bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of ophthalmic measurements obtained via high-frequency ultrasound imaging in four species of snakes
Authors: Hollingsworth Steven R. , Holmberg Bradford J. , Strunk Anneliese , Oakley Alicia D. , Sickafoose Leann M. , Kass Philip H. 
Published: March 2008

Abstract
Objective—To measure the dimensions of the eyes of living snakes by use of high-frequency ultrasound imaging and correlate those measurements with age, length, and weight.
Animals—14 clinically normal snakes.
Procedures—Species, age, length, weight, and horizontal spectacle diameter were recorded, and each snake underwent physical and ophthalmic examinations; ultrasonographic examination of both eyes was performed by use of a commercially available ultrasound unit and a 50-MHz transducer. Ultrasonographic measurements included spectacle thickness, subspectacular space depth, corneal thickness, anterior chamber depth, lens thickness, vitreous cavity depth, and globe length. All measurements were made along the visual axis.
Results—2 corn snakes, 5 California king snakes, 1 gopher snake, and 6 ball pythons were examined. There were no significant differences within or between the species with regard to mean spectacle thickness, corneal thickness, or subspectacular space depth. However, mean horizontal spectacle diameter, anterior chamber depth, and axial globe length differed among the 4 species; for each measurement, ball pythons had significantly larger values than California king snakes.
Conclusions and Clinical Relevance—Spectacle thickness, subspectacular space depth, and corneal thickness were similar among the species of snake examined and did not vary significantly with age, length, or weight. Measurements of these dimensions can potentially serve as baseline values to evaluate snakes of these species with a retained spectacle, subspectacular abscess, or subspectacular fluid accumulation. Anterior chamber depth and axial length appeared variable among species, but axial length did not vary with age, length, or weight in the species studied.
Pharmacokinetics of voriconazole following intravenous and oral administration and body fluid concentrations of voriconazole following repeated oral administration in horses
Authors: Colitz Carmen M. H. , Latimer Federico G. , Cheng Hao , Chan Ken K. , Reed Stephen M. , Pennick Genneth J. 
Published: March 2008

Abstract
Objective—To determine the pharmacokinetics of voriconazole following IV and PO administration and assess the distribution of voriconazole into body fluids following repeated PO administration in horses.
Animals—6 clinically normal adult horses.
Procedures—All horses received voriconazole (10 mg/kg) IV and PO (2-week interval between treatments). Plasma voriconazole concentrations were determined prior to and at intervals following administration. Subsequently, voriconazole was administered PO (3 mg/kg) twice daily for 10 days to all horses; plasma, synovial fluid, CSF, urine, and preocular tear film concentrations of voriconazole were then assessed.
Results—Mean ± SD volume of distribution at steady state was 1,604.9 ± 406.4 mL/kg. Systemic bioavailability of voriconazole following PO administration was 95 ± 19%; the highest plasma concentration of 6.1 ± 1.4 μg/mL was attained at 0.6 to 2.3 hours. Mean peak plasma concentration was 2.57 μg/mL, and mean trough plasma concentration was 1.32 μg/mL. Mean plasma, CSF, synovial fluid, urine, and preocular tear film concentrations of voriconazole after long-term PO administration were 5.163 ± 1.594 μg/mL, 2.508 ± 1.616 μg/mL, 3.073 ± 2.093 μg/mL, 4.422 ± 0.8095 μg/mL, and 3.376 ± 1.297 μg/mL, respectively.
Conclusions and Clinical Relevance—Results indicated that voriconazole distributed quickly and widely in the body; following a single IV dose, initial plasma concentrations were high with a steady and early decrease in plasma concentration. Absorption of voriconazole after PO administration was excellent, compared with absorption after IV administration. Voriconazole appears to be another option for the treatment of fungal infections in horses.
Effects of foodborne Fusarium mycotoxins with and without a polymeric glucomannan mycotoxin adsorbent on food intake and nutrient digestibility, body weight, and physical and clinicopathologic variables of mature dogs
Authors: Leung Maxwell C. K. , Smith Trevor K. , Karrow Niel A. , Boermans Herman J. 
Published: March 2008

Abstract
Objective—To investigate the effects of feeding cereal-based diets that are naturally contaminated with Fusarium mycotoxins to dogs and assess the efficacy of a polymeric glucomannan mycotoxin adsorbent (GMA) in prevention of Fusarium mycotoxicosis.
Animals—12 mature female Beagles.
Procedures—Dogs received each of 3 cereal-based diets for 14 days. One diet was uncontaminated (control diet), and the other 2 contained contaminated grains; one of the contaminated diets also contained 0.2% GMA. Contaminants included deoxynivalenol, 15-acetyl deoxynivalenol, zearalenone, and fusaric acid. Food intake and nutrient digestibility, body weight, blood pressure, heart rate, and clinicopathologic variables of the dogs were assessed at intervals during the feeding periods.
Results—Food intake and body weight of dogs fed the contaminated diet without GMA were significantly decreased, compared with effects of the control diet. Reductions in blood pressure; heart rate; serum concentrations of total protein, globulin, and fibrinogen; and serum activities of alkaline phosphatase and amylase as well as increases in blood monocyte count and mean corpuscular volume were detected. Consumption of GMA did not ameliorate the effects of the Fusarium mycotoxins. For the GMA-contaminated diet, digestibility of carbohydrate, protein, and lipid was significantly higher than that associated with the control diet, possibly because of physiologic adaptation of the recipient dogs to reduced food intake.
Conclusions and Clinical Relevance—Results indicated that consumption of grains naturally contaminated with Fusarium mycotoxins can adversely affect dogs' feeding behaviors and metabolism. As a food additive, GMA was not effective in prevention of Fusarium mycotoxicosis in dogs.
Test-Retest Reliability and Minimal Detectable Change on Balance and Ambulation Tests, the 36-Item Short-Form Health Survey, and the Unified Parkinson Disease Rating Scale in People With Parkinsonism
Authors: Steffen Teresa , Seney Megan 
Published: March 2008

Background and PurposeDistinguishing between a clinically significant change and change due to measurement error can be difficult. The purpose of this study was to determine test-retest reliability and minimal detectable change for the Berg Balance Scale (BBS), forward and backward functional reach, the Romberg Test and the Sharpened Romberg Test (SRT) with eyes open and closed, the Activities-specific Balance Confidence (ABC) Scale, the Six-Minute Walk Test (6MWT), comfortable and fast gait speed, the Timed “Up & Go” Test (TUG), the Medical Outcomes Study 36-Item Short-Form Health Survey (SF-36), and the Unified Parkinson Disease Rating Scale (UPDRS) in people with parkinsonism.SubjectsThirty-seven community-dwelling adults with parkinsonism (mean age=71 years) participated. The Hoehn and Yahr Scale median score of 2 was on the lower end of the scale; however, the scores ranged from 1 to 4.MethodsSubjects were tested twice by the same raters, with 1 week between tests. Test-retest reliability was calculated using intraclass correlation coefficients (ICCs). Minimal detectable change was calculated using a 95% confidence interval (MDC95).ResultsThe ICCs for test-retest reliability were above .90 for the BBS, ABC Scale, SRT with eyes closed, 6MWT, and comfortable and fast gait speeds. The MDC95 values for those functional tests were: BBS=5/56, ABC Scale=13%, SRT with eyes closed=19 seconds, 6MWT=82 m, comfortable gait speed=0.18 m/s, and fast gait speed=0.25 m/s. The ICCs for test-retest reliability of SF-36 scores were above .80, with the exception of the social functioning subscale. The MDC95 values for the SF-36 ranged between 19% and 45%. The MDC95 values for the UPDRS Activities of Daily Living section, Motor Examination section, and total scores were 4/52, 11/108, and 13/176, respectively.Discussion and ConclusionMinimal detectable change values are useful to therapists in rehabilitation and wellness programs in determining whether change during or after intervention is clinically significant. High test-retest reliability of scores for the BBS, ABC Scale, SRT with eyes closed, 6MWT, and gait speed make them trustworthy functional assessments in people with parkinsonism. The SF-36 and UPDRS provide quality-of-life and disease severity rating values in the ongoing assessment of people with parkinsonism.
Synthesis of a 4‐Selenothymidine Phosphoramidite and Incorporation into Oligonucleotides
Authors: Sheng Jia , Huang Zhen 
Published: March 2008

AbstractThe detailed synthetic protocol for a 4‐selenothymidine phosphoramidite and its use to prepare modified oligonucleotides is described here. The Se‐phosphoramidite synthesis was achieved by developing a useful protection and deprotection system for the selenium functionality. The coupling reaction of the Se‐phosphoramidite during solid‐phase oligonucleotide synthesis is quantitative, and the oligonucleotides containing the Se‐modification are stable. Based on crystal structure analysis, the selenium‐modified oligonucleotides retain base‐pairing like their native counterparts, and the derivatized DNA structure is virtually identical to the native structure. This achievement will present a novel opportunity for structural studies of nucleic acids and their protein complexes, because selenium can resolve the phase problem in macromolecular X‐ray crystallography. In addition, this atom‐specific replacement of oxygen with selenium will provide a useful tool for investigating biochemical and biophysical properties of nucleic acids and their protein complexes. Curr. Protoc. Nucleic Acid Chem. 32:1.19.1‐1.19.13. © 2008 by John Wiley & Sons, Inc.
Photoactivation and Imaging of Photoactivatable Fluorescent Proteins
Authors: Patterson George H. 
Published: March 2008

AbstractA major advance in the microscopic study of cells and tissues is the introduction of photoactivatable fluorescent proteins, which can specifically mark proteins of interest within a living cell. Fluorescent proteins are now available that allow a pool of molecules to be “turned on” by photoactivation. This unit discusses technical aspects for the general use of photoactivatable fluorescent proteins and introduces some specific applications in the concluding remarks. Curr. Protoc. Cell Biol. 38:21.6.1‐21.6.10. © 2008 by John Wiley & Sons, Inc.
Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence
Authors: Schug Jonathan 
Published: March 2008

AbstractThis unit describes how to use the Transcription Element Search System (TESS). This Web site predicts transcription factor binding sites (TFBS) in DNA sequence using two different kinds of models of sites, strings and positional weight matrices. The binding of transcription factors to DNA is a major part of the control of gene expression. Transcription factors exhibit sequence‐specific binding; they form stronger bonds to some DNA sequences than to others. Identification of a good binding site in the promoter for a gene suggests the possibility that the corresponding factor may play a role in the regulation of that gene. However, the sequences transcription factors recognize are typically short and allow for some amount of mismatch. Because of this, binding sites for a factor can typically be found at random every few hundred to a thousand base pairs. TESS has features to help sort through and evaluate the significance of predicted sites. Curr. Protoc. Bioinform. 21:2.6.1‐2.6.15. © 2008 by John Wiley & Sons, Inc.
Analysis of Gene‐Expression Data Using J‐Express
Authors: Stavrum Anne Kristin , Petersen Kjell , Jonassen Inge , Dysvik Bjarte 
Published: March 2008

AbstractThe J‐Express package has been designed to facilitate the analysis of microarray data with an emphasis on efficiency, usability, and comprehensibility. The J‐Express system provides a powerful and integrated platform for the analysis of microarray gene expression data. It is platform‐independent in that it requires only the availability of a Java virtual machine on the system. The system includes a range of analysis tools and a project management system supporting the organization and documentation of an analysis project. This unit describes the J‐Express tool, emphasizing central concepts and principles, and gives examples of how it can be used to explore gene expression data sets. Curr. Protoc. Bioinform. 21:7.3.1‐7.3.25. © 2008 by John Wiley & Sons, Inc.
Using the Proteomics Identifications Database (PRIDE)
Authors: Martens Lennart , Jones Phil , Côté Richard 
Published: March 2008

AbstractThe Proteomics Identifications Database (PRIDE) is a public data repository designed to store, disseminate, and analyze mass spectrometry based proteomics datasets. The PRIDE database can accommodate any level of detailed metadata about the submitted results, which can be queried, explored, viewed, or downloaded via the PRIDE Web interface. The PRIDE database also provides a simple, yet powerful, access control mechanism that fully supports confidential peer‐reviewing of data related to a manuscript, ensuring that these results remain invisible to the general public while allowing referees and journal editors anonymized access to the data. This unit describes in detail the functionality that PRIDE provides with regards to searching, viewing, and comparing the available data, as well as different options for submitting data to PRIDE. Curr. Protoc. Bioinform. 21:13.8.1‐13.8.19. © 2008 by John Wiley & Sons, Inc.
Using GFS to Identify Encoding Genomic Loci from Protein Mass Spectral Data
Authors: Holmes Mark R. , Giddings Morgan C. 
Published: March 2008

AbstractGenome‐based peptide fingerprint scanning (GFS) directly maps several types of protein mass spectral (MS) data to the loci in the genome that may have encoded for the protein. This process can be used either for protein identification or for proteogenomic mapping, which is gene‐finding and annotation based on proteomic data. Inputs to the program are one or more mass spectrometry files from peptide mass fingerprinting and/or tandem MS (MS/MS) along with one or more sequences to search them against, and the output is the coordinates of any matches found. This unit describes the use of GFS and subsequent results analysis. Curr. Protoc. Bioinform. 21:13.9.1‐13.9.20. © 2008 by John Wiley & Sons, Inc.
Preparation of Autogenic Human Feeder Cells for Growth of Human Embryonic Stem Cells
Authors: Gonzalez Rodolfo , Loring Jeanne F. , Snyder Evan Y. 
Published: March 2008

AbstractHuman embryonic stem cells (hESCs) that are currently distributed under NIH guidelines, as well as many of those that are not on the NIH registry, have been derived and maintained in coculture with growth‐arrested mouse embryonic fibroblasts (MEFs). Using this mouse support system may compromise the therapeutic potential of these hESCs because of the risk of transmitting xenopathogens. Alternatively, to reduce this risk, methods to culture undifferentiated hESCs on autologous hESC‐derived human feeder layers have now been developed. This feeder cell system derived from hESCs successfully prolongs growth of undifferentiated hESCs and eliminates risk factors and concerns about using xenogeneic or unknown allogeneic feeders. In this unit, we provide the necessary protocols for an autogeneic human feeder system that efficiently supports hESC growth and maintenance of pluripotency. Curr. Protoc. Stem Cell Biol. 4:1C.5.1‐1C.5.15. © 2008 by John Wiley & Sons, Inc.
Purification and Culture of Human Blood Vessel–Associated Progenitor Cells
Authors: Crisan Mihaela , Huard Johnny , Zheng Bo , Sun Bin , Yap Solomon , Logar Alison , Giacobino Jean‐Paul , Casteilla Louis , Péault Bruno 
Published: March 2008

AbstractMultilineage progenitor cells, diversely designated as MSC, MAPC, or MDSC, have been previously extracted from long‐term cultures of fetal and adult organs (e.g., bone marrow, brain, lung, pancreas, muscle, adipose tissue, and several others). The identity and location, within native tissues, of these elusive stem cells are described here. Subsets of endothelial cells and pericytes, which participate in the architecture of human blood vessels, exhibit, following purification to homogeneity, developmental multipotency. The selection from human tissues, by flow cytometry using combinations of positive and negative cell surface markers, of endothelial and perivascular cells is described here. In addition, a rare subset of myoendothelial cells that express markers of both endothelial and myogenic cell lineages and exhibit dramatic myogenic and cardiomyogenic potential has been identified and purified from skeletal muscle. The culture conditions amenable to the long‐term proliferation of these blood vessel–associated stem cells in vitro are also described. Curr. Protoc. Stem Cell Biol. 4:2B.2.1‐2B.2.13. © 2008 by John Wiley & Sons, Inc.
Rural adult literacy in a community context: From the margin to the mainstream
Authors: Ziegler Mary F. , Davis Dent C. 
Published: March 2008

AbstractLegislation over the past two decades has shaped the dominant view of adult literacy as addressing gaps in well‐defined, measurable skills. As rural communities face unprecedented challenges, this one‐size‐fits‐all view of adult literacy does not consider the unique local context of rural communities or involve those communities in defining their own needs and goals.
A nasal proteosome adjuvant activates microglia and prevents amyloid deposition
Authors: Frenkel Dan , Puckett Lindsay , Petrovic Sanja , Xia Weiming , Chen Guiquan , Vega Jose , Dembinsky‐Vaknin Adi , Shen Jie , Plante Martin , Burt David S. , Weiner Howard L. 
Published: March 2008

AbstractObjectiveWe assessed whether peripheral activation of microglia by a nasal proteosome‐based adjuvant (Protollin) that has been given safely to humans can prevent amyloid deposition in young mice and affect amyloid deposition and memory function in old mice with a large amyloid load.MethodsAmyloid precursor protein (APP) transgenic (Tg) J20 mice received nasal treatment with Protollin weekly for 8 months beginning at age 5 months. Twenty‐four‐month‐old J20 mice were treated weekly for 6 weeks.ResultsWe found reduction in the level of fibrillar amyloid (93%), insoluble β‐amyloid (Aβ; 68%), and soluble Aβ (45%) fragments in 14‐month‐old mice treated with Protollin beginning at age 5 months. Twenty‐four‐month‐old mice treated with nasal Protollin for 6 weeks had decreased soluble and insoluble Aβ (1‐40) and (1‐42) and improved memory function. Activated microglia (CD11b+ cells) colocalized with Aβ fibrils in the 24‐month‐old animals, and microglial activation correlated with the decrease in Aβ. No microglial activation was observed in 14‐month‐old mice, suggesting that once Aβ is cleared, there is downregulation of microglial activation. Both groups had reduction in astrocytosis. Protollin was observed in the nasal cavity and cervical lymph node but not in the brain. Activated CD11b+SRA+ (scavenger receptor A) cells were found in blood and cervical lymph node and increased interleukin‐10 in cervical lymph node. No toxicity was associated with treatment.InterpretationOur results demonstrate a novel antibody‐independent immunotherapy for both prevention and treatment of Alzheimer's disease that is mediated by peripheral activation of microglia with no apparent toxicity. Ann Neurol 2008;63:591–601
Fatal familial insomnia: Clinical features and early identification
Authors: Krasnianski Anna , Bartl Mario , Sanchez Juan Pascual J. , Heinemann Uta , Meissner Bettina , Varges Daniela , Schulze‐Sturm Ulf , Kretzschmar Haus A. , Schulz‐Schaeffer Walter J. , Zerr Inga 
Published: March 2008

AbstractOur aim was to develop a detailed clinical description of fatal familial insomnia in a large patient group with respect to the M129V genotype. Data on 41 German fatal familial insomnia patients were analyzed. Clinical features, 14‐3‐3 proteins in the cerebrospinal fluid, magnetic resonance imaging, positron emission tomography, single‐photon emission computed tomography, polysomnography, and electroencephalography were studied. Age at disease onset, disease duration, and clinical syndrome varied depending on the codon 129 genotype. Because the sensitivity of the most diagnostic tests is low in fatal familial insomnia, detailed clinical investigation is extremely important. Polysomnography may help to support the diagnosis. Ann Neurol 2008
Effects of depth and eutrophication on the zooxanthella clades of Stylophora pistillata from the Gulf of Eilat (Red Sea)
Authors: Lampert‐Karako Sarit , Stambler Noga , Katcoff Don J. , Achituv Yair , Dubinsky Zvy , Simon‐Blecher Noa 
Published: March 2008

Abstract
The symbiotic association between corals and zooxanthellae has been a major contributing factor in the success of reef‐building corals.
The diversity of zooxanthellae harboured in the hermatypic coral Stylophora pistillata in the Gulf of Eilat (Aqaba), northern Red Sea, was investigated on the basis of the length and sequence variation of the 18S small subunit ribosomal DNA. Of several clades found worldwide, only clades A and C were found to be associated with this coral species in the Gulf.
No correlation between the pink and brown colour morphs of the coral S. pistillata and the zooxanthella clade was found. Shallow‐water colonies (5 m) harbour clade A while deeper‐water colonies (17 m) harbour either clade A or C. This coral is a brooding species that associates with different zooxanthellae at different depths.
Eutrophication from fish farms did not affect clade identity associated with Stylophora.
Copyright © 2008 John Wiley & Sons, Ltd.
Spatio‐temporal modeling of nanoparticle delivery to multicellular tumor spheroids
Authors: Goodman Thomas T. , Chen Jingyang , Matveev Konstantin , Pun Suzie H. 
Published: March 2008

AbstractThe inefficiency of nanoparticle penetration in tissues limits the therapeutic efficacy of such formulations for cancer applications. Recent work has indicated that modulation of tissue architecture with enzymes such as collagenase significantly increases macromolecule delivery. In this study we developed a mathematical model of nanoparticle penetration into multicellular spheroids that accounts for radially dependent changes in tumor architecture, as represented by the volume fraction of tissue accessible to nanoparticle diffusion. Parameters such as nanoparticle binding, internalization rate constants, and accessible volume fraction were determined experimentally. Unknown parameters of nanoparticle binding sites per cell in the spheroid and pore shape factor were determined by fitting to experimental data. The model was correlated with experimental studies of the penetration of 40 nm nanoparticles in SiHa multicellular spheroids with and without collagenase treatment and was able to accurately predict concentration profiles of nanoparticles within spheroids. The model was also used to investigate the effects of nanoparticle size. This model contributes toward the understanding of the role of tumor architecture on nanoparticle delivery efficiency. Biotechnol. Bioeng. 2008;101: 388–399. © 2008 Wiley Periodicals, Inc.