bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collection of Embryos from Short-Tailed Fruit Bats (Carollia perspicillata): Figure 1.
Authors: Rasweiler John J. , Cretekos Chris J. , Behringer Richard R. 
Published: March 2009

INTRODUCTIONEmbryos from the short-tailed fruit bat (Carollia perspicillata) can be collected from females that are pregnant as a result of matings established in a laboratory colony or during the breeding season in the wild. The entire reproductive tract containing the single conceptus is dissected from the female, and the uterus is measured. If the uteri contain embryos that can be dissected out, measured, and staged, this information can be compared to published data for normal pregnancies. The results can then be used to predict when conceptuses at other stages of development might be collected. Such data, by themselves, do not establish whether those pregnancies may have previously included a period of delay at the primitive streak stage. As described in this protocol, the embryo is usually dissected from the reproductive tract free of decidual tissue and its extraembryonic membranes, including the yolk sac and amnion. Once isolated, the embryo can then be processed for subsequent analysis.
Fixation and Storage of Embryos from Short-Tailed Fruit Bat (Carollia perspicillata)
Authors: Rasweiler John J. , Cretekos Chris J. , Behringer Richard R. 
Published: March 2009

INTRODUCTIONThis protocol describes fixation of embryos and tissues of the short-tailed fruit bat C. perspicillata. The fixed embryos can be stored at −20°C for prolonged periods and can be used for whole-mount in situ hybridization, whole-mount immunohistochemistry, or for embedding and sectioning in paraffin or frozen blocks for a variety of histological procedures.
Alcian Blue/Alizarin Red Staining of Cartilage and Bone of Short-Tailed Fruit Bat (Carollia perspicillata)
Authors: Rasweiler John J. , Cretekos Chris J. , Behringer Richard R. 
Published: March 2009

INTRODUCTIONThis protocol is used to stain embryo skeleton with alcian blue and alizarin red at later stages of development, when there is significant replacement of the cartilaginous early skeleton with ossified bone. It has been used with good results on the short-tailed fruit bat Carollia perspicillata and other bat species from CS 20 through neonatal stages.
Alcian Blue/Alizarin Red Staining of Cartilage and Bone in Mouse: Figure 1.
Authors: Ovchinnikov Dmitry 
Published: March 2009

INTRODUCTIONThe vertebrate skeleton forms by endochondral and intramembranous bone formation. During endochondral bone formation, mesenchyme condensations give rise to cartilages that are eventually replaced by bone. However, there are some permanent cartilages that do not ossify, such as the cartilage of the trachea and articular cartilage of the joints, and intramembranous bone formation occurs directly without a cartilage template. This article describes a method for simultaneously visualizing cartilage and mineralized tissues (notably bone) in the developing mouse. It makes use of alcian blue and alizarin red stains, and it is best used for later fetal, newborn, and early post-natal stages of development. Neonatal skeletons are especially well suited for this technique.
Collection of Embryos from Darwin’s Finches (Thraupidae, Passeriformes)
Authors: Abzhanov Arhat 
Published: March 2009

INTRODUCTIONThere are no breeding colonies of Darwin’s finches anywhere in the world. Thus, all of the embryonic material is collected in the wild. This protocol describes how, in a field setting, fertilized eggs are collected and incubated at a precise temperature and how the resulting embryos are harvested and processed for in situ hybridization, antibody staining, and microarray analyses. In addition, the protocol includes steps for preparing the heads of older embryos for histological staining of bone and cartilage with alcian blue and alizarin red. It is likely that the same or similar methods can be used to obtain embryonic tissue from other species of songbirds. The main limitation of this protocol is that, when used in the field without external constant electricity sources, it requires power generators that need to run on a more or less constant basis, as well as stockpiles of supplies (fuel, oil, and fresh water).
Cetyltrimethyl Ammonium Bromide (CTAB) DNA Miniprep for Plant DNA Isolation
Authors: Clarke Joseph D. 
Published: March 2009

INTRODUCTIONThe presence of polysaccharides in a DNA preparation can inhibit use of techniques such as polymerase chain reaction (PCR). Cetyltrimethyl ammonium bromide (CTAB) is a surfactant useful for isolation of DNA from tissues containing high amounts of polysaccharides. Under the high-salt conditions used in this protocol, the CTAB binds the polysaccharides, removing them from the solution. When used with Arabidopsis, this procedure yields quite pure DNA that is suitable for thermal asymmetric interlaced PCR (TAIL-PCR).
Dellaporta Miniprep for Plant DNA Isolation
Authors: Weigel Detlef , Glazebrook Jane 
Published: March 2009

INTRODUCTIONThis procedure provides a quick and inexpensive method for plant DNA isolation. When used with Arabidopsis, this procedure yields quite good-quality DNA that is suitable as a polymerase chain reaction (PCR) template for cleaved amplified polymorphic sequences (CAPS) or simple sequence length polymorphism (SSLP) markers. It yields enough DNA to test a large number of markers. It is recommended in cases when many markers will be tested on the same samples.
Quick Miniprep for Plant DNA Isolation
Authors: Weigel Detlef , Glazebrook Jane 
Published: March 2009

INTRODUCTIONThis procedure describes a quick miniprep for plant DNA isolation. It yields a small quantity of poorly purified DNA. However, many samples can be processed in a short time. When used with Arabidopsis, the method generally provides DNA of sufficient quality for polymerase chain reaction (PCR) amplification of cleaved amplified polymorphic sequences (CAPS) and simple sequence length polymorphism (SSLP) markers. Repeated freeze-thaw cycles should be avoided, because they result in samples that will no longer work as PCR templates.
Mass Spectrometry Characterization of Multiprotein Complexes: Figure 1.
Authors: Robinson Carol V. 
Published: March 2009

INTRODUCTIONAlthough mass spectrometry measures species in the gas phase, it is becoming widely accepted that, under the appropriate conditions, noncovalent features of protein structure and interactions can be retained in mass spectra. Recent applications have shown that mass spectrometry can provide information not only about the stoichiometry of subunits within a complex, but also about subsets of interacting proteins within macromolecular complexes, the component oligomers in polydisperse assemblies, and changes in quaternary structure in response to phosphorylation of subunits. An important advance in this field has been the recent extension of established techniques to examine protein complexes isolated directly from cells, rather than assembled from recombinant subunits. This protocol provides guidance for setup and use of a mass spectrometer to analyze multiprotein complexes.
Transduction of Vertebrate Cells with Recombinant Baculovirus
Authors: Airenne Kari J. , Laitinen Olli H. , Mähönen Anssi J. , Ylä-Herttuala Seppo 
Published: March 2009

INTRODUCTIONThe baculoviral expression vector system (BEVS) has become one of the most popular systems to produce recombinant proteins. The finding that a modified baculovirus bearing a suitable promoter was able to efficiently transduce hepatocytes stimulated further interest in BEVS as a potential gene delivery vector for cells other than those of insect origin. Indeed, a wide variety of vertebrate cells can be transduced by recombinant baculoviruses. Such viruses can also mediate efficient gene delivery into several tissues of mammals in vivo. The popularity of BEVS over other expression systems is based on several unique features such as safety, ability to accommodate large transgenes, and low cytotoxicity in vertebrate cells even at very high virus load. This protocol describes a method for transformation of vertebrate cells with recombinant baculovirus.
Potent antitumor activity of double‐regulated oncolytic adenovirus‐mediated ST13 for colorectal cancer
Authors: Yu De Bin , Zhong Su Yang , Yang Min , Wang Yi Gang , Qian Qi Jun , Zheng Shu , Liu Xin Yuan 
Published: March 2009

Following targeted gene virotherapy, the suppression of tumorigenicity 13 (ST13) gene was inserted into the double‐regulated oncolytic adenovirus SG500 to ensure more safety and potent antitumor activity against colorectal cancer in vitro and in vivo. We generated the ST13‐expressing oncolytic adenovirus SG500‐ST13, with which colorectal carcinoma cell lines SW620 and HCT116, and the lung fibroblast cell line WI38, were infected. Crystal violet staining was carried out to detect the cytopathic effect in cells, and the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide method was used to assay cell viability. The effect of apoptosis induced by SG500‐ST13 was confirmed by Hoechst staining and the TdT‐mediated dUTP‐biotin nick‐end labeling method. To further identify the antitumor effects of SG500‐ST13 on HCT116 xenografts in Balb/c nude mice, the induction of cell death was assessed by hematoxylin–eosin staining. Immunohistochemical study was also carried out. (Cancer Sci 2009; 100: 678–683)
Cost‐effective mammography screening in Korea: High incidence of breast cancer in young women
Authors: Lee Soon Young , Jeong Seong Hwa , Kim Youn Nam , Kim Jinheum , Kang Dae Ryong , Kim Hyeon‐Chang , Nam Chung Mo 
Published: March 2009

The epidemiological characteristics of breast cancer in Korean women are different from the characteristics reported in Western women. The highest incidence rate occurs in Korean women in their 40s. The purpose of this study was to determine the most cost‐effective screening interval and target age range for Korean women from the perspective of the national healthcare system. A stochastic model was used to simulate breast cancer screenings by varying both the screening intervals and the age ranges. The effectiveness of mammography screening was defined as the probability of detecting breast cancer in the preclinical state and the cost was based on the direct cost of mammography screening and the confirmative tests. The age‐specific mean sojourn times and the sensitivity of the mammography were applied in the stochastic model. An optimal cost‐effectiveness was determined by the incremental cost‐effectiveness ratio and lifetime schedule sensitivity. Sensitivity analyses were undertaken to assess parameter uncertainty. The selected cost‐effective strategies were: (1) the current biennial mammography screenings for women who are at least 40 years old; (2) biennial screening for women between the ages of 35 and 75 years; and (3) a combination strategy consisting of biennial screening for women aged between 45 and 54 years, and 3‐year interval screening for women aged between 40 and 44 years and 55 and 65 years. Further studies should follow to investigate the effectiveness of mammography screening in women younger than 40 years in Asia as well as in Korea. (Cancer Sci 2009; 100: 1105–1111)
Risk of upper gastrointestinal bleeding with oral bisphosphonates and non steroidal anti‐inflammatory drugs: a case‐control study
Authors: ETMINAN M. , LÉVESQUE L. , FITZGERALD J. M. , BROPHY J. M. 
Published: March 2009

SummaryBackground  Gastrointestinal injuries including gastric ulcers have been reported with oral bisphosphonate therapy. However, the risk of the more serious upper gastrointestinal bleeding (UGB) especially in the community setting with these drugs remains unknown. Similarly, the risk of UGB among users of both bisphosphonates and non steroidal anti‐inflammatory drugs (NSAIDs) in the community is also unknown.Aim  To explore the risk of more serious UGB among users of bisphosphonates and the risk of UGB among users of both bisphosphonates and NSAIDs in the community.Methods  We conducted a case‐control study within a cohort of Quebec residents who had received a revascularization procedure from 1995 to 2004. Cohort members were followed up from the date of their first procedure until the earliest of: (1) study outcome, (2) date of death or (3) end of health care coverage. Cases were defined as those with the first diagnosis of a UGB. For each case, 20 controls were selected and matched to the cases by index date, age and cohort entry. Adjusted odds ratios for current use of bisphosphonates, NSAIDs and co‐therapy of both drugs were computed.Results  Within the initial cohort, 3253 incident cases of UGBs and corresponding 65 060 matched controls were identified. The adjusted odds ratio (OR) for UGB by current users of bisphosphonates was 1.01 (95% CI, 0.72–1.43). Current NSAID use was associated with an increased risk of UGB OR = 1.75; 95% CI, 1.53–1.99. The OR for use of bisphosphonates and NSAIDs was elevated OR = 2.00; 95% CI, 1.12–3.57. This risk was still elevated for users of bisphosphonates and COX‐2 inhibitors [OR = 2.38 (95% CI, 1.26–4.50)].Conclusion  We found no evidence of an increase in the risk of UGB among current users of bisphosphonates. The risk of combined NSAID and bisphosphonate therapy was increased, but this risk was not higher than the risk for NSAID users alone.
Therapeutic opportunities for counteracting apoptosis resistance in childhood leukaemia
Authors: Fulda Simone 
Published: March 2009

SummaryEvasion of apoptosis is a hallmark of human cancers, for example in haematological malignancies. Apoptosis is an intrinsic cell death program that is crucial in maintaining tissue homeostasis, for example in the haematopoietic system where there is a high turnover rate of cells. As a result, a decrease in the rate of apoptosis as well as an increase in proliferation favours tumorigenesis as well as tumour progression. Further, the anti‐leukaemic action of current treatment approaches, including chemo‐, radio‐ or immunotherapy, critically relies on intact cell death programs in cancer cells. Therefore, defects in apoptosis pathways are frequently associated with the resistance to anticancer therapies. In recent years, the identification and characterization of the molecules and pathways that are involved in the regulation and execution of cell death in leukaemia and lymphoma cells, for example tumour necrosis factor‐related apoptosis inducing ligand (TRAIL), ‘inhibitor of apoptosis’ (IAP) proteins and Bcl‐2, have set the ground for the development of novel diagnostic tools and molecular therapeutics targeting apoptosis pathways in haematological malignancies.
Notoriety to respectability: a short history of arsenic prior to its present day use in haematology
Authors: Doyle Derek 
Published: March 2009

SummaryThis paper looks at arsenic, and in particular the trioxide, from the days of the ancient Chinese, Egyptians, Greeks and Romans, through the 17th–20th centuries to its adoption by today’s haematologists. It looks at its commercial and medical uses, past and present, its notoriety as a poison, it’s reputation as a ‘tonic’ and therapeutic agent, many of the famous people associated with it including Thomas Fowler, William Withering and Robert Christison, and the promise an 18th century panacea now offers 21st century patients under the care of today’s haematologists and tomorrow’s oncologists.
A novel view on stem cell development: analysing the shape of cellular genealogies
Authors: Glauche I. , Lorenz R. , Hasenclever D. , Roeder I. 
Published: March 2009

AbstractObjectives:  The analysis of individual cell fates within a population of stem and progenitor cells is still a major experimental challenge in stem cell biology. However, new monitoring techniques, such as high‐resolution time‐lapse video microscopy, facilitate tracking and quantitative analysis of single cells and their progeny. Information on cellular development, divisional history and differentiation are naturally comprised into a pedigree‐like structure, denoted as cellular genealogy. To extract reliable information concerning effecting variables and control mechanisms underlying cell fate decisions, it is necessary to analyse a large number of cellular genealogies.Materials and Methods:  Here, we propose a set of statistical measures that are specifically tailored for the analysis of cellular genealogies. These measures address the degree and symmetry of cellular expansion, as well as occurrence and correlation of characteristic events such as cell death. Furthermore, we discuss two different methods for reconstruction of lineage fate decisions and show their impact on the interpretation of asymmetric developments. In order to illustrate these techniques, and to circumvent the present shortage of available experimental data, we obtain cellular genealogies from a single‐cell‐based mathematical model of haematopoietic stem cell organization.Results and Conclusions:  Based on statistical analysis of cellular genealogies, we conclude that effects of external variables, such as growth conditions, are imprinted in their topology. Moreover, we demonstrate that it is essential to analyse timing of cell fate‐specific changes and of occurrence of cell death events in the divisional context in order to understand the mechanisms of lineage commitment.
Lability of organic carbon in lakes of different trophic status
Authors: OSTAPENIA A. P. , PARPAROV A. , BERMAN T. 
Published: March 2009

Summary1. We used first‐order kinetic parameters of biological oxygen demand (BOD), the constant of aerobic decomposition (k) and the asymptotic value of BOD (BODult), to characterise the lability of organic carbon pools in six lakes of different trophic state: L. Naroch, L. Miastro and L. Batorino (Belarus), L. Kinneret (Israel), L. Ladoga (Russia) and L. Mendota (U.S.A.). The relative contributions of labile and refractory organic carbon fractions to the pool of total organic carbon (TOC) in these lakes were quantified. We also determined the amounts of labile organic carbon within the dissolved and particulate TOC pools in the three Belarus lakes.2. Mean annual chlorophyll concentrations (used as a proxy for lake trophic state) ranged from 2.3 to 50.6 μg L−1, labile organic carbon (OCL = 0.3BODult) from 0.75 to 2.95 mg C L−1 and k from 0.044 to 0.14 day−1.3. Our data showed that there were greater concentrations of OCL but lower k values in more productive lakes.4. In all cases, the DOC fraction dominated the TOC pool. OCL was a minor component of the TOC pool averaging about 20%, irrespective of lake trophic state.5. In all the lakes, most (c. 85%) of the DOC pool was refractory, corresponding with published data based on measurements of bacterial production and DOC depletion. In contrast, a larger fraction (27–55%) of the particulate organic carbon (POC) pool was labile. The relative amount of POC in the TOC pool tended to increase with increasing lake productivity.6. Long‐term BOD incubations can be valuable in quantifying the rates of breakdown of the combined particulate and dissolved organic carbon pools and in characterising the relative proportions of the labile and recalcitrant fractions of these pools. If verified from a larger number of lakes our results could have important general implications.
Human mid‐gestation amniotic fluid contains interleukin‐16 bioactivity
Authors: Thornton Catherine A. , Holloway Judith A. , Shute Janis K. , Holloway John W. , Diaper Norma D. , Warner John O. 
Published: March 2009

SummaryCD4‐positive cells are detectable in the human fetal gastrointestinal tract from 11 weeks of gestation. Interleukin‐16 (IL‐16) is a chemoattractant for CD4+ cells and, via fetal swallowing of amniotic fluid, could mediate the influx of CD4+ cells into the fetal gut. We have shown that IL‐16 was detectable in human amniotic fluid at 16–18 weeks of gestation (mid‐pregnancy) but was not detectable at term (late pregnancy; > 37 weeks of gestation). Similarly, mid‐pregnancy, but not late pregnancy, amniotic fluid contained chemotactic activity for CD4+ T cells, this activity was reduced by 58% in the presence of a neutralizing anti‐IL‐16 antibody. The levels of IL‐16 in fetal plasma at 16–24 weeks of gestation were very high, and decreased significantly by 25–36 weeks but at > 37 weeks remained significantly higher than adult levels. IL‐16 transcripts were detectable in whole tissue extracts of fetal gut, skin and placenta but not in amniocytes, and IL‐16 immunoreactivity was detectable in cells within the lamina propria of the fetal gut and within the skin, where it was associated with the basement membrane. Neither IL‐16 levels nor chemotactic activity for CD4+ T cells in mid‐pregnancy amniotic fluid was related to atopic outcomes at 1 year of age. IL‐16 might have an important role in the early development of the human immune system and/or in regulating fetal and maternal immunological responsiveness during pregnancy.
New dimensions in endodontic imaging: part 1. Conventional and alternative radiographic systems
Authors: Patel S. , Dawood A. , Whaites E. , Pitt Ford T. 
Published: March 2009

AbstractConventional radiographs used for the management of endodontic problems yield limited information because of the two‐dimensional nature of images produced, geometric distortion and anatomical noise. These factors often act in combination. This review paper assesses the limitations of periapical radiographs and seeks to clarify three‐dimensional imaging techniques that have been suggested as adjuncts to conventional radiographs. These include tuned aperture computed tomography, magnetic resonance imaging, ultrasound, computed tomography and cone beam computed tomography (CBCT). Of these techniques, CBCT appears to be an effective and safe way to overcome some of the problems associated with conventional radiographs.
Detection of periapical bone defects in human jaws using cone beam computed tomography and intraoral radiography
Authors: Patel S. , Dawood A. , Mannocci F. , Wilson R. , Pitt Ford T. 
Published: March 2009

AbstractAim  To compare the diagnostic accuracy of intraoral digital periapical radiography with that of cone beam computed tomography (CBCT) for the detection of artificial periapical bone defects in dry human jaws.Methodology  Small and large artificial periapical lesions were prepared in the periapical region of the distal root of six molar teeth in human mandibles. Scans and radiographs were taken with a charged couple device (CCD) digital radiography system and a CBCT scanner before and after each periapical lesion had been created. Sensitivity, specificity, positive predictive values, negative predictive values and Receiver Operator Characteristic (ROC) curves as well as the reproducibility of each technique were determined.Results  The overall sensitivity was 0.248 and 1.0 for intraoral radiography and CBCT respectively, i.e. these techniques correctly identified periapical lesions in 24.8% and 100% of cases, respectively. Both imaging techniques had specificity values of 1.0. The ROC Az values were 0.791 and 1.000 for intraoral radiography and CBCT, respectively.Conclusions  With intraoral radiography, external factors (i.e. anatomical noise and poor irradiation geometry), which are not in the clinician’s control, hinder the detection of periapical lesions. CBCT removes these external factors. In addition, it allows the clinician to select the most relevant views of the area of interest resulting in improved detection of the presence and absence of artificial periapical lesions.