bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recombinant adeno-associated virus-mediated transfer of shRNA against Notch3 ameliorates hepatic fibrosis in rats
Authors: Zheng Shao-Ping , Chen Yi-Xiong , Guo Jun-Li , Qi Dan , Zheng Shao-Jiang , Zhang Shu-Ling , Weng Zhi-Hong 
Published: August 2013

Liver fibrosis, a wound healing process following all kinds of liver injuries, is characterized by excessive deposition of extracellular matrix (ECM). Our previous study revealed that Notch3 might participate in liver fibrogenesis by regulating the activation of hepatic stellate cells (HSCs). The aim of this study was to assess the effects of Notch3 shRNA on hepatic fibrosis in a rat model induced by carbon tetrachloride (CCl4) and to clarify the mechanisms underlying those effects. Recombinant adeno-associated virus type 1 (rAAV1) vector carrying Notch3 shRNA (rAAV1-Notch3-shRNA) was generated and transferred to rat livers via the tail vein. The expression of Notch3, Jagged1, Hes1 and α-SMA were detected by real-time RT-PCR and immunofluorescence. The effects of rAAV1-Notch3-shRNA on fibrosis was investigated by pathological and immunohistochemical examination. Our findings showed that Notch3, Jagged1, Hes1 and α-SMA were downregulated. This downregulation was accompanied by improved hepatic fibrosis after the inhibition of Notch3 in vivo. rAAV1-Notch3-shRNA treatment reversed the epithelial-mesenchymal transition (EMT) in fibrotic livers by decreasing the expression of transforming growth factor β1 (TGF-β1) and vimentin in a line with the increased expression of E-cadherin. The inhibition of Notch3 was not found to play a role in hepatocyte proliferation. Rather, it inhibited hepatocyte apoptosis in vivo to some extent. The results of the present study suggest that the inhibition of Notch3 can protect hepatocytes from undergoing apoptosis and attenuate liver fibrogenesis. This may be a viable therapeutic option for hepatic fibrosis.
Genome-wide analysis of the Populus Hsp90 gene family reveals differential expression patterns, localization, and heat stress responses
Authors: Zhang Jin , Li Jianbo , Liu Bobin , Zhang Li , Chen Jun , Lu Mengzhu 
Published: August 2013

Abstract

Background
Members of the heat shock protein 90 (Hsp90) class of proteins are evolutionarily conserved molecular chaperones. They are involved in protein folding, assembly, stabilization, activation, and degradation in many normal cellular processes and under stress conditions. Unlike many other well-characterized molecular chaperones, Hsp90s play key roles in signal transduction, cell-cycle control, genomic silencing, and protein trafficking. However, no systematic analysis of genome organization, gene structure, and expression compendium has been performed in the Populus model tree genus to date.

Results
We performed a comprehensive analysis of the Populus Hsp90 gene family and identified 10 Populus Hsp90 genes, which were phylogenetically clustered into two major groups. Gene structure and motif composition are relatively conserved in each group. In Populus trichocarpa, we identified three paralogous pairs, among which the PtHsp90-5a/PtHsp90-5b paralogous pair might be created by duplication of a genome segment. Subcellular localization analysis shows that PtHsp90 members are localized in different subcellular compartments. PtHsp90-3 is localized both in the nucleus and in the cytoplasm, PtHsp90-5a and PtHsp90-5b are in chloroplasts, and PtHsp90-7 is in the endoplasmic reticulum (ER). Furthermore, microarray and semi-quantitative real-time RT-PCR analyses show that a number of Populus Hsp90 genes are differentially expressed upon exposure to various stresses.

Conclusions
The gene structure and motif composition of PtHsp90s are highly conserved among group members, suggesting that members of the same group may also have conserved functions. Microarray and RT-PCR analyses show that most PtHsp90s were induced by various stresses, including heat stress. Collectively, these observations lay the foundation for future efforts to unravel the biological roles of PtHsp90 genes.
Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae
Authors: Wei Li , Xin Yi , Wang Dongmei , Jing Xiaoyan , Zhou Qian , Su Xiaoquan , Jia Jing , Ning Kang , Chen Feng , Hu Qiang , Xu Jian 
Published: August 2013

Abstract

Background
Microalgae are promising feedstock for production of lipids, sugars, bioactive compounds and in particular biofuels, yet development of sensitive and reliable phylotyping strategies for microalgae has been hindered by the paucity of phylogenetically closely-related finished genomes.

Results
Using the oleaginous eustigmatophyte Nannochloropsis as a model, we assessed current intragenus phylotyping strategies by producing the complete plastid (pt) and mitochondrial (mt) genomes of seven strains from six Nannochloropsis species. Genes on the pt and mt genomes have been highly conserved in content, size and order, strongly negatively selected and evolving at a rate 33% and 66% of nuclear genomes respectively. Pt genome diversification was driven by asymmetric evolution of two inverted repeats (IRa and IRb): psbV and clpC in IRb are highly conserved whereas their counterparts in IRa exhibit three lineage-associated types of structural polymorphism via duplication or disruption of whole or partial genes. In the mt genomes, however, a single evolution hotspot varies in copy-number of a 3.5 Kb-long, cox1-harboring repeat. The organelle markers (e.g., cox1, cox2, psbA, rbcL and rrn16_mt) and nuclear markers (e.g., ITS2 and 18S) that are widely used for phylogenetic analysis obtained a divergent phylogeny for the seven strains, largely due to low SNP density. A new strategy for intragenus phylotyping of microalgae was thus proposed that includes (i) twelve sequence markers that are of higher sensitivity than ITS2 for interspecies phylogenetic analysis, (ii) multi-locus sequence typing based on rps11_mt-nad4, rps3_mt and cox2-rrn16_mt for intraspecies phylogenetic reconstruction and (iii) several SSR loci for identification of strains within a given species.

Conclusion
This first comprehensive dataset of organelle genomes for a microalgal genus enabled exhaustive assessment and searches of all candidate phylogenetic markers on the organelle genomes. A new strategy for intragenus phylotyping of microalgae was proposed which might be generally applicable to other microalgal genera and should serve as a valuable tool in the expanding algal biotechnology industry.
Copper-containing amine oxidases contribute to terminal polyamine oxidation in peroxisomes and apoplast of Arabidopsis thaliana
Authors: Planas-Portell Joan , Gallart Marta , Tiburcio Antonio F , Altabella Teresa 
Published: August 2013

Abstract

Background
Polyamines (PAs) are oxidatively deaminated at their primary or secondary amino-groups by copper-containing amine oxidases (CuAOs) or FAD-dependent amine oxidases (PAOs), respectively. Both enzymes have long been considered to be apoplastic proteins. However, three out of five PAO isoforms in Arabidopsis thaliana are localized in peroxisomes, while the other two PAOs are predicted to be cytosolic. Interestingly, most of these PAOs do not contribute to terminal PA oxidation, but instead are involved in the back-conversion pathway, producing spermidine from spermine and putrescine from spermidine, which in turn is inhibited by putrescine. This opens the question as to whether PAs are catabolized in the apoplast of Arabidopsis and if the terminal oxidation occurs in the peroxisomes. The main objective of this study was to know if these catabolic processes are mediated by CuAOs.

Results

A. thaliana contains ten genes annotated as CuAOs, but only one (ATAO1) has been characterized at the protein level. Reported herein is the characterization of three genes encoding putative Arabidopsis CuAOs (AtCuAO1, AtCuAO2 and AtCuAO3). These genes encode functional CuAOs that use putrescine and spermidine as substrates. AtCuAO1, like ATAO1, is an extracellular protein, while AtCuAO2 and AtCuAO3 are localized in peroxisomes. The three genes present a different expression profile in response to exogenous treatments, such as application of abcisic acid, methyl jasmonate, salycilic acid, flagellin 22 and wounding.

Conclusions
PA catabolism in the Arabidopsis apoplast is mediated predominantly by CuAOs, while in peroxisomes the co-localization of CuAO-dependent terminal catabolism with PAO-back-conversion machineries might contribute to modulating putrescine-mediated inhibition of the back-conversion, suggesting the occurrence of a tight coordination between both catabolic pathways. The expression profile of AtCuAO1-3 in response to different exogenous treatments, together with the different localization of the corresponding proteins, provides evidence for the functional diversification of Arabidopsis CuAO proteins.
Giant gastrointestinal stromal tumor (GIST) of the stomach cause of high bowel obstruction: surgical management
Authors: Cappellani Alessandro , Piccolo Gaetano , Cardì Francesco , Cavallaro Andrea , Lo Menzo Emanuele , Cavallaro Vincenzo , Zanghì Antonio , Di Vita Maria , Berretta Massimiliano 
Published: August 2013

Abstract

Background
Gastrointestinal stromal tumors (GISTs) represent 85% of all mesenchymal neoplasms that affect the gastrointestinal (GI) tract. These GISTs range in size from small lesions to large masses. Often they are clinically silent until they reach a significant size, so their discovery is usually incidental.

Case presentation
A 67-year-old man was admitted at our general surgery department with a persistent abdominal pain in the left hypochondrium, associated with nausea and vomiting. Clinical examination revealed a palpable mass in the epigastrium and in the left hypochondrium, which was approximately 40 cm long. Ultrasonography and computed tomography of the abdomen showed a large mass of 40 × 25 cm, which extended from the posterior wall of the stomach to the spleen, involving the body and the tail of the pancreas. The patient underwent en-block resection of the mass, sleeve resection of the stomach, and distal pancreatectomy-splenectomy. The histopathology of the resected specimen was consistent with a gastrointestinal stromal tumor of the stomach (positive for CD 117) with a high risk of malignancy (mitotic count >5/50 high-power fieldand Ki67/Mib1 >10%). The postoperative course was uneventful and treatment with imatinib mesylate began immediately. The patient appears to be disease free after four years.

Conclusions
Giant GISTs of the stomach are rare. Surgical resection with curative intent is feasible. The combination of surgical resection and imatinib can provide long-termdisease-free survival. An R0 resection is the best achievable treatment, therefore the patient should be evaluated over time for potential resectability.
An unexpected but interesting response to a novel therapy for malignant extragastrointestinal stromal tumor of the mesoileum: a case report and review of the literature
Authors: Li Hengping , Li Jun , Li Xingwen , Kang Yaqiong , Wei Qiang 
Published: August 2013

Abstract

Background
Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. Extragastrointestinal stromal tumors (eGISTs) of the mesoileum are extremely rare and are usually treated with surgery combined with imatinib therapy.

Case presentation
We present the case of a 43-year-old man who developed a large eGIST in the mesoileum. Abdominal/pelvic computed tomography revealed a large heterogeneous mass with cystic and solid components that measured 20.0 × 12.0 × 8.0 cm. Three cycles of neoadjuvant chemotherapy with epirubicin, cyclophosphamide and hydroxycamptothecin; en bloc resection; and three more cycles of adjuvant chemotherapy with the same regimen and drugs resulted in five years of disease-free survival without any symptoms.

Conclusions
Although imatinib treatment is usually chosen for eGISTs, resistance to imatinib remains a concern; these patients may receive neoadjuvant or adjuvant chemotherapy. In case of the former, further treatment, that is, surgery or adjuvant chemotherapy, depends on tumor response to the neoadjuvant chemotherapy. In addition, this treatment for eGIST is not only beneficial but also economical for patients compared with imatinib. A novel treatment approach that combined neoadjuvant chemotherapy, surgery and adjuvant chemotherapy resulted in long-term survival in our patient, thus showing promise as a potential therapy for eGISTs.
Pilot study of a robotic protocol to treat shoulder subluxation in patients with chronic stroke
Authors: Dohle Carolin I , Rykman Avrielle , Chang Johanna , Volpe Bruce T 
Published: August 2013

AbstractBackgroundShoulder subluxation is a frequent complication of motor impairment after stroke, leading to soft tissue damage, stretching of the joint capsule, rotator cuff injury, and in some cases pain, thus limiting use of the affected extremity beyond weakness. In this pilot study, we determined whether robotic treatment of chronic shoulder subluxation can lead to functional improvement and whether any improvement was robust.Methods18 patients with chronic stroke (3.9 ± 2.9 years from acute stroke), completed 6 weeks of robotic training using the linear shoulder robot. Training was performed 3 times per week on alternate days. Each session consisted of 3 sets of 320 repetitions of the affected arm, and the robotic protocol alternated between training vertical arm movements, shoulder flexion and extension, in an anti-gravity plane, and training horizontal arm movements, scapular protraction and retraction, in a gravity eliminated plane.ResultsTraining with the linear robot improved shoulder stability, motor power, and resulted in improved functional outcomes that were robust 3 months after training.ConclusionIn this uncontrolled pilot study, the robotic protocol effectively treated shoulder subluxation in chronic stroke patients. Treatment of subluxation can lead to improved functional use of the affected arm, likely by increasing motor power in the trained muscles.
Extrauterine adenomyoma of the liver with a focally cellular smooth muscle component occurring in a patient with a history of myomectomy: case report and review of the literature
Authors: Huanwen Wu , Hui Zhang , Xiaowei Xue , Zhaohui Lu 
Published: August 2013

Abstract

Virtual Slides

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1327125766102291.
Since first reported in 1986, 14 cases of extrauterine adenomyoma have been reported in the English literature, most often occurring in the ovaries. In this report, we present the first case of extrauterine adenomyoma involving the liver in a 29-year-old woman who presented with a 2-year history of low back pain with recent worsening and a history of laparoscopic myomectomy 5 years previously. Gross inspection of the specimen revealed a subcapsular mass that had a well-circumscribed margin with the adjacent liver tissue. By histopathologic examination, the multilobular mass was composed of a smooth muscle component and benign endometrioid glands and stroma. The smooth muscle component was focally cellular, and the endometrioid glands had secretory features. Both the smooth muscle component and endometrioid tissue were positive for ER and PR. The smooth muscle component was also positive for desmin and SMA, while the endometrioid stroma was positive for CD10. Other extrauterine lesions composed of a mixture of smooth muscle tissue and heterotopic endometrioid tissue, including endometriosis with a smooth muscle component, leiomyomatosis/leiomyomas associated with endometriosis and uterus-like masses, should be included in differential diagnoses. The patient was free from recurrence 5 months after liver tumor resection.
Phytosynthesis of silver nanoparticles using Pterocarpus santalinus leaf extract and their antibacterial properties
Authors: Gopinath Kasi , Gowri Shanmugam , Arumugam Ayyakannu 
Published: August 2013

AbstractGreen synthesis is one of the rapid, reliable, and best routes for the synthesis of silver nanoparticles (Ag NPs). The current study revealed that the aqueous leaf extract ofPterocarpus santalinus, which contains steroids, saponins, tannins, phenols, triterpenoids, flavonoids, glycosides, and glycerides, is found to be responsible for bioreduction during the synthesis of spherical Ag nanoparticles. The formed Ag NPs were characterized by ultraviolet-visible (UV-vis), Fourier transform-infrared (FT-IR), X-ray diffraction (XRD), atomic force microscopy (AFM), energy-dispersive X-ray spectroscopy (EDX), and scanning electron microscopy (SEM) analysis. UV-vis spectra of the aqueous medium containing silver nanoparticles showed a surface plasmon resonance peak at 418 nm. FT-IR analysis was performed to analyze the biomolecules responsible for the reduction of Ag NPs. XRD results confirmed the presence of silver nanoparticles with face-centered cubic structure. The EDX analysis showed the completed inorganic composition of the synthesized Ag NPs. AFM analysis exemplified the results of particle sizes (41 nm). The calculated crystallite sizes are in the range of 20 to 50 nm, and the spherical nature of the Ag NPs was ascertained by SEM. The synthesized Ag NPs exhibited good antibacterial potential against gram-positive and gram-negative bacterial strains. The zone of inhibition effect of antibacterial activity depends upon the concentration of Ag NPs.
Three-dimensional reconstruction and analysis of the tubular system of vertebrate skeletal muscle
Authors: Jayasinghe Izzy , Launikonis Bradley S. 
Published: August 2013

Summary
Skeletal muscle fibres are very large and elongated. In response to excitation there must be a rapid and uniform release of Ca2+ throughout for contraction. To ensure a uniform spread of excitation throughout the fibre to all the Ca2+ release sites, the muscle internalizes the plasma membrane, to form the tubular (t-) system. Hence the t-system forms a complex and dense network throughout the fibre that is responsible for excitation–contraction coupling and other signalling mechanisms. However, we currently do not have a very detailed view of this membrane network because of limitations in previously used imaging techniques to visualize it. In this study we serially imaged fluorescent dye trapped in the t-system of fibres from rat and toad muscle using the confocal microscope, and deconvolved and reconstructed these images to produce the first three-dimensional reconstructions of large volumes of the vertebrate t-system. These images showed complex arrangements of tubules that have not been described previously and also allowed the association of the t-system with cellular organelles to be visualized. There was a high density of tubules close to the nuclear envelope because of the close and parallel alignment of the long axes of the myofibrils and the nuclei. Furthermore local fluorescence intensity variations from sub-resolution tubules were converted to tubule diameters. Mean diameters of tubules were 85.9±6.6 and 91.2±8.2 nm, from rat and toad muscle under isotonic conditions, respectively. Under osmotic stress the distribution of tubular diameters shifted significantly in toad muscle only, with change specifically occurring in the transverse but not longitudinal tubules.
Like mother, like offspring: maternal and offspring wound healing correlate in snakes
Authors: Hopkins Brittney C. , Chin Stephanie Y. , Willson John D. , Hopkins William A. 
Published: August 2013

SUMMARY
Immune function early in life can be influenced by parental effects and the environment, but it remains unclear how these two factors may interact to influence immunocompetence. We evaluated maternal and environmental contributions to offspring healing ability in a viviparous reptile, the northern watersnake (Nerodia sipedon). We measured wound healing rates, a highly integrative and biologically relevant measure of innate immunity, of females and their offspring collected from sites contaminated with a toxic heavy metal and compared them with those of individuals from reference sites. We found that female watersnakes that healed the fastest produced offspring that also exhibited faster healing rates. However, we detected no influence of environmental pollution on maternal or offspring healing rates. To our knowledge, our study is the first to correlate maternal and offspring wound healing ability in a wild vertebrate.
Gas exchange patterns and water loss rates in the Table Mountain cockroach,Aptera fusca(Blattodea: Blaberidae)
Authors: Groenewald Berlizé , Bazelet Corinna S. , Potter C. Paige , Terblanche John S. 
Published: August 2013

SummaryThe importance of metabolic rate and/or spiracle modulation for saving respiratory water is contentious. One major explanation for gas exchange pattern variation in terrestrial insects is to effect a respiratory water loss (RWL) saving. To test this, we measured V·CO2 and V·H2O in a previously unstudied, mesic cockroach, Aptera fusca, and compared gas exchange and water loss parameters among the major gas exchange patterns (continuous, cyclic, discontinuous gas exchange (DGE)) at a range of temperatures. Mean V·CO2, V·H2O, and V·H2O per unit V·CO2 did not differ among the gas exchange patterns at all temperatures (p&gt;0.09). There was no significant association between temperature and gas exchange pattern type (p=0.63). Percentage of RWL (relative to total water loss) was typically low (9.79±1.84%) and did not differ significantly among gas exchange patterns at 15°C (p=0.26). The method of estimation had a large impact on the %RWL and of three techniques investigated (traditional, regression, hyperoxic switch), the traditional method generally performed best. In many respects, A. fusca has typical gas exchange for what might be expected from other insects studied to date (e.g. V·CO2, V·H2O, RWL and CWL). However, we found for A. fusca that V·H2O expressed as a function of metabolic rate was significantly higher than the expected consensus relationship for insects, suggesting it is under considerable pressure to save water. Despite this, we found no consistent evidence supporting the conclusion that transitions in pattern type yield reductions in RWL in this mesic cockroach.
Petroleum quaternary ammonium surfactants mixture synthesized from light naphtha as corrosion inhibitors for carbon steel in 1 m HCl
Authors: Hamitouche Houria , Khelifa Abdellah , Kouache Amel , Moulay Saâd 
Published: August 2013

AbstractA quaternary ammonium cationic surfactants mixture was synthesized from light naphtha, petroleum fraction. The mixture was analyzed by Fourier transform infrared spectroscopy and UV/Visible spectroscopy and was evaluated as a corrosion inhibitor for carbon steel in 1mHCl, by gravimetry, potentiodynamic polarization and electrochemical impedance spectroscopy. The results showed that inhibiting efficiency increased with inhibitor concentration and temperature, and was independent of pH (in the range of 0–4) and immersion time; its optimal value was up to 84% for 560 mg/l at 25°C. Experimental data showed that the cationic surfactants mixture acts as a mixed (anodic and cathodic) inhibitor and conformed to the Langmuir adsorption isotherm. Scanning electron microscopy images revealed the inhibiting capacity of the mixture against carbon steel acid corrosion.
A Solid-State Fault Current Limiting Device for VSC-HVDC Systems
Authors: Larruskain D. Marene , Zamora Inmaculada , Abarrategui, Oihane , Iturregi Araitz 
Published: August 2013

Abstract
Faults in the DC circuit constitute one of the main limitations of voltage source converter VSC-HVDC systems, as the high fault currents can damage seriously the converters. In this article, a new design for a fault current limiter (FCL) is proposed, which is capable of limiting the fault current as well as interrupting it, isolating the DC grid. The operation of the proposed FCL is analysed and verified with the most usual faults that can occur in overhead lines.