bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotype–phenotype analysis and natural history of left ventricular hypertrophy in LEOPARD syndrome
Authors: Limongelli Giuseppe , Sarkozy Anna , Pacileo Giuseppe , Calabrò Paolo , Digilio Maria Cristina , Maddaloni Valeria , Gagliardi Giulia , Di Salvo Giovanni , Iacomino Maria , Marino Bruno , Dallapiccola Bruno , Calabrò Raffaele 
Published: February 2008

AbstractBecause it is unclear whether the genotype may influence the clinical course in patients with LEOPARD syndrome (LS), we analyzed clinical and molecular predictors of adverse cardiac events in patients with left ventricular hypertrophy (LVH). A comprehensive cardiovascular evaluation, including baseline electrocardiogram, echocardiography, exercise test and 24 hr Holter monitoring at the time of clinical diagnosis and during follow‐up was conducted on 24 patients referred to our departments. Phenotypical examination and diagnosis were performed by expert clinical geneticists. The entire PTPN11 and RAF1 coding regions were screened for mutations by DHPLC analysis, followed by sequencing. Patients without PTPN11 mutations (34%) showed a higher frequency of family history of sudden death (P = 0.007), increased left atrial dimensions (P = 0.05), bradyarrhythmias (P = 0.04), episodes of supraventricular tachycardias (P = 0.06), atrial fibrillation (P = 0.009), and nonsustained ventricular tachycardias (P = 0.05) during Holter monitoring. Six patients (25%) had adverse cardiac events during follow‐up (including sudden deaths, resuscitated cardiac arrest, septal myectomy, and heart failure). LVH, New York Heart Association Class, left ventricular outflow tract obstruction, and nonsustained ventricular tachycardias were associated to adverse cardiac events. Of note, three patients with mutations in exon 13 showed a severe obstructive cardiomyopathy, with serious cardiac complications during follow‐up (heart failure, septal myectomy, and sudden death). In conclusion, patients with LVH associated with LS seem to carry a relatively high risk of adverse (arrhythmic and nonarrhythmic) events. Further genotype–phenotype studies are warranted to fully elucidate the impact of the genotype on the natural history of patients with LS and LVH. © 2008 Wiley‐Liss, Inc.
Clinical and radiographic delineation of odontochondrodysplasia
Authors: Unger Sheila , Antoniazzi Franco , Brugnara Milena , Alanay Yasemin , Caglayan Ahmet , Lachlan Katherine , Ikegawa Shiro , Nishimura Gen , Zabel Bernhard , Spranger Jürgen , Superti‐Furga Andrea 
Published: February 2008

AbstractThe association of dentinogenesis imperfecta (DI) with a distinct form of chondrodysplasia in a boy was reported by Goldblatt et al. [1991; Am J Med Genet 39:170–172] and has been given the name of Goldblatt syndrome or odontochondrodysplasia (ODCD; OMIM#184260). Since the original description, only four further individuals have been reported (one sib pair and two unrelated cases). We report on an additional six individuals, including a second sib pair (brother and sister), with clinical and radiographic features that cluster and thus confirm the nosologic status of this entity. The main radiographic features are congenital platyspondyly with coronal clefts, severe metaphyseal changes particularly of the hands, wrists, and knees, mesomelic limb shortening, and coxa valga. The main physical signs are short stature, joint laxity, narrow chest, scoliosis, and DI. This combination of clinical and radiographic findings allows clear recognition of this syndrome in early childhood. Of note, the signs that are present in the newborn period are not entirely specific and the differential diagnosis includes spondylometaphyseal dysplasia (SMD) Sedaghatian type or platyspondylic lethal dysplasia (PSLD) Torrance type. The occurrence of two sib pairs in a group of only 11 patients suggests an autosomal recessive inheritance pattern. Overmodification of cartilage‐extracted collagen 2 has been reported in two sibs, but mutation analysis of COL2A1 as well as of COMP, FGFR3, RMRP, and SBDS in one or more patients have given negative results, and the molecular etiology is as yet unknown. © 2008 Wiley‐Liss, Inc.
Health‐related quality of life of children with a positive carrier status for inherited cardiovascular diseases
Authors: Smets Ellen M.A. , Stam Marinka M.H. , Meulenkamp Tineke M. , van Langen Irene M. , Wilde Arthur A.M. , Wiegman Albert , de Wert Guido M. , Tibben Aad 
Published: February 2008

AbstractFamilial hypercholesterolemia, hypertrophic cardiomyopathy, and long QT Syndrome are genetic cardiovascular conditions which may lead to sudden cardiac death at a young age. Preventive measures include lifestyle modifications, medications, and/or cardiac devices. Hence, identification of carrier children can protect them for the potentially life threatening consequences at a young age. Yet, informing children about their genetic risk status and subjecting them to treatment may have negative consequences. This preliminary study aimed to explore (1) how the health‐related quality of life of carrier children compares to the quality of life of Dutch children in general; and (2) to what extent the carrier children's quality of life and their parents' perception thereof concur. Our method involved carrier children (n = 35), aged between 8 and 18 years, and their parents (n = 37) who completed a self‐report questionnaire. Children's health‐related quality of life was assessed with a children and parent version of the KIDSCREEN. Dutch reference data were available from a representative national sample. Our results show no statistically significant differences in scores between carrier children and the reference group. Also, no differences were found between carrier children and their parents' ratings, with the exception of the scale “psychological well being”. Parents rated their child's psychological well being significantly lower. We identified no problems with the well‐being of carrier children as compared to a representative sample of peers. This may offer some initial reassurance to those who have concerns about the implications of genetically testing children for one of these cardiovascular conditions. Yet, attention to possible problems in these children remains warranted. © 2008 Wiley‐Liss, Inc.
Fermentative production of l‐glycerol 3‐phosphate utilizing a Saccharomyces cerevisiae strain with an engineered glycerol biosynthetic pathway
Authors: Popp A. , Nguyen H.T.T. , Boulahya K. , Bideaux C. , Alfenore S. , Guillouet S.E. , Nevoigt E. 
Published: February 2008

AbstractInterest in l‐glycerol 3‐phosphate (l‐G3P) production via microbial fermentation is due to the compound's potential to replace the unstable substrate dihydroxyacetone phosphate (DHAP) in one‐pot enzymatic carbohydrate syntheses. A Saccharomyces cerevisiae strain with deletions in both genes encoding specific l‐G3Pases (GPP1 and GPP2) and multicopy overexpression of l‐glycerol 3‐phosphate dehydrogenase (GPD1) was studied via small‐scale (100 mL) batch fermentations under quasi‐anaerobic conditions. Intracellular accumulation of l‐G3P reached extremely high levels (roughly 200 mM) but thereafter declined. Extracellular l‐G3P was also detected and its concentration continuously increased throughout the fermentation, such that most of the total l‐G3P was found outside the cells as fermentation concluded. Moreover, in spite of the complete elimination of specific l‐G3Pase activity, the strain showed considerable glycerol formation suggesting unspecific dephosphorylation as a mechanism to relieve cells of intracellular l‐G3P accumulation. Up‐scaling the process employed fed‐batch fermentation with repeated glucose feeding, plus an aerobic growth phase followed by an anaerobic product accumulation phase. This produced a final product titer of about 325 mg total l‐G3P per liter of fermentation broth. Biotechnol. Bioeng. 2008;100: 497–505. © 2008 Wiley Periodicals, Inc.
Viral clearance using disposable systems in monoclonal antibody commercial downstream processing
Authors: Zhou Joe X. , Solamo Felix , Hong Tony , Shearer Michael , Tressel Tim 
Published: February 2008

AbstractOnce highly selective protein A affinity is chosen for robust mAb downstream processing, the major role of polishing steps is to remove product related impurities, trace amounts of host cell proteins, DNA/RNA, and potential viral contaminants. Disposable systems can act as powerful options either to replace or in addition to polishing column chromatography to ensure product purity and excellent viral clearance power for patients' safety. In this presentation, the implementation of three disposable systems such as depth filtration, membrane chromatography, and nanometer filtration technology in a commercial process are introduced. The data set of viral clearance with these systems is presented. Application advantages and disadvantages including cost analysis are further discussed. Biotechnol. Bioeng. 2008;100: 488–496. © 2008 Wiley Periodicals, Inc.
Biomaterial‐loaded allograft threaded cage for the treatment of femoral head osteonecrosis in a goat model
Authors: Yang Shuhua , Wu Xinghuo , Mei Rongcheng , Yang Cao , Li Jin , Xu Weihua , Ye Shunan 
Published: February 2008

AbstractThe purpose of this study was to evaluate the efficacy of core decompression with a biomaterial‐loaded allograft threaded cage (ATC) for the treatment of femoral head osteonecrosis in an established goat model. First, bilateral early‐stage osteonecrosis was induced. After core decompression, the remaining goats were randomly divided into three groups: Group A, the goats were left without any treatment; Group B, the goats were treated with implanting a composite of autologous bone and decalcified bone matrix (DBM); Group C, the goats were treated using insertion of ATC loaded with DBM and autogenous bone graft. Then radiographic, histological and biomechanical analysis were taken in each group at 5, 10, and 20 weeks postoperation. In Group A, the classical signs of osteonecrosis of the femoral head were identified 10 weeks after the induction. Twenty weeks later, the density, surface and biomechanical stability of the femoral head were normal in Group C, while an irregular surface and an inhomogeneous microstructure or variation of density/hardness were identified in Group B. The specimens revealed a continuous trabaecular bone structure throughout the cage and extensive bone ingrowth and remodeling in Group C, while fibrous tissue was evident in Group B. Core decompression with a biomaterial loaded ATC almost uniformly delays or arrests the progression of the disease before articular collapse, and it could help to get the balance between bone resorption and new bone formation, strengthen structural mechanics of the femoral head, provide structure support of articular cartilage. Biotechnol. Bioeng. 2008;100: 560–566. © 2008 Wiley Periodicals, Inc.
Impact of target mRNA structure on siRNA silencing efficiency: A large‐scale study
Authors: Gredell Joseph A. , Berger Angela K. , Walton S. Patrick 
Published: February 2008

AbstractThe selection of active siRNAs is generally based on identifying siRNAs with certain sequence and structural properties. However, the efficiency of RNA interference has also been shown to depend on the structure of the target mRNA, primarily through studies using exogenous transcripts with well‐defined secondary structures in the vicinity of the target sequence. While these studies provide a means for examining the impact of target sequence and structure independently, the predicted secondary structures for these transcripts are often not reflective of structures that form in full‐length, native mRNAs where interactions can occur between relatively remote segments of the mRNAs. Here, using a combination of experimental results and analysis of a large dataset, we demonstrate that the accessibility of certain local target structures on the mRNA is an important determinant in the gene silencing ability of siRNAs. siRNAs targeting the enhanced green fluorescent protein were chosen using a minimal siRNA selection algorithm followed by classification based on the predicted minimum free energy structures of the target transcripts. Transfection into HeLa and HepG2 cells revealed that siRNAs targeting regions of the mRNA predicted to have unpaired 5′‐ and 3′‐ends resulted in greater gene silencing than regions predicted to have other types of secondary structure. These results were confirmed by analysis of gene silencing data from previously published siRNAs, which showed that mRNA target regions unpaired at either the 5′‐end or 3′‐end were silenced, on average, ∼10% more strongly than target regions unpaired in the center or primarily paired throughout. We found this effect to be independent of the structure of the siRNA guide strand. Taken together, these results suggest minimal requirements for nucleation of hybridization between the siRNA guide strand and mRNA and that both mRNA and guide strand structure should be considered when choosing candidate siRNAs. Biotechnol. Bioeng. 2008;100: 744–755. © 2008 Wiley Periodicals, Inc.
Increased phenotypic stability and ethanol tolerance of recombinant Escherichia coli KO11 when immobilized in continuous fluidized bed culture
Authors: Zhou Bin , Martin Gregory J.O. , Pamment Neville B. 
Published: February 2008

AbstractThe recombinant Escherichia coli B strain KO11, containing chromosomally‐integrated genes for ethanol production, was developed for use in lignocellulose‐to‐ethanol bioconversion processes but suffers from instability in continuous culture and a low ethanol tolerance compared to yeast. Here we report the ability cell immobilization to improve its phenotypic stability and ethanol tolerance during continuous culture on a 50 g/L xylose feed. Experiments conducted in a vertical tubular fermentor operated as a liquid‐fluidized bed with the cells immobilized on porous glass microspheres were compared to control experiments in the same reactor operated as a chemostat without the support particles. Without cell immobilization the ethanol yield fell sharply following start‐up, declining to 60% of theoretical after only 8–9 days of continuous fermentation. While immobilizing the cells did not prevent this decline, it delayed its onset and slowed its rate. With immobilization, a stable high ethanol yield (>85%) was maintained for at least 10 days, thereafter declining slowly, but remaining above 70% even after up to 40 days of fermentation. The ethanol tolerance of E. coli KO11 cells was substantially increased by immobilization on the glass microspheres. In ethanol tolerance tests, immobilized cells released from the microspheres had survival rates 2.3‐ to 15‐fold higher than those of free cells isolated from the same broth. Immobilization is concluded to be an effective means of increasing ethanol tolerance in E. coli KO11. While immobilization was only partially effective in combating its phenotypic instability, further improvements can be expected following optimization of the immobilization conditions. Biotechnol. Bioeng. 2008;100: 627–633. © 2008 Wiley Periodicals, Inc.
Neural differentiation and potential use of stem cells from the human umbilical cord for central nervous system transplantation therapy
Authors: Low Choon Bing , Liou Yih‐Cherng , Tang Bor Luen 
Published: February 2008

AbstractThe human umbilical cord is a rich source of autologous stem and progenitor cells. Interestingly, subpopulations of these, particularly mesenchymal‐like cells from both cord blood and the cord stroma, exhibited a potential to be differentiated into neuron‐like cells in culture. Umbilical cord blood stem cells have demonstrated efficacy in reducing lesion sizes and enhancing behavioral recovery in animal models of ischemic and traumatic central nervous system (CNS) injury. Recent findings also suggest that neurons derived from cord stroma mesenchymal cells could alleviate movement disorders in hemiparkinsonian animal models. We review here the neurogenic potential of umbilical cord stem cells and discuss possibilities of their exploitation as an alternative to human embryonic stem cells or neural stem cells for transplantation therapy of traumatic CNS injury and neurodegenerative diseases. © 2008 Wiley‐Liss, Inc.
Investigation of Barcelona and Du Chilly filbert nuts. I. Chemical study of Barcelona and Du Chilly filbert nuts and oils
Authors: Fang S. C. , Bullis D. E. 
Published: February 2008

SummaryBarcelona and Du Chilly fibert nuts have been analyzed for their principal constituents. The characteristics of the oils obtained by solvent extraction and by cold expression have been determined and their fatty acid composition has been ascertained. Most of the chemical and physical characteristics of the oils as determined in this laboratory agree well with values previously reported by other investigators on European varieties. However, our study of the oil components shows a considerable difference in fatty acid composition.
Clarifying co‐rumination: Associations with internalizing symptoms and romantic involvement among adolescent girls
Authors: Starr Lisa R. , Davila Joanne 
Published: February 2008

AbstractCo‐rumination, or excessive discussion of problems within friendships, has been associated with internalizing symptoms and is especially prevalent among adolescent girls. Eighty‐three early adolescent girls participated in a prospective study further examining this construct. Co‐rumination was positively correlated with depressive symptoms and positive aspects of friendship, but did not predict longitudinal changes in depressive symptoms. Co‐rumination was negatively related to social anxiety when controlling for depressive symptoms. Co‐rumination correlated positively with romantic experiences, and the two interacted to predict longitudinal changes in depressive symptoms, implying that co‐rumination may only be depressogenic under certain circumstances. Theoretical ramifications for the construct of co‐rumination and interpersonal aspects of adolescent internalizing symptoms are discussed.
Developmental expression of glycine receptor subunits in rat cerebellum
Authors: García‐Alcocer Guadalupe , Mejía Carmen , Berumen Laura C. , Miledi Ricardo , Martínez‐Torres Ataúlfo 
Published: February 2008

AbstractThe distribution of the glycine receptor subunits α1–3 and β in the developing rat cerebellum was studied from postnatal day 1 to adulthood by means of quantitative RT‐PCR and immunohistochemistry. qRT‐PCR of postnatal cerebella indicated the presence of mRNA for each subunit, with a relative expression of α2 > α3 > α1 > β. The immunohistochemistry indicated a strong α2 signal in the Purkinje cells, internal and external granular layers. The α1–3 subunits had weak signals in the Purkinje cells and molecular layer. The α1 subunit was expressed at a low level and was also found in the white matter. The function of these receptors in neuronal and glial plasma membranes in early postnatal development remains to be determined.
Using flowViz to visualize flow cytometry data
Authors: Sarkar D. , Le Meur N. , Gentleman R. 
Published: February 2008

Abstract
Summary: Automated analysis of flow cytometry (FCM) data is essential for it to become successful as a high throughput technology. We believe that the principles of Trellis graphics can be adapted to provide useful visualizations that can aid such automation. In this article, we describe the R/Bioconductor package flowViz that implements such visualizations.
Availability: flowViz is available as an R package from the Bioconductor project: http://bioconductor.org
Contact: dsarkar@fhcrc.org
SVM-HUSTLE—an iterative semi-supervised machine learning approach for pairwise protein remote homology detection
Authors: Shah Anuj R. , Oehmen Christopher S. , Webb-Robertson Bobbie-Jo 
Published: February 2008

Abstract
Motivation: As the amount of biological sequence data continues to grow exponentially we face the increasing challenge of assigning function to this enormous molecular ‘parts list’. The most popular approaches to this challenge make use of the simplifying assumption that similar functional molecules, or proteins, sometimes have similar composition, or sequence. However, these algorithms often fail to identify remote homologs (proteins with similar function but dissimilar sequence) which often are a significant fraction of the total homolog collection for a given sequence. We introduce a Support Vector Machine (SVM)-based tool to detect homology using semi-supervised iterative learning (SVM-HUSTLE) that identifies significantly more remote homologs than current state-of-the-art sequence or cluster-based methods. As opposed to building profiles or position specific scoring matrices, SVM-HUSTLE builds an SVM classifier for a query sequence by training on a collection of representative high-confidence training sets, recruits additional sequences and assigns a statistical measure of homology between a pair of sequences. SVM-HUSTLE combines principles of semi-supervised learning theory with statistical sampling to create many concurrent classifiers to iteratively detect and refine, on-the-fly, patterns indicating homology.
Results: When compared against existing methods for identifying protein homologs (BLAST, PSI-BLAST, COMPASS, PROF_SIM, RANKPROP and their variants) on two different benchmark datasets SVM-HUSTLE significantly outperforms each of the above methods using the most stringent ROC1 statistic with P-values less than 1e-20. SVM-HUSTLE also yields results comparable to HHSearch but at a substantially reduced computational cost since we do not require the construction of HMMs.
Availability: The software executable to run SVM-HUSTLE can be downloaded from http://www.sysbio.org/sysbio/networkbio/svm_hustle
Contact: anuj.shah@pnl.gov
Factors influencing the recruitment and abundance of Didemnum in Narragansett Bay, Rhode Island
Authors: Auker Linda A. , Oviatt Candace A. 
Published: February 2008

Abstract
Auker, L. A., and Oviatt, C. A. 2008. Factors influencing the recruitment and abundance of Didemnum in Narragansett Bay, Rhode Island. – ICES Journal of Marine Science, 65: 765–769. The non-indigenous colonial tunicate Didemnum sp. A has been observed in Narragansett Bay, Rhode Island, since 2000. We compared weekly recruitment of the species and environmental parameters (i.e. temperature, salinity, chlorophyll a, dissolved oxygen, pH, and nutrient concentrations) over a 6-month period among three sites: (i) the University of Rhode Island Graduate School of Oceanography dock (GSO), (ii) the Department of Environmental Management pier at Fort Wetherill (FW), and (iii) the Prudence Island T-wharf. At the GSO and FW, divers surveyed the sites for percentage cover of Didemnum. To assess the spread of Didemnum in the bay and what factors may predict the tunicate’s presence, we also surveyed intertidal sites in October and November 2005, noting Didemnum presence, salinity, number of boats and moorings, and distances to major ports at each site. GSO had the highest percentage cover of adults and the highest recruitment of the tunicate (p < 0.01), reaching average peak values of 319 individuals per 100 cm2 in September 2005. Temperature and salinity demonstrated the best correlation with recruitment, and higher boat and mooring numbers may be a reliable predictor of tunicate presence. Further monitoring is needed to assess the potential spread of Didemnum throughout Narragansett Bay.