bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of an Electro-Optic Scanner for Potential Endoscope Application
Authors: Wang W. , Lee S. , Jen A. , Reinhall P. , Nuckley D. 
Published: July 2009

Technological advancements in endoscopy design are in current development due to the increased demand for minimally invasive medical procedures. One such advancement is reducing the overall size of the endoscope system while maintaining the resolution and field-of-view (FOV). Reduction of size results in less tissue damage and trauma during operation as well as faster recovery times for patients. Additionally, areas that are inaccessible by today's endoscope designs will be possible to examine. Current endoscopes use either a bundle of optical fibers (optical waveguides) and/or one or more cameras having an array of detectors to capture an image. Thus, the diameter of these devices employed for remote imaging cannot be reduced to smaller than the image size. Even if one ignores additional optical fibers used for illumination of a region of interest, the scope diameter is therefore limited by the individual pixel size of a camera or by the diameter of optical fibers used to acquire the image. Therefore, it is apparent to achieve scopes with less than 3 mm overall diameter using current technologies, resolution and/or FOV must be sacrificed by having fewer pixel elements. All commercially available scopes suffer from this fundamental tradeoff between high image quality and small size. More recently, our research has been working on developing a 2-D electro-optic scanner potentially be implemented for clinical endoscopic imaging application. The proposed optical device has several unique advantages. Electro-optical scanning offers a sensitive, facile, accurate, and superb quality method to capture images of physical and biological tissues. In addition, the minute physical size of the imaging system has a much needed advantage over conventional imaging systems. The proposed design is based on the fact that the propagation direction of a light beam can be changed when the index of refraction of an electro-optic medium is altered by the application of an external electric field. The basic design of the system consists of a thin film electro-optic polymer waveguide with built-in cascaded prisms structure for horizontal beam deflection and an electro-optic grating structure for vertical beam deflection. The cascaded prisms are combined with the electro-optic polymer to create a voltage-controlled horizontal beam deflection. A grating coupler, a structure that is commonly used as light coupling device for dielectric waveguide, is combined with the EO polymer to create the vertical controlled beam deflection. A collimated light beam coupled into the waveguide by a mechanical coupler via an optical fiber cascaded down these two deflection stages. When the beam exits, the emitted light beam is displaced along two orthogonal directions in a raster pattern. A photodetector array integrated in the same substrate captured the reflected intensity. The scanned imaged is then analyzed and reconstruct based on the received signal.
Endothelial colony-forming cells from patients with chronic myeloproliferative disorders lack the disease-specific molecular clonality marker
Authors: Piaggio Giovanna , Rosti Vittorio , Corselli Mirko , Bertolotti Francesca , Bergamaschi Gaetano , Pozzi Sarah , Imperiale Davide , Chiavarina Barbara , Bonetti Elisa , Novara Francesca , Sessarego Mario , Villani Laura , Garuti Anna , Massa Margherita , Ghio Riccardo , Campanelli Rita , Bacigalupo Andrea , Pecci Alessandro , Viarengo Gianluca , Zuffardi Orsetta , Frassoni Francesco , Barosi Giovanni 
Published: July 2009

AbstractTwo putative types of circulating endothelial progenitor cells have been recently identified in vitro: (1) endothelial colony-forming cell (ECFC) and (2) colony-forming unit–endothelial cell (CFU-EC). Only the former is now recognized to belong to endothelial lineage. We have used the ECFC and CFU-EC assays to readdress the issue of the clonal relation between endothelial progenitor cells and hematopoietic stem cells in patients with Philadelphia-positive and Philadelphia-negative chronic myeloproliferative disorders. Both ECFCs and CFU-ECs were cultured from peripheral blood mononuclear cells, and either BCR-ABL rearrangement or JAK2-V617F mutation were assessed in both types of endothelial colonies. We found that ECFCs lack the disease-specific markers, which are otherwise present in CFU-ECs, thus reinforcing the concept that the latter belongs to the hematopoietic lineage, and showing that in chronic myeloproliferative disorders the cell that gives rise to circulating ECFC has a distinct origin from the cell of the hematopoietic malignant clone.
CalDAG-GEFI is at the nexus of calcium-dependent platelet activation
Authors: Stefanini Lucia , Roden R. Claire , Bergmeier Wolfgang 
Published: July 2009

AbstractThe importance of the second messengers calcium (Ca2+) and diacylglycerol (DAG) in platelet signal transduction was established more than 30 years ago. Whereas protein kinase C (PKC) family members were discovered as the targets of DAG, little is known about the molecular identity of the main Ca2+ sensor(s). We here identify Ca2+ and DAG-regulated guanine nucleotide exchange factor I (CalDAG-GEFI) as a critical molecule in Ca2+-dependent platelet activation. CalDAG-GEFI, through activation of the small GTPase Rap1, directly triggers integrin activation and extracellular signal-regulated kinase-dependent thromboxane A2 (TxA2) release. CalDAG-GEFI–dependent TxA2 generation provides crucial feedback for PKC activation and granule release, particularly at threshold agonist concentrations. PKC/P2Y12 signaling in turn mediates a second wave of Rap1 activation, necessary for sustained platelet activation and thrombus stabilization. Our results lead to a revised model for platelet activation that establishes one molecule, CalDAG-GEFI, at the nexus of Ca2+-induced integrin activation, TxA2 generation, and granule release. The preferential activation of CalDAG-GEFI over PKC downstream of phospholipase C activation, and the different kinetics of CalDAG-GEFI– and PKC/P2Y12-mediated Rap1 activation demonstrate an unexpected complexity to the platelet activation process, and they challenge the current model that DAG/PKC-dependent signaling events are crucial for the initiation of platelet adhesion.
An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels
Authors: Nassir Rami , Kosoy Roman , Tian Chao , White Phoebe A , Butler Lesley M , Silva Gabriel , Kittles Rick , Alarcon-Riquelme Marta E , Gregersen Peter K , Belmont John W , De La Vega Francisco M , Seldin Michael F 
Published: July 2009

Abstract

Background
Case-control genetic studies of complex human diseases can be confounded by population stratification. This issue can be addressed using panels of ancestry informative markers (AIMs) that can provide substantial population substructure information. Previously, we described a panel of 128 SNP AIMs that were designed as a tool for ascertaining the origins of subjects from Europe, Sub-Saharan Africa, Americas, and East Asia.

Results
In this study, genotypes from Human Genome Diversity Panel populations were used to further evaluate a 93 SNP AIM panel, a subset of the 128 AIMS set, for distinguishing continental origins. Using both model-based and relatively model-independent methods, we here confirm the ability of this AIM set to distinguish diverse population groups that were not previously evaluated. This study included multiple population groups from Oceana, South Asia, East Asia, Sub-Saharan Africa, North and South America, and Europe. In addition, the 93 AIM set provides population substructure information that can, for example, distinguish Arab and Ashkenazi from Northern European population groups and Pygmy from other Sub-Saharan African population groups.

Conclusion
These data provide additional support for using the 93 AIM set to efficiently identify continental subject groups for genetic studies, to identify study population outliers, and to control for admixture in association studies.
Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty
Authors: Longo Mark S , Carone Dawn M ,   NISC Comparative Sequencing Program, Green Eric D , O'Neill Michael J , O'Neill Rachel J 
Published: July 2009

Abstract

Background
Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB), are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined.

Results
To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, Macropus eugenii, derived from centromeric regions (CEN), euchromatic regions (EU), and an evolutionary breakpoint (EB) that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s) and endogenous retroviruses (ERVs) and a depletion of short interspersed nucleotide elements (SINEs) shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33), known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements.

Conclusion
Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the divergence of marsupials and eutherians that may have predisposed these genomic regions to large-scale chromosomal instability.
A comparative genomics approach to understanding the biosynthesis of the sunscreen scytonemin in cyanobacteria
Authors: Soule Tanya , Palmer Kendra , Gao Qunjie , Potrafka Ruth M , Stout Valerie , Garcia-Pichel Ferran 
Published: July 2009

Abstract

Background
The extracellular sunscreen scytonemin is the most common and widespread indole-alkaloid among cyanobacteria. Previous research using the cyanobacterium Nostoc punctiforme ATCC 29133 revealed a unique 18-gene cluster (NpR1276 to NpR1259 in the N. punctiforme genome) involved in the biosynthesis of scytonemin. We provide further genomic characterization of these genes in N. punctiforme and extend it to homologous regions in other cyanobacteria.

Results
Six putative genes in the scytonemin gene cluster (NpR1276 to NpR1271 in the N. punctiforme genome), with no previously known protein function and annotated in this study as scyA to scyF, are likely involved in the assembly of scytonemin from central metabolites, based on genetic, biochemical, and sequence similarity evidence. Also in this cluster are redundant copies of genes encoding for aromatic amino acid biosynthetic enzymes. These can theoretically lead to tryptophan and the tyrosine precursor, p-hydroxyphenylpyruvate, (expected biosynthetic precursors of scytonemin) from end products of the shikimic acid pathway. Redundant copies of the genes coding for the key regulatory and rate-limiting enzymes of the shikimic acid pathway are found there as well. We identified four other cyanobacterial strains containing orthologues of all of these genes, three of them by database searches (Lyngbya PCC 8106, Anabaena PCC 7120, and Nodularia CCY 9414) and one by targeted sequencing (Chlorogloeopsis sp. strain Cgs-089; CCMEE 5094). Genomic comparisons revealed that most scytonemin-related genes were highly conserved among strains and that two additional conserved clusters, NpF5232 to NpF5236 and a putative two-component regulatory system (NpF1278 and NpF1277), are likely involved in scytonemin biosynthesis and regulation, respectively, on the basis of conservation and location. Since many of the protein product sequences for the newly described genes, including ScyD, ScyE, and ScyF, have export signal domains, while others have putative transmembrane domains, it can be inferred that scytonemin biosynthesis is compartmentalized within the cell. Basic structural monomer synthesis and initial condensation are most likely cytoplasmic, while later reactions are predicted to be periplasmic.

Conclusion
We show that scytonemin biosynthetic genes are highly conserved among evolutionarily diverse strains, likely include more genes than previously determined, and are predicted to involve compartmentalization of the biosynthetic pathway in the cell, an unusual trait for prokaryotes.
Antinociception Induced by Chronic Glucocorticoid Treatment is Correlated to Local Modulation of Spinal Neurotransmitter Content
Authors: Pinto-Ribeiro Filipa , Moreira Vitor , Pěgo José M , Leão Pedro , Almeida Armando , Sousa Nuno 
Published: July 2009

BackgroundWhile acute effects of stress on pain are well described, those produced by chronic stress are still a matter of dispute. Previously we demonstrated that chronic unpredictable stress results in antinociception in the tail-flick test, an effect that is mediated by increased levels of corticosteroids. In the present study, we evaluated nociception in rats after chronic treatment with corticosterone (CORT) and dexamethasone (DEX) in order to discriminate the role of each type of corticosteroid receptors in antinociception.ResultsBoth experimental groups exhibited a pronounced antinociceptive effect after three weeks of treatment when compared to controls (CONT); however, at four weeks the pain threshold in CORT-treated animals returned to basal levels whereas in DEX-treated rats antinociception was maintained. In order to assess if these differences are associated with altered expression of neuropeptides involved in nociceptive transmission we evaluated the density of substance P (SP), calcitonin gene-related peptide (CGRP), somatostatin (SS) andB2-γ-aminobutiric acid receptors (GABAB2) expression in the spinal dorsal horn using light density measurements and stereological techniques. After three weeks of treatment the expression of CGRP in the superficial dorsal horn was significantly decreased in both CORT and DEX groups, while GABAB2was significantly increased; the levels of SP for both experimental groups remained unchanged at this point. At 4 weeks, CGRP and SP are reduced in DEX-treated animals and GABAB2unchanged, but all changes were restored to CONT levels in CORT-treated animals. The expression of SS remained unaltered throughout the experimental period.ConclusionThese data indicate that corticosteroids modulate nociception since chronic corticosteroid treatment alters the expression of neuropeptides involved in nociceptive transmission at the spinal cord level. As previously observed in some supraspinal areas, the exclusive GR activation resulted in more profound and sustained behavioural and neurochemical changes, than the one observed with a mixed ligand of corticosteroid receptors. These results might be of relevance for the pharmacological management of certain types of chronic pain, in which corticosteroids are used as adjuvant analgesics.
Simultaneous integrated boost radiotherapy for bilateral breast: a treatment planning and dosimetric comparison for volumetric modulated arc and fixed field intensity modulated therapy
Authors: Nicolini Giorgia , Clivio Alessandro , Fogliata Antonella , Vanetti Eugenio , Cozzi Luca 
Published: July 2009

Abstract

Purpose
A study was performed comparing dosimetric characteristics of volumetric modulated arcs (RapidArc, RA) and fixed field intensity modulated therapy (IMRT) on patients with bilateral breast carcinoma.

Materials and methods
Plans for IMRT and RA, were optimised for 10 patients prescribing 50 Gy to the breast (PTVII, 2.0 Gy/fraction) and 60 Gy to the tumour bed (PTVI, 2.4 Gy/fraction). Objectives were: for PTVs V90%>95%, Dmax<107%; Mean lung dose MLD<15 Gy, V20 Gy<22%; heart involvement was to be minimised. The MU and delivery time measured treatment efficiency. Pre-treatment dosimetry was performed using EPID and a 2D-array based methods.

Results
For PTVII minus PTVI, V90% was 97.8 ± 3.4% for RA and 94.0 ± 3.5% for IMRT (findings are reported as mean ± 1 standard deviation); D5%-D95% (homogeneity) was 7.3 ± 1.4 Gy (RA) and 11.0 ± 1.1 Gy (IMRT). Conformity index (V95%/VPTVII) was 1.10 ± 0.06 (RA) and 1.14 ± 0.09 (IMRT). MLD was <9.5 Gy for all cases on each lung, V20 Gy was 9.7 ± 1.3% (RA) and 12.8 ± 2.5% (IMRT) on left lung, similar for right lung. Mean dose to heart was 6.0 ± 2.7 Gy (RA) and 7.4 ± 2.5 Gy (IMRT). MU resulted in 796 ± 121 (RA) and 1398 ± 301 (IMRT); the average measured treatment time was 3.0 ± 0.1 minutes (RA) and 11.5 ± 2.0 (IMRT). From pre-treatment dosimetry, % of field area with γ <1 resulted 98.8 ± 1.3% and 99.1 ± 1.5% for RA and IMRT respectively with EPID and 99.1 ± 1.8% and 99.5 ± 1.3% with 2D-array (ΔD = 3% and DTA = 3 mm).

Conclusion
RapidArc showed dosimetric improvements with respect to IMRT, delivery parameters confirmed its logistical advantages, pre-treatment dosimetry proved its reliability.
Solving a Hamiltonian Path Problem with a bacterial computer
Authors: Baumgardner Jordan , Acker Karen , Adefuye Oyinade , Crowley Samuel Thomas , DeLoache Will , Dickson James O , Heard Lane , Martens Andrew T , Morton Nickolaus , Ritter Michelle , Shoecraft Amber , Treece Jessica , Unzicker Matthew , Valencia Amanda , Waters Mike , Campbell AMalcolm , Heyer Laurie J , Poet Jeffrey L , Eckdahl Todd T 
Published: July 2009

Abstract

Background
The Hamiltonian Path Problem asks whether there is a route in a directed graph from a beginning node to an ending node, visiting each node exactly once. The Hamiltonian Path Problem is NP complete, achieving surprising computational complexity with modest increases in size. This challenge has inspired researchers to broaden the definition of a computer. DNA computers have been developed that solve NP complete problems. Bacterial computers can be programmed by constructing genetic circuits to execute an algorithm that is responsive to the environment and whose result can be observed. Each bacterium can examine a solution to a mathematical problem and billions of them can explore billions of possible solutions. Bacterial computers can be automated, made responsive to selection, and reproduce themselves so that more processing capacity is applied to problems over time.

Results
We programmed bacteria with a genetic circuit that enables them to evaluate all possible paths in a directed graph in order to find a Hamiltonian path. We encoded a three node directed graph as DNA segments that were autonomously shuffled randomly inside bacteria by a Hin/hixC recombination system we previously adapted from Salmonella typhimurium for use in Escherichia coli. We represented nodes in the graph as linked halves of two different genes encoding red or green fluorescent proteins. Bacterial populations displayed phenotypes that reflected random ordering of edges in the graph. Individual bacterial clones that found a Hamiltonian path reported their success by fluorescing both red and green, resulting in yellow colonies. We used DNA sequencing to verify that the yellow phenotype resulted from genotypes that represented Hamiltonian path solutions, demonstrating that our bacterial computer functioned as expected.

Conclusion
We successfully designed, constructed, and tested a bacterial computer capable of finding a Hamiltonian path in a three node directed graph. This proof-of-concept experiment demonstrates that bacterial computing is a new way to address NP-complete problems using the inherent advantages of genetic systems. The results of our experiments also validate synthetic biology as a valuable approach to biological engineering. We designed and constructed basic parts, devices, and systems using synthetic biology principles of standardization and abstraction.
Enhanced production of bacterial cellulose by using a biofilm reactor and its material property analysis
Authors: Cheng Kuan-Chen , Catchmark Jeff M , Demirci Ali 
Published: July 2009

Abstract
Bacterial cellulose has been used in the food industry for applications such as low-calorie desserts, salads, and fabricated foods. It has also been used in the paper manufacturing industry to enhance paper strength, the electronics industry in acoustic diaphragms for audio speakers, the pharmaceutical industry as filtration membranes, and in the medical field as wound dressing and artificial skin material. In this study, different types of plastic composite support (PCS) were implemented separately within a fermentation medium in order to enhance bacterial cellulose (BC) production by Acetobacter xylinum. The optimal composition of nutritious compounds in PCS was chosen based on the amount of BC produced. The selected PCS was implemented within a bioreactor to examine the effects on BC production in a batch fermentation. The produced BC was analyzed using X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), thermogravimetric analysis (TGA), and dynamic mechanical analysis (DMA). Among thirteen types of PCS, the type SFYR+ was selected as solid support for BC production by A. xylinum in a batch biofilm reactor due to its high nitrogen content, moderate nitrogen leaching rate, and sufficient biomass attached on PCS. The PCS biofilm reactor yielded BC production (7.05 g/L) that was 2.5-fold greater than the control (2.82 g/L). The XRD results indicated that the PCS-grown BC exhibited higher crystallinity (93%) and similar crystal size (5.2 nm) to the control. FESEM results showed the attachment of A. xylinum on PCS, producing an interweaving BC product. TGA results demonstrated that PCS-grown BC had about 95% water retention ability, which was lower than BC produced within suspended-cell reactor. PCS-grown BC also exhibited higher T
max compared to the control. Finally, DMA results showed that BC from the PCS biofilm reactor increased its mechanical property values, i.e., stress at break and Young's modulus when compared to the control BC. The results clearly demonstrated that implementation of PCS within agitated fermentation enhanced BC production and improved its mechanical properties and thermal stability.