bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assignment of relevés to pre‐defined classes by supervised clustering of plant communities using a new composite index
Authors: van Tongeren Onno , Gremmen Niek , Hennekens Stephan 
Published: March 2008

AbstractQuestion:How does a newly designed method of supervised clustering perform in the assignment of relevé (species composition) data to a previously established classification. How do the results compare to the assignment by experts and to the assignment using a completely different numerical method?Material:Relevés analysed represent 4186 Czech grassland plots and 4990 plots from a wide variety of vegetation types (359 different associations or basal communities) in The Netherlands. For both data sets we had at our disposal an expert classification, and for the Czech data we also had available a numerical classification as well as a classification based on a neural network method (multi‐layer perceptron).Methods:Two distance indices, one qualitative and one quantitative, are combined into a single index by weighted multiplication. The composite index is a distance index for the dissimilarity between relevés and vegetation types. For both data sets the classifications by the new method were compared with the existing classifications.Results:For the Czech grasslands we correctly classified 81% of the plots to the classes of an expert classification at the alliance level and 71% to the classes of the numerical classification. Correct classification rates for the Dutch relevés were 64, 78 and 83 % for the lowest (subassociation or association), association, and alliance level, respectively.Conclusion:Our method performs well in assigning community composition records to previously established classes. Its performance is comparable to the performance of other methods of supervised clustering. Compared with a multi‐layer perceptron (a type of artificial neural network), fewer parameters have to be estimated. Our method does not need the original relevé data for the types, but uses synoptic tables. Another practical advantage is the provision of directly interpretable information on the contributions of separate species to the result.
Genetic analysis of 14 families with Schnyder crystalline corneal dystrophy reveals clues to UBIAD1 protein function
Authors: Weiss Jayne S. , Kruth Howard S. , Kuivaniemi Helena , Tromp Gerard , Karkera Jayaprakash , Mahurkar Sunil , Lisch Walter , Dupps William J , White Peter S. , Winters R. Scott , Kim Chaesik , Rapuano Christopher J. , Sutphin John , Reidy Jim , Hu Fung‐Rong , Lu Da Wen , Ebenezer Neil , Nickerson Michael L. 
Published: March 2008

AbstractSchnyder crystalline corneal dystrophy (SCCD) is a rare autosomal dominant disease characterized by progressive corneal opacification resulting from abnormal deposition of cholesterol and phospholipids. Recently, six different mutations on the UBIAD1 gene on chromosome 1p36 were found to result in SCCD. The purpose of this article is to further characterize the mutation spectrum of SCCD and identify structural and functional consequences for UBIAD1 protein activity. DNA sequencing was performed on samples from 36 individuals from 14 SCCD families. One affected individual was African American and SCCD has not been previously reported in this ethnic group. We identified UBIAD1 mutations in all 14 families which had 30 affected and 6 unaffected individuals. Eight different UBIAD1 mutations, 5 novel (L121F, D118G, and S171P in exon 1, G186R and D236E in exon 2) were identified. In four families with DNA samples from both affected and unaffected individuals, the D118G, G186R, T175I, and G177R mutations cosegregated with SCCD. In combination with our previous report, we have identified the genetic mutation in UBIAD1 in 20 unrelated families with 10 (including 5 reported here), having the N102S mutation. The results suggest that N102S may be a mutation hot spot because the affected families were unrelated including Caucasian and Asian individuals. There was no genotype phenotype correlation except for the T175I mutation which demonstrated prominent diffuse corneal haze, typically without corneal crystals. Protein analysis revealed structural and functional implications of SCCD mutations which may affect UBIAD1 function, ligand binding and interaction with binding partners, like apo E. © 2008 Wiley‐Liss, Inc.
Array comparative genomic hybridization in global developmental delay
Authors: Shevell M.I. , Bejjani B.A. , Srour M. , Rorem E.A. , Hall N. , Shaffer L.G. 
Published: March 2008

AbstractObjective: Array‐based comparative genomic hybridization (array CGH) is an emerging technology that allows for the genome‐wide detection of DNA copy number changes (CNC) such as deletions or duplications. In this study, array‐based CGH was applied to a consecutive series of children with previously undiagnosed non‐syndromal global developmental delay (GDD) to assess potential etiologic yield. Methods: The children in this study were drawn from a previously reported consecutive series of children with well‐defined GDD. Almost all subjects had undergone prior karyotyping and neuroimaging studies with non‐diagnostic results. Array‐based CGH was undertaken using the SignatureChip® (1887 BACs representing 622 loci) with abnormalities verified by subsequent FISH analysis and testing of parents to distinguish between pathogenic and familial non‐pathogenic variants. Results: On CGH analysis in our study, 6 of 94 children (6.4%) had a causally related pathogenic CNC. Three were sub‐telomeric in location. An analysis of a variety of clinical factors revealed that only the presence of minor dysmorphic features (<3) was predictive of etiologic yield on CGH analysis (4/26 vs. 2/68, P = 0.05). Severity of delay was not found to be predictive. Interpretation: In children with non‐syndromal GDD, array‐based CGH has an etiologic yield of 6.4%. This suggests that this emerging technology may be of diagnostic value when applied subsequent to detailed history, physical examination, and targeted laboratory testing. Array CGH may merit consideration as a first‐tier test in the context of a child with unexplained GDD. © 2008 Wiley‐Liss, Inc.
Candidate genes for schizophrenia: A survey of association studies and gene ranking
Authors: Sun Jingchun , Kuo Po‐Hsiu , Riley Brien P. , Kendler Kenneth S. , Zhao Zhongming 
Published: March 2008

AbstractMore than 500 genes have been reported with positive or negative association with schizophrenia. The wealth of this information, along with the complex nature of psychiatric disorders, provides a challenging but also unique opportunity for the investigation of molecular and cellular mechanisms in schizophrenia. In this study, we performed a comprehensive survey of the published association studies collected in the SchizophreniaGene database. We observed over time a strong trend for increases in the number of published reports, the number of studied genes, and the sample size of the studies. We also examined the studies, genes, and sample sizes in different ethnic populations and the distribution of these association studies and their employed markers among these susceptibility genes. We then selected and ranked candidate genes using a combined odds ratio method. The evaluation of this candidate gene set against sets selected by other methods suggested its utility in follow‐up association studies and in further bioinformatics analysis. We also examined the functional biases of the selected genes. © 2008 Wiley‐Liss, Inc.
Exclusion of linkage to chromosome 14q in a large South Tyrolean family with idiopathic basal ganglia calcification (IBGC)
Authors: Volpato Claudia Béu , De Grandi Alessandro , Buffone Ebba , Pichler Irene , Gebert Uwe , Schifferle Günther , Schönhuber Rudolf , Pramstaller Peter P. 
Published: March 2008

AbstractFamilial Idiopathic Basal Ganglia Calcification (FIBGC) is a neurodegenerative syndrome that usually follows an autosomal dominant pattern of inheritance. Linkage to only one locus on chromosome 14q (IBCG1) has been described so far. We identified and characterized a large multigenerational Italian family from a population isolate with 14 FIBGC affected members. Linkage analysis excluded the IBCG1 locus, thus demonstrating further locus heterogeneity for this disease. © 2008 Wiley‐Liss, Inc.
A genome‐wide linkage scan provides evidence for both new and previously reported loci influencing common migraine
Authors: Ligthart Lannie , Nyholt Dale R. , Hottenga Jouke‐Jan , Distel Marijn A. , Willemsen Gonneke , Boomsma Dorret I. 
Published: March 2008

AbstractLatent class analysis was performed on migraine symptom data collected in a Dutch population sample (N = 12,210, 59% female) in order to obtain empirical groupings of individuals suffering from symptoms of migraine headache. Based on these heritable groupings (h2 = 0.49, 95% CI: 0.41–0.57) individuals were classified as affected (migrainous headache) or unaffected. Genome‐wide linkage analysis was performed using genotype data from 105 families with at least 2 affected siblings. In addition to this primary phenotype, linkage analyses were performed for the individual migraine symptoms. Significance levels, corrected for the analysis of multiple traits, were determined empirically via a novel simulation approach. Suggestive linkage for migrainous headache was found on chromosomes 1 (LOD = 1.63; pointwise P = 0.0031), 13 (LOD = 1.63; P = 0.0031), and 20 (LOD = 1.85; P = 0.0018). Interestingly, the chromosome 1 peak was located close to the ATP1A2 gene, associated with familial hemiplegic migraine type 2 (FHM2). Individual symptom analysis produced a LOD score of 1.97 (P = 0.0013) on chromosome 5 (photo/phonophobia), a LOD score of 2.13 (P = 0.0009) on chromosome 10 (moderate/severe pain intensity) and a near significant LOD score of 3.31 (P = 0.00005) on chromosome 13 (pulsating headache). These peaks were all located near regions previously reported in migraine linkage studies. Our results provide important replication and support for the presence of migraine susceptibility genes within these regions, and further support the utility of an LCA‐based phenotyping approach and analysis of individual symptoms in migraine genetic research. Additionally, our novel “2‐step” analysis and simulation approach provides a powerful means to investigate linkage to individual trait components. © 2008 Wiley‐Liss, Inc.
A hybrid approach to Web forum interactional coherence analysis
Authors: Fu Tianjun , Abbasi Ahmed , Chen Hsinchun 
Published: March 2008

AbstractDespite the rapid growth of text‐based computer‐mediated communication (CMC), its limitations have rendered the media highly incoherent. This poses problems for content analysis of online discourse archives. Interactional coherence analysis (ICA) attempts to accurately identify and construct CMC interaction networks. In this study, we propose the Hybrid Interactional Coherence (HIC) algorithm for identification of web forum interaction. HIC utilizes a bevy of system and linguistic features, including message header information, quotations, direct address, and lexical relations. Furthermore, several similarity‐based methods including a Lexical Match Algorithm (LMA) and a sliding window method are utilized to account for interactional idiosyncrasies. Experiments results on two web forums revealed that the proposed HIC algorithm significantly outperformed comparison techniques in terms of precision, recall, and F‐measure at both the forum and thread levels. Additionally, an example was used to illustrate how the improved ICA results can facilitate enhanced social network and role analysis capabilities.
Assessment of the Embryonic Stem Cell Test and application and use in the pharmaceutical industry
Authors: Paquette Jennifer A. , Kumpf Steven W. , Streck Randal D. , Thomson Jason J. , Chapin Robert E. , Stedman Donald B. 
Published: March 2008

AbstractBACKGROUND: The European Centre for the Validation of Alternative Methods (ECVAM) designed the Embryonic Stem Cell Test (EST) as a tool for classifying developmentally toxic compounds. An in vitro tool to assess developmental toxicity would be of great value to the pharmaceutical industry to help with toxicity‐associated attrition. METHODS: ECVAM's EST protocol was used, but employing a different mouse embryonic stem cell (ESC) line and an alternative differentiation medium. A subset of the compounds used to validate the EST assay along with a number of in‐house pharmaceutical compounds plus marketed pharmaceutical compounds were used to assess the EST performance with receptor‐mediated compounds. RESULTS: Our results with ECVAM compounds mirrored ECVAM's. Compounds that were developmentally toxic in vivo were classified by the EST as moderate risk. Overall, the accuracy was 75% with the current set of data and the predictivity of low‐, moderate‐, and high‐risk compounds was 90, 71, and 60% while the precision was 59, 86, and 100%, respectively. Interestingly, a number of the non‐developmentally toxic compounds had values for the 3T3 IC50 values, which were lower than the ESC IC50 and ID50, a situation not taken into account by ECVAM when designing the EST algorithm. CONCLUSIONS: The assay as currently constructed has a significant false‐positive rate (∼40%), but a very low false‐negative rate (∼7%). Additional moderate‐ and high‐risk compounds need to be assessed to increase confidence, accuracy, and understanding in the EST's predictivity. Birth Defects Res (Part B), 2008. © 2008 Wiley‐Liss, Inc.
Salvage chemotherapy with CPT‐11 for recurrent temozolomide‐refractory anaplastic astrocytoma
Authors: Chamberlain Marc C. , Wei‐Tsao Denice D. , Blumenthal Deborah T. , Glantz Michael J. 
Published: March 2008

AbstractBACKGROUND.The primary objective of this prospective phase 2 study of CPT‐11 in adult patients with recurrent temozolomide‐refractory anaplastic astrocytoma (AA) was to evaluate 6‐month progression‐free survival (PFS).METHODS.Forty patients (27 men and 13 women) ages 17 to 58 years (median age, 38 years) with radiographically recurrent AA were treated. All patients had been treated previously with surgery, involved‐field radiotherapy, and adjuvant chemotherapy. Fifteen patients were treated at first recurrence with an alternative chemotherapy. All patients were treated at either first or second recurrence with CPT‐11 administered intravenously once every 3 weeks, which was defined operationally as a single cycle. Neurologic and neuroradiographic evaluations were performed every 9 weeks.RESULTS.All patients were evaluable for toxicity, and 39 patients were evaluable for response. In total, 302 cycles of CPT‐11 (median, 6 cycles; range, 1–22 cycles) were administered. CPT‐11‐related toxicity included diarrhea (19 cycles), leukopenia (16 cycles), fatigue (11 cycles), anemia (6 cycles), delayed nausea/vomiting (5 cycles), neutropenia (5 cycles), and renal failure (1 patient, 1 toxic death). Two patients (5%) patients required erythrocyte transfusions. Nine patients (23%) demonstrated a radiographic complete response (1 patient) or partial response (8 patients), 16 patients (41%) demonstrated stable disease, and 14 patients (36%) had progressive disease after 3 cycles of CPT‐11. The median time to tumor progression was 4.1 month. The median survival was 6.9 months, and the 6‐month and 12‐month PFS rates were 40% and 5%, respectively.CONCLUSIONS.CPT‐11 demonstrated modest efficacy with acceptable toxicity in this cohort of adult patients with recurrent AA, all of whom had failed on prior temozolomide chemotherapy. Cancer 2008. © 2008 American Cancer Society.
Genetic counseling for the 22q11.2 deletion
Authors: McDonald‐McGinn Donna M. , Zackai Elaine H. 
Published: March 2008

AbstractBecause of advances in palliative medical care, children with the 22q11.2 deletion syndrome are surviving into adulthood. An increase in reproductive fitness will likely follow necessitating enhanced access to genetic counseling for these patients and their families. Primary care physicians/obstetric practitioners are in a unique position to identify previously undiagnosed patients as they reach reproductive age and to refer them for genetic counseling. To date, most deletions are de novo, secondary to homologous recombination between low‐copy repeat sequences located within 22q11.2. Nonetheless, both somatic and germ line mosaicism has been observed giving unaffected parents a small risk of recurrence. Once present though there is a 50% chance for a person with this contiguous deletion to have an affected child. With this in mind, a variety of prenatal monitoring techniques, as well as, preimplantation genetic diagnosis are available depending on the specific level of risk. © 2008 Wiley‐Liss, Inc. Dev Disabil Res Rev 2008;14:69–74.
Velo‐cardio‐facial syndrome: 30 Years of study
Authors: Shprintzen Robert J. 
Published: March 2008

AbstractVelo‐cardio‐facial syndrome is one of the names that has been attached to one of the most common multiple anomaly syndromes in humans. The labels DiGeorge sequence, 22q11 deletion syndrome, conotruncal anomalies face syndrome, CATCH 22, and Sedlačková syndrome have all been attached to the same disorder. Velo‐cardio‐facial syndrome has an expansive phenotype with more than 180 clinical features described that involve essentially every organ and system. The syndrome has drawn considerable attention because a number of common psychiatric illnesses are phenotypic features including attention deficit disorder, schizophrenia, and bipolar disorder. The expression is highly variable with some individuals being essentially normal at the mildest end of the spectrum, and the most severe cases having life‐threatening and life‐impairing problems. The syndrome is caused by a microdeletion from chromosome 22 at the q11.2 band. Although the large majority of affected individuals have identical 3 megabase deletions, less than 10% of cases have smaller deletions of 1.5 or 2.0 megabases. The 3 megabase deletion encompasses a region containing 40 genes. The syndrome has a population prevalence of approximately 1:2,000 in the United States, although incidence is higher. Although initially a clinical diagnosis, today velo‐cardio‐facial syndrome can be diagnosed with extremely high accuracy by fluorescence in situ hybridization and several other laboratory techniques. Clinical management is age dependent with acute medical problems such as congenital heart disease, immune disorders, feeding problems, cleft palate, and developmental disorders occupying management in infancy and preschool years. Management shifts to cognitive, behavioral, and learning disorders during school years, and then to the potential for psychiatric disorders including psychosis in late adolescence and adult years. Although the majority of people with velo‐cardio‐facial syndrome do not develop psychosis, the risk for severe psychiatric illness is 25 times higher for people affected with velo‐cardio‐facial syndrome than that of the general population. Therefore, interest in understanding the nature of psychiatric illness in the syndrome remains strong. © 2008 Wiley‐Liss, Inc. Dev Disabil Res Rev 2008;14:3–10.
Developmental downregulation of GABAergic drive parallels formation of functional synapses in cultured mouse neocortical networks
Authors: Klueva Julia , Meis Susanne , de Lima Ana D. , Voigt Thomas , Munsch Thomas 
Published: March 2008

AbstractNetworks of cortical neurons in vitro spontaneously develop synchronous oscillatory electrical activity at around the second week in culture. However, the underlying mechanisms and in particular the role of GABAergic interneurons in initiation and synchronization of oscillatory activity in developing cortical networks remain elusive. Here, we examined the intrinsic properties and the development of GABAergic and glutamatergic input onto presumed projection neurons (PNs) and large interneurons (L‐INs) in cortical cultures of GAD67‐GFP mice. Cultures developed spontaneous synchronous activity already at 5–7 days in vitro (DIV), as revealed by imaging transient changes in Fluo‐3 fluorescence. Concurrently, spontaneous glutamate‐mediated and GABAA‐mediated postsynaptic currents (sPSCs) occured at 5 DIV. For both types of neurons the frequency of glutamatergic and GABAergic sPSCs increased with DIV, whereas the charge transfer of glutamatergic sPSCs increased and the charge transfer of GABAergic sPSCs decreased with cultivation time. The ratio between GABAergic and the overall charge transfer was significantly reduced with DIV for L‐INs and PNs, indicating an overall reduction in GABAergic synaptic drive with maturation of the network. In contrast, analysis of miniature PSCs (mPSCs) revealed no significant changes of charge transfer with DIV for both types of neurons, indicating that the reduction in GABAergic drive was not due to a decreased number of functional synapses. Our data suggest that the global reduction in GABAergic synaptic drive together with more synaptic input to PNs and L‐INs during maturation may enhance rhythmogenesis of the network and increase the synchronization at the level of population bursts. © 2008 Wiley Periodicals, Inc. Develop Neurobiol, 2008
Transthoracic echocardiography for suspected pulmonary embolism in the intensive care unit: Unjustly underused or rightfully ignored?
Authors: Stawicki S. Peter , Seamon Mark J. , Meredith Denise M. , Chovanes John , Paszczuk Anna , Kim Patrick K. , Gracias Vicente H. 
Published: March 2008

AbstractTransthoracic echocardiography (TTE) is an established part of modern medical practice, and its use in documenting cardiac disorders has long been recognized. Since the introduction of 2‐dimensional TTE, the right‐sided heart chambers have become amenable to fairly accurate analysis, enabling the evaluation of morphologic and functional abnormalities associated with many cardiopulmonary diseases, including pulmonary embolism (PE). The availability of small, portable echocardiographic units combined with an increasing number of intensive care specialists trained in echocardiography makes TTE an attractive modality for the diagnosis of PE in the intensive care unit (ICU). In the ICU setting, prompt decision‐making and appropriate triage of critically ill patients can facilitate early institution of therapy for PE while awaiting patient stabilization and further definitive testing. Although several prior reviews incorporate TTE in the overall approach and clinical decision algorithms pertaining to the diagnosis and treatment of pulmonary embolism, no dedicated review exists that focuses purely on TTE. We attempt to fill that gap by reviewing the available literature pertaining to use of TTE in the diagnosis of suspected PE, and by better defining the use of TTE in the ICU setting. Emphasis is placed on the use of TTE as a clinical triage tool for suspected PE. © 2008 Wiley Periodicals, Inc. J Clin Ultrasound, 2008.