bluuebunny/crossref_metadata_2025_split huggingface dataset:
An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era
Authors: Su Zhenqiang , Fang Hong , Hong Huixiao , Shi Leming , Zhang Wenqian , Zhang Wenwei , Zhang Yanyan , Dong Zirui , Lancashire Lee J , Bessarabova Marina , Yang Xi , Ning Baitang , Gong Binsheng , Meehan Joe , Xu Joshua , Ge Weigong , Perkins Roger , Fischer Matthias , Tong Weida 
Published: December 2014

Abstract
Background
Gene expression microarray has been the primary biomarker platform ubiquitously applied in biomedical research, resulting in enormous data, predictive models, and biomarkers accrued. Recently, RNA-seq has looked likely to replace microarrays, but there will be a period where both technologies co-exist. This raises two important questions: Can microarray-based models and biomarkers be directly applied to RNA-seq data? Can future RNA-seq-based predictive models and biomarkers be applied to microarray data to leverage past investment?

Results
We systematically evaluated the transferability of predictive models and signature genes between microarray and RNA-seq using two large clinical data sets. The complexity of cross-platform sequence correspondence was considered in the analysis and examined using three human and two rat data sets, and three levels of mapping complexity were revealed. Three algorithms representing different modeling complexity were applied to the three levels of mappings for each of the eight binary endpoints and Cox regression was used to model survival times with expression data. In total, 240,096 predictive models were examined.

Conclusions
Signature genes of predictive models are reciprocally transferable between microarray and RNA-seq data for model development, and microarray-based models can accurately predict RNA-seq-profiled samples; while RNA-seq-based models are less accurate in predicting microarray-profiled samples and are affected both by the choice of modeling algorithm and the gene mapping complexity. The results suggest continued usefulness of legacy microarray data and established microarray biomarkers and predictive models in the forthcoming RNA-seq era.
Systematic evaluation of connectivity map for disease indications
Authors: Cheng Jie , Yang Lun , Kumar Vinod , Agarwal Pankaj 
Published: December 2014

Abstract
Background
Connectivity map data and associated methodologies have become a valuable tool in understanding drug mechanism of action (MOA) and discovering new indications for drugs. One of the key ideas of connectivity map (CMAP) is to measure the connectivity between disease gene expression signatures and compound-induced gene expression profiles. Despite multiple impressive anecdotal validations, only a few systematic evaluations have assessed the accuracy of this aspect of CMAP, and most of these utilize drug-to-drug matching to transfer indications across the two drugs.

Methods
To assess CMAP methodologies in a more direct setting, namely the power of classifying known drug-disease relationships, we evaluated three CMAP-based methods on their prediction performance against a curated dataset of 890 true drug-indication pairs. The disease signatures were generated using Gene Logic BioExpress™ system and the compound profiles were derived from the Connectivity Map database (CMAP, build 02, http://www.broadinstitute.org/CMAP/).

Results
The similarity scoring algorithm called eXtreme Sum (XSum) performs better than the standard Kolmogorov-Smirnov (KS) statistic in terms of the area under curve and can achieve a four-fold enrichment at 0.01 false positive rate level, with AUC = 2.2E-4, P value = 0.0035.

Conclusion
Connectivity map can significantly enrich true positive drug-indication pairs given an effective matching algorithm.
Thyroid Dysfunction Associated With Follicular Cell Steatosis in Obese Male Mice and Humans
Authors: Lee Min Hee , Lee Jung Uee , Joung Kyong Hye , Kim Yong Kyung , Ryu Min Jeong , Lee Seong Eun , Kim Soung Jung , Chung Hyo Kyun , Choi Min Jeong , Chang Joon Young , Lee Sang-Hee , Kweon Gi Ryang , Kim Hyun Jin , Kim Koon Soon , Kim Seong-Min , Jo Young Suk , Park Jeongwon , Cheng Sheue-Yann , Shong Minho 
Published: January 2015

AbstractAdult thyroid dysfunction is a common endocrine disorder associated with an increased risk of cardiovascular disease and mortality. A recent epidemiologic study revealed a link between obesity and increased prevalence of hypothyroidism. It is conceivable that excessive adiposity in obesity might lead to expansion of the interfollicular adipose (IFA) depot or steatosis in thyroid follicular cells (thyroid steatosis, TS). In this study, we investigated the morphological and functional changes in thyroid glands of obese humans and animal models, diet-induced obese (DIO), ob/ob, and db/db mice. Expanded IFA depot and TS were observed in obese patients. Furthermore, DIO mice showed increased expression of lipogenesis-regulation genes, such as sterol regulatory element binding protein 1 (SREBP-1), peroxisome proliferator-activated receptor γ (PPARγ), acetyl coenzyme A carboxylase (ACC), and fatty acid synthetase (FASN) in the thyroid gland. Steatosis and ultrastructural changes, including distension of the endoplasmic reticulum (ER) and mitochondrial distortion in thyroid follicular cells, were uniformly observed in DIO mice and genetically obese mouse models, ob/ob and db/db mice. Obese mice displayed a variable degree of primary thyroid hypofunction, which was not corrected by PPARγ agonist administration. We propose that systemically increased adiposity is associated with characteristic IFA depots and TS and may cause or influence the development of primary thyroid failure.
Auxin transporters and binding proteins at a glance
Authors: Grones Peter , Friml Jiří 
Published: January 2015

ABSTRACT
The plant hormone auxin is a key regulator of plant growth and development. Differences in auxin distribution within tissues are mediated by the polar auxin transport machinery, and cellular auxin responses occur depending on changes in cellular auxin levels. Multiple receptor systems at the cell surface and in the interior operate to sense and interpret fluctuations in auxin distribution that occur during plant development. Until now, three proteins or protein complexes that can bind auxin have been identified. SCFTIR1 [a SKP1–cullin-1–F-box complex that contains transport inhibitor response 1 (TIR1) as the F-box protein] and S-phase-kinase-associated protein 2 (SKP2) localize to the nucleus, whereas auxin-binding protein 1 (ABP1), predominantly associates with the endoplasmic reticulum and cell surface. In this Cell Science at a Glance article, we summarize recent discoveries in the field of auxin transport and signaling that have led to the identification of new components of these pathways, as well as their mutual interaction.
Schur Products
Authors: Constantinescu Corneliu 
Published: December 2014

Abstract
We call Schur products (in analogy to crossed products which inspired the present construction) a C*-algebra obtained from a given unital C*-algebra E and a discrete group T. This new C*-algebra consists of operators acting on the Hilbert right E-module E ⊗ l
2(T) and are defined by a twisted representation of T.
Role of vitamin D and sFlt-1/PlGF ratio in the development of early- and late-onset preeclampsia
Authors: Álvarez-Fernández Indira , Prieto Belén , Rodríguez Verónica , Ruano Yolanda , Escudero Ana I. , Álvarez Francisco V. 
Published: December 2014

AbstractThe imbalanced production of placental biomarkers and vitamin D deficiency have been proposed as risk factors for the development of preeclampsia (PE). However, little is known about the relationship between them and their role in early- versus late-onset PE. The objectives were to assess the role of 25-hydroxyvitamin D [25(OH)D] concentrations and the soluble fms-like tyrosine kinase 1 (sFlt-1) to placental growth factor (PlGF) ratio in the development of early- and late-onset PE; and to evaluate the relationship between 25(OH)D and the biomarkers.A retrospective, full-blinded cohort study was conducted at the Obstetric Emergency Service of a tertiary care hospital. Pregnant women (n=257) attending obstetric triage with suspicion of PE were included. sFlt-1, PlGF and 25(OH)D concentrations were measured by electrochemoluminescence (ECLIA) immunoassay and pregnancy outcome (development of PE) was registered from patients records.PE women showed lower 25(OH)D concentrations at clinical presentation than non-PE women (median: 35.0 nmol/L and 39.6 nmol/L, respectively; p=0.027). Women with 25(OH)D levels <50 nmol/L experienced an increased risk of developing late-onset PE [odds ratio (OR) 4.6, 95% confidence interval (CI) 1.4–15], but no association was found for early-onset PE. However, a sFlt-1/PlGF ratio above the corresponding cutpoints increased the risk of developing both early- and late-onset PE [ORs 58 (95% CI 11–312) and 12 (95% CI 5.0–27), respectively]. No association was found between 25(OH)D levels and sFlt-1/PlGF ratio.Low vitamin D status in women with suspected late-onset PE increases the risk of imminent development of the disease.
Ahlfors–Weill extensions in several complex variables
Authors: Chuaqui Martin , Hernández Rodrigo 
Published: January 2015

Abstract
We derive an Ahlfors–Weill type extension for a class of holomorphic mappings defined in the ball 𝔹
n
, generalizing the formula for Nehari mappings in the disk. The class of mappings holomorphic in the ball is defined in terms of the Schwarzian operator. Convexity relative to the Bergman metric plays an essential role, as well as the concept of a weakly linearly convex domain. The extension outside the ball takes values in the projective dual to ℂ
n
, that is, in the set of complex hyperplanes.
Synthesis, characterization and formulation of sodium calcium silicate bioceramic for drug delivery applications
Authors: Reddy P. Manohar , Lakshmi Ravy , Dass Febin Prabhu , Sasikumar Swamiappan 
Published: December 2014

AbstractSodium calcium silicate (Na2CaSiO4) is a bioactive silicate with Na2O, CaO and SiO2 as its basic components, which is similar to that of the composition of bioactive glasses. In the present study, pure sodium calcium silicate was synthesized by rapid combustion technique, and the synthesized sample was characterized by powder X-ray diffraction to check the phase purity. The scaffolds were prepared by varying the ratio of sodium calcium silicate and polyvinyl alcohol, and the apatite-formation ability of the scaffolds was examined by soaking them in a simulated body fluid. The results revealed the formation of hydroxyapatite on the surface of the scaffold after 5 days, which is found to be rapid when compared with the bioactivity of the calcium silicates and calcium magnesium silicates. The scaffolds were also loaded with ciprofloxacin as a model drug and analyzed for its drug release profile using UV spectrophotometer. The release profile did not vary with the change in bioceramic-to-biopolymer ratio, and 60% of the drug was released in 10 days, which is within the appreciable range for a targeted drug delivery system. Moreover, the experimental and simulated values of the release kinetics were compared by applying the existing mathematical model.
The Evolving Puzzle of AutosomalVersusY-linked Male Determination inMusca domestica
Authors: Hamm Ronda L , Meisel Richard P , Scott Jeffrey G 
Published: January 2015

AbstractSex determination is one of the most rapidly evolving developmental pathways, but the factors responsible for this fast evolution are not well resolved. The house fly, Musca domestica, is an ideal model for studying sex determination because house fly sex determination is polygenic and varies considerably between populations. Male house flies possess a male-determining locus, the M factor, which can be located on the Y or X chromosome or any of the five autosomes. There can be a single M or multiple M factors present in an individual male, in heterozygous or homozygous condition. Males with multiple copies of M skew the sex ratio toward the production of males. Potentially in response to these male-biased sex ratios, an allele of the gene transformer, Md-traD, promotes female development in the presence of one or multiple M factors. There have been many studies to determine the linkage and frequency of these male determining factors and the frequency of Md-traD chromosomes in populations from around the world. This review provides a summary of the information available to date regarding the patterns of distribution of autosomal, X-linked and Y-linked M factors, the relative frequencies of the linkage of M, the changes in frequencies found in field populations, and the fitness of males with autosomal M factors vs. Y-linked M. We evaluate this natural variation in the house fly sex determination pathway in light of models of the evolution of sex determination.
Optofluidically Tuned Fluorescence Enhancement by Plasmonic Nanocup Arrays
Authors: Seo Sujin , Ameen Abid , Liu Gang Logan 
Published: January 2015

ABSTRACTWe demonstrate fluidically tuned fluorescence enhancement on the colorimetric substrate with the plasmonic effects induced by the periodic gold nanocup arrays. The fluorescence enhancement by the plasmonic effect has been studied extensively by varying the geometries of nanostructures or the morphology of nanoparticles. In this study, however, the fluorescence enhancement without changing these parameters but simply by varying surrounding media on the colorimetric plasmonic surface is accomplished. The dynamic responses of fluorescence from self-assembled monolayer of dyes on the surface were monitored by flowing various fluids with different refractive indices. The dependence of the radiative decay rate as well as the scattering cross-section on the surrounding dielectric properties results into the selective enhancement of the fluorescence intensity, having a maximum at different surrounding refractive index for different fluorophores with different emission band centers.
Optofluidic Waveguiding for Biomedical Sensing
Authors: Wall Thomas A. , Parks Joshua , Leake Kaelyn D. , Schmidt Holger , Hawkins Aaron R. 
Published: January 2015

ABSTRACTWe review an optofluidic waveguiding lab-on-a-chip used to sense bioparticles. The sensor uses a liquid filled Anti-Resonant Reflecting Optical Waveguide (ARROW) that is interfaced with standard ridge waveguides. The ridge waveguides are coupled to off-chip lasers and detectors via optical fiber. A perpendicular intersection between the ARROW and a ridge waveguide is especially useful for detecting fluorescently tagged particles. Light coupled into the ridge waveguide can fluorescently excite these particles within a very small volume. Fluorescent signal can then be guided within the ARROW and subsequently off chip to a detector.We also discuss how such devices are fabricated. Both the ARROW and ridge waveguides are made using alternating thin films of tantalum oxide and silicon dioxide on silicon substrates. These thin films are deposited by either sputtering or plasma enhanced chemical vapor deposition (PECVD). The waveguides are patterned using a combination of standard photolithographic processes, reactive ion etching, and sacrificial etching. Low-loss optical guiding is very dependent on both the waveguide structure and the materials used. The latest processes for maximizing detection sensitivity are reviewed.We also present results using the optofluidic waveguiding sensor for detecting a variety of different types of particles such as fluorescently labeled nanobeads, viruses, ribosomes, and RNA.
Electrophoretic Deposition of Single Wall Carbon Nanotube Films and Characterization
Authors: Lim Junyoung , Jalali Maryam , Campbell Stephen A. 
Published: January 2015

ABSTRACTElectrophoretic deposition enables the rapid deposition of single wall carbon nanotube films at room temperature. An accurate, reproducible film thickness can be obtained by controlling electric field strength, suspension concentration, and time. To investigate the electrical and mechanical properties of such films, we recorded electric resistance and Young’s modulus using I-V characterization and a nanoindenter, respectively. The measured resistivity of the films varied from 2.14 × 10-3 to 7.66 × 10-3 Ω·cm, and the Young’s modulus was 4.72 to 5.67 GPa, independent of film thickness from 77 to 134 nm. These results indicated that the mechanical and electrical properties of film are comparable with previously reported methods such as layer by layer deposition even though we achieved much higher deposition rates. We also measured the film mass density which is usually unrecorded even though it is an important parameter for MEMS/NEMS device actuation. The film density was found with conventional thickness measurement and Rutherford backscattering spectrometry. It varied from 0.12 to 0.54 g/cm3 as the film thickness increased. This method could be extended to applications of CNT films for flexible electronics or high frequency RF MEMS devices.
Single Walled Carbon Nanotube Assisted Thermal Sensor
Authors: Chandrasekar S. , Santhanam K.S.V. , Yue Y. , Kalaiazagan K. , Fuller L. 
Published: January 2015

ABSTRACTA nano thermal sensor was made by depositing carbon nanotubes from a medium containing a) methylene chloride b)sodium dodecyl sulfate and c) Baytron-P (polymer) assisted sodium dodecyl sulfate. The nano thermal sensors showed d.c. electrical resistance as independent of temperature when the sensors were made by procedures (a) or (b). The electrical resistivity in both the situations has been independent of temperature. When the nanosensor is made with carbon nanotubes by assisted method (c), the d.c. electrical resistance decreased with temperature. The negative temperature coefficient (TCR) is manifested in the semiconducting property of the active material. The sensor behavior is reproducible and varies linearly with temperature. The nanosensor made by non assisted carbon nanotube showed zero TCR. This is probably the first instance of assisted thermal sensor made with single walled carbon nanotubes.
Effects of Carbon Content, Annealing Condition and Internal Defects on the nucleation, growth and coarsening of P-type Carbides in High Niobium Containing TiAl Alloys
Authors: Wang Li , Pyczak Florian , Gabrisch Heike , Lorenz Uwe , Münch Mathias , Schimansky Frank-Peter , Schreyer Andreas , Stark Andreas 
Published: January 2015

ABSTRACTThe nucleation, growth and coarsening of carbides is investigated in high niobium containing TiAl alloys by diffraction and transmission electron microscopy. Higher carbon content increases the dissolution temperature of carbides. The solubility of carbon is much higher in a γ/α2-phase alloy than in the γ phase alone. Hereby no significant influence of Nb on carbon solubility is found. Crystallographic defects as grain boundaries and dislocations promote carbide nucleation which results in a carbide precipitation sequence starting first at grain boundaries, then at dislocations and only later in the γ matrix away from crystallographic defects. The consumption of carbon by grain boundary carbides or neighboring α2 grains also generates a precipitate free zone in γ grains near the grain boundary.
Como Proust foi moderno: entre debates literários e conflitos culturais
Authors: Haiduke Paulo Rodrigo Andrade 
Published: December 2014

Neste artigo são discutidas questões relacionadas ao hoje famoso ciclo romanesco de Marcel Proust (1871-1922) intitulado Em busca do tempo perdido (A la recherche du temps perdu) e a sua recepção como um dos maiores cânones da literatura moderna no século XX. Tomando como referência comentadores contemporâneos ao lançamento do romance (os volumes foram publicados orginalmente entre 1913 e 1927), pretendo introduzir os leitores nos debates que buscaram arrogar a Proust o papel de arauto do modernismo literário. Dessa forma, apresentarei alguns debates tematizados pelos contemporâneos e que engajaram Proust e sua obra não apenas em querelas literárias, artísticas e estéticas, mas em discussões de maior amplitude social e cultural concernentes à Terceira República Francesa. Utilizarei historiografia específica, bem como bibliografia mais ampla, para mostrar que as querelas nas quais Proust e seu romance foram envolvidos concerniam não apenas ao debate literário e estético, mas também às temporalidades e historicidades de maior amplitude que permearam a sociedade e a cultura francesas.
Quando a literatura fala à história: a ficção de Barbosa Lessa e a memória pública no Rio Grande do Sul
Authors: Zalla Jocelito 
Published: December 2014

O objetivo deste trabalho é analisar as intervenções de Luiz Carlos Barbosa Lessa, escritor, folclorista e militante fundador do movimento tradicionalista gaúcho, no debate público rio-grandense pela literatura de imaginação. Para tanto, parte-se de um episódio que agitou a produção letrada local na década de 1950, o chamado “caso Sepé”, em torno do qual foi ponderada a conveniência ou inviabilidade de incorporar a experiência missioneira guarani na narração do passado gaúcho. Buscase, portanto, não somente averiguar as posições do autor no debate, mas avaliar as possibilidades e escolhas formais de confronto, em especial a escrita literária como contraponto ao discurso histórico. A tomada de posição de Lessa sobre a questão indígena leva a críticas mais amplas ao modelo dominante de memória histórica no estado, orientando seu projeto literário para criações até então pouco comuns, como a figuração de grupos e segmentos tidos como marginais (indígenas, negros, mulheres), além da reafirmação do caráter popular do gaúcho rio-grandense.
Um grão de sal: autenticidade, felicidade e relações de amizade na correspondência de Mário de Andrade com Carlos Drummond
Authors: De Araújo Ricardo Benzaquen 
Published: December 2014

O texto em pauta pretende examinar a forma pela qual Mário de Andrade elabora a sua subjetividade na correspondência que troca com Carlos Drummond de Andrade. O seu argumento central é o de que a personalidade sanguínea, forte e autêntica de Mário não desconhece momentos de insegurança, abandono e até desilusão, momentos que, paradoxalmente, só conseguem ser superados pelo recurso a experiências marcadas pela dor física e espiritual a que ele, nas próprias relações de amizade – em função, por exemplo, das críticas que lhe são endereçadas pelos amigos –, não deixa de se submeter. Assim, longe de procurar a felicidade em um terreno utópico, no futuro ou no além, nosso autor se arrisca a confrontar diretamente o infortúnio, convicto de que os desafios e a alteridade embutidos nesse gesto serão capazes de gerar uma energia em condições de aperfeiçoar a sua intensa, fecunda e quase excessiva identidade pessoal.