bluuebunny/crossref_metadata_2025_split huggingface dataset:
Independent component analysis: recent advances
Authors: Hyvärinen Aapo 
Published: January 2013

Independent component analysis is a probabilistic method for learning a linear transform of a random vector. The goal is to find components that are maximally independent and non-Gaussian (non-normal). Its fundamental difference to classical multi-variate statistical methods is in the assumption of non-Gaussianity, which enables the identification of original, underlying components, in contrast to classical methods. The basic theory of independent component analysis was mainly developed in the 1990s and summarized, for example, in our monograph in 2001. Here, we provide an overview of some recent developments in the theory since the year 2000. The main topics are: analysis of causal relations, testing independent components, analysing multiple datasets (three-way data), modelling dependencies between the components and improved methods for estimating the basic model.
Network Inference Analysis Identifies an APRR2-Like Gene Linked to Pigment Accumulation in Tomato and Pepper Fruits
Authors: Pan Yu , Bradley Glyn , Pyke Kevin , Ball Graham , Lu Chungui , Fray Rupert , Marshall Alexandra , Jayasuta Subhalai , Baxter Charles , van Wijk Rik , Boyden Laurie , Cade Rebecca , Chapman Natalie H. , Fraser Paul D. , Hodgman Charlie , Seymour Graham B. 
Published: January 2013

Abstract
Carotenoids represent some of the most important secondary metabolites in the human diet, and tomato (Solanum lycopersicum) is a rich source of these health-promoting compounds. In this work, a novel and fruit-related regulator of pigment accumulation in tomato has been identified by artificial neural network inference analysis and its function validated in transgenic plants. A tomato fruit gene regulatory network was generated using artificial neural network inference analysis and transcription factor gene expression profiles derived from fruits sampled at various points during development and ripening. One of the transcription factor gene expression profiles with a sequence related to an Arabidopsis (Arabidopsis thaliana) ARABIDOPSIS PSEUDO RESPONSE REGULATOR2-LIKE gene (APRR2-Like) was up-regulated at the breaker stage in wild-type tomato fruits and, when overexpressed in transgenic lines, increased plastid number, area, and pigment content, enhancing the levels of chlorophyll in immature unripe fruits and carotenoids in red ripe fruits. Analysis of the transcriptome of transgenic lines overexpressing the tomato APPR2-Like gene revealed up-regulation of several ripening-related genes in the overexpression lines, providing a link between the expression of this tomato gene and the ripening process. A putative ortholog of the tomato APPR2-Like gene in sweet pepper (Capsicum annuum) was associated with pigment accumulation in fruit tissues. We conclude that the function of this gene is conserved across taxa and that it encodes a protein that has an important role in ripening.
Repression of Essential Chloroplast Genes Reveals New Signaling Pathways and Regulatory Feedback Loops inChlamydomonas
Authors: Ramundo Silvia , Rahire Michèle , Schaad Olivier , Rochaix Jean-David 
Published: January 2013

AbstractAlthough reverse genetics has been used to elucidate the function of numerous chloroplast proteins, the characterization of essential plastid genes and their role in chloroplast biogenesis and cell survival has not yet been achieved. Therefore, we developed a robust repressible chloroplast gene expression system in the unicellular alga Chlamydomonas reinhardtii based mainly on a vitamin-repressible riboswitch, and we used this system to study the role of two essential chloroplast genes: ribosomal protein S12 (rps12), encoding a plastid ribosomal protein, and rpoA, encoding the α-subunit of chloroplast bacterial-like RNA polymerase. Repression of either of these two genes leads to the arrest of cell growth, and it induces a response that involves changes in expression of nuclear genes implicated in chloroplast biogenesis, protein turnover, and stress. This response also leads to the overaccumulation of several plastid transcripts and reveals the existence of multiple negative regulatory feedback loops in the chloroplast gene circuitry.
A Dominant Point Mutation in a RINGv E3 Ubiquitin Ligase Homoeologous Gene Leads to Cleistogamy inBrassica napus
Authors: Lu Yun-Hai , Arnaud Dominique , Belcram Harry , Falentin Cyril , Rouault Patricia , Piel Nathalie , Lucas Marie-Odile , Just Jérémy , Renard Michel , Delourme Régine , Chalhoub Boulos 
Published: January 2013

AbstractIn the allopolyploid Brassica napus, we obtained a petal-closed flower mutation by ethyl methanesulfonate mutagenesis. Here, we report cloning and characterization of the Bn-CLG1A (CLG for cleistogamy) gene and the Bn-clg1A-1D mutant allele responsible for the cleistogamy phenotype. Bn-CLG1A encodes a RINGv E3 ubiquitin ligase that is highly conserved across eukaryotes. In the Bn-clg1A-1D mutant allele, a C-to-T transition converts a Pro at position 325 to a Leu (P325L), causing a dominant mutation leading to cleistogamy. B. napus and Arabidopsis thaliana plants transformed with a Bn-clg1A-1D allele show cleistogamous flowers, and characterization of these flowers suggests that the Bn-clg1A-1D mutation causes a pronounced negative regulation of cutin biosynthesis or loading and affects elongation or differentiation of petal and sepal cells. This results in an inhibition or a delay of petal development, leading to folded petals. A homoeologous gene (Bn-CLG1C), which shows 99.5% amino acid identity and is also constitutively and equally expressed to the wild-type Bn-CLG1A gene, was also identified. We showed that P325L is not a loss-of-function mutation and did not affect expression of Bn-clg1A-1D or Bn-CLG1C. Our findings suggest that P325L is a gain-of-function semidominant mutation, which led to either hyper- or neofunctionalization of a redundant homoeologous gene.
GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis
Authors: Seren Ümit , Vilhjálmsson Bjarni J. , Horton Matthew W. , Meng Dazhe , Forai Petar , Huang Yu S. , Long Quan , Segura Vincent , Nordborg Magnus 
Published: January 2013

AbstractArabidopsis thaliana is an important model organism for understanding the genetics and molecular biology of plants. Its highly selfing nature, small size, short generation time, small genome size, and wide geographic distribution make it an ideal model organism for understanding natural variation. Genome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in A. thaliana. Previously genotyped accessions (natural inbred lines) can be grown in replicate under different conditions and phenotyped for different traits. These important features greatly simplify association mapping of traits and allow for systematic dissection of the genetics of natural variation by the entire A. thaliana community. To facilitate this, we present GWAPP, an interactive Web-based application for conducting GWAS in A. thaliana. Using an efficient implementation of a linear mixed model, traits measured for a subset of 1386 publicly available ecotypes can be uploaded and mapped with a mixed model and other methods in just a couple of minutes. GWAPP features an extensive, interactive, and user-friendly interface that includes interactive Manhattan plots and linkage disequilibrium plots. It also facilitates exploratory data analysis by implementing features such as the inclusion of candidate polymorphisms in the model as cofactors.
Associations of acanthosis nigricans with metabolic abnormalities in polycystic ovary syndrome women with normal body mass index
Authors: Dong Zhe , Huang Jia , Huang Lili , Chen Xiaoli , Yin Qianqian , Yang Dongzi 
Published: January 2013

AbstractAcanthosis nigricans (AN) usually correlates to insulin resistance (IR) or obesity in obese populations, but adequate studies on the significance of AN in people with normal body mass index (BMI) have not been performed and discussed. Three hundred and thirty‐nine polycystic ovary syndrome (PCOS) patients with normal BMI (<23 kg/m2) were recruited. The anthropometric and biochemical parameters of these patients were measured. In these patients with normal BMI, 33 (9.7%) women had AN, and six (1.77%) women were diagnosed with metabolic syndrome. Most of the anthropometric and biochemical variables associated with metabolic status were more unfavorable in the AN‐positive group compared with the AN‐negative groups. The prevalence of central obesity, IR and reduced high‐density lipoprotein cholesterol (HDL‐C) level were also significantly higher in the AN‐positive group (P < 0.05). In multiple regression analysis, presence of AN was still significantly associated with IR (odds ratio [OR] = 2.952, 95% confidence intervals [CI] = 1.367–6.376] and reduced HDL‐C level (OR = 2.668, 95% CI = 1.160–6.135) after adjustments for age and BMI. Sensitivity, specificity, and positive and negative predictive values for AN to detect IR were 18.6%, 92.6%, 39.4% and 81.4%, respectively. In conclusion, presence of AN correlated with IR and reduced HDL‐C level in PCOS women with normal BMI. AN status had high specificity to detect IR, but lack of sensitivity.
Developmental‐ and food‐dependent foraging transcript levels in the desert locust
Authors: Tobback Julie , Verlinden Heleen , Vuerinckx Kristel , Vleugels Rut , Vanden Broeck Jozef , Huybrechts Roger 
Published: January 2013

AbstractDrastic changes in the environment during a lifetime require developmental and physiological flexibility to ensure animal survival. Desert locusts, Schistocerca gregaria, live in an extremely changeable environment, which alternates between periods of rainfall and abundant food and periods of drought and starvation. In order to survive, locusts display an extreme form of phenotypic plasticity that allows them to rapidly cope with these changing conditions by converting from a cryptic solitarious phase to a swarming, voracious gregarious phase. To accomplish this, locusts possess different conserved mediators of phenotypic plasticity. Recently, attention has been drawn to the possible roles of protein kinases in this process. In addition to cyclic AMP‐dependent protein kinase (PKA), also cyclic GMP‐dependent protein kinase (PKG), which was shown to be involved in changes of food‐related behavior in a variety of insects, has been associated with locust phenotypic plasticity. In this article, we study the transcript levels of the S. gregaria orthologue of the foraging gene that encodes a PKG in different food‐related, developmental and crowding conditions. Transcript levels of the S. gregaria foraging orthologue are highest in different parts of the gut and differ between isolated and crowd‐reared locusts. They change when the availability of food is altered, display a distinct pattern with higher levels after a moult and decrease with age during postembryonic development.
Multidisciplinary osteoporosis management of post low‐energy trauma hip‐fracture patients
Authors: Skorupski Nicole , Alexander Ivy M. 
Published: January 2013

AbstractPurposeThe purpose of this article is to increase awareness of osteoporosis incidence in patients with hip fracture among providers and allied health professionals, to increase osteoporosis recognition and treatment in post hip‐fracture patients, and to provide guidance on how to improve continuity of care and collaboration between members of the multidisciplinary healthcare team.Data sourcesRecent evidence from the literature is reviewed to identify effective management strategies for post low‐energy trauma hip‐fracture patients and prevention of future osteoporotic fracture, regardless of osteoporosis diagnosis prior to the initial fracture.ConclusionsDespite the availability of accurate screening technologies and highly efficacious antiosteoporosis medications, implementation of these measures for low‐energy trauma hip‐fracture patients remains critically low. This is because of a number of factors including hesitancy to integrate care across specialty lines, lack of reliable referral systems, and resistance to change. There is also a lack of recognition of the connection between low‐energy trauma hip fracture and osteoporosis by many healthcare professionals.Implications for practiceAll members of the multidisciplinary care team are called to action to adopt osteoporosis evaluation and treatment strategies that research has shown to be effective on a larger scale in the post hip‐fracture setting.
A prospective longitudinal study on rotation thromboelastometry in women with uncomplicated pregnancies and postpartum
Authors: van Rheenen‐Flach Leonie E. , Zweegman Sonja , Boersma Fleur , Lenglet Joris E. , Twisk Jos W. R. , Bolte Antoinette C. 
Published: January 2013

BackgroundRotation thromboelastometry (ROTEM) is an easy, fast and complete method of measuring coagulation.AimsOur goal was to obtain longitudinal values on ROTEM in uncomplicated pregnancies and in the puerperium.Materials and MethodsHealthy women, who visited our outpatient clinic for antenatal checks and who accomplished an uncomplicated pregnancy were tested three times during pregnancy and one time postpartum. Intrinsic and extrinsic pathway tests were carried out.ResultsIn total, 62 women were analysed, and 298 measurements were taken. With increasing gestational age, there are significant changes towards hypercoagulability.ConclusionThis study provides a better knowledge about physiological changes in ROTEM measurements during pregnancy. These normative data may serve as assistance for future studies and interventions.
Enlargement of the levator hiatus in female pelvic organ prolapse: Cause or effect?
Authors: Andrew Bronwyn P. , Shek Ka L. , Chantarasorn Varisara , Dietz Hans P. 
Published: January 2013

AimThis study was undertaken to investigate whether female pelvic organ prolapse repair changes levator hiatal biometry.MethodsRetrospective analysis of clinical and translabial ultrasound volume data of women who underwent prolapse surgery at a tertiary urogynaecological unit between March 2005 and April 2009. Data sets of 81 women were analysed who had undergone an interview, clinical assessment using POP‐Q staging and 3D translabial ultrasound before and after prolapse surgery. Imaging data were obtained preoperatively and 3–12 months postoperatively to determine potential changes in levator hiatal dimensions. Type of surgery, mesh use, symptoms of recurrent prolapse, age, significant recurrent prolapse and length of follow‐up were tested in linear regression as potential confounders.ResultsThe mean preoperative hiatal area on Valsalva was 31.9 cm2 (range 13.5–58.1 cm2, SD 10.0 cm2). Mean postoperative hiatal area on Valsalva was 28.9 cm2 (range 13.9–47.4 cm2; SD 7.3 cm2), which implies a significant reduction of 9% (P = 0.001). None of the tested potential confounders were found to be significantly associated with a perioperative change in hiatal area on Valsalva on linear regression analysis.ConclusionsSurgery for female pelvic organ prolapse is associated with a small but significant reduction in hiatal area, but abnormal hiatal distensibility persists in most cases. This suggests that excessive hiatal distensibility is more likely the cause rather than the effect of prolapse.
Comparison of 23‐gauge sutureless sclerotomy architecture and clinical outcomes in macular and non‐macular surgery using spectral‐domain optical coherence tomography
Authors: Tahiri Joutei Hassani Rachid , El Sanharawi Mohamed , Adam Raphael , Monin Claire , Dupont‐Monod Sylvère , Baudouin Christophe 
Published: January 2013

Abstract.Purpose:  To compare the 23‐gauge (23‐G) sutureless vitrectomy incision architecture in macular and non‐macular surgery, using anterior segment spectral‐domain optical coherence tomography (SD‐OCT), and to evaluated its influence on clinical outcomes.Methods:  A prospective, observational case series of 43 patients who underwent primary transconjunctival 23‐G pars plana vitrectomy (PPV) for macular and non‐macular diseases. All sclerotomy wounds were imaged 1 day after surgery using the anterior segment module of SD‐OCT (OCT Spectralis; Heidelberg Engineering, Heidelberg, Germany). Sclerotomy architecture, including good wound apposition, presence of gaping and misalignment of the roof and floor of the incisions were evaluated. Preoperative, intraoperative and postoperative medical record data were also prospectively collected.Results:  Incision gaping and misalignment of the roof and floor occurred more frequently in the superotemporal and superonasal quadrants than in the inferotemporal quadrant (p < 0.05) and was more frequent in the non‐macular group than in the macular group (p < 0.05). The incidence of incision gaping increased significantly as the incision angle increased. In the macular group, the mean postoperative intraocular pressure (IOP) did not change from the preoperative value, whereas in the non‐macular group, the mean IOP decreased significantly from 15.09 ± 2.58 mmHg preoperatively to 12.18 ± 3.25 mmHg on the first postoperative day (p < 0.005). The mean IOP did not differ significantly between the two groups of surgery at 1 week, and at 1 month postoperatively.Conclusions:  In 23‐G PPV, non‐macular surgery is associated with a significant postoperative IOP decrease in comparison with macular surgery, which could be explained by the most remodelled wound architecture.
Understanding the impact of uveitis on health‐related quality of life in adolescents
Authors: Maca Saskia M. , Amirian Arsine , Prause Carolin , Gruber Kathrin , Mejdoubi Lamiss , Barisani‐Asenbauer Talin 
Published: January 2013

Abstract.Purpose:  A reduction in quality of life (QoL) during an active phase of disease has been shown for patients with uveitis of various age groups. Adult uveitis patients were shown to also have reduced QoL‐values despite disease being quiescent, but adolescents have not been investigated in this respect.Methods:  This clinic‐based, cross‐sectional pilot study assessed the overall health‐related quality of life (HRQoL) in adolescents (11–18 years) with a history of inactive uveitis and good visual function. Two independent generic (non‐disease‐specific) instruments were applied, the Inventory for Assessing the Quality of Life and the German KINDL‐R‐questionnaire.Results:  Thirty‐seven adolescents, 20 females (54%) and 17 males with a mean age of 15 ± 3 years and diagnosis since 5 ± 2 years participated. Subgroups with a reduced HRQoL were those with anterior and intermediate localization of uveitis, bilateral disease, application of immunosuppressive therapy, a short time since diagnosis, and a high number of recurrences.Conclusion:  Even despite quiescence of disease and good visual function, certain risk factors may result in a decreased HRQoL in juvenile uveitis patients. Our findings support the need of further evaluation of HRQoL in this patient group, the validation of specific psychometric inventories for this disease and the establishment of interdisciplinary collaboration including psychological counselling.
Late in‐the‐bag intraocular lens dislocation in eyes with pseudoexfoliation syndrome
Authors: Østern Atle Einar , Sandvik Gunhild Falleth , Drolsum Liv 
Published: January 2013

Abstract.Purpose: To assess preoperative features, frequency, surgical approaches and outcomes of late in‐the‐bag dislocation of posterior chamber intraocular lenses (IOLs) in eyes with pseudoexfoliation syndrome.Methods: Seventy‐seven patients (81 eyes) were enrolled. Inclusion criteria were patients with pre‐existing pseudoexfoliation syndrome who underwent surgery for late in‐the‐bag IOL dislocation between March 2004 and April 2010. Medical records were reviewed. Data from before and after secondary surgery were analysed.Results: Mean time between cataract extraction and secondary surgery for late in‐the‐bag dislocation of posterior chamber IOLs was 8.5 years. The increase in frequency within the reviewed period was statistically significant, ranging from six patients in the first year to 25 patients in the final year (p = 0.004). When surgical correction was performed within 1 month of referral, deterioration of the dislocation occurred in only one of 23 patients (4.3%). Complications, especially vitreous loss, occurred significantly more frequently during exchange surgery (n = 23) when compared with scleral suturing (n = 50) (p < 0.0001). After surgery, however, no differences in complications (p = 0.98) or best‐corrected visual acuity (p = 0.74) was found. In general, following secondary surgery, there was a statistically significant improvement in best‐corrected visual acuity (p < 0.0001).Conclusion: The frequency of late in‐the‐bag dislocation of posterior chamber IOLs in eyes with pseudoexfoliation syndrome increased during the observation period. Our study suggests that surgical repair should not be delayed beyond 1 month and that scleral suturing is preferable to exchange surgery, because of less intraoperative complications.
Positioning of the posterior intraocular lens in the longer term following cataract surgery in eyes with and without pseudoexfoliation syndrome
Authors: Østern Atle Einar , Sandvik Gunhild Falleth , Drolsum Liv 
Published: January 2013

Abstract.Purpose:  To assess long‐term positioning of posterior chamber intraocular lenses within the capsular bag in eyes with pseudoexfoliation syndrome.Methods:  The study includes 44 patients with pseudoexfoliation syndrome and 85 age‐matched controls, who underwent cataract surgery in 2001 and 2002 at the Eye Department, Oslo University Hospital. In 2008, all patients were re‐examined. A comparison of the extent of possible decentration in eyes with and without pseudoexfoliation syndrome was made by evaluating Scheimpflug images (Pentacam) of the anterior segment.Results:  It was found that, 6–7 years following cataract surgery, posterior chamber intraocular lenses were positioned lower in eyes with pseudoexfoliation syndrome than in control eyes. The difference was statistically significant (p = 0.01). Downward shift was associated with presence of glaucoma only in eyes with pseudoexfoliation syndrome (p = 0.01). No patients had visual disturbances related to displacement of the intraocular lens. Three of the patients with pseudoexfoliation syndrome (6.8%) had observable pseudophacodonesis by slit‐lamp examination, compared to one in the control group (1.2%). The study demonstrated that Pentacam is an appropriate instrument to measure decentration of intraocular lenses.Conclusion:  The study suggests that, 6–7 years after cataract surgery, the intraocular lenses within the capsular bag are more prone to decentration in pseudoexfoliation syndrome eyes, compared to controls.