bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatically identifying and annotating mouse embryo gene expression patterns
Authors: Han Liangxiu , van Hemert Jano I. , Baldock Richard A. 
Published: February 2011

Abstract
Motivation: Deciphering the regulatory and developmental mechanisms for multicellular organisms requires detailed knowledge of gene interactions and gene expressions. The availability of large datasets with both spatial and ontological annotation of the spatio-temporal patterns of gene expression in mouse embryo provides a powerful resource to discover the biological function of embryo organization. Ontological annotation of gene expressions consists of labelling images with terms from the anatomy ontology for mouse development. If the spatial genes of an anatomical component are expressed in an image, the image is then tagged with a term of that anatomical component. The current annotation is done manually by domain experts, which is both time consuming and costly. In addition, the level of detail is variable, and inevitably errors arise from the tedious nature of the task. In this article, we present a new method to automatically identify and annotate gene expression patterns in the mouse embryo with anatomical terms.
Results: The method takes images from in situ hybridization studies and the ontology for the developing mouse embryo, it then combines machine learning and image processing techniques to produce classifiers that automatically identify and annotate gene expression patterns in these images. We evaluate our method on image data from the EURExpress study, where we use it to automatically classify nine anatomical terms: humerus, handplate, fibula, tibia, femur, ribs, petrous part, scapula and head mesenchyme. The accuracy of our method lies between 70% and 80% with few exceptions. We show that other known methods have lower classification performance than ours. We have investigated the images misclassified by our method and found several cases where the original annotation was not correct. This shows our method is robust against this kind of noise.
Availability: The annotation result and the experimental dataset in the article can be freely accessed at http://www2.docm.mmu.ac.uk/STAFF/L.Han/geneannotation/.
Contact: l.han@mmu.ac.uk
Supplementary Information: Supplementary data are available at Bioinformatics online.
aCGH.Spline—an R package for aCGH dye bias normalization
Authors: Fitzgerald Tomas W. , Larcombe Lee D. , Le Scouarnec Solena , Clayton Stephen , Rajan Diana , Carter Nigel P. , Redon Richard 
Published: February 2011

Abstract
Motivation: The careful normalization of array-based comparative genomic hybridization (aCGH) data is of critical importance for the accurate detection of copy number changes. The difference in labelling affinity between the two fluorophores used in aCGH—usually Cy5 and Cy3—can be observed as a bias within the intensity distributions. If left unchecked, this bias is likely to skew data interpretation during downstream analysis and lead to an increased number of false discoveries.
Results: In this study, we have developed aCGH.Spline, a natural cubic spline interpolation method followed by linear interpolation of outlier values, which is able to remove a large portion of the dye bias from large aCGH datasets in a quick and efficient manner.
Conclusions: We have shown that removing this bias and reducing the experimental noise has a strong positive impact on the ability to detect accurately both copy number variation (CNV) and copy number alterations (CNA).
Contact: l.larcombe@cranfield.ac.uk; tf2@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Composition and Sensory Evaluation of Popcorn Flake Polymorphisms for a Select Butterfly‐Type Hybrid
Authors: Sweley Jess C. , Rose Devin J. , Jackson David S. 
Published: March 2011

ABSTRACTThe objective of this study was to identify and characterize different popped popcorn flake shapes, or polymorphisms, arising from a yellow butterfly popcorn hybrid (YP‐213), and then to determine the impact of popcorn flake shape on composition and sensory characteristics. Kernels were popped using a microwave oven and visually sorted into three different polymorphisms depending on whether the appendages were expanded unilaterally, bilaterally, or multilaterally. When popped, 9.0 ± 3.1%, 71.2 ± 5.9%, and 12.3 ± 3.8% of kernels were expanded unilaterally, bilaterally, and multilaterally, respectively, while 7.6 ± 1.4% of kernels remained unpopped. Expansion volumes for unilaterally, bilaterally, and multilaterally expanded polymorphisms were 28.6 ± 3.84, 43.0 ± 0.84, and 53.5 ± 2.5 cm3/g, respectively. Unilateral popcorn flakes retained the most fat, saturated fat, and sodium, while multilaterally expanded flakes had the highest levels of protein, total carbohydrate, and popcorn‐like aromatic pyrazines. Sensory evaluation revealed significant differences among polymorphisms for flavor and texture attributes, with the unilaterally expanded polymorphism receiving the highest overall product liking. These data show that different popcorn flake polymorphisms produced from a single hybrid of popcorn affect sensory and compositional profiles. More research is necessary to elucidate the factors that affect popcorn flake polymorphisms and support development of new varieties or techniques to produce the most desirable microwave popcorn.
Healthcare experiences of women who have been diagnosed with a sexually transmitted infection
Authors: East Leah , Jackson Debra , O’Brien Louise , Peters Kathleen 
Published: March 2011

Aim.  This paper reports the healthcare experiences of women who have been diagnosed with a sexually transmitted infection.Background.  The incidence of sexually transmitted infections is increasing throughout the globe on an annual basis. To effectively curb this trend and reduce the spread of these infections, effective education and treatment is essential.Design.  This study used a feminist approach.Methods.  Ten women participated in this study. Interviews were conducted online and transcripts were thematically analysed.Results.  Findings from this study revealed that the women generally characterised their healthcare experiences as negative. Some women perceived being negatively judged by healthcare professionals and felt they were not provided with sufficient information or support when diagnosed with a sexually transmitted infection.Conclusion.  This paper reveals how healthcare professionals have the ability to exacerbate the adversity felt by women diagnosed with a sexually transmitted infection and how providing appropriate therapeutic care can assist young women who have been diagnosed with these types of infections.Relevance to clinical practice.  Nurses and other healthcare professionals can better serve patients by providing emotional and therapeutic support and information about the possible effects and long‐term sequelae of sexually transmitted infections. Further, by providing sufficient information and support, the negative effects of having a sexually transmitted infection can be reduced and women’s ability to cope with a sexually transmitted infection can be enhanced.
Activation of cerebral peroxisome proliferator‐activated receptors γ (PPARγ) reduces neuronal damage in the substantia nigra after transient focal cerebral ischaemia in the rat
Authors: Zuhayra M. , Zhao Y. , von Forstner C. , Henze E. , Gohlke P. , Culman J. , Lützen U. 
Published: March 2011

M. Zuhayra, Y. Zhao, C. von Forstner, E. Henze, P. Gohlke, J. Culman and U. Lützen (2011) Neuropathology and Applied Neurobiology37, 738–752Activation of cerebral peroxisome proliferator‐activated receptors γ (PPARγ) reduces neuronal damage in the substantia nigra after transient focal cerebral ischaemia in the ratAim: The function of brain (neuronal) peroxisome proliferator‐activated receptor(s) γ (PPARγ) in the delayed degeneration and loss of neurones in the substantia nigra (SN) was studied in rats after transient occlusion of the middle cerebral artery (MCAO). Methods: The PPARγ agonist, pioglitazone, or vehicle was infused intracerebroventricularly over a 5‐day period before, during and 5 days after MCAO (90 min). The neuronal degeneration in the SN pars reticularis (SNr) and pars compacta (SNc), the analysis of the number of tyrosine hydroxylase‐immunoreactive (TH‐IR) neurones and the expression of the PPARγ in these neurones were studied by immunohistochemistry and immunofluorescence staining. The effects of PPARγ activation on excitotoxic and oxidative neuronal damage induced by glutamate and 6‐hydroxydopamine were investigated in primary cortical neurones expressing PPARγ. Results: Pioglitazone reduced the total and striatal infarct size, neuronal degeneration in both parts of the ipsilateral SN, the loss of TH‐IR neurones in the SNc and increased the number of PPARγ‐positive TH‐IR neurones. Pioglitazone protected primary cortical neurones against oxidative and excitotoxic damage, prevented the loss of neurites and supported the formation of synaptic networks in neurones exposed to glutamate or 6‐hydroxydopamine by a PPARγ‐dependent mechanism. Conclusions: Activation of cerebral PPARγ confers neuroprotection after ischaemic stroke by preventing both, neuronal damage within the peri‐infarct zone and delayed degeneration of neurones and neuronal death in areas remote from the site of ischaemic injury. Pioglitazone and other PPARγ agonists may be useful therapeutic agents to prevent progression of brain damage after cerebral ischaemia.
Use of specific airway resistance to assess bronchodilator response in children
Authors: MAHUT BRUNO , PEIFFER CLAUDINE , BOKOV PLAMEN , DELCLAUX CHRISTOPHE , BEYDON NICOLE 
Published: March 2011

ABSTRACTBackground and objective:  Changes in specific airway resistance (ΔsRaw) after bronchodilation, as measured by plethysmography and FEV1, are frequently considered to be interchangeable indices of airway obstruction. However, the baseline relationship between these two indices is weak, and the value of ΔsRaw that best predicts FEV1 reversibility in children has yet to be determined. The aim of this study was (i) to establish the sRaw cut‐off value that best distinguishes between positive and negative bronchodilator responses, as measured by FEV1 reversibility; (ii) to determine whether the discrepancy between ΔsRaw and ΔFEV1 might be explained by independent correlations between ΔFEV1 and both ΔsRaw (mainly airway obstruction) and ΔFVC (airway closure); and (iii) to assess the effect of height and age on the relationship between ΔsRaw and ΔFEV1.Methods:  A retrospective study was performed in 481 children (median age 10.5 years, range 6.1–17.6) with actual or suspected asthma, for whom sRaw and spirometry data were obtained at baseline and after administration of a bronchodilator.Results:  The sRaw cut‐off value that best predicted FEV1 reversibility was a 42% decrease from baseline (P = 0.0001, area under the curve 0.70, sensitivity 55%, specificity 77%) and was independent of height and age. Changes in FEV1 were significantly but independently related to ΔsRaw and ΔFVC (index of air trapping) (r = 0.40, P < 0.0001 and r = 0.39, P < 0.0001, respectively).Conclusions:  A 42% decrease in sRaw predicted FEV1 reversibility reasonably well, whereas a smaller decrease in sRaw failed to detect approximately one out of two positive responses detected by FEV1, with no influence of height or age.
Nocturia as a manifestation of systemic disease
Authors: Gulur Dev Mohan , Mevcha Amit M. , Drake Marcus J. 
Published: March 2011

What’s known on the subject? and What does the study add? Waking at night to pass urine, nocturia, is widely regarded as urological, but many medical conditions can be responsible. Overproduction of urine overnight on the frequency volume chart, “nocturnal polyuria”, is a key feature signifying possible contribution of systemic disease; renal, endocrine, neurological, or cardiovascular malfunction may be responsible.Failure to evaluate the potential medical basis risks poor treatment outcomes for a bothersome symptom. Inappropriately instigating surgical treatment, such as TURP, can lead to harm in a patient whose nocturia is caused by nocturnal polyuria. Global and nocturnal polyuria should be fully investigated, in case a potentially serious illness is responsible.Nocturia is commonly referred to urologists, but the mechanisms underlying the problem, together with the appropriate clinical assessment and management, may lie outside the ordinary scope of the specialty. Some serious conditions may manifest nocturia as an early feature, often as a consequence of nocturnal polyuria (NP). Voiding frequency is influenced by rate of urine output, reservoir capacity of the bladder, lower urinary tract (LUT) sensation and psychological response. Polyuria can result from polydipsia or endocrine dysfunction. NP can result from endogenous fluid and solute shifts, cardiovascular and autonomic disease, obstructive sleep apnoea, and chronic kidney disease. Nocturia without polyuria occurs in the presence of LUT pathology, pelvic masses and sleep disturbance. Drug intake can contribute to, or counteract, each of these problems. In assessing nocturia, clinicians need to consider an undiagnosed serious condition that may manifest nocturia as an early feature, or suboptimal management of a known condition. The frequency‐volume chart is a key tool in categorizing the basis of nocturia, identifying those patients with global polyuria or NP, for whom involvement of other specialties is often necessary for assessment and management. Treatment should be directed at the cause of the problem, with a view to improving long‐term health and health‐related quality of life. Simple steps should be undertaken by all patients, including improvement of the sleep environment and behaviour modification. Evaluation of treatment response requires objective data to corroborate subjective impressions. Some mechanisms of nocturia do not reliably improve with treatment, leading to refractory symptoms.
Therapeutic hypothermia during neonatal transport
Authors: O’Reilly Kathleen M , Tooley James , Winterbottom Sharon 
Published: March 2011

AbstractAim:  To compare the effectiveness of different cooling methods used during neonatal transport in maintaining target temperature.Methods:  Retrospective review of transport data for all infants centralized for therapeutic hypothermia between April 2008 and October 2009.Results:  A total of 46 infants were retrieved for therapeutic hypothermia during the study period. During transport, 10 infants were passively cooled, 17 infants were actively cooled with adjuncts and 19 infants were actively cooled with a purpose‐built cooling machine. On arrival at the tertiary unit, 84% of infants who were actively cooled with a purpose‐built cooling machine had temperatures within the therapeutic range compared with 47% of infants who were actively cooled with adjuncts and 20% of infants who were passively cooled.Conclusion:  Passive cooling and cooling with adjuncts often fail to achieve temperatures within the desired therapeutic range. Therapeutic hypothermia during transport can be reliably achieved using a purpose‐built cooling machine. We recommend that cooling during transport should only be undertaken using a purpose‐built cooling machine.
Relational regulation in the Brazilian Ministério Publico: The organizational basis of regulatory responsiveness
Authors: Coslovsky Salo V. 
Published: March 2011

AbstractRecent research on regulatory enforcement has been showing that the best way to enforce protective regulations is to thoroughly adapt the remedy to the problem at hand. Unfortunately, this is far from easy, as organizations and work environments all too often encourage street‐level bureaucrats to standardize and simplify their practices. In an attempt to bridge this gap, many scholars equate responsiveness to preprogrammed escalation. This article analyzes how the Brazilian Ministério Público (MP) promotes a more ambitious form of responsiveness, here called relational regulation. While most of the formal features of the MP encourage routinization, groups of reformist prosecutors identify important cases, recruit external allies, and jointly devise innovative and context‐specific solutions to problems of non‐compliance. Crucially, this mode of action is not an anomaly, the result of individual proclivities or specific and formal job assignments. Rather, it is systematically produced by a mostly parallel and covert organization that operates within and expands beyond the MP itself. These two logics – routinized and custom‐made responses – compete, cooperate, interpenetrate, and find common ground within the same organizational umbrella, and through their interaction they create an enforcement agency that is more robust, reliable, and responsive than allowed by current theory.
Population growth and colonization of Steller sea lions in the Glacier Bay region of southeastern Alaska: 1970s–2009
Authors: Mathews Elizabeth A. , Womble Jamie N. , Pendleton Grey W. , Jemison Lauri A. , Maniscalco John M. , Streveler Greg 
Published: March 2011

AbstractWe estimated trends in numbers of Steller sea lions in the Glacier Bay region of the eastern population from the 1970s to 2009. We documented the colonization of several new haul‐outs and the transition of one haul‐out (Graves Rocks) to a rookery, assessed seasonal patterns in distribution, and compared counts from different observation platforms. Sea lions increased in the region by 8.2%/yr (95%CI = 6.4%–10.0%), with the most growth at South Marble Island in Glacier Bay (16.6%/yr, 1991–2009) and rapid growth in Cross Sound. Seasonal patterns in the distribution of sea lions were likely influenced by new breeding opportunities and the seasonal availability of prey. Factors that likely contributed to the exceptional growth include availability of new habitat following deglaciation, immigration, redistribution, decreases in mortality, and ecosystem‐level changes. The rapid increase in sea lion numbers in this region is of particular interest in light of dramatic declines in the western population and evidence that Steller sea lions from both the eastern and western populations colonized the Graves Rocks rookery. The colonization and rookery development in this dynamic area may signal the reversal of the reproductive isolation of the two populations.
Group‐Based Shame and Guilt: Emerging Directions in Research
Authors: Lickel Brian , Steele Rachel R. , Schmader Toni 
Published: March 2011

AbstractResearch on the role of emotion in social identity, group processes, and intergroup conflict is burgeoning. This paper examines recent research on group‐based shame and guilt and describes important themes in this research. Guilt and shame are distinguished by different appraisals and motivations in intergroup contexts. Group‐based shame is associated with threats to group‐image and motivations to protect and repair that image. In contrast, group‐based guilt is associated with efforts to repair and apologize for ingroup wrongdoing. Current research is expanding in several important directions. First, the scope of emotions is expanding beyond that of shame and guilt to consider the roles of emotions such as ingroup‐directed anger in situations that may also provoke group‐based shame and guilt. Second, people’s motivations to avoid feeling group‐based shame and guilt are becoming better understood, particularly in relation to different aspects of social identification. Finally, we argue that dynamic processes in emotion expression and experience, particularly due to the relation between perpetrator and victim groups, are an important future direction in research on group‐based shame and guilt.
A measure for describing and comparing postreproductive life span as a population trait
Authors: Levitis Daniel A , Lackey Laurie Bingaman 
Published: March 2011

Summary1. While classical life‐history theory does not predict postreproductive life span (PRLS), it has been detected in a great number of taxa, leading to the view that it is a broadly conserved trait and attempts to reconcile theory with these observations. We suggest an alternative: the apparently wide distribution of significant PRLS is an artefact of insufficient methods.2. PRLS is traditionally measured in units of time between each individual’s last parturition and death, after excluding those individuals for whom this interval is short. A mean of this measure is then calculated as a population value. We show this traditional population measure (which we denote PrT) to be inconsistently calculated, inherently biased, strongly correlated with overall longevity, uninformative on the importance of PRLS in a population’s life history, unable to use the most commonly available form of relevant data and without a realistic null hypothesis. Using data altered to ensure that the null hypothesis is true, we find a false‐positive rate of 0·47 for PrT.3. We propose an alternative population measure, using life‐table methods. Postreproductive representation (PrR) is the proportion of adult years lived which are postreproductive. We briefly derive PrR and discuss its properties. We employ a demographic simulation, based on the null hypothesis of simultaneous and proportional decline in survivorship and fecundity, to produce a null distribution for PrR based on the age‐specific rates of a population.4. In an example analysis, using data on 84 populations of human and nonhuman primates, we demonstrate the ability of PrR to represent the effects of artificial protection from mortality and of humanness on PRLS. PrR is found to be higher for all human populations under a wide range of conditions than for any nonhuman primate in our sample. A strong effect of artificial protection is found, but humans under the most adverse conditions still achieve PrR of >0·3.5. PrT should not be used as a population measure and should be used as an individual measure only with great caution. The use of PrR as an intuitive, statistically valid and intercomparable population life‐history measure is encouraged.
Fyn Is Downstream of the HGF/MET Signaling Axis and Affects Cellular Shape and Tropism in PC3 Cells
Authors: Jensen Ana R. , David Saito Y. , Liao Chuanhong , Dai Jinlu , Keller Evan T. , Al-Ahmadie Hikmat , Dakin-Haché Kelly , Usatyuk Peter , Sievert Margarit F. , Paner Gladell P. , Yala Soheil , Cervantes Gustavo M. , Natarajan Viswanathan , Salgia Ravi , Posadas Edwin M. 
Published: March 2011

Abstract
Purpose: Fyn is a member of the Src family of kinases that we have previously shown to be overexpressed in prostate cancer. This study defines the biological impact of Fyn inhibition in cancer using a PC3 prostate cancer model.
Experimental Design: Fyn expression was suppressed in PC3 cells using an shRNA against Fyn (PC3/FYN-). Knockdown cells were characterized using standard growth curves and time-lapse video microscopy of wound assays and Dunn Chamber assays. Tissue microarray analysis was used to verify the physiologic relevance of the HGF/MET axis in human samples. Flank injections of nude mice were performed to assess in vivo growth characteristics.
Results: HGF was found to be sufficient to drive Fyn-mediated events. Compared to control transductants (PC3/Ctrl), PC3/FYN- showed a 21% decrease in growth at 4 days (P = 0.05). PC3/FYN- cells were 34% longer than control cells (P = 0.018) with 50% increase in overall surface area (P &lt; 0.001). Furthermore, when placed in a gradient of HGF, PC3/FYN- cells showed impaired directed chemotaxis down an HGF gradient in comparison to PC3/Ctrl (P = 0.001) despite a 41% increase in cellular movement speed. In vivo studies showed 66% difference of PC3/FYN- cell growth at 8 weeks using bidimensional measurements (P = 0.002).
Conclusions: Fyn plays an important role in prostate cancer biology by facilitating cellular growth and by regulating directed chemotaxis—a key component of metastasis. This finding bears particular translational importance when studying the effect of Fyn inhibition in human subjects. Clin Cancer Res; 17(10); 3112–22. ©2011 AACR.