bluuebunny/crossref_metadata_2025 huggingface dataset:
An Evaluation of the Responsiveness and Discriminant Validity of Shoulder Questionnaires among Patients Receiving Surgical Correction of Shoulder Instability
Authors: Kemp Kyle A. R. , Sheps David M. , Beaupre Lauren A. , Styles-Tripp Fiona , Luciak-Corea Charlene , Balyk Robert
Published: May 2012

Health-related quality-of-life (HRQL) measures must detect clinically important changes over time and between different patient subgroups. Forty-three patients (32 M, 13 F; mean age  =  26.00  ±  8.19 years) undergoing arthroscopic Bankart repair completed three validated shoulder questionnaires (Western Ontario Shoulder Instability index (WOSI), American Shoulder and Elbow Surgeons Standardized Shoulder Assessment form (ASES), Constant score) preoperatively, and at 6, 12, and 24 months postoperatively. Responsiveness and discriminant validity was assessed between those with a satisfactory outcome and those with (1) a major recurrence of instability, (2) a single episode of subluxation, (3) any postoperative episode of instability. Eight (20%) patients reported recurrent instability. Compared to baseline, the WOSI detected improvement at the 6- (P<0.001) and 12-month (P=0.011) evaluations. The ASES showed improvement at 6 months (P=0.003), while the Constant score did not report significant improvement until 12 months postoperatively (P=0.001). Only the WOSI detected differential shoulder function related to shoulder instability. Those experiencing even a single episode of subluxation reported a 10% drop in their WOSI score, attaining the previously established minimal clinically important difference (MCID). Those experiencing a frank dislocation or multiple episodes of subluxation reported a 20% decline. The WOSI allows better discrimination of the severity of postoperative instability symptoms following arthroscopic Bankart repair.
Umbilical Cord Serum Erythropoietin Levels and Maternal Smoking in Pregnancy
Authors: Sazak Soner , Kayıran Sinan Mahir , Paksoy Yahya
Published: May 2012

Objective. To evaluate the effect of maternal smoking during pregnancy on levels of umbilical cord erythropoietin.Methods. Erythropoietin levels were measured in umbilical cord sera of 60 newborns who were delivered vaginally at term. There were 20 (33%) smoking and 40 (67%) nonsmoking mothers.Results. Mean cord serum erythropoietin levels were significantly lower in the nonsmokers (nonsmokers, 24 ± 9 IU/L; smokers, 61 ± 46 IU/L;P<.001). There was a significant positive correlation between the number of cigarettes smoked per day and cord serum erythropoietin levels (r, 0.58;P≤.05).Conclusions. Smoking during pregnancy is associated with increased levels of umbilical cord erythropoietin at birth. This may indicate a risk of fetal hypoxia and growth restriction. Education and encouragement of cessation of smoking during pregnancy are important to avoid associated fetal and maternal morbidity and mortality.
Microarchitecture Parameters Describe Bone Structure and Its Strength Better Than BMD
Authors: Topoliński Tomasz , Mazurkiewicz Adam , Jung Stanislaw , Cichański Artur , Nowicki Krzysztof
Published: May 2012

Introduction and Hypothesis. Some papers have shown that bone mineral density (BMD) may not be accurate in predicting fracture risk. Recently microarchitecture parameters have been reported to give information on bone characteristics. The aim of this study was to find out if the values of volume, fractal dimension, and bone mineral density are correlated with bone strength.Methods. Forty-two human bone samples harvested during total hip replacement surgery were cut to cylindrical samples. The geometrical mesh of layers of bone mass obtained from microCT investigation and the volumes of each layer and fractal dimension were calculated. The finite element method was applied to calculate the compression forceFcausingε=0.8% strain.Results. There were stronger correlations for microarchitecture parameters with strength than those for bone mineral density. The values of determination coefficientR2for mean volume and force were 0.88 and 0.90 for mean fractal dimension and force, while for BMD and force the value was 0.53. The samples with bigger mean bone volume of layers and bigger mean fractal dimension of layers (more complex structure) presented higher strength.Conclusion. The volumetric and fractal dimension parameters better describe bone structure and strength than BMD.
Fluorescence Correlation Spectroscopy in Drug Discovery: Study of Alexa532-Endothelin 1 Binding to the Endothelin ETAReceptor to Describe the Pharmacological Profile of Natural Products
Authors: Caballero-George Catherina , Sorkalla Thomas , Jakobs Daniel , Bolaños Jessica , Raja Huzefa , Shearer Carol , Bermingham Eldredge , Häberlein Hanns
Published: May 2012

Fluorescence correlation spectroscopy and the newly synthesized Alexa532-ET1 were used to study the dynamics of the endothelin ETAreceptor-ligand complex alone and under the influence of a semisynthetic selective antagonist and a fungal extract on living A10 cells. Dose-dependent increase of inositol phosphate production was seen for Alexa532-ET1, and its binding was reduced to 8% by the selective endothelin ETAantagonist BQ-123, confirming the specific binding of Alexa532-ET1 to the endothelin ETAreceptor. Two different lateral mobilities of the receptor-ligand complexes within the cell membrane were found allowing the discrimination of different states for this complex. BQ-123 showed a strong binding affinity to the “inactive” receptor state characterized by the slow diffusion time constant. A similar effect was observed for the fungal extract, which completely displaced Alexa532-ET1 from its binding to the “inactive” receptor state. These findings suggest that both BQ-123 and the fungal extract act as inverse agonists.
Changes of Peel Essential Oil Composition of Four Tunisian Citrus during Fruit Maturation
Authors: Bourgou Soumaya , Rahali Fatma Zohra , Ourghemmi Iness , Saïdani Tounsi Moufida
Published: May 2012

The present work investigates the effect of ripening stage on the chemical composition of essential oil extracted from peel of four citrus: bitter orange (Citrus aurantium), lemon (Citrus limon), orange maltaise (Citrus sinensis), and mandarin (Citrus reticulate) and on their antibacterial activity. Essential oils yields varied during ripening from 0.46 to 2.70%, where mandarin was found to be the richest. Forty volatile compounds were identified. Limonene (67.90–90.95%) and 1,8-cineole (tr-14.72%) were the most represented compounds in bitter orange oil while limonene (37.63–69.71%),β-pinene (0.63–31.49%),γ-terpinene (0.04–9.96%), andp-cymene (0.23–9.84%) were the highest ones in lemon. In the case of mandarin, the predominant compounds were limonene (51.81–69.00%), 1,8-cineole (0.01–26.43%), andγ-terpinene (2.53–14.06%). However, results showed that orange peel oil was dominated mainly by limonene (81.52–86.43%) during ripening. The results showed that ripening stage influenced significantly the antibacterial activity of the oils againstStaphylococcus aureus,Escherichia coli, andPseudomonas aeruginosa. This knowledge could help establish the optimum harvest date ensuring the maximum essential oil, limonene, as well as antibacterial compounds yields of citrus.
An Evaluation of Leaf Biomass : Length Ratio as a Tool for Nondestructive Assessment in Eelgrass (Zostera marinaL.)
Authors: Echavarria-Heras Hector , Solana-Arellano Elena , Lee Kun-Seop , Hosokawa Shinya , Franco-Vizcaíno Ernesto
Published: May 2012

The characterization of biomass and its dynamics provides valuable information for the assessment of natural and transplanted eelgrass populations. The need for simple, nondestructive assessments has led to the use of the leaf biomass-to-length ratio for converting leaf-length measurements, which can be easily obtained, to leaf growth rates through the plastochrone method. Using data on leaf biomass and length collected in three natural eelgrass populations and a mesocosm, we evaluated the suitability of a leaf weight-to-length ratio for nondestructive assessments. For the data sets considered, the isometric scaling that sustains the weight-to-length proxy always produced inconsistent fittings, and for leaf-lengths greater than a threshold value, the conversion of leaf length to biomass generated biased estimations. In contrast, an allometric scaling of leaf biomass and length was highly consistent in all the cases considered. And these nondestructive assessments generated reliable levels of reproducibility in leaf biomass for all the ranges of variability in leaf lengths. We argue that the use of allometric scaling for the representation of leaf biomass in terms of length provides a more reliable approach for estimating eelgrass biomass.
Maternal and Cord Serum Cytokine Changes with Continuous and Intermittent Labor Epidural Analgesia: A Randomized Study
Authors: Mantha Venkat R. , Vallejo Manuel C. , Ramesh Vimala , Jones Bobby L. , Ramanathan Sivam
Published: May 2012

Background. Maternal fever during labor epidural analgesia (LEA) may cause increased maternal and cord serum inflammatory cytokines. We report the effects of intermittent and continuous LEA on these cytokines.Methods. Ninety-two women were randomly assigned to continuous (CLEA) or intermittent (ILEA) groups, 46 in each. Maternal temperature was checked and blood drawn at epidural insertion (baseline) and four-hourly until 4 h postpartum (4 PP). Cord blood was drawn after placental delivery. Interleukin-1β(IL-1β), interleukin-6 (IL-6), interleukin-8 (IL-8), granulocyte macrophage-colony stimulating factor (GM-CSF), and tumor necrosis factor-α(TNF-α) were measured and analyzed according to group randomization, and then combined and reanalyzed as febrile (temperature ≥38°C) or afebrile groups.Results. Significant intragroup changes from baseline were noted in some groups. Data are pg/mL, median (Q1/Q3). IL-6 rose at all time points in all groups.CLEA: baseline: 18.5 (12.5/31.1), 4 h: 80.0 (46.3/110.8), 8 h: 171.9 (145.3/234.3), and 4 PP: 81 (55.7/137.4).ILEA: baseline: 15.7 (10.2/27.1), 4 h: 68.2 (33.3/95.0), 8 h: 125.0 (86.3/195.0), and 4 PP: 70.2 (54.8/103.6).Febrile group: baseline: 21.6 (13.8/40.9), 4 h: 83.9 (47.5/120.8), 8 h: 186.7 (149.6/349.9), and 4 PP: 105.8 (65.7/158.8).Afebrile group: baseline: 10.9 (2.1/17.4), 4 h: 38.2 (15.0/68.2), 8 h: 93.8 (57.1/135.7), and 4 PP: 52.9 (25.1/78). IL-8 rose at all time points inCLEA: baseline: 2.68 (0.0/4.3), 4 h: 3.7 (0.0/6.5), 8 h: 6.0 (3.3/9.6), 4 PP: 5.6 (0.8/8.0), andafebrile groupbaseline: 2.5 (0.0/4.7), 4 h: 3.3 (0.0/6.2), 8 h: 5.3 (1.9/9.8), and 4 PP: 4.7 (0.0/7.6). It fell at 4 PP infebrile group: baseline: 4.1 (0.0/6.4), 4 h: 3.8 (0.0/6.5), 8 h: 5.2 (2.5/8.0), and 4 PP: 2.9 (0.0/4.0). GM-CSF increased at 8 h and decreased at 4 PP inILEAbaseline: 2.73 (0.0/7.2), 4 h: 2.73 (0.0/7.9), 8 h: 3.9 (2.7/11.5), and 4 PP: 2.0 (0.0/7.2). It increased at 4 h and 8 h and decreased at 4 PP infebrilegroup: baseline: 2.6 (0.0/4.2), 4 h: 3.2 (2.1/7.0), 8 h: 4.0 (3.2/12.3), and 4 PP: 2.4 (1.7/12.6). There were no intergroup cytokine changes in maternal or cord serum in CLEA versus ILEA or febrile versus afebrile groups.Conclusions. Some cytokines, especially IL-6, rise physiologically during labor epidural analgesia.
The Use of Geostatistics in the Study of Floral Phenology ofVulpia geniculata(L.) Link
Authors: León Ruiz Eduardo J. , García Mozo Herminia , Domínguez Vilches Eugenio , Galán Carmen
Published: May 2012

Traditionally phenology studies have been focused on changes through time, but there exist many instances in ecological research where it is necessary to interpolate among spatially stratified samples. The combined use of Geographical Information Systems (GIS) and Geostatistics can be an essential tool for spatial analysis in phenological studies. Geostatistics are a family of statistics that describe correlations through space/time and they can be used for both quantifying spatial correlation and interpolating unsampled points. In the present work, estimations based upon Geostatistics and GIS mapping have enabled the construction of spatial models that reflect phenological evolution ofVulpia geniculata(L.) Link throughout the study area during sampling season. Ten sampling points, scattered troughout the city and low mountains in the “Sierra de Córdoba” were chosen to carry out the weekly phenological monitoring during flowering season. The phenological data were interpolated by applying the traditional geostatitical method of Kriging, which was used to ellaborate weekly estimations ofV. geniculataphenology in unsampled areas. Finally, the application of Geostatistics and GIS to create phenological maps could be an essential complement in pollen aerobiological studies, given the increased interest in obtaining automatic aerobiological forecasting maps.
Improving Growth and Productivity of Oleiferous Brassicas under Changing Environment: Significance of Nitrogen and Sulphur Nutrition, and Underlying Mechanisms
Authors: Anjum Naser A. , Gill Sarvajeet S. , Umar Shahid , Ahmad Iqbal , Duarte Armando C. , Pereira Eduarda
Published: May 2012

Mineral nutrients are the integral part of the agricultural systems. Among important plant nutrients, nitrogen (N) and sulphur (S) are known essential elements for growth, development, and various physiological functions in plants. Oleiferous brassicas (rapeseed and mustard) require higher amounts of S in addition to N for optimum growth and yield. Therefore, balancing S-N fertilization, optimization of nutrient replenishment, minimization of nutrient losses to the environment, and the concept of coordination in action between S and N could be a significant strategy for improvement of growth and productivity of oleiferous brassicas. Additionally, positive interaction between S and N has been reported to be beneficial for various aspects of oilseed brassicas. The current paper updates readers on the significance of N and S for the improvement of plant growth, development, and productivity in detail. In addition, S-N nutrition-mediated control of major plant antioxidant defense system components involved in the removal and/or metabolism of stress-induced/generated reactive oxygen species in plants (hence, the control of plant growth, development, and productivity) has been overviewed.
Rapid Prototyping in Orthopaedic Surgery: A User's Guide
Authors: Frame Mark , Huntley James S.
Published: May 2012

Rapid prototyping (RP) is applicable to orthopaedic problems involving three dimensions, particularly fractures, deformities, and reconstruction. In the past, RP has been hampered by cost and difficulties accessing the appropriate expertise. Here we outline the history of rapid prototyping and furthermore a process using open-source software to produce a high fidelity physical model from CT data. This greatly mitigates the expense associated with the technique, allowing surgeons to produce precise models for preoperative planning and procedure rehearsal. We describe the method with an illustrative case.
Lipids and All-Cause Mortality among Older Adults: A 12-Year Follow-Up Study
Authors: Cabrera Marcos Aparecido Sarria , de Andrade Selma Maffei , Dip Renata Maciulis
Published: May 2012

This is a 12-year follow-up cohort study with 800 people (60–85 years old). The association between lipid disorders and mortality was analysed by Cox proportional hazard adjusted model. All-cause mortality was considered the dependent variable, and lipid disorders as independent variables: total cholesterol (TC) >200 and <170 mg/dl, HDL-c <35 and 40, LDL-c >100 and 130, and triglycerides (TG) >50. An initial analysis of all subjects was performed and a second was carried out after having excluded individuals with a body mass index (BMI) <20 kg/m2or mortality in ≤2 years. The mortality showed a positive association with low TC and a negative association with high TC and high LDL-c. After the exclusion of underweight and premature mortality, there was a positive association only with TC <170 mg/dl (HR = 1.36, CI95%: 1.02–1.82). The data did not show a higher risk with high levels of TC, LDL-c, and TG. However, they showed higher mortality among older adults with low TC.
A Learning-Based Approach for Biomedical Word Sense Disambiguation
Authors: Al-Mubaid Hisham , Gungu Sandeep
Published: May 2012

In the biomedical domain, word sense ambiguity is a widely spread problem with bioinformatics research effort devoted to it being not commensurate and allowing for more development. This paper presents and evaluates a learning-based approach for sense disambiguation within the biomedical domain. The main limitation with supervised methods is the need for a corpus of manually disambiguated instances of the ambiguous words. However, the advances in automatic text annotation and tagging techniques with the help of the plethora of knowledge sources like ontologies and text literature in the biomedical domain will help lessen this limitation. The proposed method utilizes the interaction model (mutual information) between the context words and the senses of the target word to induce reliable learning models for sense disambiguation. The method has been evaluated with the benchmark dataset NLM-WSD with various settings and in biomedical entity species disambiguation. The evaluation results showed that the approach is very competitive and outperforms recently reported results of other published techniques.
Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis
Authors: Pontvianne Frédéric , Blevins Todd , Chandrasekhara Chinmayi , Feng Wei , Stroud Hume , Jacobsen Steven E. , Michaels Scott D. , Pikaard Craig S.
Published: May 2012

Eukaryotes have hundreds of nearly identical 45S ribosomal RNA (rRNA) genes, each encoding the 18S, 5.8S, and 25S catalytic rRNAs. Because cellular demands for ribosomes and protein synthesis vary during development, the number of active rRNA genes is subject to dosage control. In genetic hybrids, one manifestation of dosage control is nucleolar dominance, an epigenetic phenomenon in which the rRNA genes of one progenitor are repressed. For instance, in Arabidopsis suecica, the allotetraploid hybrid of Arabidopsis thaliana and Arabidopsis arenosa, the A. thaliana-derived rRNA genes are selectively silenced. An analogous phenomenon occurs in nonhybrid A. thaliana, in which specific classes of rRNA gene variants are inactivated. An RNA-mediated knockdown screen identified SUVR4 {SUPPRESSOR OF VARIEGATION 3-9 [SU(VAR)3-9]-RELATED 4} as a histone H3 Lys 9 (H3K9) methyltransferase required for nucleolar dominance in A. suecica. H3K9 methyltransferases are also required for variant-specific silencing in A. thaliana, but SUVH5 [SU(VAR)3-9 HOMOLOG 5] and SUVH6, rather than SUVR4, are the key activities in this genomic context. Mutations disrupting the H3K27 methyltransferases ATXR5 or ATXR6 affect which rRNA gene variants are expressed or silenced, and in atxr5 atxr6 double mutants, dominance relationships among variants are reversed relative to wild type. Interestingly, these changes in gene expression are accompanied by changes in the relative abundance of the rRNA gene variants at the DNA level, including overreplication of the normally silenced class and decreased abundance of the normally dominant class. Collectively, our results indicate that histone methylation can affect both the doses of different variants and their differential silencing through the choice mechanisms that achieve dosage control.
A molecular wound response program associated with regeneration initiation in planarians
Authors: Wenemoser Danielle , Lapan Sylvain W. , Wilkinson Alex W. , Bell George W. , Reddien Peter W.
Published: May 2012

Planarians are capable of regenerating any missing body part and present an attractive system for molecular investigation of regeneration initiation. The gene activation program that occurs at planarian wounds to coordinate regenerative responses remains unknown. We identified a large set of wound-induced genes during regeneration initiation in planarians. Two waves of wound-induced gene expression occurred in differentiated tissues. The first wave includes conserved immediate early genes. Many second-wave genes encode conserved patterning factors required for proper regeneration. Genes of both classes were generally induced by wounding, indicating that a common initial gene expression program is triggered regardless of missing tissue identity. Planarian regeneration uses a population of regenerative cells (neoblasts), including pluripotent stem cells. A class of wound-induced genes was activated directly within neoblasts, including the Runx transcription factor-encoding runt-1 gene. runt-1 was required for specifying different cell types during regeneration, promoting heterogeneity in neoblasts near wounds. Wound-induced gene expression in neoblasts, including that of runt-1, required SRF (serum response factor) and sos-1. Taken together, these data connect wound sensation to the activation of specific cell type regeneration programs in neoblasts. Most planarian wound-induced genes are conserved across metazoans, and identified genes and mechanisms should be important broadly for understanding wound signaling and regeneration initiation.
Meiotic DNA double-strand breaks and chromosome asynapsis in mice are monitored by distinct HORMAD2-independent and -dependent mechanisms
Authors: Wojtasz Lukasz , Cloutier Jeffrey M. , Baumann Marek , Daniel Katrin , Varga János , Fu Jun , Anastassiadis Konstantinos , Stewart A. Francis , Reményi Attila , Turner James M.A. , Tóth Attila
Published: May 2012

Meiotic crossover formation involves the repair of programmed DNA double-strand breaks (DSBs) and synaptonemal complex (SC) formation. Completion of these processes must precede the meiotic divisions in order to avoid chromosome abnormalities in gametes. Enduring key questions in meiosis have been how meiotic progression and crossover formation are coordinated, whether inappropriate asynapsis is monitored, and whether asynapsis elicits prophase arrest via mechanisms that are distinct from the surveillance of unrepaired DNA DSBs. We disrupted the meiosis-specific mouse HORMAD2 (Hop1, Rev7, and Mad2 domain 2) protein, which preferentially associates with unsynapsed chromosome axes. We show that HORMAD2 is required for the accumulation of the checkpoint kinase ATR along unsynapsed axes, but not at DNA DSBs or on DNA DSB-associated chromatin loops. Consistent with the hypothesis that ATR activity on chromatin plays important roles in the quality control of meiotic prophase, HORMAD2 is required for the elimination of the asynaptic Spo11−/−, but not the asynaptic and DSB repair-defective Dmc1−/− oocytes. Our observations strongly suggest that HORMAD2-dependent recruitment of ATR to unsynapsed chromosome axes constitutes a mechanism for the surveillance of asynapsis. Thus, we provide convincing evidence for the existence of a distinct asynapsis surveillance mechanism that safeguards the ploidy of the mammalian germline.
Astrocytes and disease: a neurodevelopmental perspective
Authors: Molofsky Anna V. , Krenick Robert , Ullian Erik , Tsai Hui-hsin , Deneen Benjamin , Richardson William D. , Barres Ben A. , Rowitch David H.
Published: May 2012

Astrocytes are no longer seen as a homogenous population of cells. In fact, recent studies indicate that astrocytes are morphologically and functionally diverse and play critical roles in neurodevelopmental diseases such as Rett syndrome and fragile X mental retardation. This review summarizes recent advances in astrocyte development, including the role of neural tube patterning in specification and developmental functions of astrocytes during synaptogenesis. We propose here that a precise understanding of astrocyte development is critical to defining heterogeneity and could lead advances in understanding and treating a variety of neuropsychiatric diseases.
Links between metabolism and cancer
Authors: Dang Chi V.
Published: May 2012

Metabolism generates oxygen radicals, which contribute to oncogenic mutations. Activated oncogenes and loss of tumor suppressors in turn alter metabolism and induce aerobic glycolysis. Aerobic glycolysis or the Warburg effect links the high rate of glucose fermentation to cancer. Together with glutamine, glucose via glycolysis provides the carbon skeletons, NADPH, and ATP to build new cancer cells, which persist in hypoxia that in turn rewires metabolic pathways for cell growth and survival. Excessive caloric intake is associated with an increased risk for cancers, while caloric restriction is protective, perhaps through clearance of mitochondria or mitophagy, thereby reducing oxidative stress. Hence, the links between metabolism and cancer are multifaceted, spanning from the low incidence of cancer in large mammals with low specific metabolic rates to altered cancer cell metabolism resulting from mutated enzymes or cancer genes.
Hybridization to Tissues on Slides or Coverslips for Whole-Mount FISH in Drosophila: Figure 1.
Authors: Dernburg Abby F.
Published: May 2012

Many Drosophila tissues (other than embryos or egg chambers) are too large, delicate, transparent, or buoyant for manipulation in suspension. Tissues such as spermatocytes, spermatids, and imaginal disks are difficult to handle in suspension and are more appropriately fixed on slides or coverslips for whole-mount fluorescent in situ hybridization (FISH). As described in this protocol, the hybridization reaction can be performed in Coplin jars (which require 50–60 mL of solution to cover the sample), larger staining jars (which require 200 mL), or coverslip-staining jars (which hold ∼7–10 mL). Following hybridization, staining with antibodies or other detection reagents can be performed in a humid chamber and staining solution can be applied directly to the tissue.
In Vitro Transfection with Oligonucleotide DNA Using Polylysine Copolymers
Authors: Kim Sung Wan
Published: May 2012

The terplex system for delivering DNA to targeted cells comprises three components: stearyl polylysine (PLL), low-density lipoprotein (LDL), and DNA. This article describes transfection of A7R5 cells or CCD-32 cells with a terplex complex containing c-myb antisense oligonucleotide to analyze the antiproliferative effect of the transfected sequence.
In Vivo Delivery of Plasmid DNA into Rabbit Myocardium Using Polylysine Copolymers
Authors: Kim Sung Wan
Published: May 2012

The terplex system for delivering DNA to targeted cells comprises three components—stearyl polylysine (PLL), low-density lipoprotein (LDL), and DNA. This article describes the use of a terplex complex to deliver plasmid DNA carrying the vascular endothelial growth factor VEGF165 into rabbit myocardium. Transfection with VEGF is assessed by comparing tissue pathology and pumping function of the heart in control and experimental animals after induced myocardial infarction.
Optical Window Preparation for Two-Photon Imaging of Microglia in Mice: Figure 1.
Authors: Nimmerjahn Axel
Published: May 2012

Microglia are the primary immune effector cells of the brain parenchyma. They are distributed throughout the brain at various densities. Two-photon fluorescence microscopy, together with expression of fluorescent proteins in microglia, has enabled the study of these fascinating cells in vivo. Imaging studies have shown, for example, that microglia continually survey their cellular environment and immediately respond to injury. However, we still know very little about their roles in various parts of the developing and adult brain or their diverse effector functions in aging and different disease states. Experimental procedures have been developed for minimally invasive short- and long-term two-photon imaging of microglial cells in cortical regions of the intact mouse brain. This protocol presents two methods for the preparation of the optical window that is needed for two-photon imaging of microglia. The thinned skull method should be used whenever possible. Skull thinning enables transcranial two-photon imaging while minimizing external influences that might disturb normal microglia physiology and brain homeostasis. The sealed craniotomy preparation is useful for short-term investigation of microglia.
Oncogenomics Methods and Resources
Authors: Furney Simon J. , Gundem Gunes , Lopez-Bigas Nuria
Published: May 2012

Today, cancer is viewed as a genetic disease and many genetic mechanisms of oncogenesis are known. The progression from normal tissue to invasive cancer is thought to occur over a timescale of 5–20 years. This transformation is driven by both inherited genetic factors and somatic genetic alterations and mutations, and it results in uncontrolled cell growth and, in many cases, death. In this article, we review the main types of genomic and genetic alterations involved in cancer, namely copy-number changes, genomic rearrangements, somatic mutations, polymorphisms, and epigenomic alterations in cancer. We then discuss the transcriptomic consequences of these alterations in tumor cells. The use of “next-generation” sequencing methods in cancer research is described in the relevant sections. Finally, we discuss different approaches for candidate prioritization and integration and analysis of these complex data.
Orientation and Rotational Motions of Single Molecules by Polarized Total Internal Reflection Fluorescence Microscopy (polTIRFM)
Authors: Beausang John F. , Sun Yujie , Quinlan Margot E. , Forkey Joseph N. , Goldman Yale E.
Published: May 2012

In this article, we describe methods to detect the spatial orientation and rotational dynamics of single molecules using polarized total internal reflection fluorescence microscopy (polTIRFM). polTIRFM determines the three-dimensional angular orientation and the extent of wobble of a fluorescent probe bound to the macromolecule of interest. We discuss single-molecule versus ensemble measurements, as well as single-molecule techniques for orientation and rotation, and fluorescent probes for orientation studies. Using calmodulin (CaM) as an example of a target protein, we describe a method for labeling CaM with bifunctional rhodamine (BR). We also describe the physical principles and experimental setup of polTIRFM. We conclude with a brief introduction to assays using polTIRFM to assess the interaction of actin and myosin.
(5,7-Dimethyl-2-oxo-2H-chromen-4-yl)methyl pyrrolidine-1-carbodithioate
Authors: Mahabaleshwaraiah N. M. , Kumar K. Mahesh , Kotresh O. , Al-eryani Waleed Fadl Ali , Devarajegowda H. C.
Published: May 2012

In the title compound, C17H19NO2S2, the 2H-chromene ring system is almost planar, with a maximum deviation of 0.044 (2) Å, and the pyrrolidine ring adopts an envelope conformation. The dihedral angle between the 2H-chromene system and the planar part of the pyrrolidine ring is 83.65 (8)°. A weak intramolecular C—H...S hydrogen bond occurs. The crystal structure features C—H...O hydrogen bonds and π–π interactions, with a centroid–centroid distance of 3.5728 (16) Å.
Dichlorido(5,10,15,20-tetraphenylporphyrinato-κ4
N)antimony(V) hemi{di-μ-chlorido-bis[trichloridoantimonate(III)]} dichloromethane monosolvate
Authors: Soury Raoudha , Belkhiria Mohamed Sahah , Nasri Habib , Parvez Masood
Published: May 2012

The asymmetric unit of the title complex, [Sb(C44H28N4)Cl2][Sb2Cl8]0.5·CH2Cl2, is composed of a SbV complex cation wherein the Sb atom is hexacoordinated by four N atoms of the pyrrole rings of the tetraphenylporphyrinate (TPP) ligands and two chloride ions, a half di-μ-chlorido-bis[trichloridoantimonate(III)] counter-anion and a dichloromethane solvent molecule. In the cation, the average Sb—N distance is 2.066 (2) Å, while the Sb—Cl distances are 2.3410 (11) and 2.3639 (12) Å. The central unit of the cation, SbN4C20, is far from being planar, with deviations of atoms from the least-squares plane ranging from −0.110 (4) to 0.124 (4) Å. The Sb—Cl distances in the anion, which is located about an inversion center, lie in the wide range 2.3715 (13)–2.7489 (13) Å, the longest distances being between the Sb and bridging Cl atoms. The crystal structure is stabilized by intermolecular C—H...Cl interactions involving the cations, the anions and the solvent molecules. The solvent molecule is disordered over two orientations in a 0.901 (13):0.099 (13) ratio.
(2R,4R)-4-(2-Ethoxy-2-oxoethyl)-2,6,6-trimethyl–2-oxo-1,3,6,2λ5-dioxazaphosphocan-6-ium iodide
Authors: Fulfer Bradford W. , Fronczek Frank R. , Watkins Steven F.
Published: May 2012

The title compound, C11H23NO5P+·I−, consists of an eight-membered cationic heterocyclic ring in a boat–chair conformation. The ring features a tetraalkylammonium N and a methylphosphonate P atom. A –CH2(CO)OC2H5 ester side chain at the C adjacent to oxygen produces two chiral centers at that substituted C atom and the P atom, both of which were determined to have absolute R,R configurations. A previously determined racemic bromide analog has exactly the same ring but with a –C15H31 side chain. In that structure, both chiral centers show the same relative R/S,R/S configurations, but the ring in the bromide analog is in a boat conformation.
Brusatol
Authors: Hu Shu-Zhi , Jin Lu , Yu Tong , Tian Hai-Yan , Jiang Ren-Wang
Published: May 2012

The title compound, C26H32O11, is composed of an α,β-unsaturated cyclohexanone ring (A), two cyclohexane rings (B and C), a six-membered lactone ring (D) and tetrahydrofuran ring (E). Ring A exists in a half-chair conformation with a C atom displaced by 0.679 (2) Å from the mean plane through the remaining five atoms. Ring B exists in a normal chair conformation. Both rings C and D exist in a twisted-chair conformation due to the O-atom bridge and the carbonyl group in rings C and D, respectively. Ring E shows an envelope conformation with a C atom displaced by 0.761 (1) Å from the mean plane through the remaining five atoms. The ring junctions are A/B trans, B/C trans, C/D cis and D/E cis. An intramolecular O—H...O hydrogen bond occurs. In the crystal, O—H...O hydrogen bonds involving the hydroxy, lactone and ester groups and C—H...O interactions are observed.
Bis[2-(2-aminoethyl)-1H-benzimidazole-κ2
N
2,N
3](nitrato-κ2
O,O′)cobalt(II) chloride trihydrate
Authors: Zhao Jing , Zhang Heng , Zhu Guoyi
Published: May 2012

In the title compound, [Co(NO3)(C9H11N3)2]Cl·3H2O, the CoII atom is coordinated by four N atoms from two chelating 2-(2-aminoethyl)-1H-benzimidazole ligands and two O atoms from one nitrate anion in a distorted octahedral coordination environment. In the crystal, N—H...Cl, N—H...O, O—H...Cl and O—H...O hydrogen bonds link the complex cations, chloride anions and solvent water molecules into a three-dimensional network. π–π interactions between the imidazole and benzene rings and between the benzene rings are observed [centroid–centroid distances = 3.903 (3), 3.720 (3), 3.774 (3) and 3.926 (3) Å].
2-Chloro-4-(3,3-dichloroallyloxy)-1-nitrobenzene
Authors: Yu Xiao-feng , Xia Zheng-jun , Li Chun-ya
Published: May 2012

In the crystal structure of the title compound, C9H6Cl3NO3, molecules are connected by C—H...O hydrogen bonds, forming chains along the b axis. The dihedral angle between the benzene ring and the plane of the nitro group is 16.2 (1)° and that between the benzene ring and the plane of the dichloroallyl group is 10.2 (1)°.
Bis(2,2′-bipyridyl-κ2
N,N′)dichloridorhodium(III) perchlorate
Authors: Dikhtiarenko Alla , Torre-Fernández Laura , García-Granda Santiago , García José R. , Gimeno José
Published: May 2012

The asymmetric unit of the title compound, [RhCl2(C10H8N2)2]ClO4, consists of one unit of the cationic complex [RhCl2(bipy)2]+ and one uncoordinated perchlorate anion. The RhIII atom is coordinated by four N atoms from two bipyridyl ligands and two Cl atoms, forming a distorted octahedral environment. The Cl ligands are cis. Two intramolecular C—H...Cl hydrogen bonds occur in the cationic complex . In the crystal, molecules are linked together by a hydrogen-bond network involving the H atoms of bipyridyl rings and perchlorate anions. An O atom of the perchlorate anion is disordered over two sites, with an occupancy-factor ratio of 0.78 (3):0.22 (3).
Methyl 2-[(3,5-di-tert-butyl-4-hydroxybenzyl)sulfanyl]pyridine-3-carboxylate n-hexane hemisolvate
Authors: Ariffin Azhar , Nordin Nordiana , Yehye Wagee A. , Ng Seik Weng
Published: May 2012

The title solvated ester, C22H29NO3S·0.5C6H14, crystallizes with two independent molecules along with a hexane molecule in the asymmetric unit. The two aromatic rings are separated by an –CH2–S– linkage; the rings are aligned at 83.27 (4)° in one molecule and 47.66 (7)° in the other. The hydroxy group of one molecule forms an O—H...O hydrogen bond to the other molecule.
catena-Poly[[[diaqua(1,10-phenanthroline-κ2
N,N′)zinc]-μ-4-hydroxy-3-sulfonatobenzoato-κ2
O
3:O
1] sesquihydrate]
Authors: Fang Xiang-Qian , Gao Shan , Ng Seik Weng
Published: May 2012

The 1,10-phenanthroline-chelated Zn atom in the polymeric title compound, {[Zn(C7H4O6S)(C12H8N2)(H2O)2]·1.5H2O}
n
, is connected to the sulfonate O atom of one 4-hydroxy-3-sulfonatobenzoate dianion and to the carboxylate O atom of another dianion. It is also coordinated by two water molecules in an overall octahedral environment. The dianion links adjacent metal atoms into a chain running along [110]. The chains are linked by O—H...O hydrogen bonds into a three-dimensional network.
catena-Poly[[[diaqua(1,10-phenanthroline-κ2
N,N′)cobalt(II)]-μ-4-hydroxy-3-sulfonatobenzoato-κ2
O
3:O
1] sesquihydrate]
Authors: Fang Xiang-Qian , Gao Shan , Ng Seik Weng
Published: May 2012

The 1,10-phenanthroline-chelated CoII atom in the polymeric title compound, {[Co(C7H4O6S)(C12H8N2)(H2O)2]·1.5H2O}
n
, is connected to the sulfonate O atom of one 4-hydroxy-3-sulfonatobenzoate dianion and to the carboxylate O atom of another dianion. It is also coordinated by two water molecules in a trans-CoN2O4 octahedral environment. The dianion links adjacent metal atoms into a chain running along [110]. The chains are linked by O—H...O hydrogen bonds into a three-dimensional network.
5-Diethylamino-2-[(E)-(2,4-dimethoxyphenyl)iminomethyl]phenol
Authors: Kantar Esen Nur , Köysal Yavuz , Gümüş Sümeyye , Ağar Erbil , Soylu Mustafa Serkan
Published: May 2012

The title Schiff base, C19H24N2O3, exists in the crystal structure in the phenol–imine tautomeric form with an intramolecular O—H...N hydrogen bond. The planes of the aromatic rings form a dihedral angle of 36.8 (8)°. The crystal packing is characterized by C—H...O hydrogen bonds and π–π stacking interactions [centroid–centroid distance = 3.478 (4)Å].
10-(Prop-2-yn-1-yl)-2,7-diazaphenothiazine
Authors: Morak-Młodawska Beata , Suwińska Kinga , Pluta Krystian , Jeleń Małgorzata
Published: May 2012

In the title molecule [systematic name: 10-(prop-2-yn-1-yl)dipyrido[3,4-b:3′,4′-e][1,4]thiazine], C13H9N3S, the dihedral angle between the two pyridine rings is 146.33 (7)° and the angle between two halves of the thiazine ring is 138.84 (8)°, resulting in a butterfly shape for the tricyclic system. The central thiazine ring adopts a boat conformation, with the 2-propynyl substituent at the thiazine N atom located in a pseudo-equatorial position and oriented to the concave side of the diazaphenothiazine system. In the crystal, molecules are arranged via π–π interactions between the pyridine rings [centroid–centroid distances = 3.838 (1) and 3.845 (1) Å] into stacks extending along [001]. There are C—H...C and C—H...N interactions between molecules of neighbouring stacks.
Bis(butan-1-aminium) naphthalene-1,5-disulfonate
Authors: Jin Yu
Published: May 2012

In the title compound, 2C4H12N+·C10H6O6S2
2−, the anion lies on an inversion center, so the asymmetric unit contains half an anion and one cation which are linked by a strong N—H...O hydrogen bond. The crystal structure comprises discrete ions, which are linked into centrosymmetric R
4
4(12) loops by N—H...O interactions.
2-Amino-3-carboxypyridinium perchlorate
Authors: Berrah Fadila , Bouacida Sofiane , Anana Hayet , Roisnel Thierry
Published: May 2012

The asymmetric unit includes two crystallographically independent equivalents of the title salt, C6H7N2O2
+·ClO4
−. The cations and anions form separate layers alternating along the c axis, which are linked by N—H...O, O—H...O and C—H...O hydrogen bonds into a two-dimensional network parallel to (100). Further C—H...O contacts connect these layers, forming a three-dimensional network, in which R
4
4(20) rings and C
2
2(11) infinite chains can be identified.
N,N,N′,N′-Tetrakis(pyridin-4-yl)methanediamine monohydrate
Authors: Shin Jong Won , Min Kil Sik
Published: May 2012

In the title compound, C21H18N6·H2O, two 4,4′-dipyridylamine groups are linked by a methylene C atom, which sits on a twofold axis. The lattice water molecule is located slightly off a twofold axis, and is therefore disordered over two positions. In the crystal, the organic molecules and the water molecule are linked by O—H...N hydrogen bonds. The organic molecules exhibit extensive offset face-to-face π–π interactions to symmetry equivalents [centroid–centroid distances = 3.725 (3) and 4.059 (3) Å].
Unconstrained simultaneous source land data processing*
Authors: Huo Shoudong , Tsingas Constantine , Kelamis Panos G. , Pecholcs Peter I. , Xu Hai
Published: May 2012

In the past few years, significant effort has been put into developing land acquisition field techniques that can improve production performance, reduce acquisition cost and increase seismic data quality. In 2010, Saudi Aramco conducted a high‐productivity, unconstrained, simultaneous source acquisition field test. A fixed, active super‐spread continuously recorded 18 single vibrators operating simultaneously in 18 separate quadrants. The test employed high source density, unique up‐sweep lengths and spatial source separation to maximize the seismic data quality and minimize the effects of crosstalk. This test achieved an optimum productivity rate of 45,000 vibrator points (VP) per 24 hours with real time QC. In this paper, we demonstrate that the conventional processing techniques produced acceptable images despite noise interference or crosstalk. In addition, we illustrate suitable deblending processing workflows and algorithms for attenuating source interference noise. The objective of the deblending processing is to attenuate random uncompressed crosstalk and to improve the resolution of the prestack migrated time image. Finally, comparisons with legacy 3D seismic data acquired over the same area are depicted. This paper reviews how this unique integration of data acquisition and deblending processing yields a superior seismic image.
Strong divergence in trait means but not in plasticity across hatchery and wild populations of sea‐run brown troutSalmo trutta
Authors: ROGELL BJÖRN , DANNEWITZ JOHAN , PALM STEFAN , PETERSSON ERIK , DAHL JONAS , PRESTEGAARD TORE , JÄRVI TORBJÖRN , LAURILA ANSSI
Published: May 2012

There is ample evidence that organisms adapt to their native environment when gene flow is restricted. However, evolution of plastic responses across discrete environments is less well examined. We studied divergence in means and plasticity across wild and hatchery populations of sea‐run brown trout (Salmo trutta) in a common garden experiment with two rearing environments (hatchery and a nearly natural experimental stream). Since natural and hatchery environments differ, this arrangement provides an experiment in contemporary adaptation across the two environments. AQST − FSTapproach was used to investigate local adaptation in survival and growth over the first summer. We found evidence for divergent selection in survival in 1 year and in body length in both years and rearing environments. In general, the hatchery populations had higher survival and larger body size in both environments.QSTin body size did not differ between the rearing environments, and constitutive divergence in the means was in all cases stronger than divergence in the plastic responses. These results suggest that in this system, constitutive changes in mean trait values are more important for local adaptation than increased plasticity. In addition,ex siturearing conditions induce changes in trait means that are adaptive in the hatchery, but potentially harmful in the wild, suggesting that hatchery rearing is likely to be a suboptimal management strategy for trout populations facing selection in the stream environment.
Dispersal and gene flow in the rare, parasitic Large Blue butterflyMaculinea arion
Authors: UGELVIG L. V. , ANDERSEN A. , BOOMSMA J. J. , NASH D. R.
Published: May 2012

Dispersal is crucial for gene flow and often determines the long‐term stability of meta‐populations, particularly in rare species with specialized life cycles. Such species are often foci of conservation efforts because they suffer disproportionally from degradation and fragmentation of their habitat. However, detailed knowledge of effective gene flow through dispersal is often missing, so that conservation strategies have to be based on mark–recapture observations that are suspected to be poor predictors of long‐distance dispersal. These constraints have been especially severe in the study of butterfly populations, where microsatellite markers have been difficult to develop. We used eight microsatellite markers to analyse genetic population structure of the Large Blue butterflyMaculinea arionin Sweden. During recent decades, this species has become an icon of insect conservation after massive decline throughout Europe and extinction in Britain followed by reintroduction of a seed population from the Swedish island of Öland. We find that populations are highly structured genetically, but that gene flow occurs over distances 15 times longer than the maximum distance recorded from mark–recapture studies, which can only be explained by maximum dispersal distances at least twice as large as previously accepted. However, we also find evidence that gaps between sites with suitable habitat exceeding ∼20 km induce genetic erosion that can be detected from bottleneck analyses. Although further work is needed, our results suggest thatM. arioncan maintain fully functional metapopulations when they consist of optimal habitat patches that are no further apart than ∼10 km.
Genotypic variation in yellow autumn leaf colours explains aphid load in silver birch
Authors: Sinkkonen Aki , Somerkoski Eeva , Paaso Ulla , Holopainen Jarmo K. , Rousi Matti , Mikola Juha
Published: May 2012

See also the Commentary by Lev‐Yadun and Keasar
Establishment of Fabaceae Tree Species in a Tropical Pasture: Influence of Seed Size and Weeding Methods
Authors: Pereira Silvia R. , Laura Valdemir A. , Souza Andréa L. T.
Published: May 2012

The successful establishment of trees in pastures may be related to species, seed size, and weed control treatments. This study experimentally evaluated the emergence, establishment after 2 years, and growth of individuals of 7 tree species with different seed sizes sowed under three weeding methods (no weeding, grasses clipped, and grasses removed). The experiment was carried out in a tropical abandoned pasture in Midwestern Brazil, dominated by the exotic invasive grass Urochloa brizantha. The effect of seed size on seedling emergence was significant and was more intense in the no weeding and weeding treatment plots than in grasses clipped. Furthermore, an increase in seed size resulted in an increase in the probability of establishment of tree species, although this pattern also differed among weeding treatments. The increase in seed size reflected negatively on tree growth in the absence of grasses, whereas in the presence of grasses there was an inverse relationship. The experimental results suggested that the use of seeds of different sizes for direct seeding in pastures is a possible strategy of Fabaceae tree species reintroduction in pastures within the Cerrado. Fabaceae species with seeds larger than 100 mg can establish in areas with no weeding, whereas species with seeds smaller than 50 mg can establish preferentially in areas with weeding, growing faster than larger ones. Thus, weeding strategies can determine the success of direct seeding of different species in restoration projects of tropical pastures.