bluuebunny/crossref_metadata_2025_split huggingface dataset:
The GMOseek matrix: a decision support tool for optimizing the detection of genetically modified plants
Authors: Block Annette , Debode Frédéric , Grohmann Lutz , Hulin Julie , Taverniers Isabel , Kluga Linda , Barbau-Piednoir Elodie , Broeders Sylvia , Huber Ingrid , Van den Bulcke Marc , Heinze Petra , Berben Gilbert , Busch Ulrich , Roosens Nancy , Janssen Eric , Žel Jana , Gruden Kristina , Morisset Dany 
Published: August 2013

Abstract

Background
Since their first commercialization, the diversity of taxa and the genetic composition of transgene sequences in genetically modified plants (GMOs) are constantly increasing. To date, the detection of GMOs and derived products is commonly performed by PCR-based methods targeting specific DNA sequences introduced into the host genome. Information available regarding the GMOs’ molecular characterization is dispersed and not appropriately organized. For this reason, GMO testing is very challenging and requires more complex screening strategies and decision making schemes, demanding in return the use of efficient bioinformatics tools relying on reliable information.

Description
The GMOseek matrix was built as a comprehensive, online open-access tabulated database which provides a reliable, comprehensive and user-friendly overview of 328 GMO events and 247 different genetic elements (status: 18/07/2013). The GMOseek matrix is aiming to facilitate GMO detection from plant origin at different phases of the analysis. It assists in selecting the targets for a screening analysis, interpreting the screening results, checking the occurrence of a screening element in a group of selected GMOs, identifying gaps in the available pool of GMO detection methods, and designing a decision tree. The GMOseek matrix is an independent database with effective functionalities in a format facilitating transferability to other platforms. Data were collected from all available sources and experimentally tested where detection methods and certified reference materials (CRMs) were available.

Conclusions
The GMOseek matrix is currently a unique and very valuable tool with reliable information on GMOs from plant origin and their present genetic elements that enables further development of appropriate strategies for GMO detection. It is flexible enough to be further updated with new information and integrated in different applications and platforms.
Systematic review and meta-analysis of the association between childhood overweight and obesity and primary school diet and physical activity policies
Authors: Williams Andrew James , Henley William E , Williams Craig Anthony , Hurst Alison Jane , Logan Stuart , Wyatt Katrina Mary 
Published: August 2013

Abstract
Obesity is a major public health concern and there are increasing calls for policy intervention. As obesity and the related health conditions develop during childhood, schools are being seen as important locations for obesity prevention, including multifaceted interventions incorporating policy elements. The objective of this systematic review was to evaluate the effects of policies related to diet and physical activity in schools, either alone, or as part of an intervention programme on the weight status of children aged 4 to 11 years. A comprehensive and systematic search of medical, education, exercise science, and social science databases identified 21 studies which met the inclusion criteria. There were no date, location or language restrictions. The identified studies evaluated a range of either, or both, diet and physical activity related policies, or intervention programmes including such policies, using a variety of observational and experimental designs. The policies were clustered into those which sought to affect diet, those which sought to affect physical activity and those which sought to affect both diet and physical activity to undertake random effects meta-analysis. Within the diet cluster, studies of the United States of America National School Lunch and School Breakfast Programs were analysed separately; however there was significant heterogeneity in the pooled results. The pooled effects of the physical activity, and other diet related policies on BMI-SDS were non-significant. The multifaceted interventions tended to include policy elements related to both diet and physical activity (combined cluster), and although these interventions were too varied to pool their results, significant reductions in weight-related outcomes were demonstrated. The evidence from this review suggests that, when implemented alone, school diet and physical activity related policies appear insufficient to prevent or treat overweight or obesity in children, however, they do appear to have an effect when developed and implemented as part of a more extensive intervention programme. Additional evidence is required before recommendations regarding the focus of policies can be made and therefore, increased effort should be made to evaluate the effect of policies and policy containing intervention programmes upon weight status.
Dirac fermion heating, current scaling, and direct insulator-quantum Hall transition in multilayer epitaxial graphene
Authors: Liu Fan-Hung , Hsu Chang-Shun , Chuang Chiashain , Woo Tak-Pong , Huang Lung-I , Lo Shun-Tsung , Fukuyama Yasuhiro , Yang Yanfei , Elmquist Randolph E , Liang Chi-Te 
Published: August 2013

Abstract
We have performed magnetotransport measurements on multilayer epitaxial graphene. By increasing the driving current I through our graphene devices while keeping the bath temperature fixed, we are able to study Dirac fermion heating and current scaling in such devices. Using zero-field resistivity as a self thermometer, we are able to determine the effective Dirac fermion temperature (T
DF) at various driving currents. At zero field, it is found that T
DF ∝ I
≈1/2. Such results are consistent with electron heating in conventional two-dimensional systems in the plateau-plateau transition regime. With increasing magnetic field B, we observe an I-independent point in the measured longitudinal resistivity ρ
xx which is equivalent to the direct insulator-quantum Hall (I-QH) transition characterized by a temperature-independent point in ρ
xx. Together with recent experimental evidence for direct I-QH transition, our new data suggest that such a transition is a universal effect in graphene, albeit further studies are required to obtain a thorough understanding of such an effect.
The Hyperferritinemic Syndrome: macrophage activation syndrome, Still’s disease, septic shock and catastrophic antiphospholipid syndrome
Authors: Rosário Cristina , Zandman-Goddard Gisele , Meyron-Holtz Esther G , D’Cruz David P , Shoenfeld Yehuda 
Published: August 2013

Abstract

Background
Over the last few years, accumulating data have implicated a role for ferritin as a signaling molecule and direct mediator of the immune system. Hyperferritinemia is associated with a multitude of clinical conditions and with worse prognosis in critically ill patients.

Discussion
There are four uncommon medical conditions characterized by high levels of ferritin, namely the macrophage activation syndrome (MAS), adult onset Still’s disease (AOSD), catastrophic antiphospholipid syndrome (cAPS) and septic shock, that share a similar clinical and laboratory features, and also respond to similar treatments, suggesting a common pathogenic mechanism. Ferritin is known to be a pro-inflammatory mediator inducing expression of pro-inflammatory molecules, yet it has opposing actions as a pro-inflammatory and as an immunosuppressant. We propose that the exceptionally high ferritin levels observed in these uncommon clinical conditions are not just the product of the inflammation but rather may contribute to the development of a cytokine storm.

Summary
Here we review and compare four clinical conditions and the role of ferritin as an immunomodulator. We would like to propose including these four conditions under a common syndrome entity termed “Hyperferritinemic Syndrome”.
Cohesin loading factor Nipbl localizes to chromosome axes during mammalian meiotic prophase
Authors: Kuleszewicz Katarzyna , Fu Xiangwei , Kudo Nobuaki R 
Published: August 2013

Abstract

Background
Sister chromatid cohesion mediated by the cohesin complex is essential for accurate chromosome segregation during mitosis and meiosis. Loading of cohesin onto chromosomes is dependent on another protein complex called kollerin, containing Nipbl/Scc2 and Mau2/Scc4. Nipbl is an evolutionarily conserved large protein whose haploinsufficiency in humans causes a developmental disorder called Cornelia de Lange syndrome. Although the function of Nipbl homologues for chromosome cohesion in meiotic cells of non-vertebrate models has been elucidated, Nipbl has not been characterized so far in mammalian spermatocytes or oocytes.

Findings
Here we describe our analyses on the expression and localization of Nipbl in nuclei of mouse spermatocytes and oocytes at different stages of meiotic prophase. In both spermatocytes and oocytes we found that Nipbl is associated with the axial/lateral element of the synaptonemal complex (AE/LE) to which cohesin also localizes. Interestingly, Nipbl in spermatocytes, but not in oocytes, dissociates from the AE/LE at mid-pachytene stage coincident with completion of DNA double-strand break repair.

Conclusions
Our data propose that cohesin loading activity is maintained during early stages of meiotic prophase in mammalian spermatocytes and oocytes.
De novo likelihood-based measures for comparing genome assemblies
Authors: Ghodsi Mohammadreza , Hill Christopher M , Astrovskaya Irina , Lin Henry , Sommer Dan D , Koren Sergey , Pop Mihai 
Published: August 2013

Abstract

Background
The current revolution in genomics has been made possible by software tools called genome assemblers, which stitch together DNA fragments “read” by sequencing machines into complete or nearly complete genome sequences. Despite decades of research in this field and the development of dozens of genome assemblers, assessing and comparing the quality of assembled genome sequences still relies on the availability of independently determined standards, such as manually curated genome sequences, or independently produced mapping data. These “gold standards” can be expensive to produce and may only cover a small fraction of the genome, which limits their applicability to newly generated genome sequences. Here we introduce a de novo probabilistic measure of assembly quality which allows for an objective comparison of multiple assemblies generated from the same set of reads. We define the quality of a sequence produced by an assembler as the conditional probability of observing the sequenced reads from the assembled sequence. A key property of our metric is that the true genome sequence maximizes the score, unlike other commonly used metrics.

Results
We demonstrate that our de novo score can be computed quickly and accurately in a practical setting even for large datasets, by estimating the score from a relatively small sample of the reads. To demonstrate the benefits of our score, we measure the quality of the assemblies generated in the GAGE and Assemblathon 1 assembly “bake-offs” with our metric. Even without knowledge of the true reference sequence, our de novo metric closely matches the reference-based evaluation metrics used in the studies and outperforms other de novo metrics traditionally used to measure assembly quality (such as N50). Finally, we highlight the application of our score to optimize assembly parameters used in genome assemblers, which enables better assemblies to be produced, even without prior knowledge of the genome being assembled.

Conclusion
Likelihood-based measures, such as ours proposed here, will become the new standard for de novo assembly evaluation.
Transcranial doppler assessment of cerebral perfusion in critically ill septic patients: a pilot study
Authors: Pierrakos Charalampos , Antoine Aurélie , Velissaris Dimitrios , Michaux Isabelle , Bulpa Pierre , Evrard Patrick , Ossemann Michel , Dive Alain 
Published: August 2013

Abstract

Background
The aim of this study is to evaluate the feasibility and efficacy of Transcranial Doppler (TCD) in assessing cerebral perfusion changes in septic patients.

Methods
Using TCD, we measured the mean velocity in the middle cerebral artery (VmMCA, cm/sec) and calculated the pulsatility index (PI), resistance index (RI) and cerebral blood flow index (CBFi = 10*MAP/1.47PI) on the first day of patients’ admission or on the first day of sepsis development; measurements were repeated on the second day. Sepsis was defined according to standard criteria.

Results
Forty-one patients without any known neurologic deficit treated in our 24-bed Critical Care Unit were assessed (Sepsis Group = 20, Control Group = 21). Examination was feasible in 91% of septic and 85% of non-septic patients (p = 0.89). No difference was found between the two groups in mean age, mean arterial pressure (MAP) or APACHE II score. The pCO2 values were higher in septic patients (46 ± 12 vs. 39 ± 4 mmHg p < 0.01). No statistically significant higher values of VmMCA were found in septic patients (110 ± 34 cm/sec vs. 99 ± 28 cm/sec p = 0.17). Higher values of PI and RI were found in septic patients (1.15 ± 0.25 vs. 0.98 ± 0.16 p < 0.01, 0.64 ± 0.08 vs. 0.59 ± 0.06 p < 0.01, respectively). No statistically significant lower values of CBFi were found in septic patients (497 ± 116 vs. 548 ± 110 p = 0.06).

Conclusions
Our results suggest cerebral vasoconstriction in septic compared to non-septic patients. TCD is an efficient and feasible exam to evaluate changes in cerebral perfusion during sepsis.
A Cross-Sectional Association Between Bone Mineral Density and Parathyroid Hormone and Other Biomarkers in Community-Dwelling Young Adults: The CARDIA Study
Authors: Fujiyoshi Akira , Polgreen Lynda E. , Hurley Daniel L. , Gross Myron D. , Sidney Stephen , Jacobs David R. 
Published: August 2013

Abstract

Context:
Most association studies of bone-related biomarkers (BBMs) with bone mineral density (BMD) have been conducted in postmenopausal women.

Objective:
We tested whether the following BBMs were cross-sectionally associated with BMD among young adults: serum 1,25-dihydroxyvitamin D (1,25(OH)2D), 25-hydroxyvitamin D (25OHD), PTH, osteocalcin, bone-specific alkaline phosphatase (BAP), and urinary pyridinoline/urinary creatinine.

Setting and Participants:
We studied 319 individuals (134 women, 149 black, 24–36 years) recruited during 1992 through 1993 in Oakland, California. BMD was assessed with dual-energy x-ray absorptiometry. Linear regression models estimated the association between BMD and each BBM.

Results:
1,25(OH)2D was inversely associated with all BMDs. 25OHD was positively, and PTH inversely, associated with lumbar spine, total hip, and whole-body BMD. BAP was inversely associated with left arm, right arm, and whole-body BMD but not with spine or hip BMD. Neither osteocalcin nor urinary pyridinoline/urinary creatinine was associated with BMD. When we placed all BBMs (including 1,25(OH)2D) in one model, the pattern and magnitude of association was similar except for PTH, which was attenuated. The association of BMD and BBMs did not differ significantly by race or sex.

Conclusions:
In this cross-sectional study of healthy young men and women who had PTH levels considered normal in clinical practice, higher PTH was associated with lower BMD, particularly in weight-bearing sites (ie, spine and hip). The inverse association of 1,25(OH)2D, together with the attenuation of PTH, suggests that the observed association of PTH is mediated by 1,25(OH)2D. BAP was inversely associated with arm BMD. BBMs can be important markers of skeletal activity in young adults, but their clinical role on bone health among this population is yet to be fully determined.
Effects of Combustible Stacking in Large Compartments
Authors: Gentili Filippo , Giuliani Luisa , Bontempi Franco 
Published: August 2013

This paper focuses on the modelling of fire in case of various distributions of combustible materials in a large compartment.Large compartments often represent a challenge for structural fire safety, because of lack of prescriptive rules to follow and difficulties of taking into account the effect of non uniform distribution of the combustible materials and fire propagation.These aspects are discussed in this paper with reference to an industrial steel building, taken as case study. Fires triggered by the burning of wooden pallets stored in the premises have been investigated with respect to different stacking configurations of the pallets with the avail of a CFD code. The results in term of temperatures of the hot gasses and of the steel elements composing the structural system are compared with simplified analytical model of localized and post-flashover fires, with the aim of highlighting limitation and potentiality of different modelling approaches.
Professors’ Beauty, Ability, and Teaching Evaluations in Italy
Authors: Ponzo Michela , Scoppa Vincenzo 
Published: August 2013

Abstract
Using data from an Italian University, we relate student evaluations of teaching quality to the physical attractiveness of instructors (as evaluated by external raters using photos), controlling for a number of teacher and course characteristics. We first show that teachers’ beauty significantly affects evaluations of their teaching. We carry out a number of checks to tackle threats to internal validity: course fixed effects and individual research productivity are controlled for; an IV estimation strategy is undertaken using a second measure of beauty as an instrument; and measures of grooming and fastidiousness are introduced. Notwithstanding these controls, we find that more attractive teachers receive much better evaluations.
Category-specific uncertainty modeling in clinical laboratory measurement processes
Authors: Ramamohan Varun , Yih Yuehwern , Abbott James T. , Klee George G. 
Published: August 2013

Abstract

Background: A statement of measurement uncertainty describes the quality of a clinical assay analysis result, and uncertainty models of clinical assays can be used to evaluate and optimize laboratory protocols designed to minimize the measurement uncertainty associated with an assay. In this study, we propose a methodology to lend systematic structure to the uncertainty modeling process.

Methods: Clinical laboratory assays are typically classified based on the chemical reaction involved, and therefore, based on the assay analysis methodology. We use this fact to demonstrate that uncertainty models for assays within the same category are structurally identical in all respects except for the values of certain model parameters. This is accomplished by building uncertainty models for assays belonging to two categories – substrate assays based on optical absorbance analysis of endpoint reactions, and ion selective electrode (ISE) assays based on potentiometric measurements of electromotive force.

Results: Uncertainty models for the substrate assays and the ISE assays are built, and for each category, a general mathematical framework for the uncertainty model is developed. The parameters of the general framework that vary from assay to assay for each category are identified and listed.

Conclusions: Estimates of measurement uncertainty from the models were compared with estimates of uncertainty from quality control data from the clinical laboratory. We demonstrate that building a general modeling framework for each assay category and plugging in parameter values for each assay is sufficient to generate uncertainty models for an assay within a given category.
Searching for genes involved in hypertension development in special populations: children and pre-eclamptic women. Where are we standing now?
Authors: Danese Elisa , Montagnana Martina , Fava Cristiano 
Published: August 2013

Abstract
Primary hypertension is a very common disorder particularly in the aging population but hypertensive disorders can appear earlier in life, especially when obesity and unhealthy lifestyle are present. Also pregnant women can be at risk of developing gestational hypertension and/or pre-eclampsia, which causes complications in nearly 7% of pregnancies. These “special” populations could be regarded as natural models suited to reveal mechanisms of hypertension development which are either common to other forms of hypertension, including primary hypertension or specific to these populations. Recent studies in the field of genetics of primary hypertension have used new powerful tools, such as genome-wide association studies (GWAS) and sequencing, but studies about hypertension during childhood and in pregnancy have seldom used high-throughput technologies and the knowledge in this field comes mostly from the candidate gene approach. In this review we summarize some interesting results from genetic studies conducted in childhood and adolescence and during pregnancy and underline the need to apply modern technologies in these potentially very fruitful populations.
Analytic varieties with finite volume amoebas are algebraic
Authors: Madani Farid , Nisse Mounir 
Published: August 2013

Abstract
In this paper, we study the amoeba volume of a given k-dimensional generic analytic variety V of the complex algebraic torus

(

ℂ
*

)

n

$(\mathbb {C}^*)^n$

. When

n
≥
2
k

$n\ge 2k$

, we show that V is algebraic if and only if the volume of its amoeba is finite. Moreover, in this case, we establish a comparison theorem for the volume of the amoeba and the coamoeba. Examples and applications to the k-dimensional affine linear spaces are also given.
Arithmetic moduli and lifting of Enriques surfaces
Authors: Liedtke Christian 
Published: August 2013

Abstract

We construct the moduli space of Enriques surfaces in positive characteristic and
eventually over the integers,
and determine its local and global structure.
As an application, we show lifting of Enriques surfaces to characteristic zero. The key observation is that the canonical double
cover of an Enriques surface is birational to the
complete intersection of three quadrics in ℙ5, even
in characteristic 2.
Granule proteases of hematopoietic cells, a family of versatile inflammatory mediators – an update on their cleavage specificity, in vivo substrates, and evolution
Authors: Hellman Lars , Thorpe Michael 
Published: August 2013

Abstract
Cells from several of the hematopoietic cell lineages including mast cells, basophils, neutrophils, cytotoxic T cells, and natural killer (NK) cells store proteases at very high levels within their cytoplasmic granules. In mast cells, these proteases can account for up to 35% of the total cellular protein, and the absolute majority of these belong to the chymotrypsin-related serine protease family. A number of very diverse functions have been identified for these proteases, including apoptosis induction, blood pressure regulation, inactivation of insect and snake toxins, intestinal parasite expulsion, killing of bacteria and fungi, induction, mobilization, or degradation of cytokines, and the degradation of connective tissue components. A very broad spectrum of primary cleavage specificities has also been observed, including chymase, tryptase, asp-ase, elastase, and met-ase specificities, which highlights the large flexibility in the active site of these proteases. Mast cells primarily express chymases and tryptases with chymotryptic or tryptic primary cleavage specificities, respectively. Neutrophils have several enzymes with chymase, elastase, and tryptase specificities. T cells and NK cells express between 5 and 14 different granzymes, depending on the species, and these enzymes have tryptase, asp-ase, chymase, and met-ase specificities. This review focuses on the appearance of these proteases during vertebrate evolution, their primary and extended cleavage specificities, and their potential in vivo substrates. The in vivo substrates and functions are a particular challenging issue because several of these enzymes have a relatively broad specificity and may therefore cleave a wide range of different substrates.