bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rembrandt: Helping Personalized Medicine Become a Reality through Integrative Translational Research
Authors: Madhavan Subha , Zenklusen Jean-Claude , Kotliarov Yuri , Sahni Himanso , Fine Howard A. , Buetow Kenneth 
Published: February 2009

Abstract
Finding better therapies for the treatment of brain tumors is hampered by the lack of consistently obtained molecular data in a large sample set and the ability to integrate biomedical data from disparate sources enabling translation of therapies from bench to bedside. Hence, a critical factor in the advancement of biomedical research and clinical translation is the ease with which data can be integrated, redistributed, and analyzed both within and across functional domains. Novel biomedical informatics infrastructure and tools are essential for developing individualized patient treatment based on the specific genomic signatures in each patient's tumor. Here, we present Repository of Molecular Brain Neoplasia Data (Rembrandt), a cancer clinical genomics database and a Web-based data mining and analysis platform aimed at facilitating discovery by connecting the dots between clinical information and genomic characterization data. To date, Rembrandt contains data generated through the Glioma Molecular Diagnostic Initiative from 874 glioma specimens comprising ∼566 gene expression arrays, 834 copy number arrays, and 13,472 clinical phenotype data points. Data can be queried and visualized for a selected gene across all data platforms or for multiple genes in a selected platform. Additionally, gene sets can be limited to clinically important annotations including secreted, kinase, membrane, and known gene-anomaly pairs to facilitate the discovery of novel biomarkers and therapeutic targets. We believe that Rembrandt represents a prototype of how high-throughput genomic and clinical data can be integrated in a way that will allow expeditious and efficient translation of laboratory discoveries to the clinic. (Mol Cancer Res 2009;7(2):157–67)
Magnesium Sulfate for the Treatment of Eclampsia
Authors: Euser Anna G. , Cipolla Marilyn J. 
Published: February 2009

Background and Purpose—Magnesium sulfate is used extensively for prevention of eclamptic seizures. Empirical and clinical evidence supports the effectiveness of magnesium sulfate; however, questions remain as to its safety and mechanism. This review summarizes current evidence supporting the possible mechanisms of action and several controversies for magnesium sulfate treatment.Summary of Review—Several mechanisms are presented, including the effects of magnesium sulfate on peripheral and cerebral vasodilation, blood-brain barrier protection, and as an anticonvulsant.Conclusions—Though the specific mechanisms of action remain unclear, the effect of magnesium sulfate in the prevention of eclampsia is likely multi-factorial. Magnesium sulfate may act as a vasodilator, with actions in the peripheral vasculature or the cerebrovasculature, to decrease peripheral vascular resistance or relieve vasoconstriction. Additionally, magnesium sulfate may also protect the blood-brain barrier and limit cerebral edema formation, or it may act through a central anticonvulsant action.
Escape tactic plasticity of two sympatric Norops (Beta Anolis) species in Northeast Costa Rica
Authors: Lattanzio Matthew 
Published: February 2009

AbstractOptimal Escape Theory (OET) has been used extensively to predict escape responses of lizards facing predation, yet few studies have examined the responses of two species that share the same habitat, even though such lizards may exhibit distinct patterns of spatial habitat use and behaviour. Furthermore, while OET may predict when escape behaviour should occur, it does not account for any variation in tactics used. Here, the escape behaviour of sympatric Norops humilis and N. limifrons lizards were studied. Lizard microhabitats were categorized and approach speeds were randomised such that each lizard was approached at one of two speeds, slow or fast. Approach speed of a simulated predator had no significant effect on approach distances for either species. Ambient and surface temperatures varied throughout the study period, yet had no significant effect on the escape responses of either species. Species differences in escape tactics correlated with microhabitat: Norops humilis were found more often on small shrubs and typically escaped by jumping to adjacent shrub branches or leaves. Norops limifrons, on the other hand, were typically found on tree trunks and thicker stems, and used squirrelling (horizontal movement around a trunk, branch, or stem) as a primary escape tactic. Additionally, all lizards encountered at ground-level ran. These results thus illustrate the variety of escape tactics used by sympatric N. humilis and N. limifrons within their structurally diverse habitat.
Phospholipase A2 activity of crocodile serum
Authors: Nevalainen Timo J. , Kanchanapangka Sumolya , Youngprapakorn Panya , Webb Grahame J. W. , Manolis S. Charlie , Scott Kieran F. 
Published: February 2009

Abstract
The catalytic activity of phospholipase A2 (PLA2) was measured in serum
samples from 32 crocodiles in Thailand and Australia by a method using
14C-oleic acid-labelled autoclaved Escherichia coli membranes as a
substrate. The highest PLA2 activity was measured in the serum of Crocodylus
siamensis (n = 9, mean ± SD), 13.3 ± 3.1 U/l followed by hybrid C. siamensis
× C. porosus (n = 6), 10.4 ± 8.7 U/l and Crocodylus porosus (n = 17), 4.3 ±
3.0 U/l. The difference between C. siamensis and C. porosus was highly
significant (P < 0.001). The gender of the animals and the geographical
location of the crocodile farms were not significant variables affecting
serum PLA2 levels. It was concluded that PLA2 is present in crocodilian
serum and may have an antimicrobial role.
Effects of predation risk factors on escape behavior by Balearic lizards (Podarcis lilfordi) in relation to optimal escape theory
Authors: Cooper, Jr. William E. , Hawlena Dror , Pérez-Mellado Valentín 
Published: February 2009

Abstract
Escape theory predicts that flight initiation distance (FID = predator-prey
distance when escape begins) increases as predation risk increases. We
tested effects of variation of approach speed and directness, predator
persistence, concealment, and weather conditions on FID in the Balearic
lizard (Podarcis lilfordi) by ourselves simulating predators. We examined
effects of directness of approach on probability of fleeing and of repeated
approach on entering refuge and distance fled. As predicted, FID was greater
for faster approach speed, more direct approach, during second than first
approaches, and when lizards were exposed than partially concealed. Other
effects of directness of approach and repeated approach also were as
predicted by greater assessed risk by the lizards. The proportion of
individuals that fled was greater for direct than indirect approaches. The
proportion of lizards that entered refuges and distance fled were greater
during the second of two successive approaches. Effects of weather on FID
were complex. FID was shortest in the warmest conditions with no noticeable
wind, when lizards were active. Lizards were inactive and basked in the
other conditions. FID was longest at 20°C without wind, and intermediate FID
occurred at 18°C in windy conditions. We present hypotheses for weather
effects. Tests are needed to unravel effects of temperature and wind speed.
All predictions of escape theory for simple risk factors, i.e., all except
than weather conditions, were confirmed. Escape theory successfully predicts
FID for these risks in P. lilfordi, other lacertids, and more broadly, in
ecologically and taxonomically diverse lizards.
In the Eyes of the Christian Writer al-Hārit ibn Sinān Poetics and Eloquence as a Platform of Inter-Cultural Contacts and Contrasts
Authors: Sadan Joseph 
Published: February 2009

AbstractWhile ostensibly aspects of poetics are best discussed within a purely literary perspective, in fact they can hardly be disconnected from their socio-cultural and religious frameworks. Al-Hārit ibn Sinān was a Christian scholar and writer who lived under Muslim rule towards the end of the ninth and apparently also the beginning of the tenth century, precisely at the time when the first fruits of the idea of the Qur‘ān's stylistic inimitability (i’ğāz) began to ripe. Although this concept played a role also in interfaith polemics throughout the Middle Ages, our author shows his temperance and restraint by praising the style of the Bible (he would appear not to have read the books of the Old Testament in the original Hebrew but demonstrated understanding and a feeling for the text through another Semitic language: Syriac), both because as a Christian living under Muslim rule he was loathe to arouse an overt controversy with the society in which he lived, and also because glorifying the style of Holy Scripture, which he had apparently inherited from the Syriac-Byzantine culture, was an important tendency in and of itself in both Jewish and Christian literature (in England, for example, upsurges of this tendency have occurred even in modern times). Nevertheless, we cannot ignore the fact that our author did compare the poetics of four cultures: that of the Hebrews, that of the Greek (or rather Greek-Byzantine, rūm), that of the Syriac elements and that of the Arabs. He even tries to prove, using somewhat specious arguments, that the Hebrew portions of the Bible contain rhymes. His positions thus deserve to be considered retrospectively also in an interfaith and intercultural context.
An Assessment of the Importance of Chaotic Stirring and Turbulent Mixing on the West Florida Shelf
Authors: Beron-Vera F. J. , Olascoaga M. J. 
Published: February 2009

Abstract
Application of dynamical systems tools has recently revealed in surface ocean currents produced by a Hybrid-Coordinate Ocean Model (HYCOM) simulation the presence of a persistent large-scale Lagrangian coherent structure (LCS) on the southern portion of the west Florida shelf (WFS). Consistent with satellite-tracked drifter trajectories, this LCS constitutes a cross-shelf barrier for the lateral transport of passive tracers. Because of the constraints that the above LCS, as well as smaller-scale LCSs lying shoreside, can impose on pollutant dispersal and its potentially very important biological consequences, a study was carried out on the nature of the surface ocean Lagrangian motion on the WFS. The analysis is based on the same simulated surface ocean velocity field that has been able to sustain the aforementioned persistent cross-shelf transport barrier. Examination of several diagnostics suggests that chaotic stirring dominates over turbulent mixing on time scales of up to two months or so. More specifically, it is found on those time scales that tracer evolution at a given length scale is governed to a nonnegligible extent by coarser-scale velocity field features, fluid particle dispersion is spatially inhomogeneous, and the Lagrangian evolution is more irregular than the driving Eulerian flow.
A Polar Low Pair over the Norwegian Sea
Authors: Brümmer Burghard , Müller Gerd , Noer Gunnar 
Published: February 2009

Abstract
During the Lofotes cyclone experiment (LOFZY 2005), two polar lows developed one behind the other inside a cold-air outbreak from the north in the lee of Spitsbergen on 7 March 2005. Buoys, ship, and aircraft measurements as well as satellite imagery are applied to analyze the polar low bulk properties, the horizontal and vertical structure, and the mass, moisture, and heat budget. The lifetime of the system until landfall at northern Norway was 12 h. The generation occurred under the left exit region of an upper-level jet with 70 m s−1. Both polar lows had a radius of 100–130 km and extended to a height of about 2.5 km. The propagation speeds were within 14–17 m s−1 and correspond to the vertically averaged wind velocity of the lowest 2.5 km. In the polar low centers the pressure was about 2–3 hPa lower and the air was 1–2 K warmer and drier than in the surroundings. Aircraft measurements in the second of the two polar lows show an embedded frontlike precipitation band north of the center. Here, the highest low-level winds with 25 m s−1 and the largest fluxes of sensible and latent heat with 290 and 520 W m−2, respectively, were measured (areal averages amounted to 115 and 190 W m−2). Aircraft data show mass convergence in the subcloud layer (0–900 m) and divergence in the cloud layer (900–2500 m). Moisture supply by evaporation from the sea surface was about twice as large as that by convergence in the subcloud layer. The condensation rate in the cloud layer nearly equaled the rate of evaporation at the sea surface. Almost all condensed cloud water was converted to precipitation water. Only half of the precipitation at the cloud base reached the sea surface.
MicroRNA transcriptome profiles during swine skeletal muscle development
Authors: McDaneld Tara G , Smith Timothy PL , Doumit Matthew E , Miles Jeremy R , Coutinho Luiz L , Sonstegard Tad S , Matukumalli Lakshmi K , Nonneman Dan J , Wiedmann Ralph T 
Published: February 2009

Abstract

Background
MicroRNA (miR) are a class of small RNAs that regulate gene expression by inhibiting translation of protein encoding transcripts. To evaluate the role of miR in skeletal muscle of swine, global microRNA abundance was measured at specific developmental stages including proliferating satellite cells, three stages of fetal growth, day-old neonate, and the adult.

Results
Twelve potential novel miR were detected that did not match previously reported sequences. In addition, a number of miR previously reported to be expressed in mammalian muscle were detected, having a variety of abundance patterns through muscle development. Muscle-specific miR-206 was nearly absent in proliferating satellite cells in culture, but was the highest abundant miR at other time points evaluated. In addition, miR-1 was moderately abundant throughout developmental stages with highest abundance in the adult. In contrast, miR-133 was moderately abundant in adult muscle and either not detectable or lowly abundant throughout fetal and neonate development. Changes in abundance of ubiquitously expressed miR were also observed. MiR-432 abundance was highest at the earliest stage of fetal development tested (60 day-old fetus) and decreased throughout development to the adult. Conversely, miR-24 and miR-27 exhibited greatest abundance in proliferating satellite cells and the adult, while abundance of miR-368, miR-376, and miR-423-5p was greatest in the neonate.

Conclusion
These data present a complete set of transcriptome profiles to evaluate miR abundance at specific stages of skeletal muscle growth in swine. Identification of these miR provides an initial group of miR that may play a vital role in muscle development and growth.
Inducible expression of beta defensins by human respiratory epithelial cells exposed to Aspergillus fumigatusorganisms
Authors: Alekseeva Ludmila , Huet Dominique , Féménia Françoise , Mouyna Isabelle , Abdelouahab Mahdia , Cagna Adrien , Guerrier Daniel , Tichanné-Seltzer Virginie , Baeza-Squiban Armelle , Chermette René , Latgé Jean-Paul , Berkova Nadia 
Published: February 2009

AbstractBackgroundAspergillus fumigatus, a saprophytic mould, is responsible for life-threatening, invasive pulmonary diseases in immunocompromised hosts. The role of the airway epithelium involves a complex interaction with the inhaled pathogen. Antimicrobial peptides with direct antifungal and chemotactic activities may boost antifungal immune response.ResultsThe inducible expression of defensins by human bronchial epithelial 16HBE cells and A549 pneumocyte cells exposed toA. fumigatuswas investigated. Using RT-PCR and real time PCR, we showed an activation of hBD2 and hBD9 defensin genes: the expression was higher in cells exposed to swollen conidia (SC), compared to resting conidia (RC) or hyphal fragments (HF). The kinetics of defensin expression was different for each one, evoking a putative distinct function for each investigated defensin. The decrease of defensin expression in the presence of heat-inactivated serum indicated a possible link between defensins and the proteins of the host complement system. The presence of defensin peptide hBD2 was revealed using immunofluorescence that showed a punctual cytoplasmic and perinuclear staining. Quantification of the cells stained with anti hBD2 antibody demonstrated that SC induced a greater number of cells that synthesized hBD2, compared to RC or HF. Labelling of the cells with anti-hBD-2 antibody showed a positive immunofluorescence signal around RC or SC in contrast to HF. This suggests co-localisation of hBD2 and digested conidia. The HBD2 level was highest in the supernatants of cells exposed to SC, as was determined by sandwich ELISA. Experiments using neutralising anti-interleukine-1β antibody reflect the autocrine mechanism of defensin expression induced by SC. Investigation of defensin expression at transcriptional and post-transcriptional levels demonstrated the requirement of transcription as well as new protein synthesis duringA. fumigatusdefensin induction. Finally, induced defensin expression in primary culture of human respiratory cells exposed toA. fumigatuspoints to the biological significance of described phenomena.ConclusionOur findings provide evidence that respiratory epithelium might play an important role in the immune response duringAspergillusinfection. Understanding the mechanisms of regulation of defensin expression may thus lead to new approaches that could enhance expression of antimicrobial peptides for potential therapeutic use during aspergillosis treatment.
Identification of two proteins that interact with the Erp virulence factor from Mycobacterium tuberculosis by using the bacterial two-hybrid system
Authors: Klepp Laura I , Soria Marcelo , Blanco Federico C , Bianco María V , Santangelo María P , Cataldi Angel A , Bigi Fabiana 
Published: February 2009

Abstract

Background
The exported repetitive protein (erp) gene encodes a secreted 36-kDa protein with a central domain containing several proline-glycine-leucine-threonine-serine (PGLTS) repeats. It has been demonstrated that erp is a virulence-associated factor since the disruption of this gene impairs the growth of Mycobacterium bovis and Mycobacterium tuberculosis in mice.

Results
In order to elucidate the function of Erp we searched for Erp-binding proteins from M. tuberculosis by using a bacterial two-hybrid system. Our results indicate that Erp interacts specifically with two putative membrane proteins, Rv1417 and Rv2617c. Further analysis revealed that the latter two interact with each other, indicating that Rv1417, Rv2617c and Erp are connected through multiple interactions. While Rv1417 is disseminated in several Actinomycetales genera, orthologues of Rv2617c are exclusively present in members of the M. tuberculosis complex (MTC). The central and amino-terminal regions of Erp were determined to be involved in the interaction with Rv1417 and Rv2627c. Erp forms from Mycobacterium smegmatis and Mycobacterium leprae were not able to interact with Rv2617c in two-hybrid assays. Immunolocalization experiments showed that Rv1417 and Rv2617c are found on the cell membrane and Erp on the bacterial cell wall. Finally, comparative genomics and expression studies revealed a possible role of Rv1417 in riboflavin metabolism.

Conclusion
We identified interactive partners of Erp, an M. tuberculosis protein involved in virulence, which will be the focus of future investigation to decipher the function of the Erp family protein.
Extremely short duration high intensity interval training substantially improves insulin action in young healthy males
Authors: Babraj John A , Vollaard Niels BJ , Keast Cameron , Guppy Fergus M , Cottrell Greg , Timmons James A 
Published: February 2009

Abstract

Background
Traditional high volume aerobic exercise training reduces cardiovascular and metabolic disease risk but involves a substantial time commitment. Extremely low volume high-intensity interval training (HIT) has recently been demonstrated to produce improvements to aerobic function, but it is unknown whether HIT has the capacity to improve insulin action and hence glycemic control.

Methods
Sixteen young men (age: 21 ± 2 y; BMI: 23.7 ± 3.1 kg·m-2; VO2peak: 48 ± 9 ml·kg-1·min-1) performed 2 weeks of supervised HIT comprising of a total of 15 min of exercise (6 sessions; 4–6 × 30-s cycle sprints per session). Aerobic performance (250-kJ self-paced cycling time trial), and glucose, insulin and NEFA responses to a 75-g oral glucose load (oral glucose tolerance test; OGTT) were determined before and after training.

Results
Following 2 weeks of HIT, the area under the plasma glucose, insulin and NEFA concentration-time curves were all reduced (12%, 37%, 26% respectively, all P < 0.001). Fasting plasma insulin and glucose concentrations remained unchanged, but there was a tendency for reduced fasting plasma NEFA concentrations post-training (pre: 350 ± 36 v post: 290 ± 39 μmol·l-1, P = 0.058). Insulin sensitivity, as measured by the Cederholm index, was improved by 23% (P < 0.01), while aerobic cycling performance improved by ~6% (P < 0.01).

Conclusion
The efficacy of a high intensity exercise protocol, involving only ~250 kcal of work each week, to substantially improve insulin action in young sedentary subjects is remarkable. This novel time-efficient training paradigm can be used as a strategy to reduce metabolic risk factors in young and middle aged sedentary populations who otherwise would not adhere to time consuming traditional aerobic exercise regimes.
The uterine expression of SEC63gene is up-regulated at implantation sites in association with the decidualization during the early pregnancy in mice
Authors: Su Ren-wei , Sun Zhao-gui , Zhao Yue-chao , Chen Qiu-ju , Yang Zeng-ming , Li Run-sheng , Wang Jian 
Published: February 2009

Abstract

Background
Sec63 is a key component of the protein translocation machinery in the mammalian endoplasmic reticulum (ER), and involved in the post-translation processing of secretory proteins. The aim of this study was to determine the expression pattern of SEC63 gene in mouse uterus during the early pregnancy.

Methods
Real-time quantitative PCR and Western blot analyses were used to evaluate the alteration in levels of uterine SEC63 gene expression during the peri-implantation period in mice. Further, both in situ hybridization and immunohistochemical analyses were performed to examine the spatial localization of SEC63 gene expression in mouse uterine tissues. The presence of Sec63 protein in human uterine tissue was also detected by immunohistochemical analysis. Statistical analysis was carried out using Tukey test.

Results
Uterine SEC63 gene expression was up-regulated and predominantly localized in mouse decidual cells during days 5–8 of pregnancy. More interestingly, Sec63 protein was also detected in human decidua of 10-week pregnancy, whereas was not observed in human endometrial tissues both at proliferative and secretory phases of menstrual cycle.

Conclusion
The pattern of SEC63 gene expression is consistent with a possible role for SEC63 in decidualization.