bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lumican Peptides: Rational Design Targeting ALK5/TGFBRI
Authors: Gesteira Tarsis Ferreira , Coulson-Thomas Vivien J. , Yuan Yong , Zhang Jianhua , Nader Helena B. , Kao Winston W.-Y. 
Published: February 2017

AbstractLumican, a small leucine rich proteoglycan (SLRP), is a component of extracellular matrix which also functions as a matrikine regulating multiple cell activities. In the cornea, lumican maintains corneal transparency by regulating collagen fibrillogenesis, promoting corneal epithelial wound healing, regulating gene expression and maintaining corneal homeostasis. We have recently shown that a peptide designed from the 13 C-terminal amino acids of lumican (LumC13) binds to ALK5/TGFBR1 (type1 receptor of TGFβ) to promote wound healing. Herein we evaluate the mechanism by which this synthetic C-terminal amphiphilic peptide (LumC13), binds to ALK5. These studies clearly reveal that LumC13-ALK5 form a stable complex. In order to determine the minimal amino acids required for the formation of a stable lumican/ALK5 complex derivatives of LumC13 were designed and their binding to ALK5 investigated in silico. These LumC13 derivatives were tested both in vitro and in vivo to evaluate their ability to promote corneal epithelial cell migration and corneal wound healing, respectively. These validations add to the therapeutic value of LumC13 (Lumikine) and aid its clinical relevance of promoting the healing of corneal epithelium debridement. Moreover, our data validates the efficacy of our computational approach to design active peptides based on interactions of receptor and chemokine/ligand.
Elongation factor P restricts Salmonella’s growth by controlling translation of a Mg2+ transporter gene during infection
Authors: Choi Eunna , Choi Soomin , Nam Daesil , Park Shinae , Han Yoontak , Lee Jung-Shin , Lee Eun-Jin 
Published: February 2017

AbstractWhen a ribosome translates mRNA sequences, the ribosome often stalls at certain codons because it is hard to translate. Consecutive proline codons are such examples that induce ribosome stalling and elongation factor P (EF-P) is required for the stalled ribosome to continue translation at those consecutive proline codons. We found that EF-P is required for translation of the mgtB gene encoding a Mg2+ transporter in the mgtCBR virulence operon from the intracellular pathogen Salmonellaenterica serovar Typhimurium. Salmonella lacking EF-P decreases MgtB protein levels in a manner dependent on consecutive proline codons located in the mgtB coding region despite increasing transcription of the mgtCBR operon via the mgtP open reading frame in the leader RNA, resulting in an altered ratio between MgtC and MgtB proteins within the operon. Substitution of the consecutive proline codons to alanine codons eliminates EF-P-mediated control of the mgtB gene during infection and thus contributes to Salmonella’s survival inside macrophages where Salmonella experiences low levels of EF-P. This suggests that this pathogen utilizes a strategy to coordinate expression of virulence genes by an evolutionarily conserved translation factor.
A Floral Fragrance, Methyl Benzoate, is An Efficient Green Pesticide
Authors: Feng Yan , Zhang Aijun 
Published: February 2017

AbstractOver-reliance on synthetic pesticides in insect pest control has caused widespread public and scientific concerns for human health and the environment, especially since many insect pests have already developed resistances to conventional pesticides and Bt products. For this reason, there is a considerable interest in development of alternative control methods for insect pest management. Based on laboratory studies, we report that methyl benzoate (MB), a naturally-occurring compound in many plants, may possess toxicity against various stages of a variety of insect pests, including the brown marmorated stinkbug, Halyomorpha halys, diamondback moth, Plutella xylostella, and tobacco hornworm, Manduca sexta, as well as the spotted wing drosophila, Drosophila suzukii. Based on our laboratory toxicity data, MB was at least 5 to 20 times more toxic than the conventional pyrethroid (β-cyfluthrin), sulfur & pyrethrin mixture, and some organic commercial products available on the market against H. halys, P. xylostella, and M. sexta, eggs. Because MB is considered an environment-friendly, it has great potential to be used as an alternative tool to synthetic pesticide for insect pest management in crop production, thereby, reducing threats to natural ecosystems and human health caused by over-application of conventional synthetic pesticides.
High-throughput single-cell analysis for the proteomic dynamics study of the yeast osmotic stress response
Authors: Zhang Rongfei , Yuan Haiyu , Wang Shujing , Ouyang Qi , Chen Yong , Hao Nan , Luo Chunxiong 
Published: February 2017

AbstractMotorized fluorescence microscopy combined with high-throughput microfluidic chips is a powerful method to obtain information about different biological processes in cell biology studies. Generally, to observe different strains under different environments, high-throughput microfluidic chips require complex preparatory work. In this study, we designed a novel and easily operated high-throughput microfluidic system to observe 96 different GFP-tagged yeast strains in one switchable culture condition or 24 different GFP-tagged yeast strains in four parallel switchable culture conditions. A multi-pipette is the only additional equipment required for high-throughput patterning of cells in the chip. Only eight connections are needed to control 96 conditions. Using these devices, the proteomic dynamics of the yeast stress response pathway were carefully studied based on single-cell data. A new method to characterize the proteomic dynamics using a single cell’s data is proposed and compared to previous methods, and the new technique should be useful for studying underlying control networks. Our method provides an easy and systematic way to study signaling pathways at the single-cell level.
Mono-Energy Coronary Angiography with a Compact Synchrotron Source
Authors: Eggl Elena , Mechlem Korbinian , Braig Eva , Kulpe Stephanie , Dierolf Martin , Günther Benedikt , Achterhold Klaus , Herzen Julia , Gleich Bernhard , Rummeny Ernst , Noёl Peter B. , Pfeiffer Franz , Muenzel Daniela 
Published: February 2017

AbstractX-ray coronary angiography is an invaluable tool for the diagnosis of coronary artery disease. However, the use of iodine-based contrast media can be contraindicated for patients who present with chronic renal insufficiency or with severe iodine allergy. These patients could benefit from a reduced contrast agent concentration, possibly achieved through application of a mono-energetic x-ray beam. While large-scale synchrotrons are impractical for daily clinical use, the technology of compact synchrotron sources strongly advanced during the last decade. Here we present a quantitative analysis of the benefits a compact synchrotron source can offer in coronary angiography. Simulated projection data from quasi-mono-energetic and conventional x-ray tube spectra is used for a CNR comparison. Results show that compact synchrotron spectra would allow for a significant reduction of contrast media. Experimentally, we demonstrate the feasibility of coronary angiography at the Munich Compact Light Source, the first commercial installation of a compact synchrotron source.
Facing the phase problem in Coherent Diffractive Imaging via Memetic Algorithms
Authors: Colombo Alessandro , Galli Davide Emilio , De Caro Liberato , Scattarella Francesco , Carlino Elvio 
Published: February 2017

AbstractCoherent Diffractive Imaging is a lensless technique that allows imaging of matter at a spatial resolution not limited by lens aberrations. This technique exploits the measured diffraction pattern of a coherent beam scattered by periodic and non–periodic objects to retrieve spatial information. The diffracted intensity, for weak–scattering objects, is proportional to the modulus of the Fourier Transform of the object scattering function. Any phase information, needed to retrieve its scattering function, has to be retrieved by means of suitable algorithms. Here we present a new approach, based on a memetic algorithm, i.e. a hybrid genetic algorithm, to face the phase problem, which exploits the synergy of deterministic and stochastic optimization methods. The new approach has been tested on simulated data and applied to the phasing of transmission electron microscopy coherent electron diffraction data of a SrTiO3 sample. We have been able to quantitatively retrieve the projected atomic potential, and also image the oxygen columns, which are not directly visible in the relevant high-resolution transmission electron microscopy images. Our approach proves to be a new powerful tool for the study of matter at atomic resolution and opens new perspectives in those applications in which effective phase retrieval is necessary.
The mitotic checkpoint regulator RAE1 induces aggressive breast cancer cell phenotypes by mediating epithelial-mesenchymal transition
Authors: Oh Ji Hoon , Hur Ho , Lee Ji-Yeon , Kim Yeejeong , Seo Younsoo , Kim Myoung Hee 
Published: February 2017

AbstractThe gene RAE1 encodes ribonucleic acid export 1 (RAE1), which is involved in mRNA export and is known to serve as a mitotic checkpoint regulator. In addition, RAE1 haplo-insufficiency leads to chromosome missegregation and early aging-associated phenotypes. In humans, a positive correlation has been found between RAE1 copy number abnormalities and gene amplification in breast cancer cells. However, the precise functional role of RAE1 in breast cancer remains to be determined. An in silico analysis of data retrieved from GENT and cBio-Portal identified RAE1 upregulation in breast cancer tissues relative to normal breast cells. Functional studies of various cell lines showed that RAE1 induced invasive and migratory abilities by regulating epithelial-mesenchymal transition signals. A tissue microarray was constructed to demonstrate the interrelationship between clinicopathological features and RAE1 expression. Immunohistochemistry revealed a positive correlation between RAE1 expression and a high histologic grade. Furthermore, RAE1 overexpression was associated with considerably poorer disease-free survival and distant metastasis-free survival, especially in patients with oestrogen receptor-positive tumours. In summary, RAE1 may be a prognostic marker and therapeutic intervention target in malignant breast cancers.
Multiplexed transcriptome analysis to detect ALK, ROS1 and RET rearrangements in lung cancer
Authors: Rogers Toni-Maree , Arnau Gisela Mir , Ryland Georgina L. , Huang Stephen , Lira Maruja E. , Emmanuel Yvette , Perez Omar D. , Irwin Darryl , Fellowes Andrew P. , Wong Stephen Q. , Fox Stephen B. 
Published: February 2017

AbstractALK, ROS1 and RET gene fusions are important predictive biomarkers for tyrosine kinase inhibitors in lung cancer. Currently, the gold standard method for gene fusion detection is Fluorescence In Situ Hybridization (FISH) and while highly sensitive and specific, it is also labour intensive, subjective in analysis, and unable to screen a large numbers of gene fusions. Recent developments in high-throughput transcriptome-based methods may provide a suitable alternative to FISH as they are compatible with multiplexing and diagnostic workflows. However, the concordance between these different methods compared with FISH has not been evaluated. In this study we compared the results from three transcriptome-based platforms (Nanostring Elements, Agena LungFusion panel and ThermoFisher NGS fusion panel) to those obtained from ALK, ROS1 and RET FISH on 51 clinical specimens. Overall agreement of results ranged from 86–96% depending on the platform used. While all platforms were highly sensitive, both the Agena panel and Thermo Fisher NGS fusion panel reported minor fusions that were not detectable by FISH. Our proof–of–principle study illustrates that transcriptome-based analyses are sensitive and robust methods for detecting actionable gene fusions in lung cancer and could provide a robust alternative to FISH testing in the diagnostic setting.
Age-dependent Changes in the Articular Cartilage and Subchondral Bone of C57BL/6 Mice after Surgical Destabilization of Medial Meniscus
Authors: Huang Henry , Skelly Jordan D. , Ayers David C. , Song Jie 
Published: February 2017

AbstractAge is the primary risk factor for osteoarthritis (OA), yet surgical OA mouse models such as destabilization of the medial meniscus (DMM) used for evaluating disease-modifying OA targets are frequently performed on young adult mice only. This study investigates how age affects cartilage and subchondral bone changes in mouse joints following DMM. DMM was performed on male C57BL/6 mice at 4 months (4 M), 12 months (12 M) and 19+ months (19 M+) and on females at 12 M and 18 M+. Two months after surgery, operated and unoperated contralateral knees were harvested and evaluated using cartilage histology scores and μCT quantification of subchondral bone plate thickness and osteophyte formation. The 12 M and 19 M+ male mice developed more cartilage erosions and thicker subchondral bone plates after DMM than 4 M males. The size of osteophytes trended up with age, while the bone volume fraction was significantly higher in the 19 M+ group. Furthermore, 12 M females developed milder OA than males as indicated by less cartilage degradation, less subchondral bone plate sclerosis and smaller osteophytes. Our results reveal distinct age/gender-dependent structural changes in joint cartilage and subchondral bone post-DMM, facilitating more thoughtful selection of murine age/gender when using this surgical technique for translational OA research.
Plasmonically enhanced metal–insulator multistacked photodetectors with separate absorption and collection junctions for near-infrared applications
Authors: Abedini Dereshgi Sina , Sisman Zulkarneyn , Topalli Kagan , Okyay Ali Kemal 
Published: February 2017

AbstractPlasmonically enhanced metal-insulator-metal (MIM) type structures are popular among perfect absorbers and photodetectors in which the field enhancement (for increased absorption) mechanism is directly coupled with collection (photocurrent) processes. In this work we propose a device structure that decouples absorption and collection parts for independent optimization. Double-stacked MIM (i.e. MIMIM) photodetectors operating in the near-infrared (NIR) spectrum up to 1200 nm wavelength are demonstrated. In the absorbing MIM (at the top side), we have used Silver nanoparticles resulting from dewetting, yielding a very low reflection of 10% for the most part of the 400 to 1000 nm wavelength range. An unconventional plasmonic material, Chromium, exhibits an absorption peak of over 80% at 1000 nm. The complete device has been fabricated and the photo-collection tunneling MIM (at the bottom) suppresses the leakage current by metal workfunction difference. An optimized stack consisting of Silver – Hafnium Oxide – Chromium – Aluminum Oxide – Silver nanoparticles (from bottom to top) yields a dark current of 7 nA and a photoresponsivity peak of 0.962 mA/W at 1000 nm and a full width at half maximum of 300 nm, while applied bias is 50 mV and device areas are 300 μm × 600 μm.
Mycorrhizas alter sucrose and proline metabolism in trifoliate orange exposed to drought stress
Authors: Wu Hui-Hui , Zou Ying-Ning , Rahman Mohammed Mahabubur , Ni Qiu-Dan , Wu Qiang-Sheng 
Published: February 2017

AbstractArbuscular mycorrhizal fungi (AMF) can enhance drought tolerance in plants, whereas little is known regarding AMF contribution to sucrose and proline metabolisms under drought stress (DS). In this study, Funneliformis mosseae and Paraglomus occultum were inoculated into trifoliate orange (Poncirus trifoliata) under well watered and DS. Although the 71-days DS notably (P < 0.05) inhibited mycorrhizal colonization, AMF seedlings showed significantly (P < 0.05) higher plant growth performance and leaf relative water content, regardless of soil water status. AMF inoculation significantly (P < 0.05) increased leaf sucrose, glucose and fructose concentration under DS, accompanied with a significant increase of leaf sucrose phosphate synthase, neutral invertase, and net activity of sucrose-metabolized enzymes and a decrease in leaf acid invertase and sucrose synthase activity. AMF inoculation produced no change in leaf ornithine-δ-aminotransferase activity, but significantly (P < 0.05) increased leaf proline dehydrogenase activity and significantly (P < 0.05) decreased leaf both Δ1-pyrroline-5-carboxylate reductase and Δ1-pyrroline-5-carboxylate synthetase activity, resulting in lower proline accumulation in AMF plants under DS. Our results therefore suggest that AMF strongly altered leaf sucrose and proline metabolism through regulating sucrose- and proline-metabolized enzyme activities, which is important for osmotic adjustment of the host plant.
Penetration-enhancement underlies synergy of plant essential oil terpenoids as insecticides in the cabbage looper, Trichoplusia ni
Authors: Tak Jun-Hyung , Isman Murray B. 
Published: February 2017

AbstractMany plant essential oils and their terpenoid constituents possess bioactivities including insecticidal activity, and they sometimes act synergistically when mixed. Although several hypotheses for this have been proposed, the underlying mechanism has not been fully elucidated thus far. In the present study, we report that in larvae of the cabbage looper, Trichoplusia ni, most synergistic or antagonistic insecticidal activities among mixtures of plant essential oil constituents are pharmacokinetic effects, owing to changes in solubility as well as spreadability on a wax layer. Among the major constituents of rosemary (Rosmarinus officinalis) oil, in vitro analysis revealed up to a 19-fold increase in penetration of camphor in a binary mixture with 1,8-cineole through the larval integument, suggesting increased penetration as the major mechanism for synergy. A total of 138 synergistic or antagonistic interactions among 39 compounds were identified in binary mixtures via topical application, and these were highly correlated to changes in surface tension as measured by contact angle of the mixtures on a beeswax layer. Among compounds tested, trans-anethole alone showed evidence of internal synergy, whereas most of remaining synergistic or antagonistic combinations among the three most active compounds were identified as penetration-related interactions, confirmed via a divided-application bioassay.
Photoacoustic and Fluorescence Imaging of Cutaneous Squamous Cell Carcinoma in Living Subjects Using a Probe Targeting Integrin αvβ6
Authors: Zhang Chao , Zhang Yong , Hong Kai , Zhu Shu , Wan Jie 
Published: February 2017

AbstractCutaneous squamous cell carcinoma (cSCC) is the second most common non-melanoma skin cancer worldwide. Today, cSCC is diagnosed by visual inspection followed by invasive skin biopsy. There is a need to develop non-invasive diagnostic tools to achieve early and accurate detection. Photoacoustic imaging (PAI) possesses high ultrasonic resolution and strong optical contrast at new depths (<1–5 cm). Together with exogenous contrast agents, PAI has found promising use in various tumors in living subjects. The expression of integrin αvβ6is significantly up-regulated in cSCC. We fabricated an anti-integrin αvβ6antibody and labeled it with indocyanine green (ICG) to form an ICG-αvβ6antibody. The results showed that the ICG-αvβ6antibody probe could be used to detect cSCC with high specificity (3-fold over the control by PAI) and deep penetration (approximately 1 cm) by PAI. This suggests that the ICG-αvβ6antibody is a promising probe targeting the integrin αvβ6for detection of cSCC tumors by PAI and fluorescence imaging. It may find clinical application in the early diagnosis of cSCC as well as in intraoperative navigation.
Prenatal and Postnatal Management of Gastroschisis in German-Speaking Countries: Is There a Standardized Management?
Authors: Schib Katharina , Schumacher Marc , Meuli Martin , Tharakan Sasha , Subotic Ulrike 
Published: February 2017

Introduction Evidence-based guidelines or protocols regarding the perinatal management of babies born with gastroschisis are lacking. The aim of this work is to evaluate the different current treatment modalities for newborns with gastroschisis during the perinatal period in the German-speaking countries Germany, Austria, and Switzerland. These data could serve as a starting point for the development of a multicenter randomized controlled trial.
Materials and Methods A questionnaire was developed with 30 questions divided into five sections: (1) prenatal diagnosis, (2) fetal therapy, (3) mode and timing of delivery, (4) operative management, and (5) postoperative management. All pediatric surgery institutions that treat newborns with gastroschisis were identified and asked to participate. Data were categorized by country and analyzed using descriptive statistics (frequency and percentage).
Results The return rate of the questionnaire was 95% (89 hospitals). A standard procedure was identified regarding prenatal ultrasound monitoring, interdisciplinary team approach, planned delivery through cesarean section, postnatal coverage of the intestine with a silastic bag, first intervention within the first 6 hours after birth, attempt of primary abdominal wall closure, and perioperative antibiotic treatment. For many crucial parameters, management was not standardized.
Conclusions There is no gold standard in German-speaking countries on how to manage fetuses and babies with gastroschisis. Moreover, this report unveils some questionable elements of daily practice for which there is no evidence at all and which can jeopardize outcome and even prove fatal (fetal therapy, preterm delivery, lack of abdominal pressure monitoring). Prospective randomized-controlled multicenter studies are needed to set a standard.
Serpin1 and WSCP differentially regulate the activity of the cysteine protease RD21 during plant development in
Arabidopsis thaliana
Authors: Rustgi Sachin , Boex-Fontvieille Edouard , Reinbothe Christiane , von Wettstein Diter , Reinbothe Steffen 
Published: February 2017

Significance
Nature has evolved highly specific protease inhibitors comprising serpin and Kunitz proteins. In humans, loss- or gain-of-function mutations in many protease inhibitor (PI) genes lead to compromised innate immune responses, dementia, thrombosis, and other diseases. Here, we report how plants make use of serpin and Kunitz PIs to control papain-like cysteine proteases over plant development and exploit them for defense.
Cytotoxic compounds against cancer cells from Bombyx mori inoculated with Cordyceps militaris
Authors: Qiu Weitao , Wu Jing , Choi Jae-Hoon , Hirai Hirofumi , Nishida Hiroshi , Kawagishi Hirokazu 
Published: February 2017

Abstract
Two compounds, 3′-deoxyinosine and cordycepin, were isolated from Bombyx mori inoculated with Cordyceps militaris. In the bioassay examining cytotoxicity against cancer cells, both compounds showed toxicity against A549, PANC-1, and MCF-7 cancer cells.
Friends and Interveners
Authors: Collins Paul M. , McCarthy Lauren A. 
Published: February 2017

AbstractInterest groups attempt to shape the content of law and policy in a variety of venues, including the legal system. Though the bulk of research dedicated to understanding interest group participation in litigation occurs in the context of the United States, there have been growing efforts to explore this important topic from a cross-national perspective. We contribute to this literature by investigating interest group amicus curiae and intervener activity across 11 English-speaking high courts during the 1969–2002 era. Our results support our theoretical argument that institutional features of courts and nations heavily shape levels of organizational litigation, including the power of judicial review, the rules governing third-party participation, and the presence of a bill of rights. This research informs our understanding of institutional design, social movement litigation, and the democratic nature of courts.