of NDRG2 in esophageal squamous cell carcinoma
Authors: Shi Hai , Li Nanlin , Li Shujun , Chen Changsheng , Wang Weizhong , Xu Chunsheng , Zhang Jian , Jin Haifeng , Zhang Hongwei , Zhao Huadong , Song Wenjie , Feng Quanxin , Feng Xiangying , Shen Xin , Yao Libo , Zhao Qingchuan 
Published: February 2010

N‐Myc downstream‐regulated gene 2 (NDRG2), a new member of the N‐Myc downstream‐regulated gene family, has been found to be a differentially expressed gene involved in a variety of cancers. The present study aimed to investigate the expression of NDRG2 in esophageal squamous cell carcinoma (ESCC). Immunohistochemistry was performed in 154 samples from patients with ESCC to detect the expression level of NDRG2 and C‐MYC. Results indicated that the expression level of NDRG2 in the cancer samples was significantly lower than that in normal tissues; the trend of C‐MYC was the reverse. The Wilcoxon–Mann–Whitney test showed significant difference in the expression of NDRG2 in patients with different T stage, TNM stage, and differentiation degree of cancers (P = 0.036, 0.031, 0.001, respectively). Patients in stages I and II were followed up for 5 consecutive years and Kaplan–Meier survival analysis demonstrated that the survival time of ESCC patients with high expression of NDRG2 was longer than those with low expression during the 5‐year follow‐up period (P = 0.0018). Cox regression analysis indicated that low expression of NDRG2, cancer stage of pT1, and distant organ metastasis (pM1) were the independent poor prognostic factors of ESCC (P = 0.004, 0.019, 0.0013, respectively). Furthermore, up‐regulation of NDRG2 was introduced to ESCC cell lines (EC9706 and EC109) by plasmid transfection. In vivo and in vitro studies indicated that overexpression of NDRG2 markedly reduced proliferation and promoted the apoptosis of EC9706 and EC109 cells. In summary, our results demonstrated that NDRG2 played an important role in the proliferation of ESCC cells and the expression of NDRG2 in ESCC was closely related with the prognosis.(Cancer Sci 2010; 101: 1292–1299)
Response of native ungulates to drought in semi‐arid Kenyan rangeland
Authors: Augustine David J. 
Published: February 2010

AbstractThe distribution and abundance of native ungulates were measured on commercially managed, semi‐arid rangeland in central Kenya over a 3‐year period that encompassed severe drought and above‐average rainfall. Native ungulate biomass density averaged 5282 kg km−2over the study and was dominated by elephant (Loxodonta africana), impala (Aepyceros melampus) and dik‐dik (Madoqua kirkii). Biomass density of domestic cattle (Bos taurus) averaged 2280 kg km−2during the study. Responses of native ungulates to severe drought were variable. Impala densities were similar to or greater than densities for similar habitat in protected areas, and varied from 12 to 16 km−2during and following the drought to 24–29 km−2following above‐average rainfall. Dik‐dik densities were also greater than densities reported for protected areas and were surprisingly stable throughout the study despite the wide annual fluctuations in rainfall. Elephant migrated out of the region during drought but were present at high densities (2.9–5.2 km−2) during wet seasons, consistent with telemetry studies emphasizing the importance ofAcaciabushland habitat on commercial rangelands for the migratory portion of the Laikipia–Samburu elephant population. Results show that substantial densities of native browsing and mixed‐feeding ungulates can occur on rangeland managed for commercial beef production and suggest that the capacity for ungulates to move over large spatial scales (>100 km2) and to shift distributions in response to locally variable thunderstorms may be important for sustaining these populations.
Historical biogeography of the coffee family (Rubiaceae, Gentianales) in Madagascar: case studies from the tribes Knoxieae, Naucleeae, Paederieae and Vanguerieae
Authors: Wikström N. , Avino M. , Razafimandimbison S. G. , Bremer B. 
Published: February 2010

AbstractAim  In Madagascar the family Rubiaceae includes an estimated 650 species representing 95 genera. As many as 98% of the species and 30% of the genera are endemic. Several factors make the Rubiaceae a model system for developing an understanding of the origins of the Malagasy flora. Ancestral area distributions are explicitly reconstructed for four tribes (Knoxieae, Naucleeae, Paederieae and Vanguerieae) with the aim of understanding how many times, and from where, these groups have originated in Madagascar.Location  Indian Ocean Basin, with a focus on Madagascar.Methods  Bayesian phylogenetic analyses are conducted on the four tribes. The results are used for reconstructing ancestral areas using dispersal–vicariance analyses. Phylogenetic uncertainties in the reconstructions are accounted for by conducting all analyses on the posterior distribution from the analyses.Results  Altogether, 11 arrivals in Madagascar (one in Paederieae, five in Knoxieae, three in Vanguerieae, and two in Naucleeae) are reconstructed. The most common pattern is a dispersal event (followed by vicariance) from Eastern Tropical Africa. The Naucleeae and Paederieae in Madagascar differ and originate from Asia. Numerous out‐of‐Madagascar dispersals, mainly in the dioecious Vanguerieae, are reconstructed.Main conclusions  The four tribes arrived several times in Madagascar via dispersal events from Eastern Tropical Africa, Southern Africa and Tropical Asia. The presence of monophyletic groups that include a number of species only found in Madagascar indicates that much endemism in the tribes results from speciation events occurring well after their arrival in Madagascar. Madagascar is the source of origin for almost all Rubiaceae found on the neighbouring islands of the Comoros, Mascarenes and Seychelles.
Dried leaves of Rosmarinus officinalis as a treatment for streptococcosis in tilapia
Authors: Zilberg D , Tal A , Froyman N , Abutbul S , Dudai N , Golan‐Goldhirsh A 
Published: February 2010

AbstractDietary application of dried Rosmarinus officinalis (rosemary) leaves as a treatment for streptococcal infection was studied in tilapia, Oreochromis sp. Feeding with dried rosemary leaves significantly reduced mortality following infection with Streptococcus iniae: 44% mortality in the group fed 8% rosemary, similar to oxytetracycline treatment (43% mortality), and significantly lower than the control (65%). Dietary administration of 16% rosemary significantly reduced mortality because of Streptococcus agalactiae infection in 44 g fish (62% and 76% in 16% rosemary and control, respectively), but not in a similar experiment conducted with 5.5 g fish. The antibacterial effect of rosemary on S. iniae was studied. Activity of rosemary cultivar Israel was reduced during the winter, but there was no significant change in cultivars Oranit and Star. Storage of powdered rosemary leaves at 50 °C resulted in fourfold and eightfold higher MIC24 h values after 3 and 4.5 months, respectively. Storage at −20 °C, 4 °C and 25 °C and autoclaving (120 °C) each resulted in a twofold increase in MIC24 h. Repeated exposures of S. iniae to rosemary did not affect minimal inhibitory concentration, suggesting no development of resistance to rosemary.
Salmonid alphavirus (SAV) and pancreas disease (PD) in Atlantic salmon, Salmo salar L., in freshwater and seawater sites in Norway from 2006 to 2008
Authors: Jansen M D , Taksdal T , Wasmuth M A , Gjerset B , Brun E , Olsen A B , Breck O , Sandberg M 
Published: February 2010

AbstractA cohort study was initiated in the spring of 2006 to investigate epidemiological aspects and pathogenesis of salmonid alphavirus (SAV) subtype 3 infections and pancreas disease (PD). The aims were to assess involvement of the freshwater production phase, the extent and frequency of subclinical infections and to follow PD‐affected populations throughout the entire seawater production cycle, as well as investigate possible risk factors for PD outbreaks. Fish groups from 46 different Atlantic salmon freshwater sites in six counties were sampled once prior to seawater transfer and followed onto their seawater sites. A total of 51 Atlantic salmon seawater sites were included, and fish groups were sampled three times during the seawater production phase. SAV subtype 3 was not identified by real‐time RT‐PCR from samples collected in the freshwater phase, nor were any SAV‐neutralizing antibodies or histopathological changes consistent with PD. In the seawater phase, SAV was detected in samples from 23 of 36 (63.9%) studied sites located within the endemic region. No SAV subtype 3 was detected in samples from seawater sites located outside the endemic region. The cumulative incidence of PD during the production cycle amongst sites with SAV detected was 87% (20 of 23 sites). Average fish weight at time of PD diagnosis ranged from 461 to 5978 g, because of a wide variation in the timing of disease occurrence throughout the production cycle. Mortality levels following a PD diagnosis varied greatly between populations. The mean percentage mortality was 6.9% (±7.06) (range 0.7–26.9), while the mean duration of increased mortality following PD diagnosis was 2.8 months (±1.11) (range 1–6).
A novel DFNB1 deletion allele supports the existence of a distant cis‐regulatory region that controls GJB2 and GJB6 expression
Authors: Wilch E , Azaiez H , Fisher RA , Elfenbein J , Murgia A , Birkenhäger R , Bolz H , Da Silva‐Costa SM , Del Castillo I , Haaf T , Hoefsloot L , Kremer H , Kubisch C , Le Marechal C , Pandya A , Sartorato EL , Schneider E , Van Camp G , Wuyts W , Smith RJH , Friderici KH 
Published: February 2010

Wilch E, Azaiez H, Fisher RA, Elfenbein J, Murgia A, Birkenhäger R, Bolz HJ, da Silva‐Costa SM, del Castillo I, Haaf T, Hoefsloot L, Kremer H, Kubisch C, Le Marechal C, Pandya A, Sartorato EL, Schneider E, Van Camp G, Wuyts W, Smith RJH, Friderici KH. A novel DFNB1 deletion allele supports the existence of a distant cis‐regulatory region that controls GJB2 and GJB6 expression.Eleven affected members of a large German–American family segregating recessively inherited, congenital, non‐syndromic sensorineural hearing loss (SNHL) were found to be homozygous for the common 35delG mutation of GJB2, the gene encoding the gap junction protein Connexin 26. Surprisingly, four additional family members with bilateral profound SNHL carried only a single 35delG mutation. Previously, we demonstrated reduced expression of both GJB2 and GJB6 mRNA from the allele carried in trans with that bearing the 35delG mutation in these four persons. Using array comparative genome hybridization (array CGH), we have now identified on this allele a deletion of 131.4 kb whose proximal breakpoint lies more than 100 kb upstream of the transcriptional start sites of GJB2 and GJB6. This deletion, del(chr13:19,837,344–19,968,698), segregates as a completely penetrant DFNB1 allele in this family. It is not present in 528 persons with SNHL and monoallelic mutation of GJB2 or GJB6, and we have not identified any other candidate pathogenic copy number variation by arrayCGH in a subset of 10 such persons. Characterization of distant GJB2/GJB6 cis‐regulatory regions evidenced by this allele may be required to find the ‘missing’ DFNB1 mutations that are believed to exist.
Conquering the complex world of human septins: implications for health and disease
Authors: Peterson EA , Petty EM 
Published: February 2010

Peterson EA and Petty EM. Conquering the complex world of human septins: implications for health and disease.Septins are highly conserved filamentous proteins first characterized in budding yeast and subsequently identified in must eukaryotes. Septins can bind and hydrolyze GTP, which is intrinsically related to their formation of septin hexamers and functional protein interactions. The human septin family is composed of 14 loci,SEPT1‐SEPT14, which encode dozens of different septin proteins. Their central GTPase and polybasic domain regions are highly conserved but they diverge in their N‐terminus and/or C‐terminus. The mechanism by which the different isoforms are generated is not yet well understood, but one can hypothesize that the use of different promoters and/or alternative splicing could give rise to these variants.Septins perform diverse cellular functions according to tissue expression and their interacting partners. Functions identified to date include cell division, chromosome segregation, protein scaffolding, cellular polarity, motility, membrane dynamics, vesicle trafficking, exocytosis, apoptosis, and DNA damage response. Their expression is tightly regulated to maintain proper filament assembly and normal cellular functions. Alterations of these proteins, by mutation or expression changes, have been associated with a variety of cancers and neurological diseases. The association of septins with cancer results from alterations of expression in solid tumors or translocations in leukemias [mixed lineage leukemia (MLL)]. Expression changes in septins have also been associated with neurological conditions such as Alzheimer's and Parkinson's disease, as well as retinopathies, hepatitis C, spermatogenesis and Listeria infection. Pathogenic mutations ofSEPT9were identified in the autosomal dominant neurological disorder hereditary neuralgic amyotrophy (HNA).Human septin research over the past decade has established their importance in cell biology and human disease. Further functional characterization of septins is crucial to our understanding of their possible diagnostic, prognostic, and therapeutic applications.
Identification and molecular characterization of two novel chromosomal deletions associated with autism
Authors: Chien W‐H , Gau SS‐F , Wu Y‐Y , Huang Y‐S , Fang J‐S , Chen Y‐J , Soong W‐T , Chiu Y‐N , Chen C‐H 
Published: February 2010

Chien W‐H, Gau SS‐F, Wu Y‐Y, Huang Y‐S, Fang J‐S, Chen Y‐J, Soong W‐T, Chiu Y‐N, Chen C‐H. Identification and molecular characterization of two novel chromosomal deletions associated with autism.Autism is a childhood‐onset neurodevelopmental disorder with a strong genetic basis in its etiology. Conventional karyotype analysis has revealed that chromosomal structural aberrations such as translocation, inversion, deletion, and duplication play a role in causing autism spectrum disorders (ASD). In addition, recent array‐based comparative genomic hybridization (array CGH) studies discovered that submicroscopic deletion and duplication of DNA segments also contributed significantly to the genetic etiology of ASD. Together, these studies indicate that genomic rearrangement is an important genetic mechanism of ASD. Using karyotyping analysis and array CGH technology, we identified a subtelomeric deletion of approximately 6.8 Mb at 4q35.1‐35.2 and a terminal deletion of approximately 2.4 Mb at 8p23.2‐pter in two autistic boys, respectively. These two deletions were further validated using fluorescent in situ hybridization and real‐time quantitative polymerase chain reaction, and their breakpoints were delineated using high‐resolution array CGH. The 4q deletion is a rare de novo mutation, while the transmission of 8p deletion is unknown, because the father of the patient was unavailable for study. These two deletions are rare mutations and were not found in the additional 282 patients with ASD and in the 300 control subjects in our population. The identification of these two chromosomal deletions contribute to our understanding of the genetic basis of ASD, and the haploinsufficiency of several genes located at the deleted regions of chromosome 8p and 4q may contribute to the clinical phenotypes of autism.
Effects of Rapid Broadband Trills on Responses to Song Overlapping in Nightingales
Authors: Sprau Philipp , Schmidt Rouven , Roth Tobias , Amrhein Valentin , Naguib Marc 
Published: February 2010

AbstractIn communication, animals often use complex signals with different traits carrying different information. In the song of some songbirds, both trills and song overlapping signal arousal or the readiness to escalate a contest in male‐male interactions, yet they also differ inherently from each other. Song overlapping is restricted to interactions and has a clear directive function as the songs are timed specifically to the songs of a counterpart. Trills, however, can be used without opponents actively singing and do not have such a directional character unless when combined with directed traits. This difference raises the question whether trills can enhance the agonistic function of song overlapping when being used simultaneously. Here, we exposed male nightingales (Luscinia megarhynchos) prior to pairing to overlapping playback treatments differing in the presence or absence of rapid broadband trills. Males responded differently to the two playback treatments suggesting that song overlapping and rapid broadband trills have some synergistic effects. Consequently, the separate or simultaneous use of trills and of song overlapping may allow males to adjust information encoded in their singing on a fine scale. Furthermore, males that remained unpaired throughout the breeding season responded differently to the playbacks than did subsequently paired males, emphasizing the implications of differences in territory defence behaviour on males subsequent pairing success.