bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution
Authors: Apeltsin Leonard , Morris John H. , Babbitt Patricia C. , Ferrin Thomas E. 
Published: December 2010

Abstract
Motivation: Clustering protein sequence data into functionally specific families is a difficult but important problem in biological research. One useful approach for tackling this problem involves representing the sequence dataset as a protein similarity network, and afterwards clustering the network using advanced graph analysis techniques. Although a multitude of such network clustering algorithms have been developed over the past few years, comparing algorithms is often difficult because performance is affected by the specifics of network construction. We investigate an important aspect of network construction used in analyzing protein superfamilies and present a heuristic approach for improving the performance of several algorithms.
Results: We analyzed how the performance of network clustering algorithms relates to thresholding the network prior to clustering. Our results, over four different datasets, show how for each input dataset there exists an optimal threshold range over which an algorithm generates its most accurate clustering output. Our results further show how the optimal threshold range correlates with the shape of the edge weight distribution for the input similarity network. We used this correlation to develop an automated threshold selection heuristic in order to most optimally filter a similarity network prior to clustering. This heuristic allows researchers to process their protein datasets with runtime efficient network clustering algorithms without sacrificing the clustering accuracy of the final results.
Availability: Python code for implementing the automated threshold selection heuristic, together with the datasets used in our analysis, are available at http://www.rbvi.ucsf.edu/Research/cytoscape/threshold_scripts.zip.
Contact: tef@cgl.ucsf.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Microinjection of Xenopus Embryos
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M. 
Published: December 2010

INTRODUCTIONThis article describes the factors that should be considered when microinjecting Xenopus oocytes. Forward planning is particularly important for embryo injection because the frogs lay eggs only for a limited time, and once the eggs are fertilized there is a very short period during which the embryos are suitable for injection.
Imaging Neuropeptide Release in the Drosophila Neuromuscular Junction (NMJ)
Authors: Levitan Edwin S. , Shakiryanova Dinara 
Published: December 2010

INTRODUCTIONElectrophysiological studies of synaptic function cannot directly reveal the internal workings of the nerve terminal and do not robustly report release of neuropeptides and neurotrophins. These limitations can now be overcome with the presynaptic expression of green fluorescent protein (GFP) indicators of vesicle motion, release, and signaling. This protocol describes how to image single wavelength and ratiometric fluorescence resonance energy transfer (FRET)-based GFP indicators with fluorescence microscopy in living synaptic boutons of the Drosophila neuromuscular junction (NMJ). The steps for setting up the imaging equipment for epifluorescence microscopy are given, followed by special considerations for preparing the larval NMJ for peptide release studies.
Creating Zinc Finger Nucleases Using a Modular-Assembly Approach
Authors: Porteus Matthew 
Published: December 2010

INTRODUCTIONHomologous recombination is the most precise way to manipulate the genome. It has been used extensively in bacteria, yeast, murine embryonic stem cells, and a few other specialized cell lines, but has not been available in other systems such as mammalian somatic cells. However, the creation of a gene-specific DNA double-strand break can stimulate homologous recombination by several-thousandfold in mammalian somatic cells. These double-strand breaks can be created in mammalian genomes by zinc finger nucleases (ZFNs), artificial proteins in which a zinc finger DNA-binding domain is fused to a nonspecific nuclease domain. This protocol describes how to use a polymerase chain reaction (PCR) technique to assemble new three-finger proteins and how to create a new ZFN.
Testing a Three-Finger Zinc Finger Nuclease Using a GFP Reporter System
Authors: Porteus Matthew 
Published: December 2010

INTRODUCTIONHomologous recombination is the most precise way to manipulate the genome. It has been used extensively in bacteria, yeast, murine embryonic stem cells, and a few other specialized cell lines, but it has not been available in other systems such as mammalian somatic cells. However, the creation of a gene-specific DNA double-strand break can stimulate homologous recombination by several-thousandfold in mammalian somatic cells. These double-strand breaks can be created in mammalian genomes by zinc finger nucleases (ZFNs), artificial proteins in which a zinc finger DNA-binding domain is fused to a nonspecific nuclease domain. This protocol describes how to test newly designed ZFNs using a cell-based green fluorescent protein (GFP) reporter assay to determine if they are active in a mammalian cell-culture-based system.
Calibration of the Injection Volume for Microinjection of Xenopus Oocytes and Embryos
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M. 
Published: December 2010

INTRODUCTIONMicroinjection of Xenopus oocytes or embryos with messenger RNA (mRNA) or DNA is a powerful technique for studying development. Before microinjection can be performed, the injection volume must be calibrated carefully. This protocol describes the calibration procedure for a pressure injector.
Imaging Cell Movements in Egg-Cylinder Stage Mouse Embryos
Authors: Srinivas Shankar 
Published: December 2010

INTRODUCTIONCell movements in the pregastrulation egg cylinder mouse embryo play an important role in patterning. The stereotypic movement of the anterior visceral endoderm converts a proximal-distal axis to an anteroposterior axis by properly positioning the primitive streak. The epiblast at this stage is also characterized by a great deal of cell mixing, about which very little is known. Visualizing such cell movements can help us understand their role in embryonic development. This protocol describes a method to isolate and culture the egg cylinder-stage mouse embryo, as well as an approach for time-lapse imaging of embryos cultured in vivo.
Acquisition of 4D DIC Microscopic Data to Determine Cell Contacts in Caenorhabditis elegans Embryos
Authors: Walston Timothy , Hardin Jeff 
Published: December 2010

INTRODUCTIONThe Caenorhabditis elegans embryo is particularly amenable to microscopy and embryological studies because of its short developmental time, transparent shell, and nonpigmented cells. Acquisition of stacks of images throughout the thickness of the embryo over time is a crucial method for identifying the positions and contacts between cells. Such four-dimensional (4D) microscopy is a routine tool in laboratories that study early C. elegans development. Differential interference contrast (DIC) microscopy is the focus here because of its broad availability, common use for C. elegans imaging, and wide applicability to microscopic analysis of embryos of other organisms. This protocol describes the use of a custom script within μManager’s Beanshell scripting language. The script is helpful for reducing the number of shutter open/close events during 4D acquisition.
Analysis of 4D DIC Microscopic Data to Determine Cell Contacts in Caenorhabditis elegans Embryos
Authors: Walston Timothy , Hardin Jeff 
Published: December 2010

INTRODUCTIONThe Caenorhabditis elegans embryo is particularly amenable to microscopy and embryological studies because of its short developmental time, transparent shell, and nonpigmented cells. Identification of cell contacts is important for understanding how cells within the embryo can be polarized by their neighbors. This protocol describes a technique for identifying cell membranes and potential contacts between different blastomeres in the embryo and for following those contacts through development. This protocol involves manual segmentation of the membrane of each blastomere from four-dimensional (4D) differential interference contrast (DIC) data sets. Although this technique is described for use with C. elegans embryos, it will work with any 4D DIC data set. The recent development of a pleckstrin homology (PH)-domain tagged::GFP expressed in C. elegans embryos simplifies this analysis; however, many organisms lack appropriate green fluorescent protein (GFP) transgenes. The use of the GFP transgene improves on laser-mediated techniques for labeling embryonic cell membranes with fluorescent dye. Such methods require that a laser be used to carefully permeabilize the eggshell for entry of the dye into the embryo. The technique described in this protocol requires only easily obtainable 4D DIC data sets.
Fluorescence Perturbation Techniques to Study Mobility and Molecular Dynamics of Proteins in Live Cells: FRAP, Photoactivation, Photoconversion, and FLIP
Authors: Bancaud Aurélien , Huet Sébastien , Rabut Gwénaël , Ellenberg Jan 
Published: December 2010

INTRODUCTIONThe technique of fluorescence recovery after photobleaching (FRAP) was introduced in the mid-1970s to study the diffusion of biomolecules in living cells. For several years, it was used mainly by a small number of biophysicists who had developed their own photobleaching systems. Since the mid-1990s, FRAP has gained increasing popularity because of the conjunction of two factors: First, photobleaching techniques are easily implemented on confocal laser-scanning microscopes (CLSMs), and so FRAP has become available to anyone who has access to such equipment. Second, the advent of green fluorescent protein (GFP) has allowed easy fluorescent tagging of proteins and their observation in living cells. Thanks both to the versatility of modern CLSMs, which allow control of laser intensity at any point of the image, and to the development of new fluorescent probes, additional photoperturbation techniques have emerged during the last few years. After the photoperturbation event, one observes and then analyzes how the fluorescence distribution relaxes toward the steady state. Because the photochemical perturbation of suitable fluorophores is essentially irreversible, changes of fluorescence intensity in the perturbed and unperturbed regions are due to the exchange of tagged molecules between those regions. This article first discusses the materials required for performing FRAP experiments on a CLSM and the software for data analysis. It then describes general considerations on how to perform FRAP experiments as well as the necessary controls. Finally, different possible ways to analyze the data are presented.
Creating Zinc Finger Nucleases to Manipulate the Genome in a Site-Specific Manner Using a Modular-Assembly Approach
Authors: Porteus Matthew 
Published: December 2010

INTRODUCTIONHomologous recombination is the most precise way to manipulate the genome. It has been used extensively in bacteria, yeast, murine embryonic stem cells, and a few other specialized cell lines, but it has not been available in other genetic systems such as mammalian somatic cells. However, the creation of a gene-specific DNA double-strand break can stimulate homologous recombination by several-thousandfold in mammalian somatic cells. These double-strand breaks can be created in mammalian genomes by zinc finger nucleases (ZFNs), artificial proteins in which a zinc finger DNA-binding domain is fused to a nonspecific nuclease domain. This article describes how to identify potential targets for ZFN cutting. It also focuses on how to assemble ZFNs to recognize target sequences of the form 5′-GNNGNNGNN-3′. It is likely that there will be improvements in making the individual finger modules. High-throughput methods that combine both selection and assembly are being developed, which will broaden the number of sites that can be targeted, optimize the overall structure of the ZFNs, and increase the possible experimental and therapeutic uses for ZFNs.
Immunosuppressive therapies in the management of immune‐mediated marrow failures in adults: where we stand and where we are going
Authors: Risitano Antonio M. 
Published: December 2010

SummaryImmunosuppression is a key treatment strategy for aplastic anaemia (AA) and the related immune‐mediated bone marrow failure syndromes (BMFS). For the last 20 years the standard immunosuppressive regimen for AA patients has been anti‐thymocyte globulin (ATG) plus ciclosporin A (CyA), which results in response rates ranging between 50% and 70%, and even higher overall survival. However, primary and secondary failures after immunosuppressive therapy remain frequent, and to date all attempts aiming to overcome this problem have been unfruitful. This article reviews the state of the art of current immunosuppressive therapies for AA, focusing on open questions linked to standard immunosuppressive treatment, and on experimental immunosuppressive strategies which could lead to future improvement of current treatments. Specific immunosuppressive strategies employed for other BMFS, such as lineage‐restricted marrow failures, myelodysplastic syndromes and large granular lymphocyte leukaemia‐associated cytopenias, are also briefly discussed.
Factors associated with treatment restriction orders and hospice in older nursing home residents
Authors: Lu Chu‐Yun , Johantgen Meg 
Published: December 2010

Aim.  The purpose of the study is to examine factors associated with do‐not‐resuscitate orders, do‐not‐hospitalise orders and hospice care in older nursing home residents at admission.Background.  Although hospice care is viewed as the ‘gold standard,’ geographic availability and financial reimbursement limits its use. Treatment restriction orders may represent alternative approaches to defining wishes for end‐of‐life care.Design.  A descriptive correlational study design was employed to examine the use of four care directives and hospice in newly admitted older people NH residents using Maryland Minimum Data Set 2·0 and the On‐Line Survey Certification and Reporting in 2000. Analyses reflected 10 023 unduplicated admission records from 77 NHs.Results.  The prevalence of do‐not‐resuscitate and do‐not‐hospitalise orders at admission was 28 and 3·4%, respectively. A very small percentage of residents received hospice care on admission (1·7%). Appropriately, health‐related characteristics had a strong influence on use of do‐not‐resuscitate orders, do‐not‐hospitalise orders and hospice care. However, identified predictors were varied among do‐not‐resuscitate orders, do‐not‐hospitalise orders and hospice care. Moreover, multivariate logistical modelling found that non‐Medicare insurance significantly influenced the likelihood of do‐not‐resuscitate orders, do‐not‐hospitalise orders and hospice uses; White race increased the likelihood of having a do‐not‐resuscitate and do‐not‐hospitalise order. Treatment restriction orders were associated with an increased of likelihood of hospice use.Conclusions.  As policy and reimbursement barriers to hospice use are likely to persist, treatment restriction orders should be used to focus communication with residents, families and providers, with the ultimate goal of more widespread implementation of hospice care principles.Relevance to clinical practice.  White race was consistently associated with increasing the likelihood of having do‐not‐resuscitate and do‐not‐hospitalise orders, supporting the importance of cultural sensitivity in advanced care planning. With the association between do‐not‐hospitalise orders and hospice use, treatment restriction orders should be used as potential triggers to prompting end‐of‐life care.
Swedish mothers’ experience of continuous Kangaroo Mother Care
Authors: Blomqvist Ylva Thernström , Nyqvist Kerstin Hedberg 
Published: December 2010

Aims.  To characterise the first infants receiving continuous Kangaroo Mother Care from birth to discharge in a Swedish neonatal intensive care unit and to investigate their mothers’ experiences of this model of care.Background.  Admission of a newborn infant to a neonatal intensive care unit commonly implies separation of the new mother from her infant. Kangaroo Mother Care is a model of neonatal care which supports the parental role as primary care‐giver and contributes to minimising the separation between the infant and parents.Design.  A retrospective survey design.Method.  A purposive sample consisting of 23 mother–infant pairs. Relevant infant data were obtained from their medical records. A questionnaire with questions about the infant’s care and regarding Kangaroo Mother Care was designed for this study.Results.  The infants were born at a gestational age of 31–41 weeks, birth weight ranging from 1715–3700 g. The mothers of these moderately preterm and ill newborn infants showed good acceptance of the idea of providing their infants with continuous Kangaroo Mother Care during their stay at the neonatal intensive care unit. The mothers’ evaluations of this method were predominantly positive. Negative comments concerned lack of information about practical application of the method, and some mothers perceived their infants’ care during the night as exhausting. No mother would have preferred not to perform continuous Kangaroo Mother Care or to terminate Kangaroo Mother Care earlier than they did.Conclusions.  These mothers accepted this model of care very well, provided that they received the help and support they required.Relevance to clinical practice.  Mothers whose infants are admitted to an neonatal intensive care units in settings similar to the study setting should be offered opportunities to be present and provide Kangaroo Mother Care for their infants, to the extent that they are able and willing to do so and as permitted by the infant’s medical condition and care.
Factors associated with psychosocial needs of close relatives of women under treatment for breast cancer
Authors: Schmid‐Büchi Silvia , van den Borne Bart , Dassen Theo , Halfens Ruud JG 
Published: December 2010

Aims.  (1) To gain insight into the psychosocial needs and distress of close relatives of women under treatment for breast cancer and identify how they perceive the interpersonal relationship with the patient and (2) to determine factors associated with the relatives’ psychosocial needs.Background.  Breast cancer affects patients but also close relatives. Relatives need support themselves but there is still a lack of knowledge about their specific needs.Design.  Relatives of women newly diagnosed with breast cancer participated in a cross‐sectional survey.Method.  Relatives were approached by patients, who were contacted by nurses in two Swiss breast cancer clinics. The patients received the questionnaire for their closest relative, who decided independently of the patient about participation. Standardised questionnaires were completed by 107 relatives.Results.  The relatives needed help with access to information and health care professionals. They needed information about the patients’ treatment (50·9%), honest information (41·6%) and had difficulties with confidence in health care professionals (39·2%). The majority (61·0%) suffered from distress, less (26·1%) from anxiety and depression (10·9%). Distress, anxiety and conflict in their interpersonal relationship were associated with the relatives’ unmet psychosocial needs.Conclusions.  The findings increase the knowledge of the psychosocial needs of relatives of patients with breast cancer and provide the basis for purposeful support. Distress, anxiety and conflicts in the relationship are important factors that may identify more vulnerable relatives with unmet needs or a higher demand for support.Relevance to clinical practice.  Assessment of the relatives’ specific needs, distress and anxiety is important, and the relatives’ perception of their relationship should be addressed. Health care professionals are key persons in contact with relatives and should motivate the patients to involve their relatives in the illness and treatment process. Support programmes for relatives of patients with breast cancer should be developed in Swiss cancer clinics.
An evaluation of indices of gross pathology associated with the nematodeAnguillicoloides crassusin eels
Authors: Lefebvre F , Fazio G , Palstra A P , Székely C , Crivelli A J 
Published: December 2010

AbstractThis study compares two alternative indices for quantifying the gross pathology of the swimbladder of eels,Anguilla anguilla(L.), infected with the nematodeAnguillicoloides crassus. Two observers recorded twice the scores obtained by the two indices on the same set of 71 wild caught eels (from elver to silver eels, French Mediterranean lagoons). The Length Ratio Index (LRI), performed better than the Swimbladder Degenerative Index (SDI), in three of four predefined criteria of decision. First, the LRI better correlated with an estimate of the swimbladder volume reduction, a functional consequence of the infection (representativeness). Also, the LRI was less prone to subjectivity (inter‐observer variability) and more precise (intra‐observer variability), although less easy to generate (time needed for measurement/assessment). Using a sub‐sample of 32 unaffected eels (showing minor if any swimbladder damage and no living worms at autopsy), we ascertained a linear relationship between the swimbladder length and the total body length, a prerequisite of isometric growth, to definitively accept the new ratio index as a valid alternative to the SDI. Also, because the LRI can be recorded on live specimens with radio‐imagery (non‐invasive method), we recommend its use, and provide a graph of correspondence between the SDI scores, the LRI scores and the estimated proportion of gas loss in the swimbladder.
Molecular events of apical bud formation in white spruce,Picea glauca
Authors: KAYAL WALID EL , ALLEN CARMEN C. G. , JU CHELSEA J.‐T. , ADAMS ERI , KING‐JONES SUSANNE , ZAHARIA L. IRINA , ABRAMS SUZANNE R. , COOKE JANICE E. K. 
Published: December 2010

ABSTRACTBud formation is an adaptive trait that temperate forest trees have acquired to facilitate seasonal synchronization. We have characterized transcriptome‐level changes that occur during bud formation of white spruce [Picea glauca(Moench) Voss], a primarily determinate species in which preformed stem units contained within the apical bud constitute most of next season's growth. Microarray analysis identified 4460 differentially expressed sequences in shoot tips during short day‐induced bud formation. Cluster analysis revealed distinct temporal patterns of expression, and functional classification of genes in these clusters implied molecular processes that coincide with anatomical changes occurring in the developing bud. Comparing expression profiles in developing buds under long day and short day conditions identified possible photoperiod‐responsive genes that may not be essential for bud development. Several genes putatively associated with hormone signalling were identified, and hormone quantification revealed distinct profiles for abscisic acid (ABA), cytokinins, auxin and their metabolites that can be related to morphological changes to the bud. Comparison of gene expression profiles during bud formation in different tissues revealed 108 genes that are differentially expressed only in developing buds and show greater transcript abundance in developing buds than other tissues. These findings provide a temporal roadmap of bud formation in white spruce.