bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystalline lens parameters in infancy
Authors: Wood Ivan C. J. , Mutti Donald O. , Zadnik Karla 
Published: October 2010

SummaryDespite the importance of lens power to ocular development, few data are available regarding infant crystalline lens parameters. Lens and corneal radii of curvature were measured in the horizontal meridian using a video‐based keratophakometer, and refractive error was measured by cycloplegic retinoscopy in 19 out of 27 infants ranging in age from 3 to 18 months. The median refractive error was + 1.50 D, and the median corneal power was 43.5 D. Using previously reported values for axial ocular dimensions, the median anterior and posterior lens radii of curvature were 8.7 and 5.6 mm, respectively, both substantially flatter than infant schematic eye values. The median equivalent refractive index of the lens was 1.49, considerably higher than previous reported schematic values for infants or children. There was a significant reduction in hyperopia with age (r = −0.47, P = 0.043), but no age‐related trends in lens or corneal radii of curvature, suggesting that calculated values for lens power and equivalent index may undergo substantial decline with age during early childhood development as axial length increases. Most of the decrease in lens power (75%) may be due to decreases in equivalent index rather than to flattening of the surface radii of curvature. Videophakometry appears to be a feasible and useful technique for documenting the role of the crystalline lens in infant ocular development.
VEGA: variational segmentation for copy number detection
Authors: Morganella Sandro , Cerulo Luigi , Viglietto Giuseppe , Ceccarelli Michele 
Published: October 2010

Abstract
Motivation: Genomic copy number (CN) information is useful to study genetic traits of many diseases. Using array comparative genomic hybridization (aCGH), researchers are able to measure the copy number of thousands of DNA loci at the same time. Therefore, a current challenge in bioinformatics is the development of efficient algorithms to detect the map of aberrant chromosomal regions.
Methods: We describe an approach for the segmentation of copy number aCGH data. Variational estimator for genomic aberrations (VEGA) adopt a variational model used in image segmentation. The optimal segmentation is modeled as the minimum of an energy functional encompassing both the quality of interpolation of the data and the complexity of the solution measured by the length of the boundaries between segmented regions. This solution is obtained by a region growing process where the stop condition is completely data driven.
Results: VEGA is compared with three algorithms that represent the state of the art in CN segmentation. Performance assessment is made both on synthetic and real data. Synthetic data simulate different noise conditions. Results on these data show the robustness with respect to noise of variational models and the accuracy of VEGA in terms of recall and precision. Eight mantle cell lymphoma cell lines and two samples of glioblastoma multiforme are used to evaluate the behavior of VEGA on real biological data. Comparison between results and current biological knowledge shows the ability of the proposed method in detecting known chromosomal aberrations.
Availability: VEGA has been implemented in R and is available at the address http://www.dsba.unisannio.it/Members/ceccarelli/vega in the section Download.
Contact: ceccarelli@unisannio.it
Supplementary information: Supplementary information is available at Bioinformatics online.
Trends in heart failure care: has the incident diagnosis of heart failure shifted from the hospital to the emergency department and outpatient clinics?
Authors: Ezekowitz Justin A. , Kaul Padma , Bakal Jeffrey A. , Quan Hude , McAlister Finlay A. 
Published: October 2010

AimsStudies of heart failure (HF) incidence and prevalence frequently rely on hospitalization to identify patients. Our objective was to describe the incidence, prevalence, or outcomes for HF patients diagnosed in the outpatient or emergency department (ED) setting.Methods and resultsIn a population‐based study of 82 323 HF patients in a single‐payer health‐care system in Alberta, Canada from 1999 to 2007, we examined trends over time and clinical outcomes. Heart failure patients were first diagnosed in a general outpatient clinic (45.7%), a specialty outpatient clinic (4.0%), the ED (13.7%), or in hospital (36.6%). From years 2000 to 2006, the age‐standardized incidence (per 100 000 population) decreased from 538 to 403, whereas the overall prevalence increased from 1585 to 2510. One‐year mortality was significantly different among patients first diagnosed in a general outpatient clinic (6.6%), a specialty outpatient clinic (7.5%), ED (19.1%), and hospital (29.8%). Patients initially diagnosed at the time of hospitalization had the fewest median days alive and out of hospital [347, inter‐quartile range (IQR): 136–363] over the next year compared with patients in the ED (354, IQR 313–365), specialty outpatient clinic (365, IQR 355–365), and general outpatient clinics (365, IQR: 359–365, P < 0.0001). Patients in the ED had the highest rate of subsequent ED visits, and all‐cause, cardiovascular, or HF hospitalization.ConclusionsOver time, more patients were diagnosed as outpatients compared with a hospital setting. The trends observed in incidence, prevalence, and outcomes for patients with HF differ substantially depending on the location of initial diagnosis. Additionally, efforts to study patients with HF in the ED should be a priority.
Cytokinin Regulates Compound Leaf Development in Tomato
Authors: Shani Eilon , Ben-Gera Hadas , Shleizer-Burko Sharona , Burko Yogev , Weiss David , Ori Naomi 
Published: October 2010

AbstractLeaf shape diversity relies on transient morphogenetic activity in leaf margins. However, how this morphogenetic capacity is maintained is still poorly understood. Here, we uncover a role for the hormone cytokinin (CK) in the regulation of morphogenetic activity of compound leaves in tomato (Solanum lycopersicum). Manipulation of CK levels led to alterations in leaf complexity and revealed a unique potential for prolonged growth and morphogenesis in tomato leaves. We further demonstrate that the effect of CK on leaf complexity depends on proper localization of auxin signaling. Genetic analysis showed that reduction of CK levels suppresses the effect of Knotted1 like homeobox (KNOXI) proteins on leaf shape and that CK can substitute for KNOXI activity at the leaf margin, suggesting that CK mediates the activity of KNOXI proteins in the regulation of leaf shape. These results imply that CK regulates flexible leaf patterning by dynamic interaction with additional hormones and transcription factors.
Risk of recurrent myocardial infarction with the concomitant use of clopidogrel and proton pump inhibitors
Authors: Valkhoff V. E. , ‘t Jong G. W. , Van Soest E. M. , Kuipers E. J. , Sturkenboom M. C. J. M. 
Published: October 2010

Aliment Pharmacol Ther2011;33:77–88SummaryBackground The association between myocardial infarction (MI) and co‐administration of proton pump inhibitors (PPIs) and clopidogrel remains controversial.Aim To quantify the association between concomitant use of PPIs and clopidogrel and occurrence of recurrent MI.Methods We conducted a case–control study within a cohort of acute MI patients in PHARMO Record Linkage System (1999–2008). The cases were patients readmitted for MI. PPI exposure was categorized as current (3–1 days before MI), past (30–3 days before MI), or no use (>30 days before MI). We used conditional logistic regression analyses.Results Among 23 655 patients hospitalized following MI, we identified 1247 patients readmitted for MI. Among clopidogrel users, current PPI use was associated with an increased risk of recurrent MI (OR: 1.62, 95% CI: 1.15–2.27) when compared with no PPI use, but not when compared with past PPI use (OR: 0.95, 95% CI: 0.38–2.41). Among clopidogrel non‐users, current PPI use was associated with an increased risk of recurrent MI (OR: 1.38, 95% CI: 1.18–1.61) when compared with no PPI use.Conclusions The apparent association between recurrent MI and use of PPIs with clopidogrel depends on the design, and is affected by confounding by indication. The association is not present when (un)measured confounding is addressed by design.
Dynamic changes of transcript profiles after fertilization are associated with de novo transcription and maternal elimination in tobacco zygote, and mark the onset of the maternal‐to‐zygotic transition
Authors: Zhao Jing , Xin Haiping , Qu Lianghuan , Ning Jue , Peng Xiongbo , Yan Tingting , Ma Ligang , Li Shisheng , Sun Meng‐Xiang 
Published: October 2010

SummaryThe maternal‐to‐zygotic transition (MZT) is characterized by the turnover of zygote development from maternal to zygotic control, and has been extensively studied in animals. A majority of studies have suggested that early embryogenesis is maternally controlled and that the zygotic genome remains transcriptionally inactive prior to the MZT. However, little is known about the MZT in higher plants, and its timing and impact remain uncharacterized. Here, we constructed cDNA libraries from tobacco (Nicotiana tabacum) egg cells, zygotes and two‐celled embryos for gene expression profiling analysis, followed by RT‐PCR confirmation. These analyses, together with experiments using zygote microculture coupled with transcription inhibition, revealed that a marked change in transcript profiles occurs approximately 50 h after fertilization, and that the MZT is initiated prior to zygotic division in tobacco. Although maternal transcripts deposited in egg cells support several early developmental processes, they appear to be insufficient for zygotic polar growth and subsequent cell divisions. Thus, we propose that de novo transcripts are probably required to trigger embryogenesis in later zygotes in tobacco.
Temporal and spatial regulation of DROOPING LEAF gene expression that promotes midrib formation in rice
Authors: Ohmori Yoshihiro , Toriba Taiyo , Nakamura Hidemitsu , Ichikawa Hiroaki , Hirano Hiro‐Yuki 
Published: October 2010

SummaryGenes involved in the differentiation and development of tissues and organs are temporally and spatially regulated in plant development. The DROOPING LEAF (DL) gene, a member of the YABBY gene family, promotes midrib formation in the leaf and carpel specification in the flower. Consistent with these functions, DL is initially expressed in the central region of the leaf primordia (presumptive midrib) and in the presumptive carpel primordia in the meristem. To understand the regulatory mechanism underlying DL expression, we tried to identify cis‐regulatory regions required for temporal and spatial expression of this gene. We found that the cis region responsible for the presumptive midrib‐specific expression in the leaf primordia is located in intron 2. Next, we confined the region to a sequence of about 200 bp, which corresponds to a conserved non‐coding sequence (CNS) identified by phylogenetic footprinting. In addition, a sequence termed DG1, incorporating a 5′ upstream region of about 7.4 kb, and introns 1 and 2, was shown to be sufficient to induce DL in the presumptive midrib, and to suppress it in other regions in the leaf primordia. By contrast, the regulatory region required for carpel‐specific expression was not included in the DG1 sequence. We modified Oryza sativa (rice) plant architecture by expressing an activated version of DL (DL‐VP16) in a precise manner using the DG1 sequence: the resulting transgenic plant produced a midrib in the distal region of the leaf blade, where there is no midrib in wild type, and formed more upright leaves compared with the wild type.
From defense to symbiosis: limited alterations in the kinase domain of LysM receptor‐like kinases are crucial for evolution of legume–Rhizobium symbiosis
Authors: Nakagawa Tomomi , Kaku Hanae , Shimoda Yoshikazu , Sugiyama Akifumi , Shimamura Masayuki , Takanashi Kojiro , Yazaki Kazufumi , Aoki Toshio , Shibuya Naoto , Kouchi Hiroshi 
Published: October 2010

SummaryNitrogen‐fixing symbiosis between legumes and rhizobia is initiated by the recognition of rhizobial Nod factors (NFs) by host plants. NFs are diversely modified derivatives of chitin oligosaccharide, a fungal elicitor that induces defense responses in plants. Recent evidence has shown that both NFs and chitin elicitors are recognized by structurally related LysM receptor kinases. Transcriptome analyses of Lotus japonicus roots indicated that NFs not only activate symbiosis genes but also transiently activate defense‐related genes through NF receptors. Conversely, chitin oligosaccharides were able to activate symbiosis genes independently of NF receptors. Analyses using chimeric genes consisting of the LysM receptor domain of a Lotus japonicus NF receptor, NFR1, and the kinase domain of an Arabidopsis chitin receptor, CERK1, demonstrated that substitution of a portion of the αEF helix in CERK1 with the amino acid sequence YAQ from the corresponding region of NFR1 enables L. japonicus nfr1 mutants to establish symbiosis with Mesorhizobium loti. We also showed that the kinase domains of two Lotus japonicus LysM receptor kinases, Lys6 and Lys7, which also possess the YAQ sequence, suppress the symbiotic defect of nfr1. These results strongly suggest that, in addition to adaptation of extracellular LysM domains to NFs, limited alterations in the kinase domain of chitin receptors have played a crucial role in shifting the intracellular signaling to symbiosis from defense responses, thus constituting one of the key genetic events in the evolution of root nodule symbiosis in legume plants.
Necrobiotic xanthogranuloma: Response to chlorambucil
Authors: Ryan Emma , Warren Lachlan J , Szabo Ferenc 
Published: October 2010

ABSTRACTThis report of necrobiotic xanthogranuloma associated with chronic lymphocytic leukaemia describes the response of skin lesions to chlorambucil. Characteristic clinical and histological features of necrobiotic xanthogranuloma are presented, as well as a discussion regarding management and the use of chlorambucil.
Microvillous cells expressing IP3 receptor type 3 in the olfactory epithelium of mice
Authors: Hegg Colleen C. , Jia Cuihong , Chick Wallace S. , Restrepo Diego , Hansen Anne 
Published: October 2010

AbstractMicrovillous cells of the main olfactory epithelium have been described variously as primary olfactory neurons, secondary chemosensory cells or non‐sensory cells. Here we generated an IP3R3tm1(tauGFP) mouse in which the coding region for a fusion protein of tau and green fluorescent protein replaces the first exon of the Itpr3 gene. We provide immunohistochemical and functional characterization of the cells expressing IP3 receptor type 3 in the olfactory epithelium. These cells bear microvilli at their apex, and we therefore termed them IP3R3 MV cells. The cell body of these IP3R3 MV cells lies in the upper third of the main olfactory epithelium; a long thick basal process projects towards the base of the epithelium without penetrating the basal lamina. Retrograde labeling and unilateral bulbectomy corroborated that these IP3R3 MV cells do not extend axons to the olfactory bulb and therefore are not olfactory sensory neurons. The immunohistochemical features of IP3R3 MV cells varied, suggesting either developmental stages or the existence of subsets of these cells. Thus, for example, subsets of the IP3R3 MV cells make contact with substance P fibers or express the purinergic receptor P2X3. In addition, in recordings of intracellular calcium, these cells respond to ATP and substance P as well as to a variety of odors. The characterization of IP3R3 MV cells as non‐neuronal chemoresponsive cells helps to explain the differing descriptions of microvillous cells in the literature.
Basics on emulsion technologies were reviewed from the following viewpoints
Authors: Suzuki T. 
Published: October 2010

Basics on emulsion technologies were reviewed from the following viewpoints.1 Definition of the types and states of emulsions, and the differences among emulsions, nano emulsions and micro emulsions.2 Classification of emulsion formation and the summary of conventional emulsification methods.3 Instability factors and the theories of emulsion stability.4 Phase diagram and emulsions: How to understand the states of emulsions and micro emulsions and effective emulsification and solubilization.5 Summary of recent emulsion technologies for preparation of fine emulsions.
Simplified assay of diethylene glycol and ethylene glycol in various raw materials by capillary gas chromatography
Authors: Molever K. 
Published: October 2010

The FDA has recently taken steps to reduce risks due to raw materials affected by economically motivated adulteration (EMA). One area of great interest is diethylene glycol (DEG) or ethylene glycol (EG) adulteration of glycerin, propylene glycol, and solutions of sorbitol, for which the USP monographs have recently been, revised (1). Such adulterations have occurred many times and in many countries, including a tragic episode between November 2008 and January 2009 in which 84 children in Nigeria died after ingesting teething syrup contaminated with DEG (9, 10). To eliminate this problem, the FDA has required manufacturers of finished products to assay and confirm that incoming glycerin, propylene glycol, and sorbitol solutions meet the USP limits, and the FDA/USP has incorporated such testing into the identity requirements of its updated monographs.Unfortunately, even though USP test procedures detail a simultaneous DEG and EG assay for these materials, different standard solutions are specified depending upon whether the incoming sample is glycerin, propylene glycol, or a sorbitol solution; in addition, a certain gas chromatography (GC) capillary phase is detailed for sorbitol solutions, while the assays for glycerin and propylene glycol use a different capillary phase, requiring column changeovers, separate GC systems, or front/rear column configuration. In addition, NF monographs for polyethylene glycols (PEG) and polyethylene glycol monomethyl ethers (MPEG) used in pharmaceutical products also require DEG and EG testing (detailing their own specific tests); three separate test procedures for these types of raw materials (the larger PEG‐type polymers are assayed differently than their smaller counterparts), making assay at QC unwieldy.This paper describes a single, simple test procedure that is applicable to the simultaneous assay of DEG and EG in all types of the described raw materials, using one standard solution. The assay procedure involves straightforward isolation, trimethylsilylation, and simultaneous capillary gas chromatographic quantitation using capillary GC with flame ionization detection. Although the USP‐NF limits are 0.10% DEG and 0.10% EG (and 0.25% total DEG plus EG for the PEG and MPEG products), in reality any EMA would be at levels significantly higher than that, as low‐level illegal EMA would not be economically advantageous. The scope of this project was not to fully validate this technique for inclusion in USP‐NF, but just to demonstrate its applicability for those wishing to utilize it or take it further.
Disagreement and the Cost of Capital
Authors: BLOOMFIELD ROBERT , FISCHER PAUL E. 
Published: October 2010

ABSTRACTWe assess how forms of disagreement among investors affect a firm's cost of capital. Firms experience a lower cost of capital if investors perceive that other investors are ignoring relevant disclosures (perceived errors of omission), but a higher cost of capital if investors perceive that others are responding to irrelevant disclosures (perceived errors of commission). The impact of these two sources of disagreement on the cost of capital is determined by the distribution of opinion and the nature of disclosure. For example, even though aggregated disclosures reveal less to investors, aggregated disclosures may decrease the cost of capital by eliminating disagreement associated with perceived errors of commission. These and additional results arise because the cost of capital is driven not only by investors’ uncertainty about the firm's future earnings performance, but also by investors’ uncertainty about the evolution of beliefs, which partly determines the path of prices.
Negative cooperativity in binding of muscarinic receptor agonists and GDP as a measure of agonist efficacy
Authors: Jakubík J , Janíčková H , El‐Fakahany EE , Doležal V 
Published: October 2010

BACKGROUND AND PURPOSEConventional determination of agonist efficacy at G‐protein coupled receptors is measured by stimulation of guanosine‐5′‐γ−thiotriphosphate (GTPγS) binding. We analysed the role of guanosine diphosphate (GDP) in the process of activation of the M2muscarinic acetylcholine receptor and provide evidence that negative cooperativity between agonist and GDP binding is an alternative measure of agonist efficacy.EXPERIMENTAL APPROACHFiltration and scintillation proximity assays measured equilibrium binding as well as binding kinetics of [35S]GTPγS and [3H]GDP to a mixture of G‐proteins as well as individual classes of G‐proteins upon binding of structurally different agonists to the M2muscarinic acetylcholine receptor.KEY RESULTSAgonists displayed biphasic competition curves with the antagonist [3H]‐N‐methylscopolamine. GTPγS (1 µM) changed the competition curves to monophasic with low affinity and 50 µM GDP produced a similar effect. Depletion of membrane‐bound GDP increased the proportion of agonist high‐affinity sites. Carbachol accelerated the dissociation of [3H]GDP from membranes. The inverse agonist N‐methylscopolamine slowed GDP dissociation and GTPγS binding without changing affinity for GDP. Carbachol affected both GDP association with and dissociation from Gi/oG‐proteins but only its dissociation from Gs/olfG‐proteins.CONCLUSIONS AND IMPLICATIONSThese findings suggest the existence of a low‐affinity agonist‐receptor conformation complexed with GDP‐liganded G‐protein. Also the negative cooperativity between GDP and agonist binding at the receptor/G‐protein complex determines agonist efficacy. GDP binding reveals differences in action of agonists versus inverse agonists as well as differences in activation of Gi/oversus Gs/olfG‐proteins that are not identified by conventional GTPγS binding.