bluuebunny/crossref_metadata_2025 huggingface dataset:
De novo assembly and Characterisation of the Transcriptome during seed development, and generation of genic-SSR markers in Peanut (Arachis hypogaea L.)
Authors: Zhang Jianan , Liang Shan , Duan Jialei , Wang Jin , Chen Silong , Cheng Zengshu , Zhang Qiang , Liang Xuanqiang , Li Yurong
Published: March 2012

Background

The peanut (Arachis hypogaea L.) is an important oilseed crop in tropical and subtropical regions of the world. However, little about the molecular biology of the peanut is currently known. Recently, next-generation sequencing technology, termed RNA-seq, has provided a powerful approach for analysing the transcriptome, and for shedding light on the molecular biology of peanut.

Results

In this study, we employed RNA-seq to analyse the transcriptomes of the immature seeds of three different peanut varieties with different oil contents. A total of 26.1-27.2 million paired-end reads with lengths of 100 bp were generated from the three varieties and 59,077 unigenes were assembled with N50 of 823 bp. Based on sequence similarity search with known proteins, a total of 40,100 genes were identified. Among these unigenes, only 8,252 unigenes were annotated with 42 gene ontology (GO) functional categories. And 18,028 unigenes mapped to 125 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, 3,919 microsatellite markers were developed in the unigene library, and 160 PCR primers of SSR loci were used for validation of the amplification and the polymorphism.

Conclusion

We completed a successful global analysis of the peanut transcriptome using RNA-seq, a large number of unigenes were assembled, and almost four thousand SSR primers were developed. These data will facilitate gene discovery and functional genomic studies of the peanut plant. In addition, this study provides insight into the complex transcriptome of the peanut and established a biotechnological platform for future research.
Infant mortality in Brazil, 1980-2000: A spatial panel data analysis
Authors: Barufi Ana Maria , Haddad Eduardo , Paez Antonio
Published: March 2012

Background

Infant mortality is an important measure of human development, related to the level of welfare of a society. In order to inform public policy, various studies have tried to identify the factors that influence, at an aggregated level, infant mortality. The objective of this paper is to analyze the regional pattern of infant mortality in Brazil, evaluating the effect of infrastructure, socio-economic, and demographic variables to understand its distribution across the country.

Methods

Regressions including socio-economic and living conditions variables are conducted in a structure of panel data. More specifically, a spatial panel data model with fixed effects and a spatial error autocorrelation structure is used to help to solve spatial dependence problems. The use of a spatial modeling approach takes into account the potential presence of spillovers between neighboring spatial units. The spatial units considered are Minimum Comparable Areas, defined to provide a consistent definition across Census years. Data are drawn from the 1980, 1991 and 2000 Census of Brazil, and from data collected by the Ministry of Health (DATASUS). In order to identify the influence of health care infrastructure, variables related to the number of public and private hospitals are included.

Results

The results indicate that the panel model with spatial effects provides the best fit to the data. The analysis confirms that the provision of health care infrastructure and social policy measures (e.g. improving education attainment) are linked to reduced rates of infant mortality. An original finding concerns the role of spatial effects in the analysis of IMR. Spillover effects associated with health infrastructure and water and sanitation facilities imply that there are regional benefits beyond the unit of analysis.

Conclusions

A spatial modeling approach is important to produce reliable estimates in the analysis of panel IMR data. Substantively, this paper contributes to our understanding of the physical and social factors that influence IMR in the case of a developing country.
Medical advice and diabetes self-management reported by Mexican-American, Black- and White-non-Hispanic adults across the United States
Authors: Vaccaro Joan A , Feaster Daniel J , Lobar Sandra L , Baum Marianna K , Magnus Marcia , Huffman Fatma G
Published: March 2012

Background

Diabetes has reached epidemic proportions in the United States, particularly among minorities, and if improperly managed can lead to medical complications and death. Healthcare providers play vital roles in communicating standards of care, which include guidance on diabetes self-management. The background of the client may play a role in the patient-provider communication process. The aim of this study was to determine the association between medical advice and diabetes self care management behaviors for a nationally representative sample of adults with diabetes. Moreover, we sought to establish whether or not race/ethnicity was a modifier for reported medical advice received and diabetes self-management behaviors.

Methods

We analyzed data from 654 adults aged 21 years and over with diagnosed diabetes [130 Mexican-Americans; 224 Black non-Hispanics; and, 300 White non-Hispanics] and an additional 161 with 'undiagnosed diabetes' [N = 815(171 MA, 281 BNH and 364 WNH)] who participated in the National Health and Nutrition Examination Survey (NHANES) 2007-2008. Logistic regression models were used to evaluate whether medical advice to engage in particular self-management behaviors (reduce fat or calories, increase physical activity or exercise, and control or lose weight) predicted actually engaging in the particular behavior and whether the impact of medical advice on engaging in the behavior differed by race/ethnicity. Additional analyses examined whether these relationships were maintained when other factors potentially related to engaging in diabetes self management such as participants' diabetes education, sociodemographics and physical characteristics were controlled. Sample weights were used to account for the complex sample design.

Results

Although medical advice to the patient is considered a standard of care for diabetes, approximately one-third of the sample reported not receiving dietary, weight management, or physical activity self-management advice. Participants who reported being given medical advice for each specific diabetes self-management behaviors were 4-8 times more likely to report performing the corresponding behaviors, independent of race. These results supported the ecological model with certain caveats.

Conclusions

Providing standard medical advice appears to lead to diabetes self-management behaviors as reported by adults across the United States. Moreover, it does not appear that race/ethnicity influenced reporting performance of the standard diabetes self-management behavior. Longitudinal studies evaluating patient-provider communication, medical advice and diabetes self-management behaviors are needed to clarify our findings.
Knowledge, attitude and practice of emergency contraceptive among women who seek abortion care at Jimma University specialized hospital, southwest Ethiopia
Authors: Tesfaye Tatek , Tilahun Tizta , Girma Eshetu
Published: March 2012

Background

In Ethiopia maternal mortality rate is very high more than one in five women die from pregnancy or pregnancy related causes. The use of contraceptives to prevent unwanted pregnancies and unsafe abortion is an important strategy to minimize maternal mortality rate. Among various forms of contraception, emergency contraceptives are the only one that can be used after sexual intercourse offering chance to prevent unwanted pregnancy. The aim of this study was to assess the knowledge, attitude and practice of emergency contraceptive among women who seek abortion care at Jimma University specialized hospital (JUSH).

Methods

Institution base cross-sectional study on knowledge, attitude and practice of emergency contraceptive was conducted at JUSH from April to June, 2011Data was collected using structured questionnaire and analyzed using SPSS version 17.0.

Results

In this study 89 women were interviewed. More than half of them (48) were from urban area and 41 were from rural area.46 (51.7%) of them were single. Of all the respondents only nine women had awareness about emergency contraceptive. Seven of the women mentioned pills as emergency contraception and only two of them mentioned both pills and injectable as emergency contraception. All of them have positive attitude towards emergency contraception but none of them have ever used emergency contraceptives.

Conclusion and recommendation

The finding revealed pregnancy among women of 15-19 years was very common. The knowledge and practice of emergency contraception is very low. But there is high positive attitude towards emergency contraceptives. Since there is much deficit on knowledge of women on emergency contraceptives, in addition to making them accessible; programs targeted at promotion and education of emergency contraceptives is helpful to prevent unwanted pregnancy.
Engaging HIV-HCV co-infected patients in HCV treatment: the roles played by the prescribing physician and patients' beliefs (ANRS CO13 HEPAVIH cohort, France)
Authors: Salmon-Ceron Dominique , Cohen Julien , Winnock Maria , Roux Perrine , Sadr Firouze Bani , Rosenthal Eric , Martin Isabelle Poizot , Loko Marc-Arthur , Mora Marion , Sogni Philippe , Spire Bruno , Dabis François , Carrieri Maria Patrizia ,   the HEPAVIH group
Published: March 2012

Background

Treatment for the hepatitis C virus (HCV) may be delayed significantly in HIV/HCV co-infected patients. Our study aims at identifying the correlates of access to HCV treatment in this population.

Methods

We used 3-year follow-up data from the HEPAVIH ANRS-CO13 nationwide French cohort which enrolled patients living with HIV and HCV. We included pegylated interferon and ribavirin-naive patients (N = 600) at enrolment. Clinical/biological data were retrieved from medical records. Self-administered questionnaires were used for both physicians and their patients to collect data about experience and behaviors, respectively.

Results

Median [IQR] follow-up was 12[12-24] months and 124 patients (20.7%) had started HCV treatment. After multiple adjustment including patients' negative beliefs about HCV treatment, those followed up by a general practitioner working in a hospital setting were more likely to receive HCV treatment (OR[95%CI]: 1.71 [1.06-2.75]). Patients followed by general practitioners also reported significantly higher levels of alcohol use, severe depressive symptoms and poor social conditions than those followed up by other physicians.

Conclusions

Hospital-general practitioner networks can play a crucial role in engaging patients who are the most vulnerable and in reducing existing inequities in access to HCV care. Further operational research is needed to assess to what extent these models can be implemented in other settings and for patients who bear the burden of multiple co-morbidities.
Low fatness, reduced fat intake and adequate plasmatic concentrations of LDL-cholesterol are associated with high bone mineral density in women: a cross-sectional study with control group
Authors: Sarkis Karin S , Martini Lígia A , Szejnfeld Vera L , Pinheiro Marcelo M
Published: March 2012

Background

Several parameters are associated with high bone mineral density (BMD), such as overweight, black background, intense physical activity (PA), greater calcium intake and some medications. The objectives are to evaluate the prevalence and the main aspects associated with high BMD in healthy women.

Methods

After reviewing the database of approximately 21,500 BMD scans performed in the metropolitan area of São Paulo, Brazil, from June 2005 to October 2010, high BMD (over 1400 g/cm2 at lumbar spine and/or above 1200 g/cm2 at femoral neck) was found in 421 exams. Exclusion criteria were age below 30 or above 60 years, black ethnicity, pregnant or obese women, disease and/or medications known to interfere with bone metabolism. A total of 40 women with high BMD were included and matched with 40 healthy women with normal BMD, paired to weight, age, skin color and menopausal status. Medical history, food intake and PA were assessed through validated questionnaires. Body composition was evaluated through a GE-Lunar DPX MD + bone densitometer. Radiography of the thoracic and lumbar spine was carried out to exclude degenerative alterations or fractures. Biochemical parameters included both lipid and hormonal profiles, along with mineral and bone metabolism. Statistical analysis included parametric and nonparametric tests and linear regression models. P < 0.05 was considered significant.

Results

The mean age was 50.9 (8.3) years. There was no significant difference between groups in relation to PA, smoking, intake of calcium and vitamin D, as well as laboratory tests, except serum C-telopeptide of type I collagen (s-CTX), which was lower in the high BMD group (p = 0.04). In the final model of multivariate regression, a lower fat intake and body fatness as well a better profile of LDL-cholesterol predicted almost 35% of high BMD in women. (adjusted R2 = 0.347; p < 0.001). In addition, greater amounts of lean mass and higher IGF-1 serum concentrations played a protective role, regardless age and weight.

Conclusion

Our results demonstrate the potential deleterious effect of lipid metabolism-related components, including fat intake and body fatness and worse lipid profile, on bone mass and metabolism in healthy women.
A multi-layered OFDM system with parallel transmission for multicell cooperative cellular networks
Authors: Yang Jiaxin , Wang Xianbin , Park Sung Ik , Kim Heung Mook
Published: March 2012

Recent development in multicell cooperation poses significant technical challenges to the design of robust and flexible transmission techniques. A new multi-layered orthogonal frequency-division multiplexing (ML-OFDM) system is proposed in this article to provide a dynamic platform for multicell cooperation with efficient base station coordination capability. The proposed enhanced layers (ELs), which are overlaid with the cellular communication data (the base layer) in both frequency and time domains, can be used for several specific purposes indispensable to multicell cooperation. It provides an efficient way of sharing the necessary information, e.g., channel state information, user data and other transmission parameters, between the collaborative BSs without the requirement of additional signaling or control channels. Overall network efficiency is substantially enhanced due to the reduction of radio resource overhead. Furthermore, cross BS synchronization and multimedia broadcast multicast service for next generation cellular networks can be simultaneously achieved by the proposed parallel orthogonal ELs. The transceiver design for the ML-OFDM system, particularly the modulation/demodulation of the ELs and EL-induced interference cancelation is presented. Overall system performance is further optimized by proposing a power distribution scheme with a set of practical constraints. The performance of the ML-OFDM system is analyzed and verified through numerical simulations.
Characterization of the antiproliferative activity of Xylopia aethiopica
Authors: Choumessi Aphrodite T , Danel Mathieu , Chassaing Stefan , Truchet Isabelle , Penlap Véronique B , Pieme Anatole Constant , Asonganyi Tazoacha , Ducommun Bernard , Valette Annie
Published: March 2012

Background

Xylopia aethiopica, a plant found throughout West Africa, has both nutritional and medicinal uses. The present study aims to characterize the effects of extracts of this plant on cancer cells.

Results

We report that X. aethiopica extract prepared with 70% ethanol has antiproliferative activity against a panel of cancer cell lines. The IC50 was estimated at 12 μg/ml against HCT116 colon cancer cells, 7.5 μg/ml and > 25 μg/ml against U937 and KG1a leukemia cells, respectively. Upon fractionation of the extract by HPLC, the active fraction induced DNA damage, cell cycle arrest in G1 phase and apoptotic cell death. By using NMR and mass spectrometry, we determined the structure of the active natural product in the HPLC fraction as ent-15-oxokaur-16-en-19-oic acid.

Conclusion

The main cytotoxic and DNA-damaging compound in ethanolic extracts of Xylopia aethiopica is ent-15-oxokaur-16-en-19-oic acid.
Effectiveness and safety of 30 mg versus 40 mg stavudine regimens: a cohort study among HIV‐infected adults initiating HAART in South Africa
Authors: Maskew Mhairi , Westreich Daniel , Fox Matthew P , Maotoe Thapelo , Sanne Ian M
Published: March 2012

Background

As stavudine remains an important and widely prescribed drug in resource‐limited settings, the effect of a reduced dose of stavudine (from 40 mg to 30 mg) on outcomes of highly active antiretroviral therapy (HAART) remains an important public health question.

Methods

We analyzed prospectively collected data from the Themba Lethu Clinic in Johannesburg, South Africa. We assessed the relationship between stavudine dose and six‐ and/or 12‐month outcomes of stavudine substitution, failure to suppress viral load to below 400 copies/ml, development of peripheral neuropathy, lipoatrophy and hyperlactatemia/lactic acidosis. Since individuals with a baseline weight of less than 60 kg were expected to have received the same dose of stavudine throughout the study period, analysis was restricted to individuals who weighed 60 kg or more at baseline. Data were analyzed using logistic regression.

Results

Between 1 April 2004 and 30 September 2009, 3910 patients were initiated on antiretroviral therapy (ART) with a recorded stavudine dose and were included in the analysis. Of these, 2445 (62.5%) received a 40 mg stavudine dose while 1565 (37.5%) received 30 mg. In multivariate analysis, patients receiving a 40 mg dose were more likely to discontinue stavudine use (adjusted odds ratio, OR 1.71; 95% confidence limits, CI 1.13‐2.57) than those receiving 30 mg by 12 months on ART. Additionally, patients receiving 40 mg doses of stavudine were more likely to report peripheral neuropathy (OR 3.12; 95% CI 1.86‐5.25), lipoatrophy (OR 11.8; 95% CI 3.2‐43.8) and hyperlactatemia/lactic acidosis (OR 8.37; 95% CI 3.83‐18.29) in the same time period. Failure to suppress HIV viral load within 12 months of HAART initiation was somewhat more common among those given 40 mg doses (OR 1.62; 95% CI 0.88, 2.97) although this result lacked precision. Sensitivity analyses accounting for death and loss to follow up generally supported these estimates.

Conclusions

Lower stavudine dosage is associated with fewer reports of several stavudine‐associated adverse events and also a lower risk of stavudine discontinuation within the first year on ART.
Roles of histone deacetylases in epigenetic regulation: emerging paradigms from studies with inhibitors
Authors: Delcuve Geneviève P , Khan Dilshad H , Davie James R
Published: March 2012

The zinc-dependent mammalian histone deacetylase (HDAC) family comprises 11 enzymes, which have specific and critical functions in development and tissue homeostasis. Mounting evidence points to a link between misregulated HDAC activity and many oncologic and nononcologic diseases. Thus the development of HDAC inhibitors for therapeutic treatment garners a lot of interest from academic researchers and biotechnology entrepreneurs. Numerous studies of HDAC inhibitor specificities and molecular mechanisms of action are ongoing. In one of these studies, mass spectrometry was used to characterize the affinities and selectivities of HDAC inhibitors toward native HDAC multiprotein complexes in cell extracts. Such a novel approach reproducesin vivomolecular interactions more accurately than standard studies using purified proteins or protein domains as targets and could be very useful in the isolation of inhibitors with superior clinical efficacy and decreased toxicity compared to the ones presently tested or approved. HDAC inhibitor induced-transcriptional reprogramming, believed to contribute largely to their therapeutic benefits, is achieved through various and complex mechanisms not fully understood, including histone deacetylation, transcription factor or regulator (including HDAC1) deacetylation followed by chromatin remodeling and positive or negative outcome regarding transcription initiation. Although only a very low percentage of protein-coding genes are affected by the action of HDAC inhibitors, about 40% of noncoding microRNAs are upregulated or downregulated. Moreover, a whole new world of long noncoding RNAs is emerging, revealing a new class of potential targets for HDAC inhibition. HDAC inhibitors might also regulate transcription elongation and have been shown to impinge on alternative splicing.
Induction of long-term B-cell depletion in refractory rheumatoid arthritis patients preferentially affects autoreactive more than protective humoral immunity
Authors: Teng YK Onno , Wheater Gillian , Hogan Vanessa E , Stocks Philip , Levarht EW Nivine , Huizinga Tom WJ , Toes Rene EM , van Laar Jacob M
Published: March 2012

Introduction

B-cell depletion has become a common treatment strategy in anti-TNF-refractory rheumatoid arthritis (RA). Although the exact mechanism of how B-cell depletion leads to clinical amelioration in RA remains to be elucidated, repetitive treatment with B-cell-depleting agents leading to long-term B-cell depletion has been reported to be beneficial. The latter has led to the hypothesis that the beneficial effects of B-cell depletion might act through their influence on pathogenic autoreactive plasma cells.

Methods

In this study, we investigated the effects of a fixed retreatment regimen with anti-CD20 mAbs on the humoral (auto)immune system in a cohort of therapy-refractory RA patients.

Results

Fixed retreatment led to long-term B-cell depletion in peripheral blood, bone marrow and, to a lesser extent, synovium. Also, pathologic autoantibody secretion (that is, anticitrullinated peptide antibodies (ACPAs)) was more profoundly affected by long-term depletion than by physiological protective antibody secretion (that is, against measles, mumps and rubella). This was further illustrated by a significantly shorter estimated life span of ACPA-IgG secretion compared to total IgG secretion as well as protective antibody secretion.

Conclusion

By studying plasma cell function during an extensive 2-year period of B-cell depletion, autoantibody secretion was significantly shorter-lived than physiologically protective antibody secretion. This suggests that the longevity of autoreactive plasma cells is different from protective long-lived plasma cells and might indicate a therapeutic window for therapies that target plasma cells.
Characterization of synovial angiogenesis in osteoarthritis patients and its modulation by chondroitin sulfate
Authors: Lambert Cécile , Mathy-Hartert Marianne , Dubuc Jean-Emile , Montell Eulàlia , Vergés Josep , Munaut Carine , Noël Agnès , Henrotin Yves
Published: March 2012

Introduction

This work aimed at comparing the production of inflammatory and pro- and anti-angiogenic factors by normal/reactive (N/R) or inflammatory (I) areas of the osteoarthritic synovial membrane. The effects of interleukin (IL)-1β and chondroitin sulfate (CS) on the expression of pro- and anti-angiogenic factors by synovial fibroblasts cells (SFC) were also studied.

Methods

Biopsies from N/R or from I areas of osteoarthritic synovial membrane were collected at the time of surgery. The inflammatory status of the synovial membrane was characterized by the surgeon according to macroscopic criteria, including the synovial vascularization, the villi formation and the hypertrophic aspect of the tissue. We assessed the expression of CD45, von Willebrand factor and vascular endothelial growth factor (VEGF) antigen by immunohistochemistry in both N/R and I biopsies. The production of IL-6, -8, VEGF and thrombospondin (TSP)-1 by N/R or I synovial cells was quantified by ELISA. SFC were cultured in the absence or in the presence of IL-1β (1 ng/ml) and with or without CS (10, 50, 200 μg/ml). Gene expression of pro-angiogenic factors (VEGF, basic fibroblast growth factor (bFGF), nerve growth factor (NGF), matrix metalloproteinase (MMP)-2 and angiopoietin (ang)-1) and anti-angiogenic factors (vascular endothelial growth inhibitor (VEGI), TSP-1 and -2) were determined by real time RT-PCR. Production of VEGI and TSP-1 was also estimated by ELISA.

Results

Immunohistochemistry showed the increase of lymphocyte infiltration, vascular density and VEGF expression in I compared to N/R synovial biopsies. Synovial cells from I areas produced more IL-6, IL-8 and VEGF but less TSP-1 than cells isolated from N/R synovial biopsies. The expression of pro-angiogenic factors by SFC was stimulated by IL-1β. A time dependent regulation of the expression of anti-angiogenic factor genes was observed. IL-1β stimulated the expression of anti-angiogenic factor genes but inhibited it after 24 h. CS reversed the inhibitory effect of IL-1β on anti-angiogenic factors, VEGI and TSP-1.

Conclusions

We demonstrated that synovial biopsies from I areas expressed a pro-angiogenic phenotype. IL-1β induced an imbalance between pro- and anti-angiogenic factors in SFC and CS tended to normalize this IL-1β-induced imbalance, providing a new possible mechanism of action of this drug.
Impact of non-neurological complications in severe traumatic brain injury outcome
Authors: Corral Luisa , Javierre Casimiro F , Ventura Josep L , Marcos Pilar , Herrero José I , Mañez Rafael
Published: March 2012

Introduction

Non-neurological complications in patients with severe traumatic brain injury (TBI) are frequent, worsening the prognosis, but the pathophysiology of systemic complications after TBI is unclear. The purpose of this study was to analyze non-neurological complications in patients with severe TBI admitted to the ICU, the impact of these complications on mortality, and their possible correlation with TBI severity.

Methods

An observational retrospective cohort study was conducted in one multidisciplinary ICU of a university hospital (35 beds); 224 consecutive adult patients with severe TBI (initial Glasgow Coma Scale (GCS) < 9) admitted to the ICU were included. Neurological and non-neurological variables were recorded.

Results

Sepsis occurred in 75% of patients, respiratory infections in 68%, hypotension in 44%, severe respiratory failure (arterial oxygen pressure/oxygen inspired fraction ratio (PaO2/FiO2) < 200) in 41% and acute kidney injury (AKI) in 8%. The multivariate analysis showed that Glasgow Outcome Score (GOS) at one year was independently associated with age, initial GCS 3 to 5, worst Traumatic Coma Data Bank (TCDB) first computed tomography (CT) scan and the presence of intracranial hypertension but not AKI. Hospital mortality was independently associated with initial GSC 3 to 5, worst TCDB first CT scan, the presence of intracranial hypertension and AKI. The presence of AKI regardless of GCS multiplied risk of death 6.17 times (95% confidence interval (CI): 1.37 to 27.78) (P < 0.02), while ICU hypotension increased the risk of death in patients with initial scores of 3 to5 on the GCS 4.28 times (95% CI: 1.22 to15.07) (P < 0.05).

Conclusions

Low initial GCS, worst first CT scan, intracranial hypertension and AKI determined hospital mortality in severe TBI patients. Besides the direct effect of low GCS on mortality, this neurological condition also is associated with ICU hypotension which increases hospital mortality among patients with severe TBI. These findings add to previous studies that showed that non-neurological complications increase the length of stay and morbidity in the ICU but do not increase mortality, with the exception of AKI and hypotension in low GCS (3 to 5).
Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome coxidase
Authors: Szklarczyk Radek , Wanschers Bas FJ , Cuypers Thomas D , Esseling John J , Riemersma Moniek , van den Brand Mariël AM , Gloerich Jolein , Lasonder Edwin , van den Heuvel Lambert P , Nijtmans Leo G , Huynen Martijn A
Published: March 2012

Background

Orthology is a central tenet of comparative genomics and ortholog identification is instrumental to protein function prediction. Major advances have been made to determine orthology relations among a set of homologous proteins. However, they depend on the comparison of individual sequences and do not take into account divergent orthologs.

Results

We have developed an iterative orthology prediction method, Ortho-Profile, that uses reciprocal best hits at the level of sequence profiles to infer orthology. It increases ortholog detection by 20% compared to sequence-to-sequence comparisons. Ortho-Profile predicts 598 human orthologs of mitochondrial proteins from Saccharomyces cerevisiae and Schizosaccharomyces pombe with 94% accuracy. Of these, 181 were not known to localize to mitochondria in mammals. Among the predictions of the Ortho-Profile method are 11 human cytochrome c oxidase (COX) assembly proteins that are implicated in mitochondrial function and disease. Their co-expression patterns, experimentally verified subcellular localization, and co-purification with human COX-associated proteins support these predictions. For the human gene C12orf62, the ortholog of S. cerevisiae COX14, we specifically confirm its role in negative regulation of the translation of cytochrome c oxidase.

Conclusions

Divergent homologs can often only be detected by comparing sequence profiles and profile-based hidden Markov models. The Ortho-Profile method takes advantage of these techniques in the quest for orthologs.
A Framework for Solving Hybrid Influence Diagrams Containing Deterministic Conditional Distributions
Authors: Li Yijing , Shenoy Prakash P.
Published: March 2012

We describe a framework and an algorithm for approximately solving a class of hybrid influence diagrams (IDs) containing discrete and continuous chance variables, discrete and continuous decision variables, and deterministic conditional distributions for chance variables. A conditional distribution for a chance variable is said to be deterministic if its variances, for each state of its parents, are all zeroes. The solution algorithm is an extension of Shenoy's fusion algorithm for discrete influence diagrams. To mitigate the integration and optimization problems associated with solving hybrid IDs, we propose using mixture of polynomials approximations of conditional probability density and utility functions and piecewise linear approximations of nonlinear deterministic conditional distributions for continuous chance variables. The class of hybrid IDs that can be solved by our framework are those that do not involve divisions. The framework and algorithm are illustrated by solving two small examples of hybrid IDs.
Kuxa Kanema: The rise and fall of an experimental documentary series in Mozambique
Authors: Loftus Maria
Published: March 2012

The subject of this article is the monthly documentary series, Kuxa Kanema (birth of the image) produced in Mozambique from 1978 to 1986. The series recorded the blind optimism that follows the parturition of a nation, articulates cinematographic formal invention, and documents the
decline of Mozambique into civil war. It essentially traces the birth and death of a fledgling socialist democracy and the similar rise and fall of cinema itself in that country. It is noteworthy that the National Institute of Cinema was created just five months after the independence of Mozambique
in 1975, the government quickly mobilizing the power of the moving image in propagating its ideological message. As Kuxa Kanema was produced by the aforementioned state institute, it brandishes the trappings of being an official propaganda vector but its desire to allow the Mozambican people
reappropriate their image helps it overcome these limitations as does its aesthetic originality.
In the name of 'cinema action' and Third World: The intervention of foreign film-makers in Mozambican cinema in the 1970s and 1980s
Authors: Bamba Mahomed
Published: March 2012

In this article we propose a rereading of experiments in ideological and aesthetic engagement conducted by European and Latin-American film-makers in a bid to establish a post-colonial cinema in Mozambique. In order to do this we shall begin by locating this cinematographic 'Third Worldism'
within the global context of ideas, utopias, and militant idealism that configured the ethics and aesthetics of the 'cinema-action' in vogue during the 1960s and 1970s. Next, we will discuss the vicissitudes and certain disenchantments that marked the participation of these European and Latin-American
film-makers in this Mozambican adventure, hoping, by so doing, to evince the limits and contradictions of anti-colonialism and Third Worldism within the cinematographic field in general.
Ambivalent transnationality: Luso-African co-productions after independence (1988–2010)
Authors: Ferreira Carolin Overhoff
Published: March 2012

In the sequence of its adhesion to the European Community in 1986 and in search for a place in an increasingly globalized film market, Portugal established a vast amount of transnational cinematographic partnerships with the Luso-African countries Cape Verde, Mozambique, Angola and
Guinea Bissau. The partnerships, which have resulted in twenty co-productions so far, have also had a profound meaning for the discussion of colonialism and post-colonialism that cannot be overemphasized. Since the aim of this article is to give a general overview of the Luso-African feature
film landscape, it discusses the films in a resumed fashion within the context of the four co-producing PALOP (Países de Língua Oficial Portuguesa – Countries with Portuguese as Official Language). According to my understanding of transnationality as ambivalent, I will
try to comprehend how the co-productions negotiate the elements of national and transnational identity. Are they capable of holding the post-colonial tensions? Are new and multilateral perspectives that confront outdated discourses the exception or the rule?
Towards a postcolonial critical literacy: Bhimayana and the Indian graphic novel
Authors: Nayar Pramod K.
Published: March 2012

This article argues that the graphic novel of BR Ambedkar's life, Bhimayana, generates a postcolonial critical literacy. Critical literacy forces the reader to link personal experiences with socio-historical and institutional power relations, and alerts us to reflect on issues of otherness
in the text. In the first section, the article argues that Bhimayana's innovations of form and content, and its extensive metaphorization and multiple registers serve to combine a personal story with the history of a condition – of caste-based discrimination. In the second section of
the article, I focus on the critical literacy the text initiates and demands of its readers. I suggest that the work fits into an already existing interocular (where the visual intersects with images from other visual media, such as television) field, and draws upon a popular register. It
is this everyday register of comics – commonplace in the form of the comic strips in newspapers and periodicals but also as comic books – that enables Bhimayana to debate social issues in a medium that is far removed from other forms and genres such as newspaper reportage, commentaries
and Amnesty reports where human rights issues are mostly addressed. The text is therefore significant in that it situates debates about caste and human rights in the popular cultural realm. A postcolonial critical literacy is the demand made on the reader to recognize, in this supposedly non-serious
medium, a social problem.
Congenital and Postnatal Factors Inducing Malocclusions in Japanese Unilateral Cleft Lip and Palate Patients—Determination Using Logistic Regression Analysis
Authors: Kajii Takashi S. , Alam Mohammad K. , Mikoya Tadashi , Oyama Akihiko , Koshikawa-Matsuno Mino , Sugawara-Kato Yuki , Sato Yoshiaki , Iida Junichiro
Published: March 2012

Objective

To assess the congenital and postnatal factors that affect degree of malocclusion in patients with unilateral cleft lip and palate using multivariate statistical analysis.

Design

Retrospective study.

Patients

All information on 135 subjects with unilateral cleft lip and palate was obtained from an oral examination and radiograph at the initial examination at an orthodontic clinic and from surgical records. Plaster models were taken before orthodontic treatment. The ages of the subjects ranged from 5 to 8 years with a mean age of 6.9 years. All primary surgeries for the patients were performed at a university hospital.

Main Outcome Measures

The GOSLON Yardstick was used to assess the dental arch relationships (degree of malocclusion) in patients. Family history of Class III, degree of cleft, and congenitally missing upper lateral incisor on the cleft side were chosen as congenital factors inducing malocclusion. Presurgical orthopedic treatment, cheiloplasty, and palatoplasty were chosen as postnatal factors. Associations between various factors and dental arch relationships were assessed using logistic regression analysis.

Results

According to adjusted odds ratios, family history of Class III is associated with a significantly worse dental arch relationship. Palatoplasty using push-back alone correlated to a dental arch relationship that was significantly worse than palatoplasty using push-back with a buccal flap.

Conclusions

Multivariate analysis shows evidence that a positive family history of Class III and palatoplasty using push-back alone are associated with worse malocclusion of unilateral cleft lip and palate patients.
A low‐cost low‐temperature thin‐film‐transistor backplane based on oxide semiconductor
Authors: Lan Linfeng , Xiong Nana , Xiao Peng , Shi Wen , Xu Miao , Xu Wei , Yao Rihui , Peng Junbiao
Published: March 2012

Abstract— An indium‐gallium‐zinc‐oxide (IGZO) thin‐film transistor (TFT) based on an anodized aluminum‐oxide gate dielectric and photoresist passivation has been fabricated. The TFT showed a field‐effect mobility of as high as 18 cm2/V‐sec and a threshold voltage of only 0.5 V. A 50 × 50 AMOLED display based on this type of TFT was designed and fabricated. The average luminance of the panel was 150 cd/m2, and the maximum pixel luminance was 900 cd/m2.
Luminance effects influencing perception of 3‐D TV imagery
Authors: Wang Pei‐Chia , Hwang Sheue‐Ling , Chen Chin‐Sen , Chen Kuan‐Yu
Published: March 2012

Abstract— This study investigates whether screen luminance or ambient illumination has a significant effect on the perception of 3‐D TV imagery for static images and dynamic films. Two types of stimuli were shown on a multi‐view stereoscopic display: the static image, which included computer‐generated and photographic images, and dynamic film, which contained real‐life and animation images. In each treatment with a different level of screen luminance, subjects completed psychophysical and physiological measurements and subjective comfort evaluations. The results showed that when subjects viewed 3‐D static images, the ambient illumination affected psychophysical visual fatigue and screen luminance had a significant effect on subjective comfort evaluation and visual discrimination performance. However, when subjects viewed 3‐D dynamic films, screen luminance was the major factor causing psychophysical visual fatigue, and ambient illumination significantly affected subjective comfort evaluation. The outcomes contribute to knowledge concerning the suitable viewing conditions for the 3‐D viewing experience. Future work will explore the intolerance threshold of the lowest display luminance or the effect of decomposition of the screen on other physiological measurements.
Analysis of longitudinal viewing freedom of reduced‐view super multi‐view display and increased longitudinal viewing freedom using eye‐tracking technique
Authors: Nakamura Junya , Takahashi Taichi , Chen Chih‐Wei , Huang Yi‐Pai , Takaki Yasuhiro
Published: March 2012

Abstract— The viewing freedom of the reduced‐view super multi‐view (SMV) display was analyzed. It was found that there are separate multiple viewing ranges in the depth direction; thus, a technique that selects an appropriate viewing range to increase the longitudinal viewing freedom has been developed. Pixels of a flat‐panel display viewed by the viewer's eyes through a lenticular lens were determined from three‐dimensional (3‐D) positions of the viewer's eyes, which were obtained using an eye‐tracking system that employed a stereo camera. Parallax images corresponding to the 3‐D positions of the viewer's eyes were generated, which were displayed by the determined pixels. The experimental results show that the proposed technique successfully increased the longitudinal viewing freedom. It is also shown that a video camera was able to focus on the produced SMV images.
Assessing Migration Risk for Scientific Data Formats
Authors: Frisz Chris , Brown Geoffrey , Waggoner Samuel
Published: March 2012

The majority of information about science, culture, society, economy and the environment is born digital, yet the underlying technology is subject to rapid obsolescence. One solution to this obsolescence, format migration, is widely practiced and supported by many software packages, yet migration has well known risks. For example, newer formats – even where similar in function – do not generally support all of the features of their predecessors, and, where similar features exist, there may be significant differences of interpretation.There appears to be a conflict between the wide use of migration and its known risks. In this paper we explore a simple hypothesis – that, where migration paths exist, the majority of data files can be safely migrated leaving only a few that must be handled more carefully – in the context of several scientific data formats that are or were widely used. Our approach is to gather information about potential migration mismatches and, using custom tools, evaluate a large collection of data files for the incidence of these risks. Our results support our initial hypothesis, though with some caveats. Further, we found that writing a tool to identify “risky” format features is considerably easier than writing a migration tool.
Freedom of Information in the UK and its Implications for Research in the Higher Education Sector
Authors: Jubb Michael
Published: March 2012

Freedom of information legislation came into effect in the UK in 2005. All universities that receive block grants from the Higher Education Funding Councils in England, Wales, Scotland and Northern Ireland are subject to the legislation. Recent cases where universities have received requests for data and other information generated by researchers, working in areas such as climate, have given rise to controversy and widespread concern in the research community. This paper examines some of those concerns, relating to responsibilities for the ownership and holding of information, for data and records management, and for the handling of requests under the legislation. It also considers the implications relating to personal data, and to information that may affect the commercial interests of universities operating in a competitive environment, or the interests of the many other organisations which may be involved in research partnerships with universities; and it outlines concerns about the possible impact on quality assurance, peer review, and scholarly discourse. Finally, the paper emphasises the need for support and training for researchers so that they become more aware of the legislation and its implications, and how to deal with requests when they arise.
Making Data a First Class Scientific Output: Data Citation and Publication by NERC’s Environmental Data Centres
Authors: Callaghan Sarah , Donegan Steve , Pepler Sam , Thorley Mark , Cunningham Nathan , Kirsch Peter , Ault Linda , Bell Patrick , Bowie Rod , Leadbetter Adam , Lowry Roy , Moncoiffé Gwen , Harrison Kate , Smith-Haddon Ben , Weatherby Anita , Wright Dan
Published: March 2012

The NERC Science Information Strategy Data Citation and Publication project aims to develop and formalise a method for formally citing and publishing the datasets stored in its environmental data centres. It is believed that this will act as an incentive for scientists, who often invest a great deal of effort in creating datasets, to submit their data to a suitable data repository where it can properly be archived and curated. Data citation and publication will also provide a mechanism for data producers to receive credit for their work, thereby encouraging them to share their data more freely.
Developments in Research Funder Data Policy
Authors: Jones Sarah
Published: March 2012

This paper reviews developments in funders’ data management and sharing policies, and explores the extent to which they have affected practice. The Digital Curation Centre has been monitoring UK research funders’ data policies since 2008. There have been significant developments in subsequent years, most notably the joint Research Councils UK’s Common Principles on Data Policy and the Engineering and Physical Sciences Research Council’s Policy Framework on Research Data. This paper charts these changes and highlights shifting emphasises in the policies. Institutional data policies and infrastructure are increasingly being developed as a result of these changes. While action is clearly being taken, questions remain about whether the changes are affecting practice on the ground.
Sensitive and selective methods for the determination of cyproheptadine in tablets using N-bromosuccinimide and two dyes
Authors: Raghu Srinivas , Basavaiah Kanakapura
Published: March 2012

One titrimetric and two spectrophotometric methods are described for the
determination of cyproheptadine hydrochloride (CPH) in bulk drug and tablets
employing N-bromosuccinimide (NBS) as a brominating agent and two dyes,
erioglaucine (EG) and meta-cresol purple (MCP) as auxiliary reagents. In
titrimetry, a measured excess of NBS is added to an acidified solution of CPH
and the unreacted NBS is determined iodometrically. Spectrophotometry
involves the addition of a known excess of NBS to CPH in acid medium followed
by estimation of residual NBS by reacting with a fixed amount of either
erioglaucin and measuring the absorbance at 540 nm (method A) or meta-cresol
purple and measuring the absorbance at 630 nm (method B). Titrimetric
procedure is applicable over the range of 1.5-15 mg of CPH, and the reaction
stoichiometry is found to be 1: 2 (CPH: NBS). The spectrophotometric methods
are applicable over the ranges of 0.1-2.0 ?g mL-1 (method A) and 0.4-12 ?g
mL-1 (method B). The molar absorptivities are calculated to be 1.4 ? 105 and
2.2?104 Lmol-1cm-1 for method A and method B, respectively, and the
corresponding Sandell sensitivity values are 0.0023 and 0.0141 ?g cm-2. The
limits of detection are calculated and found to be 0.03 and 0.24 ?g mL-1 for
method A and method B, respectively with corresponding limits of
quantification 0.09 and 0.71. The methods were applied to the assay of CPH in
tablets, and the results were compared statistically with those of a
reference method.