bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishing quasi-steady state operations of microphysiological systems (MPS) using tissue-specific metabolic dependencies
Authors: Maass Christian , Dallas Matthew , LaBarge Matthew E. , Shockley Michael , Valdez Jorge , Geishecker Emily , Stokes Cynthia L. , Griffith Linda G. , Cirit Murat 
Published: May 2018

AbstractMicrophysiological systems (MPS), consisting of tissue constructs, biomaterials, and culture media, aim to recapitulate relevant organ functions in vitro. MPS components are housed in fluidic hardware with operational protocols, such as periodic complete media replacement. Such batch-like operations provide relevant nutrients and remove waste products but also reset cell-secreted mediators (e.g. cytokines, hormones) and potentially limit exposure to drugs (and metabolites). While each component plays an essential role for tissue functionality, MPS-specific nutrient needs are not yet well-characterized nor utilized to operate MPSs at more physiologically-relevant conditions. MPS-specific nutrient needs for gut (immortalized cancer cells), liver (human primary hepatocytes) and cardiac (iPSC-derived cardiomyocytes) MPSs were experimentally quantified. In a long-term study of the gut MPS (10 days), this knowledge was used to design operational protocols to maintain glucose and lactate at desired levels. This quasi-steady state operation was experimentally validated by monitoring glucose and lactate as well as MPS functionality. In a theoretical study, nutrient needs of an integrated multi-MPS platform (gut, liver, cardiac MPSs) were computationally simulated to identify long-term quasi-steady state operations. This integrative experimental and computational approach demonstrates the utilization of quantitative multi-scale characterization of MPSs and incorporating MPS-specific information to establish more physiologically-relevant experimental operations.
Endocide-Induced Abnormal Growth Forms of Invasive Giant Salvinia (Salvinia molesta)
Authors: Li Shiyou , Wang Ping , Su Zushang , Lozano Emily , LaMaster Olivia , Grogan Jason B. , Weng Yuhui , Decker Thomas , Findeisen John , McGarrity Monica 
Published: May 2018

AbstractGiant salvinia (Salvinia molesta) is one of the most noxious invasive species in the world. The fern is known to have primary, secondary, and tertiary growth forms, which are also commonly hypothesized as growth stages. The identification of these forms is primarily based on the size and folding status of the floating leaves. However, we identified 12 forms in the greenhouse and the field. Our experiments showed that the folding of floating leaves is a reversible trait dependent on water access. The floating leaves quickly fold in response to water shortage, reducing water loss and needs, decreasing growth, and avoiding trichome damage. The leaves re-open to allow trichomes repel water and enhance growth when having adequate water supply. Larger secondary or tertiary forms do not produce small-leaf primary forms without high intensity stress. These results do not support the hypothesis that three growth forms represent sequential growth stages. The abnormal small-leaf forms are the result of endocide-induced autotoxicity and some of them never grow into other forms. The development of abnormal forms and reversible leaf folding strategy in response to high stress along with rapid asexual reproduction are major adaptive traits contributing to the invasiveness of S. molesta.
Combined genotyping, microbial diversity and metabolite profiling studies on farmed Mytilus spp. from Kiel Fjord
Authors: Utermann Caroline , Parrot Delphine , Breusing Corinna , Stuckas Heiko , Staufenberger Tim , Blümel Martina , Labes Antje , Tasdemir Deniz 
Published: May 2018

AbstractThe blue mussel Mytilus is a popular food source with high economical value. Species of the M. edulis complex (M. edulis, M. galloprovincialis and M. trossulus) hybridise whenever their geographic ranges overlap posing difficulties to species discrimination, which is important for blue mussel aquaculture. The aim of this study was to determine the genetic structure of farmed blue mussels in Kiel Fjord. Microbial and metabolic profile patterns were studied to investigate a possible dependency on the genotype of the bivalves. Genotyping confirmed the complex genetic structure of the Baltic Sea hybrid zone and revealed an unexpected dominance of M. trossulus alleles being in contrast to the predominance of M. edulis alleles described for wild Baltic blue mussels. Culture-dependent and -independent microbial community analyses indicated the presence of a diverse Mytilus-associated microbiota, while an LC-MS/MS-based metabolome study identified 76 major compounds dominated by pigments, alkaloids and polyketides in the whole tissue extracts. Analysis of mussel microbiota and metabolome did not indicate genotypic dependence, but demonstrated high intraspecific variability of farmed mussel individuals. We hypothesise that individual differences in microbial and metabolite patterns may be caused by high individual plasticity and might be enhanced by e.g. nutritional condition, age and gender.
Spraying dynamics in continuous wave laser printing of conductive inks
Authors: Sopeña Pol , González-Torres Sergio , Fernández-Pradas Juan Marcos , Serra Pere 
Published: May 2018

AbstractLaser-induced forward transfer (LIFT), though usually associated with pulsed lasers, has been recently shown to be feasible for printing liquid inks with continuous wave (CW) lasers. This is remarkable not only because of the advantages that the new approach presents in terms of cost, but also because of the surprising transfer dynamics associated with it. In this work we carry out a study of CW-LIFT aimed at understanding the new transfer dynamics and its correlation with the printing outcomes. The CW-LIFT of lines of Ag ink at different laser powers and scan speeds revealed a range of conditions that allowed printing conductive lines with good electrical properties. A fast-imaging study showed that liquid ejection corresponds to a spraying behavior completely different from the jetting characteristic of pulsed LIFT. We attribute the spray to pool-boiling in the donor film, in which bursting bubbles are responsible for liquid ejection in the form of projected droplets. The droplet motion is then modeled as the free fall of rigid spheres in a viscous medium, in good agreement with experimental observations. Finally, thermo-capillary flow in the donor film allows understanding the evolution of the morphology of the printed lines with laser power and scan speed.
Functional analysis of eliciting plant response protein Epl1-Tas from Trichoderma asperellum ACCC30536
Authors: Yu Wenjing , Mijiti Gulijimila , Huang Ying , Fan Haijuan , Wang Yucheng , Liu Zhihua 
Published: May 2018

AbstractEliciting plant response protein (Epl) is a small Trichoderma secreted protein that acts as an elicitor to induce plant defense responses against pathogens. In the present study, the differential expression, promoter analysis, and phylogenetic tree analysis of Epl1-Tas (GenBank JN966996) from T. asperellum ACCC30536 were performed. The results showed Epl1-Tas could play an important role in the interaction between T. asperellum ACCC30536 and woody plant or woody plant pathogen. Furthermore, the effect of the Escherichia coli recombinant protein rEpl1-e and the Pichia pastoris recombinant protein rEpl1-p on Populus davidiana × P. alba var. pyramidalis (PdPap) was studied. In PdPap seedlings, rEpl1-e or rEpl1-p induction altered the expression levels of 11 genes in the salicylic acid (SA, three genes), jasmonic acid (JA, four genes) and auxin (four genes) signal transduction pathways, and five kinds of enzymes activities The induction level of rEpl1-p was significantly higher than that of rEpl1-e, indicating that rEpl1-p could be used for further induction experiment. Under 3 mg/mL rEpl1-p induction, the mean height of the PdPap seedlings increased by 57.65% and the mean lesion area on the PdPap seedlings leaves challenged with Alternaria alternata decreased by 91.22% compared with those of the control. Thus, elicitor Epl1-Tas could induce the woody plant resistance to pathogen.
Detection of Japanese Encephalitis Virus RNA in Human Throat Samples in Laos – A Pilot study
Authors: Bharucha Tehmina , Sengvilaipaseuth Onanong , Seephonelee Malee , Vongsouvath Malavanh , Vongsouvath Manivanh , Rattanavong Sayaphet , Piorkowski Géraldine , Lecuit Marc , Gorman Christopher , Pommier Jean-David , Newton Paul N. , de Lamballerie Xavier , Dubot-Pérès Audrey 
Published: May 2018

AbstractJapanese encephalitis virus (JEV) is the most commonly identified cause of acute encephalitis syndrome (AES) in Asia. The WHO recommended test is anti-JEV IgM-antibody-capture-enzyme-linked-immunosorbent-assay (JEV MAC-ELISA). However, data suggest this has low positive predictive value, with false positives related to other Flavivirus infections and vaccination. JEV RT-PCR in cerebrospinal fluid (CSF) and/or serum is highly specific, but is rarely positive; 0–25% of patients that fulfil the WHO definition of JE (clinical Acute Encephalitis Syndrome (AES) and JEV MAC-ELISA positive). Testing other body fluids by JEV RT-qPCR may improve the diagnosis. As a pilot study thirty patients admitted to Mahosot Hospital 2014–2017, recruited to the South-East-Asia-Encephalitis study, were tested by JEV MAC-ELISA and two JEV real-time RT-PCR (RT-qPCR) assays (NS2A and NS3). Eleven (36.7%) were JEV MAC-ELISA positive. Available CSF and serum samples of these patients were JEV RT-qPCR negative but 2 (7%) had JEV RNA detected in their throat swabs. JEV RNA was confirmed by re-testing, and sequencing of RT-qPCR products. As the first apparent report of JEV RNA detection in human throat samples, the provides new perspectives on human JEV infection, potentially informing improving JEV detection. We suggest that testing patients’ throat swabs for JEV RNA is performed, in combination with molecular and serological CSF and serum investigations, on a larger scale to investigate the epidemiology of the presence of JEV in human throats. Throat swabs are an easy and non-invasive tool that could be rolled out to a wider population to improve knowledge of JEV molecular epidemiology.
MiR-29c reduces the cisplatin resistance of non-small cell lung cancer cells by negatively regulating the PI3K/Akt pathway
Authors: Sun Dian-min , Tang Bu-fu , Li Zhen-xiang , Guo Hong-bo , Cheng Jin-ling , Song Ping-ping , Zhao Xin 
Published: May 2018

AbstractIn previous studies, miR-29s showed tumor suppressor properties against lung cancer, which improved the survival of patients upon the administration of chemotherapy via an unknown mechanism. Here, we investigated the regulatory effects of miR-29s on the cisplatin resistance of NSCLC cells. The expression of miR-29s was assessed in 130 clinical patients and in cisplatin-treated NSCLS cell lines. MiR-29c expression was decreased in 77% of NSCLC patients. Cisplatin treatment increased the expression of miR-29c and decreased the expression of its oncogenic target AKT2 in NSCLC cell lines. A Kaplan–Meier survival analysis indicated that higher miR-29c levels led to a longer disease-free survival. In particular, patients who experienced cancer recurrences after cisplatin chemotherapy exhibited a lower level of miR-29c expression, suggesting that miR-29c activation may contribute to the chemotherapeutic efficiency of cisplatin. The enforced expression of miR-29c enhanced the cisplatin sensitivity of NSCLC cells, while the knocking down of miR-29c led to cisplatin resistance. MiR-29c amplified the therapeutic effects of cisplatin in vivo. Rescue experiments suggested that miR-29c regulates the cisplatin resistance of NSCLS cells by negatively regulating the PI3K/Akt pathway. Overall, our results demonstrated that miR-29c enhances the sensitivity of NSCLC cells to cisplatin by targeting the PI3K/Akt pathway.
Rapid Authentication of Ginkgo biloba Herbal Products Using the Recombinase Polymerase Amplification Assay
Authors: Liu Yang , Wang Xiao-yue , Wei Xue-min , Gao Zi-tong , Han Jian-ping 
Published: May 2018

AbstractSpecies adulteration in herbal products (HPs) exposes consumers to health risks. Chemical and morphological methods have their own deficiencies when dealing with the detection of species containing the same active compounds in HPs. In this study, we developed a rapid identification method using the recombinase polymerase amplification (RPA) assay to detect two species, Ginkgo biloba and Sophora japonica (as adulteration), in Ginkgo biloba HPs. Among 36 Ginkgo biloba HP samples, 34 were found to have Ginkgo biloba sequences, and 9 were found to have Sophora japonica sequences. During the authentication process, the RPA-LFS assay showed a higher specificity, sensitivity and efficiency than PCR-based methods. We initially applied the RPA-LSF technique to detect plant species in HPs, demonstrating that this assay can be developed into an efficient tool for the rapid on-site authentication of plant species in Ginkgo biloba HPs.
Size of a plasma cloud matters
Authors: Nilsson H. , Gunell H. , Karlsson T. , Brenning N. , Henri P. , Goetz C. , Eriksson A. I. , Behar E. , Stenberg Wieser G. , Vallières X. 
Published: May 2018

Context. The cometary ionosphere is immersed in fast flowing solar wind. A polarisation electric field may arise for comets much smaller than the gyroradius of pickup ions because ions and electrons respond differently to the solar wind electric field.Aims. A situation similar to that found at a low activity comet has been modelled for barium releases in the Earth’s ionosphere. We aim to use such a model and apply it to the case of comet 67P Churyumov-Gerasimenko, the target of the Rosetta mission. We aim to explain the significant tailward acceleration of cometary ions through the modelled electric field.Methods. We obtained analytical solutions for the polarisation electric field of the comet ionosphere using a simplified geometry. This geometry is applicable to the comet in the inner part of the coma as the plasma density integrated along the magnetic field line remains rather constant. We studied the range of parameters for which a significant tailward electric field is obtained and compare this with the parameter range observed.Results. Observations of the local plasma density and magnetic field strength show that the parameter range of the observations agree very well with a significant polarisation electric field shielding the inner part of the coma from the solar wind electric field.Conclusions. The same process gives rise to a tailward directed electric field with a strength of the order of 10% of the solar wind electric field. Using a simple cloud model we have shown that the polarisation electric field, which arises because of the small size of the comet ionosphere as compared to the pick up ion gyroradius, can explain the observed significant tailward acceleration of cometary ions and is consistent with the observed lack of influence of the solar wind electric field in the inner coma.
Endoscopic mucosa-sparing lateral dissection for treatment of gastric submucosal tumors: a prospective cohort study
Authors: Li Yue , Zhang Qiang , Zhu Chaojun , Luo Yuchen , Han Zelong , Qing Haitao , Cai Jianqun , Li Ling , Huang Ying , Liu Side 
Published: May 2018

Abstract
Background In our previous work, we developed a modified method for the removal of gastric submucosal tumors (SMTs), called endoscopic mucosa-sparing lateral dissection (EMSLD). This prospective study aimed to evaluate the efficacy and postoperative outcomes of EMSLD.
Methods We prospectively enrolled 25 consecutive patients with gastric SMTs, who received EMSLD treatment. Clinicopathological characteristics and operation-related outcomes were analyzed.
Results The mean age of patients was 49.3 ± 9.7 years, and the mean tumor size was 14.6 ± 6.1 mm. En bloc resection was achieved in all cases. The mean procedure time was 47.3 ± 25.9 minutes, and the estimated blood loss was 4.8 ± 3.5 mL. Endoscopic full-thickness resection was performed in six patients (24 %) because the tumors originated from the deep muscularis propria layer. All perforations and resection defects were successfully closed by the retained mucosa and endoclips. No serious complications related to EMSLD were encountered during or after the procedure.
Conclusions EMSLD was reliable and effective for the removal of gastric SMTs. However, large-scale randomized controlled trials are needed.
Lower Extremity Limb Salvage with Cross Leg Pedicle Flap, Cross Leg Free Flap, and Cross Leg Vascular Cable Bridge Flap
Authors: Manrique Oscar J. , Bishop Sarah N. , Ciudad Pedro , Adabi Kian , Martinez-Jorge Jorys , Moran Steven L. , Huang Tony , Vijayasekaran Aparna , Chen Shih-heng , Chen Hung-chi 
Published: May 2018

Background Lower extremity salvage following significant soft tissue loss can be complicated by lack of recipient vessel for free tissue transfer. We describe our experience in lower limb salvage for patients with no recipient vessels with the use of pedicle, free and cable bridge flaps.
Methods A retrospective review from 1985 to 2017 of patients undergoing lower limb salvage using a contralateral pedicle cross leg (PCL) flaps, free cross leg (FCL) flaps, or free cable bridge (FCB) flaps was conducted. Demographics, etiology of the reconstruction, type of flap used, donor-site vessels, defect size, operating time, time of pedicle division, length of hospital stay, time to ambulation, and complications were analyzed.
Results A total of 53 patients (48 males and 5 females) with an average age of 35 years (range, 29–38 years) were identified. The etiology for the reconstruction was trauma in 52 patients and oncological resection in 1 patient. There were 18 PCL, 25 FCL, and 10 FCB completed. The recipient vessels for all flaps were the posterior tibial artery and vein. The average operating room times for PCL, FCL, and FCB flaps were 4, 9, and 10 hours, respectively. The average length of hospital stay was 5 weeks and average time to ambulation was 4 weeks. The average follow-up time was 7.5 years (range, 3–12 years). Complications encountered were hematoma (six), prolonged pain (six), total flap loss (two), reoperation (five), and infection (four). Limb salvage rates were 96.2%.
Conclusion When ipsilateral limb vessels are not available, and other reconstructive options have been exhausted, cross leg flaps can be a viable option for limb salvage in the setting of extensive defects.
Phase-Transition-Induced Pattern Formation Applied to Basic Research on Homeopathy: A Systematic Review
Authors: Scherr Claudia , Bodrova Natalia Borisovna , Baumgartner Stephan , Kokornaczyk Maria 
Published: May 2018

Background Methods based on phase-transition-induced pattern formation (PTPF) are increasingly used in medical research. Frequent application fields are medical diagnosis and basic research in homeopathy. Here, we present a systematic review of experimental studies concerning PTPF-based methods applied to homeopathy research. We also aimed at categorizing the PTPF methods included in this review.
Materials and Methods Experimental studies were collected from scientific databases (PubMed, Web of Science, Russian eLibrary) and from experts in the research field in question, following the PRISMA guidelines. The studies were rated according to pre-defined scientific criteria.
Results The review included 15 experimental studies. We identified seven different PTPF methods applied in 12 experimental models. Among these methods, phase-transition was triggered through evaporation, freezing, or solution, and in most cases led to the formation of crystals. First experimental studies concerning the application of PTPF methods in homeopathic research were performed in the first half of the 20th century; however, they were not continued in the following years. Only in the last decade, different research groups re-launched the idea, introducing new experimental approaches and computerized pattern evaluation techniques. The here-identified PTPF methods are for the first time proposed to be classified as one group of methods based on the same basic physical phenomenon.
Conclusions Although the number of experimental studies in the area is still rather limited, the long tradition in the application of PTPF methods and the dynamics of the present developments point out the high potential of these methods and indicate that they might meet the demand for scientific methods to study potentized preparations.
Inheriting power: Somaliland’s political institutions and the 2017 presidential election
Authors: Ylönen Aleksi 
Published: May 2018

SUMMARY
This briefing sheds light on Somaliland’s political institutions, election dynamics and candidates who contested the state leadership in the 2017 presidential election. It argues that in spite of recurrent postponing of parliamentary elections, the 2017 presidential election has shown that Somaliland’s democratic process and legitimacy of its political institutions have remained relatively strong in the otherwise politically unstable neighbourhood.
Integration of logistic regression and multicriteria land evaluation to simulation establishment of sustainable paddy field zone in Indramayu Regency, West Java Province, Indonesia
Authors: Nahib Irmadi , Suryanta Jaka , Niedyawati  , Kardono Priyadi , Turmudi  , Lestari Sri , Windiastuti Rizka 
Published: May 2018

Abstract
Ministry of Agriculture have targeted production of 1.718 million tons of dry grain harvest during period of 2016-2021 to achieve food self-sufficiency, through optimization of special commodities including paddy, soybean and corn. This research was conducted to develop a sustainable paddy field zone delineation model using logistic regression and multicriteria land evaluation in Indramayu Regency. A model was built on the characteristics of local function conversion by considering the concept of sustainable development. Spatial data overlay was constructed using available data, and then this model was built upon the occurrence of paddy field between 1998 and 2015. Equation for the model of paddy field changes obtained was: logit (paddy field conversion) = - 2.3048 + 0.0032*X1 – 0.0027*X2 + 0.0081*X3 + 0.0025*X4 + 0.0026*X5 + 0.0128*X6 – 0.0093*X7 + 0.0032*X8 + 0.0071*X9 – 0.0046*X10 where X1 to X10 were variables that determine the occurrence of changes in paddy fields, with a result value of Relative Operating Characteristics (ROC) of 0.8262. The weakest variable in influencing the change of paddy field function was X7 (paddy field price), while the most influential factor was X1 (distance from river). Result of the logistic regression was used as a weight for multicriteria land evaluation, which recommended three scenarios of paddy fields protection policy: standard, protective, and permissive. The result of this modelling, the priority paddy fields for protected scenario were obtained, as well as the buffer zones for the surrounding paddy fields.
SoS Notebook: an interactive multi-language data analysis environment
Authors: Peng Bo , Wang Gao , Ma Jun , Leong Man Chong , Wakefield Chris , Melott James , Chiu Yulun , Du Di , Weinstein John N 
Published: May 2018

Abstract

Motivation
Complex bioinformatic data analysis workflows involving multiple scripts in different languages can be difficult to consolidate, share and reproduce. An environment that streamlines the entire processes of data collection, analysis, visualization and reporting of such multi-language analyses is currently lacking.

Results
We developed Script of Scripts (SoS) Notebook, a web-based notebook environment that allows the use of multiple scripting language in a single notebook, with data flowing freely within and across languages. SoS Notebook enables researchers to perform sophisticated bioinformatic analysis using the most suitable tools for different parts of the workflow, without the limitations of a particular language or complications of cross-language communications.

Availability and implementation
SoS Notebook is hosted at http://vatlab.github.io/SoS/ and is distributed under a BSD license.