bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene models from ESTs (GeneModelEST): an application on the Solanum lycopersicum genome
Authors: D'Agostino Nunzio , Traini Alessandra , Frusciante Luigi , Chiusano Maria Luisa 
Published: March 2007

Abstract

Background
The structure annotation of a genome is based either on ab initio methodologies or on similaritiy searches versus molecules that have been already annotated. Ab initio gene predictions in a genome are based on a priori knowledge of species-specific features of genes. The training of ab initio gene finders is based on the definition of a data-set of gene models. To accomplish this task the common approach is to align species-specific full length cDNA and EST sequences along the genomic sequences in order to define exon/intron structure of mRNA coding genes.

Results
GeneModelEST is the software here proposed for defining a data-set of candidate gene models using exclusively evidence derived from cDNA/EST sequences.
GeneModelEST requires the genome coordinates of the spliced-alignments of ESTs and of contigs (tentative consensus sequences) generated by an EST clustering/assembling procedure to be formatted in a General Feature Format (GFF) standard file. Moreover, the alignments of the contigs versus a protein database are required as an NCBI BLAST formatted report file.
The GeneModelEST analysis aims to i) evaluate each exon as defined from contig spliced alignments onto the genome sequence; ii) classify the contigs according to quality levels in order to select candidate gene models; iii) assign to the candidate gene models preliminary functional annotations.
We discuss the application of the proposed methodology to build a data-set of gene models of Solanum lycopersicum, whose genome sequencing is an ongoing effort by the International Tomato Genome Sequencing Consortium.

Conclusion
The contig classification procedure used by GeneModelEST supports the detection of candidate gene models, the identification of potential alternative transcripts and it is useful to filter out ambiguous information. An automated procedure, such as the one proposed here, is fundamental to support large scale analysis in order to provide species-specific gene models, that could be useful as a training data-set for ab initio gene finders and/or as a reference gene list for a human curated annotation.
Matrix Metalloproteinase-9 (MMP-9) polymorphisms in patients with cutaneous malignant melanoma
Authors: Cotignola Javier , Reva Boris , Mitra Nandita , Ishill Nicole , Chuai Shaokun , Patel Ami , Shah Shivang , Vanderbeek Gretchen , Coit Daniel , Busam Klaus , Halpern Allan , Houghton Alan , Sander Chris , Berwick Marianne , Orlow Irene 
Published: March 2007

Abstract

Background
Cutaneous Malignant Melanoma causes over 75% of skin cancer-related deaths, and it is clear that many factors may contribute to the outcome. Matrix Metalloproteinases (MMPs) play an important role in the degradation and remodeling of the extracellular matrix and basement membrane that, in turn, modulate cell division, migration and angiogenesis. Some polymorphisms are known to influence gene expression, protein activity, stability, and interactions, and they were shown to be associated with certain tumor phenotypes and cancer risk.

Methods
We tested seven polymorphisms within the MMP-9 gene in 1002 patients with melanoma in order to evaluate germline genetic variants and their association with progression and known risk factors of melanoma. The polymorphisms were selected based on previously published reports and their known or potential functional relevance using in-silico methods. Germline DNA was then genotyped using pyrosequencing, melting temperature profiles, heteroduplex analysis, and fragment size analysis.

Results
We found that reference alleles were present in higher frequency in patients who tend to sunburn, have family history of melanoma, higher melanoma stage, intransit metastasis and desmoplastic melanomas among others. However, after adjustment for age, sex, phenotypic index, moles, and freckles only Q279R, P574R and R668Q had significant associations with intransit metastasis, propensity to tan/sunburn and primary melanoma site.

Conclusion
This study does not provide strong evidence for further investigation into the role of the MMP-9 SNPs in melanoma progression.
Single chain Fab (scFab) fragment
Authors: Hust Michael , Jostock Thomas , Menzel Christian , Voedisch Bernd , Mohr Anja , Brenneis Mariam , Kirsch Martina I , Meier Doris , Dübel Stefan 
Published: March 2007

AbstractBackgroundThe connection of the variable part of the heavy chain (VH) and and the variable part of the light chain (VL) by a peptide linker to form a consecutive polypeptide chain (single chain antibody, scFv) was a breakthrough for the functional production of antibody fragments inEscherichia coli. Being double the size of fragment variable (Fv) fragments and requiring assembly of two independent polypeptide chains, functional Fab fragments are usually produced with significantly lower yields inE. coli. An antibody design combining stability and assay compatibility of the fragment antigen binding (Fab) with high level bacterial expression of single chain Fv fragments would be desirable. The desired antibody fragment should be both suitable for expression as soluble antibody inE. coliand antibody phage display.ResultsHere, we demonstrate that the introduction of a polypeptide linker between the fragment difficult (Fd) and the light chain (LC), resulting in the formation of a single chain Fab fragment (scFab), can lead to improved production of functional molecules. We tested the impact of various linker designs and modifications of the constant regions on both phage display efficiency and the yield of soluble antibody fragments. A scFab variant without cysteins (scFabΔC) connecting the constant part 1 of the heavy chain (CH1) and the constant part of the light chain (CL) were best suited for phage display and production of soluble antibody fragments. Beside the expression systemE. coli, the new antibody format was also expressed inPichia pastoris. Monovalent and divalent fragments (DiFabodies) as well as multimers were characterised.ConclusionA new antibody design offers the generation of bivalent Fab derivates for antibody phage display and production of soluble antibody fragments. This antibody format is of particular value for high throughput proteome binder generation projects, due to the avidity effect and the possible use of common standard sera for detection.
High mobility group box-1 protein in patients with suspected community-acquired infections and sepsis: a prospective study
Authors: Gaïni Shahin , Pedersen Svend Stenvang , Koldkjær Ole Græsbøll , Pedersen Court , Møller Holger Jon 
Published: March 2007

Abstract
Introduction
Sepsis is a serious condition with a significant morbidity and mortality. New insight into the immunopathogenesis of sepsis could promote the development of new strategies for diagnosis and therapy. High mobility group box-1 protein (HMGB1) has been known for many years as a nuclear chromosomal protein. Its role as a pro-inflammatory cytokine in sepsis and rheumatoid arthritis has been described recently. The aim of our study was to evaluate HMGB1 as a molecular marker in patients with community-acquired infections.

Methods
Patients suspected of having infections/sepsis and admitted to a department of internal medicine were included in the study in a prospective manner. Demographic data, comorbidity, routine biochemistry, microbiological data, infection focus, severity score, and mortality on day 28 were recorded. Plasma and serum were sampled at the time of admission. HMGB1 levels were measured with a commercially available enzyme-linked immunosorbent assay (ELISA). Procalcitonin levels were measured with a TRACE (time-resolved amplified cryptate emission) assay. Lipopolysaccharide-binding protein and interleukin-6 were measured with a chemiluminiscent immunometric assay. Soluble haemoglobin scavenger receptor (sCD163) levels were measured with an in-house ELISA.

Results
One hundred and ninety-four patients were included in the study. Levels of HMGB1 are presented as medians and interquartile ranges: healthy controls (0.77 ng/ml, 0.6 to 1.46), non-infected patients (1.54 ng/ml, 0.79 to 2.88), infected patients without systemic inflammatory response syndrome (2.41 ng/ml, 0.63 to 3.44), patients with sepsis (2.24 ng/ml, 1.30 to 3.75), and patients with severe sepsis (2.18 ng/ml, 0.91 to 3.85). In a receiver operator characteristic curve analysis discriminating between non-infected patients and all infected patients, the area under the curve for HMGB1 was 0.59 (P < 0.0001). HMGB1 correlated only weakly to levels of white blood cell count, neutrophils, C-reactive protein, interleukin-6, procalcitonin, and lipopolysaccharide-binding protein (P < 0.001). HMGB1 did not correlate to sCD163.

Conclusion
In a cohort of patients with suspected community-acquired infections and sepsis, HMGB1 levels were statistically significantly higher in patients compared to the healthy controls. There was no statistically significant difference between the infected and the non-infected patients. Levels of HMGB1 correlated only very weakly to other pro-inflammatory markers and did not correlate to the anti-inflammatory marker sCD163.
GOTax: investigating biological processes and biochemical activities along the taxonomic tree
Authors: Schlicker Andreas , Rahnenführer Jörg , Albrecht Mario , Lengauer Thomas , Domingues Francisco S 
Published: March 2007

AbstractWe describe GOTax, a comparative genomics platform that integrates protein annotation with protein family classification and taxonomy. User-defined sets of proteins, protein families, annotation terms or taxonomic groups can be selected and compared, allowing for the analysis of distribution of biological processes and molecular activities over different taxonomic groups. In particular, a measure of functional similarity is available for comparing proteins and protein families, establishing functional relationships independent of evolution.
Diet of the Nonindigenous Asian Swamp Eel in Tropical Ornamental Aquaculture Ponds in West-Central Florida
Authors: Hill Jeffrey E , Watson Craig A 
Published: March 2007

Abstract
The nonindigenous Asian swamp eel Monopterus albus is established in west-central Florida, where it invades tropical ornamental fish production ponds. The economically valuable ornamental fish industry (US$42 million in 2003) is dominated by the production of small-bodied fishes cultured at high densities in small, earthen ponds. Although introduced Asian swamp eels have been described as voracious predators of fish, to date there have been no published studies containing quantitative diet information on any of the introduced populations found in the USA. The purpose of our study was to evaluate the possible effect of nonnative Asian swamp eels on the aquaculture industry by analyzing the diets of Asian swamp eels that have invaded small ponds used for the culture of ornamental fishes. We examined 71 Asian swamp eels ranging from 94 to 864 mm in total length (TL) that were taken from ornamental aquaculture farms. Fifty-two percent lacked stomach contents; otherwise, prey were relatively small and generally few in number, resulting in low values of stomach fullness. Prey items included amphipods, crayfish, fish, fish eggs, insects, oligochaetes, organic material, plant material, and a tadpole. Insects were the most frequently occurring prey and fish were second. Fish eggs dominated by number but were found in only two individuals. Fish was the heaviest prey category, closely followed by insects, fish eggs, and crayfish. Only 10 fish prey were found in 8 Asian swamp eels (including a cannibalized individual), primarily in the largest predators (≥570 mm TL). Our diet results were surprising, given the highly vulnerable prey fish found in the sampled ponds. We conclude that this species represents a low threat to the Florida ornamental aquaculture industry. We recommend that producers continue to use best management practices, but aggressive control or eradication of Asian swamp eels is not warranted.
Family, Strain, Gender, and Dietary Protein Effects on Production and Processing Traits of Norris and NWAC103 Strains of Channel Catfish
Authors: Bosworth Brian G , Silverstein Jeffery T , Wolters William R , Li Menghe H , Robinson Edwin H 
Published: March 2007

Abstract
Juvenile National Warmwater Aquaculture Center 103 (NWAC103) and Norris strain channel catfish Ictalurus punctatus (from 32 and 29 full-sib families, respectively) were individually tagged and stocked into 0.04-ha ponds at 14,400 fish/ha. Four ponds each of NWAC103 and Norris strain fish were fed a 32% protein diet and four ponds of NWAC103 fish were fed a 22% protein diet to satiation once daily for 150–178 d. Fish were harvested, counted, sexed, and weighed. Fish larger than 0.40 kg were processed and measured for yield and composition of various body components. The NWAC103 strain fish were larger at stocking than Norris strain fish; however, none of the strain-diet combinations differed with respect to survival, feed conversion ratio, or percent weight gain. The NWAC103 strain fish fed the 32% protein diet were larger at harvest and had faster growth at unit size (a) than Norris strain fish. Norris and NWAC103 strain fish fed the 32% protein diet did not differ in body component yield or composition. The NWAC103 strain fish fed the 22% and 32% protein diets did not differ in growth, but NWAC103 strain fish fed the 22% protein diet had lower processing yield (carcass, total fillet, and shank fillet) and higher visceral fat and fillet fat than NWAC103 strain fish fed the 32% protein diet. Compared with females, males had higher stocking weight, harvest weight, a, percent weight gain, head yield, fillet moisture, and nugget yield but lower visceral yield, carcass yield, fillet yield, and fillet fat. Family within strain was a significant source of variation (accounting for 10-45% of total variation) for all traits except fillet protein. The NWAC103 family rankings for most traits were consistent across diets (correlations generally &gt;0.70 among best linear unbiased predictor values across diets). These results suggest that there is potential for improving growth and processing yield traits through selective breeding and that the improvements achieved through selection would be realized on either of the diets used.
The Economic Impact of Restricting Use of Black Carp for Snail Control on Hybrid Striped Bass Farms
Authors: Wui Yong-Suhk , Engle Carole R 
Published: March 2007

Abstract
Black carp Mylopharyngodon piceus have been used in the U.S. for several decades for snail control in fish ponds. Recent concerns over the potential environmental effects of escaped fish have resulted in proposals to list black carp as an injurious species. A mixed-integer programming model was extended to evaluate the farm-level economic effects of restricting access to black carp for those farming hybrid striped bass (white bass Morone chrysops × striped bass M. saxatilis). The alternatives evaluated included (1) no snail control, (2) chemical control with hydrated lime, (3) chemical control with copper sulfate, and (4) biological control with redear sunfish Lepomis microlophus. Lack of access to black carp to control snail populations will reduce the marketability of food-size hybrid striped bass and will reduce the supply of hybrid striped bass fingerlings. Each 10% decrease in the marketability of hybrid striped bass food fish decreased net returns above variable costs by US$2,987/ha. Each 10% reduction in the supply of fingerlings further reduced net returns above variable costs by $1,107 to $1,855/ha. Net returns were lower as fingerling price increased with fingerling shortages after the first year. The industry standard of using black carp was the most cost-effective strategy. In the long run, based on the projections of our model, even with adoption of the alternative treatments analyzed in this study, small farms would go out of business, medium farms would suffer losses of 47% to 59%, and large farm would incur losses ranging from 33% to 41%. The total annual fish sales lost as a result of restrictions on the use of black carp were estimated to be $4.7-$11.96 million/year; with multiplier effects, total economic losses would be $16.45−$72.9 million/year.
Changes in Lipid and Fatty Acid Composition of Wild Freshwater Zooplankton during Enrichment and Subsequent Starvation
Authors: Lochmann S E , Goodwin K J , Racey C L 
Published: March 2007

Abstract
Concentrated wild zooplankton harvested from freshwater ponds have been used to feed the larvae of hybrid striped bass (female white bass Morone chrysops × male striped bass M. saxatilis) in tanks. However, larval growth and survival have been superior when cultured rotifers and brine shrimp Artemia spp. nauplii have been offered as first feeds. We hypothesized that enrichment with highly unsaturated fatty acids (HUFAs), which is common for cultured zooplankton, would enhance the nutritional value of wild freshwater zooplankton. Wild zooplankton were enriched for 24 h with Super Selco, a formula rich in HUFAs. Lipid and fatty acid composition changes in wild freshwater zooplankton were monitored during the enrichment period and the subsequent 72 h. Total lipids in wild zooplankton increased from a preenrichment level of 38 mg/g dry weight (DW) to 72 mg/g DW after enrichment. Although wild zooplankton were initially deficient in HUFAs, the HUFA level after enrichment was 10.41 mg/g DW, which was above the recommended level for good growth and survival of hybrid striped bass larvae. The nutritional state of wild zooplankton returned to the preenrichment level 24 h after enrichment was terminated. Therefore, enriching wild zooplankton from culture ponds for 24 h after harvesting and concentration offers producers another nutritional option for hybrid striped bass larvae during the early life history stages.
Race and ethnicity in genetic research
Authors: Sankar Pamela , Cho Mildred K. , Mountain Joanna 
Published: March 2007

AbstractUse of race and ethnicity terms in genetic research continues to generate controversy. Despite differing opinions about their basis or relevance, there is some agreement that investigators using these terms should: explain why the terms or categories were used, define them carefully, and apply them consistently. An important question is whether these recommendations are reflected in practice. Here we addressed this question based on 330 randomly selected articles published between 2001 and 2004 that reported on genetic research and used one or more words from a defined list of race, ethnicity, or population terms. The recommendation that authors using race or ethnicity terms explain the basis for assigning them to study populations was met infrequently (9.1%), and articles that used race and ethnicity as variables were no more likely than those that used them only to label a sample to provide these details. No article defined or discussed the concepts of race or ethnicity. With limited exceptions, current practice does not reflect repeated recommendations for using race or ethnicity terms in genetic research. This study provides a baseline against which to measure future trends. © 2007 Wiley‐Liss, Inc.
Isolated sagittal and coronal craniosynostosis associated with TWIST box mutations
Authors: Seto Marianne L. , Hing Anne V. , Chang Jocelyn , Hu Ming , Kapp‐Simon Kathleen A. , Patel Pravin K. , Burton Barbara K. , Kane Alex A. , Smyth Matthew D. , Hopper Richard , Ellenbogen Richard G. , Stevenson Kevin , Speltz Matthew L. , Cunningham Michael L. 
Published: March 2007

AbstractCraniosynostosis, the premature fusion of one or more cranial sutures, affects 1 in 2,500 live births. Isolated single‐suture fusion is most prevalent, with sagittal synostosis occurring in 1/5,000 live births. The etiology of isolated (nonsyndromic) single‐suture craniosynostosis is largely unknown. In syndromic craniosynostosis, there is a highly nonrandom pattern of causative autosomal dominant mutations involving TWIST1 and fibroblast growth factor receptors (FGFRs). Prior to our study, there were no published TWIST1 mutations in the anti‐osteogenic C‐terminus, recently coined the TWIST Box, which binds and inhibits RUNX2 transactivation. RUNX2 is the principal master switch for osteogenesis. We performed mutational analysis on 164 infants with isolated, single‐suture craniosynostosis for mutations in TWIST1, the IgIIIa exon of FGFR1, the IgIIIa and IgIIIc exons of FGFR2, and the Pro250Arg site of FGFR3. We identified two patients with novel TWIST Box mutations: one with isolated sagittal synostosis and one with isolated coronal synostosis. Kress et al. [2006] reported a TWIST Box “nondisease‐causing polymorphism” in a patient with isolated sagittal synostosis. However, compelling evidence suggests that their and our sequence alterations are pathogenic: (1) a mouse with a mutation of the same residue as our sagittal synostosis patient developed sagittal synostosis, (2) mutation of the same residue precluded TWIST1 interaction with RUNX2, (3) each mutation involved nonconservative amino acid substitutions in highly conserved residues across species, and (4) control chromosomes lacked TWIST Box sequence alterations. We suggest that genetic testing of patients with isolated sagittal or coronal synostosis should include TWIST1 mutational analysis. © 2007 Wiley‐Liss, Inc.
Ideen zu einer Theorie des Magneten
Authors: von Arnim L. A. 
Published: March 2007

AbstractDas Eisen ist nicht allein des Magnetismus fähig. Magnetismus des Diamanten, der Kohlen u. s. w. Zum dauernden Magnetismus des Eisens wird Sauerstoff erfordert, doch nicht die Verbindung mit Sauerstoff allein, sondern auch mit Kohlenstoff; alle beide in bestimmten Verhältnissen, weil sie sonst die Bedingung des Magnetismus, Cohärenz, aufheben. Die auszeichnende Eigernschaft des Eisens zum Magnetismus besteht darin, bei der höchsten Cohärenz, mit dem Kohlenstoffe in verschiedenen Graden der Oxydation eine Verbindung in Metallform einzugehen Ueber das Auszeichnende der Metallform Im rohen Eisen ist der Kohlenstoffstärker oxydirt als im Stahle; das rohe Eisen unterscheidet sich ferner durch Ungleichheit der Mischung mit Kohlenstoff. Chemischer Unterschied zwischen den beiden Polen des Magneten. Entgegengesetzter Unterschied der Erdpole, durch die ungleiche Erwärmung der nördlichen und südlichen Halbkugel hervorgebracht. Magnetismus des Kobalts. Kohlengehalt des Kobalts. Der Magnetismus des Diamanten, des Eisens und Kobalts lassen sich dadurch auf eine gleiche Ursache zurückführen.
On the observation of traveling acoustic waves in the solar atmosphere using a magneto‐optical filter
Authors: Haberreiter M. , Finsterle W. , Jefferies S. M. 
Published: March 2007

AbstractIn contrast to low‐frequency waves that are trapped in the cavity of the Sun, high‐frequency waves can travel freely in the solar atmosphere. By modelling the observed intensity signal in the red and blue wings of K I 7699 Å and Na I 5890 Å, we aim to better understand the measurements carried out with the Magneto‐Optical Filter at Two Heights (MOTH) experiment. We model the observed intensity signal with radiative transfer calculations carried out with the COde for Solar Irradiance (COSI). Furthermore, we derive the formation height of the lines in order to analyze to what extent the contribution functions are modulated by the acoustic waves. We find a phase lag between the red and blue filter for acoustic waves with a frequency above ≈7 mHz and conclude that a frequency dependent data analysis is required for higher frequencies. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)