bluuebunny/crossref_metadata_2025_split huggingface dataset:
Educational Inequality by Race in Brazil, 1982–2007: Structural Changes and Shifts in Racial Classification
Authors: Marteleto Leticia J. 
Published: January 2012

AbstractDespite overwhelming improvements in educational levels and opportunity during the past three decades, educational disadvantages associated with race still persist in Brazil. Using the nationally representative Pesquisa Nacional de Amostra por Domicílio (PNAD) data from 1982 and 1987 to 2007, this study investigates educational inequalities between white, pardo (mixed-race), and black Brazilians over the 25-year period. Although the educational advantage of whites persisted during this period, I find that the significance of race as it relates to education changed. By 2007, those identified as blacks and pardos became more similar in their schooling levels, whereas in the past, blacks had greater disadvantages. I test two possible explanations for this shift: structural changes and shifts in racial classification. I find evidence for both. I discuss the findings in light of the recent race-based affirmative action policies being implemented in Brazilian universities.
Union Instability as an Engine of Fertility? A Microsimulation Model for France
Authors: Thomson Elizabeth , Winkler-Dworak Maria , Spielauer Martin , Prskawetz Alexia 
Published: January 2012

Abstract
Opportunities for conceiving and bearing children are fewer when unions are not formed or are dissolved during the childbearing years. At the same time, union instability produces a pool of persons who may enter new partnerships and have additional children in stepfamilies. The balance between these two opposing forces and their implications for fertility may depend on the timing of union formation and parenthood. In this article, we estimate models of childbearing, union formation, and union dissolution for female respondents to the 1999 French Etude de l’Histoire Familiale. Model parameters are applied in microsimulations of completed family size. We find that a population of women whose first unions dissolve during the childbearing years will end up with smaller families, on average, than a population in which all unions remain intact. Because new partnerships encourage higher parity progressions, repartnering minimizes the fertility gap between populations with and those without union dissolution. Differences between the two populations are much smaller when family formation is postponed—that is, when union formation and dissolution or first birth occurs after age 30, or when couples delay childbearing after union formation.
A shortened postpartum magnesium sulfate prophylaxis regime in pre‐eclamptic women at low risk of eclampsia
Authors: Darngawn Lalthakimi , Jose Rubi , Regi Anni , Bansal Ramandeep , Jeyaseelan Laxmanan 
Published: January 2012

AbstractObjectiveTo determine whether magnesium sulfate (MgSO4) prophylaxis is needed for up to 24 hours postpartum in all patients with pre‐eclampsia.MethodsIn a randomized open clinical trial conducted in a tertiary health center in India between September 2008 and April 2010, 150 women with severe pre‐eclampsia who received intrapartum MgSO4 and delivered at more than 20 weeks gestation were enrolled. After 6 hours postpartum, the participants were randomized to continue receiving (control group) or to discontinue (intervention group) MgSO4, and outcomes were compared.ResultsAdministration of MgSO4 had to be reinstituted for 1 woman in the intervention group. Under the current protocol in the institution, all 75 women in the intervention group would have received MgSO4 for 24 hours postpartum. A significant reduction in time spent by the doctors (P < 0.001) and nurses (P < 0.001) was seen in the intervention group. The pain score in the intervention group was significantly less (P < 0.001), and women in the intervention group were able to look after themselves better (P < 0.001).ConclusionFor women at low risk for postpartum eclampsia, a shortened (6‐hour) MgSO4 regime was as effective for seizure prophylaxis as the conventional 24‐hour regime, with significant benefits in terms of cost and morbidity.
Critical care providers’ opinion on unsafe abortion in Argentina
Authors: Vasquez Daniela N. , Das Neves Andrea V. , Golubicki José L. , Di Marco Ingrid , Loudet Cecilia I. , Roberti Javier E. , Palacios‐Jaraquemada Jose , Basualdo Natalia , Varaglia Ruben , Vidal Laura ,   ; for the Critically Ill Obstetric Patients Committee of the Argentine Society of Critical Care
Published: January 2012

AbstractObjectiveTo survey the opinion of critical care providers in Argentina about abortion.MethodsAn anonymous questionnaire was distributed to critical care providers attending the 20th National Critical Care Conference in Argentina.Results149 of 1800 attendees completed the questionnaire, 69 (46.3%) of whom were members of the Argentine Society of Critical Care (ASCC). 122 (81.9%) supported abortion decriminalization in situations excluded from the current law; 142 (95.3%) in cases of congenital defects; 133 (89.3%) in cases of rape; 115 (77.2%) when women's mental health is at risk; 71 (47.7%) when pregnancy is unintended; and 61 (40.9%) for economic reasons. 126 (84.6%) supported abortion in public and private institutions, and 121 (81.2%) before 12 weeks of pregnancy. Variables independently associated with abortion support among female versus male attendees were abortion to preserve women's mental health (OR 4.47; 95% CI, 1.61–12.42; P = 0.004) and abortion before 12 weeks of pregnancy (OR 3.93; 95% CI, 1.29–11.94; P = 0.015). Abortion at request was independently associated with ASCC membership (OR 2.63; 95% CI, 1.07–6.45; P = 0.034).ConclusionCritical care providers would support abortion in situations excluded from the current abortion law and before 12 weeks of pregnancy, in both public and private hospitals.
Overexpression of annexin 1 in the development and differentiation of urothelial carcinoma
Authors: Kang Wan‐Yi , Chen Wan‐Tzu , Huang Ya‐Chun , Su Yue‐Chiu , Chai Chee‐Yin 
Published: January 2012

AbstractThis study investigates the expression of annexin 1 in urothelial carcinoma (UC) and its relation with clinicopathologic factors, and evaluates its potential clinical significance. Annexin 1 expression was analyzed by immunohistochemical staining with manual tissue microarrays and Western blot in UC. Immunohistochemical analysis of UC in tissue microarrays showed that annexin 1 protein was 76.5% (150/196) positive, which was markedly increased compared with that in the normal urothelium 20.8% (5/24) (p < 0.01). In addition, the positive expression rate of annexin 1 was higher in the high‐grade UC (81.7%; 143/175) than in the low‐grade UC (33.3%; 7/21). Western blot revealed that the expression of annexin 1 was low in low‐grade UC, and markedly increased in high‐grade UC. In conclusion, annexin 1 overexpression is observed in UC, which suggests it may be associated with tumorigenesis and its expression correlates with the differentiation of UC.
Numerical investigation and modelling of acoustically excited flow through a circular orifice backed by a hexagonal cavity
Authors: Zhang Qi , Bodony Daniel J. 
Published: January 2012

AbstractResolved simulations of the sound-induced flow through a circular orifice with a 0.99 mm diameter are examined. The orifice is backed by a hexagonal cavity and is a local model for acoustic liners commonly used for aeroengine noise reduction. The simulation data identify the role the orifice wall boundary layers play in determining the orifice discharge coefficient which, in time-domain models, is an important indicator of nonlinearity. It is observed that when the liner behaviour is not well described by linear models, the orifice boundary layers contain secondary vorticity generated from its separation from the corner on the high-pressure side of the orifice. Quantitative comparisons of the simulation-predicted impedance match available data for incident sound of 130 dB amplitude at frequencies from 1.5 to 3.0 kHz. At amplitudes of 140–160 dB, the simulation impedance is in agreement with analytical predictions when using simulation-measured quantities, including the discharge coefficient and root-mean-square velocity through the orifice, although no experimental data for this liner exist at these conditions. The simulation data are used to develop two time-domain models for the acoustic impedance wherein the velocity profile through the orifice is modelled as the product of the fluid velocity and a presumed radial shape,$\dot {\xi } V(r)$. The models perform well, predicting the in-orifice velocity and pressure, and the impedance, except for the most nonlinear cases where it is seen that the assumed shape$V(r)$can affect the backplate pressure predictions. These results suggest that future time-domain models that take the velocity profile into account, by modelling the boundary layer thickness and assuming a velocity profile shape, may be successful in predicting the nonlinear response of the liner.
Predictive value of positron emission tomography – computed tomography image fusion in the diagnosis of head and neck cancer: does it really improve staging and management?
Authors: de Casso C , Visvanathan V , Soni-Jaiswall A , Kane T , Nigam A 
Published: January 2012

AbstractAims:To determine (1) the accuracy of positron emission tomography – computed tomography in the diagnosis of head and neck cancer, (2) the learning curve involved, and (3) whether its use alters patient management.Materials and methods:A retrospective study including 80 patients with head and neck cancer who underwent positron emission tomography – computed tomography image fusion at Blackpool Victoria Hospital.Results:Fifty-three patients underwent positron emission tomography – computed tomography for staging (32 for detection of a primary tumour and 21 for detection of distant metastasis) and 27 for detection of loco-regional recurrence. Ten primary tumours and 20 recurrences were accurately diagnosed by this method. Eighteen patients had their tumour stage and management modified as a result of this method of imaging. The effect of the learning curve resulted in better true positive detection rates, one year after introduction (81 versus 61 per cent). The sensitivity and specificity of this method in detecting head and neck cancer were 70 and 42 per cent, respectively, whereas those of conventional imaging were 73 and 51 per cent, respectively.Conclusion:Compared with magnetic resonance imaging, the benefits of positron emission tomography – computed tomography may be limited to diagnosis of recurrence, as it is less hindered by tissue fibrosis, radiotherapy-related oedema, scarring and inflammation.
Morphometric characterization of the first blastomeres of rainbow trout (Oncorhynchus mykiss)
Authors: Valdebenito Iván I. , Sánchez Rubén R. , Effer Brian R. , Ubilla Andrea M. 
Published: January 2012

SummaryIn the following investigation the morphometric characteristics of the first two blastomeres of rainbow trout (Oncorhynchus mykiss) were determined. Embryos were incubated at 9°C and then fixed in a Stockard solution every 30 min starting from 8.5 to 12.5 h of incubation post fertilization. Embryonic discs were extracted and microphotographs were taken with Q Capture Pro 5.0 software using a stereomicroscope Olympus SZX7. The average size of the blastodiscs was 941.22 ± 160.42 μm. The first cleavage finished after approximately 12 h of incubation. The first two blastomeres were regularly symmetrical in their morphology. Blastomere 1 had an average length (L) of 942.68 ± 105.56 μm and width (W) of 467.34 ± 64.33 μm. Blastomere 2 had an average length of 887.60 ± 101.65 and width of 454.49 ± 47.25 μm (n = 91). Significant differences were found between the length and width of blastomeres 1 and 2. The proportion between the length of blastomeres 1 and 2 was 0.94 ± 0.07 (n = 91); between the width of blastomeres 1 and 2 it was 0.88 ± 0.11 (n = 91); and the width/length ratio was 0.51 ± 0.09 (n = 182). It was concluded that rainbow trout blastomeres tend to be asymmetrical in length with a higher dispersion of widths.
Sea ice salinity and structure: A winter time series of salinity and its distribution
Authors: Gough A. J. , Mahoney A. R. , Langhorne P. J. , Williams M. J. M. , Haskell T. G. 
Published: January 2012

We present a winter time series of Antarctic sea ice salinity from eastern McMurdo Sound, an area close to an ice shelf where a subice platelet layer forms below the sea ice late in winter. This dramatically changes the sea ice structure as the sea ice grows into the subice platelet layer. Every 2 weeks during the 5 months of sea ice formation, salinity profiles were measured, along with detailed measurements of ice structure and growth rates. Once the influence of growth rate on sea ice bulk salinity is removed, the data from 69 cores and the results of a basic parameterization demonstrate that bulk salinity for platelet ice is higher than that for columnar sea ice. We also present measurements of the salinity profile close to the ice‐water interface and use these to investigate the expected regime of fluid flow within the permeable portions of the sea ice, with particular reference to mushy layer and percolation theory. Finally, we provide a new distribution of sea ice salinity from 740 measurements, which can be interpreted as the sum of two spatial fields that we attribute to sea ice samples with and without brine channels and which should be reproduced by any realistic sea ice models. This distribution suggests that two measurements of quantities linearly linked to sea ice salinity must differ by 29% if they are to be considered different with 90% confidence.
CNGA3 is expressed in inner ear hair cells and binds to an intracellular C-terminus domain of EMILIN1
Authors: Selvakumar Dakshnamurthy , Drescher Marian J. , Dowdall Jayme R. , Khan Khalid M. , Hatfield James S. , Ramakrishnan Neeliyath A. , Drescher Dennis G. 
Published: January 2012

The molecular characteristics of CNG (cyclic nucleotide-gated) channels in auditory/vestibular hair cells are largely unknown, unlike those of CNG mediating sensory transduction in vision and olfaction. In the present study we report the full-length sequence for three CNGA3 variants in a hair cell preparation from the trout saccule with high identity to CNGA3 in olfactory receptor neurons/cone photoreceptors. A custom antibody targeting the N-terminal sequence immunolocalized CNGA3 to the stereocilia and subcuticular plate region of saccular hair cells. The cytoplasmic C-terminus of CNGA3 was found by yeast two-hybrid analysis to bind the C-terminus of EMILIN1 (elastin microfibril interface-located protein 1) in both the vestibular hair cell model and rat organ of Corti. Specific binding between CNGA3 and EMILIN1 was confirmed with surface plasmon resonance analysis, predicting dependence on Ca2+ with Kd=1.6×10−6 M for trout hair cell proteins and Kd=2.7×10−7 M for organ of Corti proteins at 68 μM Ca2+. Pull-down assays indicated that the binding to organ of Corti CNGA3 was attributable to the EMILIN1 intracellular sequence that follows a predicted transmembrane domain in the C-terminus. Saccular hair cells also express the transcript for PDE6C (phosphodiesterase 6C), which in cone photoreceptors regulates the degradation of cGMP used to gate CNGA3 in phototransduction. Taken together, the evidence supports the existence in saccular hair cells of a molecular pathway linking CNGA3, its binding partner EMILIN1 (and β1 integrin) and cGMP-specific PDE6C, which is potentially replicated in cochlear outer hair cells, given stereociliary immunolocalizations of CNGA3, EMILIN1 and PDE6C.
Effect of all‐trans‐retinoic acid on the expression of primordial germ cell differentiation‐associated genes in mESC‐derived EBs
Authors: Guo Xin , Qi Zheng‐Yu , Zhang Yan‐Min , Qin Jie , Cui Guang‐Hui , Gui Yao‐Ting , Cai Zhi‐Ming 
Published: January 2012

AbstractatRA (all‐trans‐retinoic acid) is known to induce the differentiation of mESCs (mouse embryonic stem cells) into PGCs (primordial germ cells) in vitro. However, it is not clear as to what changes occur in PGC differentiation‐associated genes or what mechanisms are involved when EBs (embryoid bodies) derived from mESCs are induced by atRA. EBs derived from mESCs were treated with 1, 2 or 5 μM atRA for 16 h, 2 days or 5 days. Real‐time PCR and Western blot analysis were performed to detect the relative levels of PGC differentiation‐associated genes (Lin28, Blimp1, Stra8 and Mvh) and the corresponding proteins respectively. Immunofluorescence was used to detect the protein location and distribution in EBs. The expression characteristics of genes could be divided into three categories: rapidly reached the peak value in 16 h and then decreased (Stra8, Lin28), initially low and then increased to reach the peak value in 5 days (Mvh) and relatively unchanged (Blimp1). A low level of Lin28 was expressed in EBs treated with atRA for 2 days or 5 days. The variation in the level of Lin28 mRNA did not influence the change in the level of Blimp1 mRNA. The changes in Stra8/Lin28 were consistent with the corresponding changes in the levels of their respective mRNAs, but the changes for Mvh/Blimp1 were not consistent with the corresponding changes in the levels of their respective mRNAs. Blimp1 expression may be independent of the effect of atRA on PGC differentiation. atRA may promote the start of a period in which there is a low level of Lin28 expression during PGC differentiation.
Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase
Authors: Fafarman Aaron T. , Sigala Paul A. , Schwans Jason P. , Fenn Timothy D. , Herschlag Daniel , Boxer Steven G. 
Published: January 2012

Understanding the electrostatic forces and features within highly heterogeneous, anisotropic, and chemically complex enzyme active sites and their connection to biological catalysis remains a longstanding challenge, in part due to the paucity of incisive experimental probes of electrostatic properties within proteins. To quantitatively assess the landscape of electrostatic fields at discrete locations and orientations within an enzyme active site, we have incorporated site-specific thiocyanate vibrational probes into multiple positions within bacterial ketosteroid isomerase. A battery of X-ray crystallographic, vibrational Stark spectroscopy, and NMR studies revealed electrostatic field heterogeneity of 8 MV/cm between active site probe locations and widely differing sensitivities of discrete probes to common electrostatic perturbations from mutation, ligand binding, and pH changes. Electrostatic calculations based on active site ionization states assigned by literature precedent and computational pK
a
prediction were unable to quantitatively account for the observed vibrational band shifts. However, electrostatic models of the D40N mutant gave qualitative agreement with the observed vibrational effects when an unusual ionization of an active site tyrosine with a pK
a
near 7 was included. UV-absorbance and
13
C NMR experiments confirmed the presence of a tyrosinate in the active site, in agreement with electrostatic models. This work provides the most direct measure of the heterogeneous and anisotropic nature of the electrostatic environment within an enzyme active site, and these measurements provide incisive benchmarks for further developing accurate computational models and a foundation for future tests of electrostatics in enzymatic catalysis.
SNP calling using genotype model selection on high-throughput sequencing data
Authors: You Na , Murillo Gabriel , Su Xiaoquan , Zeng Xiaowei , Xu Jian , Ning Kang , Zhang Shoudong , Zhu Jiankang , Cui Xinping 
Published: January 2012

Abstract
Motivation: A review of the available single nucleotide polymorphism (SNP) calling procedures for Illumina high-throughput sequencing (HTS) platform data reveals that most rely mainly on base-calling and mapping qualities as sources of error when calling SNPs. Thus, errors not involved in base-calling or alignment, such as those in genomic sample preparation, are not accounted for.
Results: A novel method of consensus and SNP calling, Genotype Model Selection (GeMS), is given which accounts for the errors that occur during the preparation of the genomic sample. Simulations and real data analyses indicate that GeMS has the best performance balance of sensitivity and positive predictive value among the tested SNP callers.
Availability: The GeMS package can be downloaded from https://sites.google.com/a/bioinformatics.ucr.edu/xinping-cui/home/software or http://computationalbioenergy.org/software.html
Contact: xinping.cui@ucr.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites
Authors: González Santi , Montserrat-Sentís Bàrbara , Sánchez Friman , Puiggròs Montserrat , Blanco Enrique , Ramirez Alex , Torrents David 
Published: January 2012

Abstract
Motivation: The prediction and annotation of the genomic regions involved in gene expression has been largely explored. Most of the energy has been devoted to the development of approaches that detect transcription start sites, leaving the identification of regulatory regions and their functional transcription factor binding sites (TFBSs) largely unexplored and with important quantitative and qualitative methodological gaps.
Results: We have developed ReLA (for REgulatory region Local Alignment tool), a unique tool optimized with the Smith–Waterman algorithm that allows local searches of conserved TFBS clusters and the detection of regulatory regions proximal to genes and enhancer regions. ReLA's performance shows specificities of 81 and 50% when tested on experimentally validated proximal regulatory regions and enhancers, respectively.
Availability: The source code of ReLA's is freely available and can be remotely used through our web server under http://www.bsc.es/cg/rela.
Contact: david.torrents@bsc.es
Supplementary information: Supplementary data are available at Bioinformatics online.
CODEX: exploration of semantic changes between ontology versions
Authors: Hartung Michael , Gross Anika , Rahm Erhard 
Published: January 2012

Abstract
Summary: Life science ontologies substantially change over time to meet the requirements of their users and to include the newest domain knowledge. Thus, an important task is to know what has been modified between two versions of an ontology (diff). This diff should contain all performed changes as compact and understandable as possible. We present CODEX (Complex Ontology Diff Explorer), a tool that allows determining semantic changes between two versions of an ontology, which users can interactively analyze in multiple ways.
Availability and implementation: CODEX is available under http://www.izbi.de/codex and is supported by all major browsers. It is implemented in Java based on Google Web Toolkit technology. Additionally, users can access a web service interface to use the diff functionality in their applications and analyses.
Contact: hartung@izbi.uni-leipzig.de