bluuebunny/crossref_metadata_2025_split huggingface dataset:
Profiling the resting venom gland of the scorpion Tityus stigmurus through a transcriptomic survey
Authors: Almeida Diego D , Scortecci Katia C , Kobashi Leonardo S , Agnez-Lima Lucymara F , Medeiros Silvia R B , Silva-Junior Arnóbio A , Junqueira-de-Azevedo Inácio de L M , Fernandes-Pedrosa Matheus de F 
Published: August 2012

Abstract

Background
The scorpion Tityus stigmurus is widely distributed in Northeastern Brazil and known to cause severe human envenoming, inducing pain, hyposthesia, edema, erythema, paresthesia, headaches and vomiting. The present study uses a transcriptomic approach to characterize the gene expression profile from the non-stimulated venom gland of Tityus stigmurus scorpion.

Results
A cDNA library was constructed and 540 clones were sequenced and grouped into 153 clusters, with one or more ESTs (expressed sequence tags). Forty-one percent of ESTs belong to recognized toxin-coding sequences, with transcripts encoding antimicrobial toxins (AMP-like) being the most abundant, followed by alfa KTx- like, beta KTx-like, beta NaTx-like and alfa NaTx-like. Our analysis indicated that 34% of the transcripts encode “other possible venom molecules”, which correspond to anionic peptides, hypothetical secreted peptides, metalloproteinases, cystein-rich peptides and lectins. Fifteen percent of ESTs are similar to cellular transcripts. Sequences without good matches corresponded to 11%.

Conclusions
This investigation provides the first global view of gene expression of the venom gland from Tityus stigmurus under resting conditions. This approach enables characterization of a large number of venom gland component molecules, which belong either to known or non yet described types of venom peptides and proteins from the Buthidae family.
Multifunctional role of dextran sulfate sodium for in vivo modeling of intestinal diseases
Authors: Rose William A , Sakamoto Kaori , Leifer Cynthia A 
Published: August 2012

Abstract

Background
Inflammatory bowel diseases (IBDs) are chronic, relapsing disorders that affect the gastrointestinal tract of millions of people and continue to increase in incidence each year. While several factors have been associated with development of IBDs, the exact etiology is unknown. Research using animal models of IBDs is beginning to provide insights into how the different factors contribute to disease development. Oral administration of dextran sulfate sodium (DSS) to mice induces a reproducible experimental colitis that models several intestinal lesions associated with IBDs. The murine DSS colitis model can also be adapted to quantify intestinal repair following injury. Understanding the mechanistic basis behind intestinal repair is critical to development of new therapeutics for IBDs because of their chronic relapsing nature.

Results
The murine DSS colitis model was adapted to provide a system enabling the quantification of severe intestinal injury with impaired wound healing or mild intestinal injury with rapid restoration of mucosal integrity, by altering DSS concentrations and including a recovery phase. We showed that through a novel format for presentation of the clinical disease data, the temporal progression of intestinal lesions can be quantified on an individual mouse basis. Additionally, parameters for quantification of DSS-induced alterations in epithelial cell populations are included to provide insights into mechanisms underlying the development of these lesions. For example, the use of the two different model systems showed that toll-like receptor 9, a nucleic acid-sensing pattern recognition receptor, is important for protection only following mild intestinal damage and suggests that this model is superior for identifying proteins necessary for intestinal repair.

Conclusions
We showed that using a murine DSS-induced experimental colitis model system, and presenting data in a longitudinal manner on a per mouse basis, enhanced the usefulness of this model, and provided novel insights into the role of an innate immune receptor in intestinal repair. By elucidating the mechanistic basis of intestinal injury and repair, we can begin to understand the etiology of IBDs, enabling development of novel therapeutics or prophylactics.
Hierarchical clustering of gene expression patterns in the Eomes + lineage of excitatory neurons during early neocortical development
Authors: Cameron David A , Middleton Frank A , Chenn Anjen , Olson Eric C 
Published: August 2012

AbstractBackgroundCortical neurons display dynamic patterns of gene expression during the coincident processes of differentiation and migration through the developing cerebrum. To identify genes selectively expressed by the Eomes + (Tbr2) lineage of excitatory cortical neurons, GFP-expressing cells from Tg(Eomes::eGFP) Gsat embryos were isolated to > 99% purity and profiled.ResultsWe report the identification, validation and spatial grouping of genes selectively expressed within the Eomes + cortical excitatory neuron lineage during early cortical development. In these neurons 475 genes were expressed ≥ 3-fold, and 534 genes ≤ 3-fold, compared to the reference population of neuronal precursors. Of the up-regulated genes, 328 were represented at the Genepaint in situ hybridization database and 317 (97%) were validated as having spatial expression patterns consistent with the lineage of differentiating excitatory neurons. A novel approach for quantifying in situ hybridization patterns (QISP) across the cerebral wall was developed that allowed the hierarchical clustering of genes into putative co-regulated groups. Forty four candidate genes were identified that show spatial expression with Intermediate Precursor Cells, 49 candidate genes show spatial expression with Multipolar Neurons, while the remaining 224 genes achieved peak expression in the developing cortical plate.ConclusionsThis analysis of differentiating excitatory neurons revealed the expression patterns of 37 transcription factors, many chemotropic signaling molecules (including the Semaphorin, Netrin and Slit signaling pathways), and unexpected evidence for non-canonical neurotransmitter signaling and changes in mechanisms of glucose metabolism. Over half of the 317 identified genes are associated with neuronal disease making these findings a valuable resource for studies of neurological development and disease.
White versus gray matter: fMRI hemodynamic responses show similar characteristics, but differ in peak amplitude
Authors: Fraser Leanne M , Stevens M Tynan , Beyea Steven D , D’Arcy Ryan C N 
Published: August 2012

Abstract

Background
There is growing evidence for the idea of fMRI activation in white matter. In the current study, we compared hemodynamic response functions (HRF) in white matter and gray matter using 4 T fMRI. White matter fMRI activation was elicited in the isthmus of the corpus callosum at both the group and individual levels (using an established interhemispheric transfer task). Callosal HRFs were compared to HRFs from cingulate and parietal activation.

Results
Examination of the raw HRF revealed similar overall response characteristics. Finite impulse response modeling confirmed that the WM HRF characteristics were comparable to those of the GM HRF, but had significantly decreased peak response amplitudes.

Conclusions
Overall, the results matched a priori expectations of smaller HRF responses in white matter due to the relative drop in cerebral blood flow (CBF) and cerebral blood volume (CBV). Importantly, the findings demonstrate that despite lower CBF and CBV, white matter fMRI activation remained within detectable ranges at 4 T.
Reproducibility of Corneal Graft Thickness measurements with COLGATE in patients who have undergone DSAEK (Descemet Stripping Automated Endothelial Keratoplasty)
Authors: Wong Melissa HY , Chew Annabel , Htoon Hla M , Lee Beng H , Cheng Jun , Liu Jiang , Tan Donald T , Mehta Jodhbir S 
Published: August 2012

Abstract

Background
The CorneaL GrAft Thickness Evaluation (COLGATE) system was recently developed to facilitate the evaluation of corneal graft thickness from OCT images. Graft thickness measurement can be a surrogate indicator for detecting graft failure or success. The purpose of this study was to determine the reproducibility of the COLGATE system in measuring DSAEK graft area between two observers.

Methods
This was a prospective case series in which 50 anterior segment OCT images of patients who had undergone DSAEK in either eye were analysed. Two observers (MW, AC) independently obtained the image analysis for the graft area using both semi automated and automated method. One week later, each observer repeated the analysis for the same set of images. Bland-Altman analysis was performed to analyze inter and intra observer agreement.

Results
There was strong intraobserver correlation between the 2 semi automated readings obtained by both observers. (r = 0.936 and r = 0.962). Intraobserver ICC for observer 1 was 0.936 (95% CI 0.890 to 0.963) and 0.967 (95% CI 0.942 to 0.981) for observer 2. Likewise, there was also strong interobserver correlation (r = 0.913 and r = 0.969). The interobserver ICC for the first measurements was 0.911 (95% CI 0.849 to 0.949) and 0.968 (95% CI 0.945 to 0.982) for the second. There was statistical difference between the automatic and the semi automated readings for both observers (p = 0.006, p = 0.003). The automatic readings gave consistently higher values than the semi automated readings especially in thin grafts.

Conclusion
The analysis from the COLGATE programme can be reproducible between different observers. Care must be taken when interpreting the automated analysis as they tend to over estimate measurements.
A systems biology approach to the global analysis of transcription factors in colorectal cancer
Authors: Pradhan Meeta P , Prasad Nagendra KA , Palakal Mathew J 
Published: August 2012

AbstractBackgroundBiological entities do not perform in isolation, and often, it is the nature and degree of interactions among numerous biological entities which ultimately determines any final outcome. Hence, experimental data on any single biological entity can be of limited value when considered only in isolation. To address this, we propose that augmenting individual entity data with the literature will not only better define the entity’s own significance but also uncover relationships with novel biological entities.To test this notion, we developed a comprehensive text mining and computational methodology that focused on discovering new targets of one class of molecular entities, transcription factors (TF), within one particular disease, colorectal cancer (CRC).MethodsWe used 39 molecular entities known to be associated with CRC along with six colorectal cancer terms as thebait list, or list of search terms, for mining the biomedical literature to identify CRC-specific genes and proteins. Using the literature-mined data, we constructed a global TF interaction network for CRC. We then developed a multi-level, multi-parametric methodology to identify TFs to CRC.ResultsThe small bait list, when augmented with literature-mined data, identified a large number of biological entities associated with CRC. The relative importance of these TF and their associated modules was identified using functional and topological features. Additional validation of these highly-ranked TF using the literature strengthened our findings. Some of the novel TF that we identified were: SLUG, RUNX1, IRF1, HIF1A, ATF-2, ABL1, ELK-1 and GATA-1. Some of these TFs are associated with functional modules in known pathways of CRC, including the Beta-catenin/development, immune response, transcription, and DNA damage pathways.ConclusionsOur methodology of using text mining data and a multi-level, multi-parameter scoring technique was able to identify both known and novel TF that have roles in CRC. Starting with just one TF (SMAD3) in the bait list, the literature mining process identified an additional 116 CRC-associated TFs. Our network-based analysis showed that these TFs all belonged to any of 13 major functional groups that are known to play important roles in CRC. Among these identified TFs, we obtained a novel six-node module consisting of ATF2-P53-JNK1-ELK1-EPHB2-HIF1A, from which the novel JNK1-ELK1 association could potentially be a significant marker for CRC.
Brahmarasayana protects against Ethyl methanesulfonate or Methyl methanesulfonate induced chromosomal aberrations in mouse bone marrow cells
Authors: Guruprasad Kanive Parashiva , Subramanian Advait , Singh Vikram Jeet , Sharma Raghavendra Sudheer Kumar , Gopinath Puthiya Mundyat , Sewram Vikash , Varier Panniyampilly Madhavankutty , Satyamoorthy Kapaettu 
Published: August 2012

Abstract

Background
Ayurveda, the traditional Indian system of medicine has given great emphasis to the promotion of health. Rasayana is one of the eight branches of Ayurveda which refers to rejuvenant therapy. It has been reported that rasayanas have immuno-modulatory, antioxidant and antitumor functions, however, the genotoxic potential and modulation of DNA repair of many rasayanas have not been evaluated.

Methods
The present study assessed the role of Brahmarasayana (BR) on Ethyl methanesulfonate (EMS)-and Methyl methanesulfonate (MMS)-induced genotoxicity and DNA repair in in vivo mouse test system. The mice were orally fed with BR (5 g or 8 mg / day) for two months and 24 h later EMS or MMS was given intraperitoneally. The genotoxicity was analyzed by chromosomal aberrations, sperm count, and sperm abnormalities.

Results
The results have revealed that BR did not induce significant chromosomal aberrations when compared to that of the control animals (p >0.05). On the other hand, the frequencies of chromosomal aberrations induced by EMS (240 mg / kg body weight) or MMS (125 mg / kg body weight) were significantly higher (p<0.05) to that of the control group. The treatment of BR for 60 days and single dose of EMS or MMS on day 61, resulted in significant (p <0.05) reduction in the frequency of chromosomal aberrations in comparison to EMS or MMS treatment alone, indicating a protective effect of BR. Constitutive base excision repair capacity was also increased in BR treated animals.

Conclusion
The effect of BR, as it relates to antioxidant activity was not evident in liver tissue however rasayana treatment was observed to increase constitutive DNA base excision repair and reduce clastogenicity. Whilst, the molecular mechanisms of such repair need further exploration, this is the first report to demonstrate these effects and provides further evidence for the role of brahmarasayana in the possible improvement of quality of life.
Pharmacokinetic profiles of artesunate following multiple intravenous doses of 2, 4, and 8 mg/kg in healthy volunteers: Phase 1b study
Authors: Miller Robert Scott , Li Qigui , Cantilena Louis R , Leary Kevin J , Saviolakis George A , Melendez Victor , Smith Bryan , Weina Peter J 
Published: August 2012

Abstract

Background
Severe malaria results in over a million deaths every year, most of them in children aged less than five years and living in sub-Saharan Africa. Injectable artesunate (AS) was recommended as initial treatment for severe malaria by WHO in 2006. The Walter Reed Army Institute of Research (WRAIR) has been developing a novel good manufacturing practice (GMP) injection of AS, which was approved by the US FDA for investigational drug use and distribution by the CDC.

Methods
Tolerability and pharmacokinetics of current GMP intravenous AS, as an anti-malarial agent, were evaluated after ascending multiple doses of 2, 4, and 8 mg/kg daily for three days with 2-minute infusion in 24 healthy subjects (divided into three groups) in the Phase 1 clinical trial study.

Results
Results showed that there were no dose-dependent increases in any adverse events. Drug concentrations showed no accumulation and no decline of the drug during the three days of treatment. After intravenous injection, parent drug rapidly declined and was converted to dihydroartemisinin (DHA) with overall mean elimination half-lives ranging 0.15-0.23 hr for AS and 1.23-1.63 hr for DHA, but the peak concentration (Cmax) of AS was much higher than that of DHA with a range of 3.08-3.78-folds. In addition, the AUC and Cmax values of AS and DHA were increased proportionally to the AS climbing multiple doses.

Discussion
The safety of injectable AS, even at the highest dose of 8 mg/kg increases the probability of therapeutic success of the drug even in patients with large variability of parasitaemia.
High-performance III-V MOSFET with nano-stacked high-k gate dielectric and 3D fin-shaped structure
Authors: Chen Szu-Hung , Liao Wen-Shiang , Yang Hsin-Chia , Wang Shea-Jue , Liaw Yue-Gie , Wang Hao , Gu Haoshuang , Wang Mu-Chun 
Published: August 2012

Abstract
A three-dimensional (3D) fin-shaped field-effect transistor structure based on III-V metal-oxide-semiconductor field-effect transistor (MOSFET) fabrication has been demonstrated using a submicron GaAs fin as the high-mobility channel. The fin-shaped channel has a thickness-to-width ratio (T
Fin/W
Fin) equal to 1. The nano-stacked high-k Al2O3 dielectric was adopted as a gate insulator in forming a metal-oxide-semiconductor structure to suppress gate leakage. The 3D III-V MOSFET exhibits outstanding gate controllability and shows a high I
on/I
off ratio > 105 and a low subthreshold swing of 80 mV/decade. Compared to a conventional Schottky gate metal–semiconductor field-effect transistor or planar III-V MOSFETs, the III-V MOSFET in this work exhibits a significant performance improvement and is promising for future development of high-performance n-channel devices based on III-V materials.
Classification of pasture habitats by Hungarian herders in a steppe landscape (Hungary)
Authors: Molnár Zsolt 
Published: August 2012

AbstractBackgroundLandscape ethnoecology focuses on the ecological features of the landscape, how the landscape is perceived, and used by people who live in it. Though studying folk classifications of species has a long history, the comparative study of habitat classifications is just beginning. I studied the habitat classification of herders in a Hungarian steppe, and compared it to classifications of botanists and laymen.MethodsFor a quantitative analysis the picture sort method was used. Twenty-three pictures of 7-11 habitat types were sorted by 25 herders.’Density’ of pictures along the habitat gradient of the Hortobágy salt steppe was set as equal as possible, but pictures differed in their dominant species, wetness, season, etc. Before sorts, herders were asked to describe pictures to assure proper recognition of habitats.ResultsHerders classified the images into three main groups: (1) fertile habitats at the higher parts of the habitat gradient (partos, lit. on the shore); (2) saline habitats (szík, lit. salt or saline place), and (3) meadows and marshes (lapos, lit. flooded) at the lower end of the habitat gradient. Sharpness of delimitation changed along the gradient. Saline habitats were the most isolated from the rest. Botanists identified 6 groups. Laymen grouped habitats in a less coherent way.As opposed to my expectations, botanical classification was not more structured than that done by herders. I expected and found high correspondence between the classifications by herders, botanists and laymen. All tended to recognize similar main groups: wetlands, ”good grass” and dry/saline habitats. Two main factors could have been responsible for similar classifications: salient features correlated (e.g. salinity recognizable by herders and botanists but not by laymen correlated with the density of grasslands or height of vegetation recognizable also for laymen), or the same salient features were used as a basis for sorting (wetness, and abiotic stress).ConclusionsDespite all the difficulties of studying habitat classifications (more implicit, more variable knowledge than knowledge on species), conducting landscape ethnoecological research will inevitably reveal a deeper human understanding of biological organization at a supraspecific level, where natural discontinuities are less sharp than at the species or population level.
Appropriate patient instructions can reduce prostate motion
Authors: Graf Reinhold , Boehmer Dirk , Nadobny Jacek , Budach Volker , Wust Peter 
Published: August 2012

Abstract

Background
Interfraction prostate motion must be compensated by increased safety margins. If filling status of rectum and bladder is constant, motion should be reduced. We attempted to reduce interfraction motion errors by proper patient instruction.

Method
In 38 patients pairs of radio-opaque fiducial markers were implanted prior to definitive radiotherapy. Patients were positioned either according to skin marks or infrared body marker. We measured prostate displacement, i.e. pelvic bones versus intraprostatic marker position, via ExacTrac (two orthogonal radiographies) in 1252 fractions. Systematic and random setup and displacement errors were determined and safety margins estimated.

Results
In our study interfraction prostate displacement is < 1 mm in RL direction, and < 2 mm in AP and SI direction. Systematic errors are slightly below random errors (< 1.5 mm). Positioning according skin marks results in higher inaccuracies of ±1.5 – 2 mm in RL and ±2 – 2.5 mm in AP/SI direction.

Conclusions
In case of appropriate patient instructions (constant organ filling) the positioning via bone fusion requires CTV-PTV margins of 2 mm in RL, 4 mm in AP, and 5 mm in SI direction. Studies without any description of patient instruction found much higher margins of > 1 cm in AP and SI direction.
Specific patterns of genetic diversity among aromatic rice varieties in Myanmar
Authors: Myint Khin Myo , Courtois Brigitte , Risterucci Ange-Marie , Frouin Julien , Soe Khin , Thet Khin Maung , Vanavichit Apichart , Glaszmann Jean-Christophe 
Published: August 2012

Abstract

Background
After observing peculiar rice varieties in Myanmar, in terms of classification in varietal groups and of grain quality, we focused on Myanmar varieties and analyzed variations at 19 microsatellite loci as well as sequences of the aroma gene BADH2.

Results
Microsatellites were able to retrieve the well-established classification into Indica (isozyme group 1), Japonica (group 6, comprising temperate and tropical forms) and specific groups from the Himalayan foothills including some Aus varieties (group 2) and some aromatic varieties (group 5). They revealed a new cluster of accessions close to, but distinct from, non-Myanmar varieties in group 5. With reference to earlier terminology, we propose to distinguish a group “5A” including group 5 varieties from the Indian subcontinent (South and West Asia) and a group “5B” including most group 5 varieties from Myanmar. In Myanmar varieties, aroma was distributed in group 1 (Indica) and in group 5B. New BADH2 variants were found. Some accessions carried a 43 bp deletion in the 3’ UTR that was not completely associated with aroma. Other accessions, all of group 5B, displayed a particular BADH2 allele with a 3 bp insertion and 100% association with aroma.

Conclusion
With the new group and the new alleles found in Myanmar varieties, our study shows that the Himalayan foothills contain series of non-Indica and non-Japonica varietal types with novel variations for useful traits.