bluuebunny/crossref_metadata_2025 huggingface dataset:
tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner
Authors: Kuscu Canan , Kumar Pankaj , Kiran Manjari , Su Zhangli , Malik Asrar , Dutta Anindya
Published: May 2018

tRNA related RNA fragments (tRFs), also known as tRNA-derived RNAs (tdRNAs), are abundant small RNAs reported to be associated with Argonaute proteins, yet their function is unclear. We show that endogenous 18 nucleotide tRFs derived from the 3′ ends of tRNAs (tRF-3) post-transcriptionally repress genes in HEK293T cells in culture. tRF-3 levels increase upon parental tRNA overexpression. This represses target genes with a sequence complementary to the tRF-3 in the 3′ UTR. The tRF-3-mediated repression is Dicer-independent, Argonaute-dependent, and the targets are recognized by sequence complementarity. Furthermore, tRF-3:target mRNA pairs in the RNA induced silencing complex associate with GW182 proteins, known to repress translation and promote the degradation of target mRNAs. RNA-seq demonstrates that endogenous target genes are specifically decreased upon tRF-3 induction. Therefore, Dicer-independent tRF-3s, generated upon tRNA overexpression, repress genes post-transcriptionally through an Argonaute-GW182 containing RISC via sequence matches with target mRNAs.
Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study
Authors: Lees John A. , Kendall Michelle , Parkhill Julian , Colijn Caroline , Bentley Stephen D. , Harris Simon R.
Published: May 2018

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made.

Methods: We simulated data from a defined 'true tree' using a realistic evolutionary model. We  built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree.

Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other.

Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. For the most accurate tree, use of either RAxML or IQ-TREE with an alignment of variable sites produced by mapping to a reference genome is best. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology.  We have publicly released our simulated data and code to enable further comparisons.
DOLORisk: study protocol for a multi-centre observational study to understand the risk factors and determinants of neuropathic pain
Authors: Pascal Mathilde M.V. , Themistocleous Andreas C. , Baron Ralf , Binder Andreas , Bouhassira Didier , Crombez Geert , Finnerup Nanna B. , Gierthmühlen Janne , Granovsky Yelena , Groop Leif , Hebert Harry L. , Jensen Troels S. , Johnsen Kristinn , McCarthy Mark I. , Meng Weihua , Palmer Colin N.A. , Rice Andrew S.C. , Serra Jordi , Solà Romà , Yarnitsky David , Smith Blair H. , Attal Nadine , Bennett David L.H.
Published: May 2018

Background: Neuropathic pain is an increasingly prevalent condition and has a major impact on health and quality of life. However, the risk factors for the development and maintenance of neuropathic pain are poorly understood. Clinical, genetic and psychosocial factors all contribute to chronic pain, but their interactions have not been studied in large cohorts. The DOLORisk study aims to study these factors.

Protocol: Multicentre cross-sectional and longitudinal cohorts covering the main causes leading to neuropathic pain (e.g. diabetes, surgery, chemotherapy, traumatic injury), as well as rare conditions, follow a common protocol for phenotyping of the participants. This core protocol correlates answers given by the participants on a set of questionnaires with the results of their genetic analyses. A smaller number of participants undergo deeper phenotyping procedures, including neurological examination, nerve conduction studies, threshold tracking, quantitative sensory testing, conditioned pain modulation and electroencephalography.

Ethics and dissemination: All studies have been approved by their regional ethics committees as required by national law. Results are disseminated through the DOLORisk website, scientific meetings, open-access publications, and in partnership with patient organisations.

Strengths and limitations:

Large cohorts covering many possible triggers for neuropathic pain

Multi-disciplinary approach to study the interaction of clinical, psychosocial and genetic risk factors

High comparability of the data across centres thanks to harmonised protocols

One limitation is that the length of the questionnaires might reduce the response rate and quality of responses of participants
Can improved diagnostics reduce mortality from Tuberculous meningitis? Findings from a 6.5-year cohort in Uganda
Authors: Cresswell Fiona V. , Bangdiwala Ananta S. , Bahr Nathan C. , Trautner Emily , Nuwagira Edwin , Ellis Jayne P. , Rajasingham Radha , Rhein Joshua , Williams Darlisha A. , Muzoora Conrad , Elliott Alison M. , Meya David B. , Boulware David R.
Published: May 2018

Background: Tuberculous meningitis (TBM) is the second most common cause of meningitis in sub-Saharan Africa and is notoriously difficult to diagnose. We describe the impact of improved TBM diagnostics over 6.5 years at two Ugandan referral hospitals.

Methods: Cohort one received cerebrospinal fluid (CSF) smear microscopy only (2010-2013). Cohort two received smear microscopy and Xpert MTB/Rif (Xpert) on 1ml unprocessed CSF at physician discretion (2011-2013). Cohort three received smear microscopy, routine liquid-media culture and Xpert on large volume centrifuged CSF (2013-2017) for all meningitis suspects with a negative CSF cryptococcal antigen. We compared rates of microbiologically confirmed TBM and hospital outcomes over time.

Results: 1672 HIV-infected adults presenting with suspected meningitis underwent lumbar puncture, of which 33% (558/1672) had negative CSF cryptococcal antigen and 12% (195/1672) were treated for TB meningitis. Over the study period, microbiological confirmation of TBM increased from 3% to 41% (P<0.01) and there was a decline in in-hospital mortality from 57% to 41% (P=0.27) amongst those with a known outcome. Adjusting for definite TBM diagnosis and antiretroviral therapy use, and using imputed data, assuming 50% of those with an unknown outcome died, the odds of dying were nearly twice as high in cohort one (adjusted odds ratio 1.7, 95% CI 0.7 to 4.4) compared to cohort three.  Sensitivity of Xpert was 63% (38/60) and culture was 65% (39/60) against a composite reference standard.

Conclusions: As TBM diagnostics have improved, microbiologically-confirmed TBM diagnoses have increased and in-hospital mortality has declined. Yet, mortality due to TB meningitis remains unacceptably high and further measures are needed to improve outcomes from TBM in Uganda.
Botanical and floristic composition of the Historical Herbarium of Leonhard Rauwolf collected in the Near East (1573­1575)
Authors: Ghorbani Abdolbaset , Wieringa Jan J. , Boer Hugo J. de , Porck Henk , Kardinaal Adriaan , Andel Tinde van
Published: May 2018

The German doctor and botanist Leonhard Rauwolf (1535­1596) was the first post­medieval European to travel to the Levant and Mesopotamia. The travel account that he published on his hazardous journey (1573­1575) is well studied, but the plants he collected during his travels have hardly been subjected to scientific study. The fourth volume of Rauwolf’s 16th century book herbarium includes plant specimens collected from the area encompassing modern­day Lebanon, Syria and Iraq. We digitized this valuable historic collection, identified all specimens in the herbarium, analyzed its floristic composition, transcribed and translated the Latin and German texts accompanying each specimen and updated the names with the latest accepted nomenclature. The herbarium book includes 191 specimens representing 183 species belonging to 64 families. It includes original specimens of Linnaean type illustrations as well as historical crop cultivars from the Near East. The Rauwolf Herbarium gives a unique insight in the exotic, unknown and useful species of the Near East from the perspective of a 16th century European botanist.
Helping Merchants to Assess the Profitability of Deal-of-the-Day Promotions
Authors: Reiner Jochen , Skiera Bernd
Published: May 2018

The ability to calculate and understand the profitability of deal-of-the-day promotions (DoDs) is of vital importance for merchants. It is also challenging because it requires these merchants to consider long-term, cross-selling, and cannibalization effects and select an appropriate discount for the promotion. The authors develop and implement a model as a free online calculator ( http://www.coupon-calculator.com ) to help merchants to determine the profit they can generate from these promotions. This calculator evaluated almost 3,700 DoDs from the merchants’ and providers’ perspectives. To gain insight on the expected profitability of DoDs, the authors analyzed 627 of these planned promotions and 30 realized promotions. The results indicate that two-thirds of the planned and all realized DoDs are expected to be profitable in the long term. Yet, DoDs are unlikely to pay off in the short term. The findings also show that unredeemed coupons strongly increase profit, particularly those of the provider.
No Firm Is an Island: The Role of Population-Level Actors in Organizational Learning from Failure
Authors: Madsen Peter M. , Desai Vinit
Published: May 2018

When a serious failure occurs within a population of organizations, members of individual organizations in the population attempt to learn vicariously from the event so that future failures may be avoided. This organization-level vicarious learning process has been extensively studied in the organizational learning literature. However, following a serious failure in one organization, a parallel process also plays out at the population level as population-level actors draw lessons from the failure and exert influence over organizations in the population in the interest of preventing future failures. Such population-level processes may exert powerful influences on organization-level learning, but have only begun to be explored in the literature. This paper begins to fill this gap by theorizing and studying the role of population-level actors in organizational learning from failure within and across organizational populations. It examines these issues in a global sample of large airlines operating between 1981 and 2011. The findings indicate that population-level forces are a major driver of improvement and learning in members of organizational populations—specifically, that the monitoring strength and activity of population-level actors influence the rates of organizational learning from failure within their populations.
What is cardiac distress and how should we measure it?
Authors: Jackson Alun C , Murphy Barbara M , Thompson David R , Ski Chantal F , Alvarenga Marlies E , Le Grande Michael R , Amerena John , Higgins Rosemary O , Barton David A
Published: May 2018

After cardiac events, rates of depression and anxiety of 20–30% have been reported, along with elevated rates of post-traumatic stress disorder and higher rates of suicide. As unresolved negative affect is associated with greater morbidity and mortality, attempts have been made to understand the complexity of emotional and psychological responses to cardiac events. Although many studies purport to measure ‘cardiac distress’, they are often limited by adopting a definition of distress as depression plus anxiety. Following the lead of the oncology and diabetes fields in the development of condition-specific distress measures, this article argues for a multidimensional approach to cardiac distress and its measurement; it builds on the concept of the ‘cardiac blues’, to show the importance of understanding and measuring how this transient phenomenon of adjustment can become a persistent negative state which challenges the ability to cope with living after a cardiac event.
Cross-generational syntactic variation in Mundaka Basque: the influence of the language of instruction
Authors: Gondra Ager
Published: May 2018

This article examines syntactic variation in relative clause (RC) constructions in Mundaka Basque among two groups of Mundaka Basque speakers. The language of instruction the Mundaka Basque speakers had in school draws the line that separates the two populations: the first group (Mundaka Basque I) had Spanish as the language of instruction and no Basque as a subject, while the second one (Mundaka Basque II) had Standard Basque as the language of instruction and Spanish as a subject. The results of an experiment involving a cloze test show that differences in production between these populations depends on the grammaticality of RCs with an indirect object or adjunct gap and a subject or direct object RC head: for Mundaka Basque I relativization under this configuration is grammatical, while for Mundaka Basque II, it is not. This variation is due to simplification of relativization accessibility in Mundaka Basque II caused by Standard Basque.
Pradoluengo y Paderluengo. ¿Un híbrido vascorrománico camuflado? / Pradoluengo and Paderluengo. A hidden Romano-basque hybrid?
Authors: Peterson David
Published: May 2018

Pradoluengo would seem to be one of the most transparently Romance place-names in the province of Burgos, from the Latin etyma pratum and longus. However, all the medieval references to the town, from various sources, insist on quite different forms —essentially Paderluengo— which it is difficult to derive from pratum, obliging us to consider alternatives. Within the context of the Sierra de la Demanda, an area teeming with Basque place-names, a Basque origin seems a plausible alternative, and in fact the name would appear to be a hybrid, formed from Basque padur(a) ‘water-meadow’ and Latin longus. Hybrids of this type are useful in that they allow us to understand and potentially even contextualise in chronological terms the period of Basque-Romance bilingualism in this area.
Análise da sustentabilidade hidroambiental dos municípios com sede totalmente contida na bacia hidrográfica do Rio Mogi Guaçu, SP
Authors: Bozzini Aloisio Calsoni , De Oliveira Prado Fernanda Carla , Pereira João Paulo , Borri Menoti , Paschoalado Cristina Filomena Pereira Rosa
Published: May 2018

Os gestores municipais e os cidadãos, a partir de suas instituições representativas, devem participar do Comitê de Bacia Hidrográfica da sua região, e, nesse sentido, têm o dever de promover melhorias na qualidade de vida e o equilíbrio ecológico. Alguns indicadores, agrupados nas dimensões/categorias desenvolvimento humano; econômico; abastecimento humano; pressões da irrigação, pecuária, abastecimento rural, aquicultura e lazer; coleta de esgoto; atendimento de coleta de lixo; e estado qualitativo da água, podem permitir uma análise e contribuir para a gestão dos recursos hídricos na bacia hidrográfica. O objetivo deste trabalho foi analisar a sustentabilidade hidroambiental dos municípios com sede totalmente contida na bacia hidrográfica do rio Mogi Guaçu, SP (Águas da Prata, Engenheiro Coelho, Luís Antônio, Mogi Mirim, Pitangueiras, São João da Boa Vista, Serra Negra, Sertãozinho, Socorro e Taquaral). A metodologia utilizada consistiu em uma pesquisa exploratória e documental, a partir do uso da estatística descritiva dentro de critérios e parâmetros de avaliação pré-definidos. Notou-se quanto ao Desenvolvimento Humano e os Indicadores Econômicos, uma situação preocupante na bacia, já que as médias dos municípios apresentaram performance de alerta. Em contrapartida, os indicadores de Saneamento apresentaram performance aceitável ou ideal. Finalmente, quanto aos indicadores referentes às Pressões da Irrigação, Pecuária, Abastecimento Rural, Aquicultura e Lazer a performance foi ideal na maioria dos municípios.
Dislipidemias en niños y adolescentes: factores determinantes y recomendaciones para su diagnóstico y manejo.
Authors: Noreña-Peña Ana , García de las Bayonas López Patricia , Sospedra López Isabel , Martínez-Sanz José Miguel , Martínez-Martínez Gerardo
Published: May 2018

El presente artículo tiene como objetivoidentificar los factores y determinantes que inciden en la dislipidemia infantil y adolescente, así como las recomendaciones existentes sobre el diagnóstico, manejo y seguimiento clínico. Se realizó una revisión narrativa consultando en PubMed, Web of Science y SciELO de artículos publicados entre 2010-2017, en población infantil y adolescente, que incluyan descripción de la patología, programas, manejo y tratamiento. Se hallaron 193 artículos. Se seleccionaron 32 que cumplían los criterios de inclusión, distribuidos en 2 grupos: uno que contiene 19 estudios originales describiendo factores para la aparición de esta patología y otro que agrupa 13 estudios correspondientes a recomendaciones para su diagnóstico y manejo. Respecto a los determinantes de las dislipidemias, el sobrepeso y/u obesidad en niños se ha descrito como el principal factor desencadenante. Aunque se observan avances sobre los tratamientos recomendados y cierto consenso acerca de las fases del mismo, todavía no existen recomendaciones unificadas con respecto a su detección precoz. Algunos autores apoyan la realización del cribado en toda la población infantil, mientras otros únicamente lo consideran necesario en niños con riesgo elevado. El tratamiento de primera línea se basa en cambios dietéticos y de actividad física, relegando al farmacológico como última opción.
Hacia la investigación basada en la evidencia
Authors: Marqués María Elena , Herrero Aitor , Baladia Eduard , Martínez-Rodríguez Rodrigo , Cervera Andrea , Buhring Kristian , Aguilar-Barrera Eliud , Durán-Agüero Samuel
Published: May 2018

ARTÍCULO ORIGINALLund H, Brunnhuber K, Juhl C, Robinson K, Leenaars M, Dorch BF, Jamtvedt G, Nortvedt MW, Christensen R, Chalmers I. Towards evidence based research. BMJ. 2016;355:i5440. doi: 10.1136/bmj.i5440Fecha de publicación del artículo original: 21 de octubre de 2016DERECHOS Y EXENCIÓN DE RESPONSABILIDADESTraducido con el permiso de BMJ Publishing Group Ltd. Lund H, Brunnhuber K, Juhl C, Robinson K, Leenaars M, Dorch BF, Jamtvedt G, Nortvedt MW, Christensen R, Chalmers I. Towards Evidence Based Research, BMJ 2016;355 :i5440 © 2016 BMJ Publishing Group Ltd.Los autores originales no han revisado ni verificado la traducción del manuscrito al español, y no necesariamente están de acuerdo con su contenidoBMJ no se hace responsable de la exactitud de la traducción publicada ni de los errores que pueda contener. No se asume responsabilidad alguna por parte de BMJ por cualquier lesión o daño a personas o propiedad por responsabilidad del producto, negligencia o de otra forma, ni de cualquier uso u operación de métodos, productos, instrucciones o ideas presentadas en el contenido original.MENSAJES CLAVEAventurarse en investigación sin revisar de manera sistemática lo ya conocido, especialmente cuando la investigación implica personas o animales, no es ético, carece de rigor científico y es un desperdicio.Una revisión sistemática de pruebas imparciales (evidencias) relevantes puede determinar si la investigación propuesta es realmente necesaria.Algunos organismos de financiación ahora requieren que los solicitantes hagan referencia a revisiones sistemáticas de investigaciones existentes.El desperdicio en investigación también se puede reducir mediante la producción, actualización y difusión eficientes de revisiones sistemáticas.
Grassroots Agency: Participation and Conflict in Buenos Aires Shantytowns seen through the Pilot Plan for Villa 7 (1971–1975)
Authors: Massidda Adriana Laura
Published: May 2018

In 1971, after more than a decade of national and municipal policies aimed at the top-down removal of shantytowns, the Buenos Aires City Council approved the Plan Piloto para la Relocalización de Villa 7 (Pilot Plan for the Relocation of Shantytown 7; 1971–1975, referred to as the Pilot Plan hereinafter). This particular plan, which resulted in the construction of the housing complex, Barrio Justo Suárez, endures in the collective memory of Argentines as a landmark project regarding grassroots participation in state housing initiatives addressed at shantytowns. Emerging from a context of a housing shortage for the growing urban poor and intense popular mobilizations during the transition to democracy, the authors of the Pilot Plan sought to empower shantytown residents in novel ways by: 1) maintaining the shantytown’s location as opposed to eradication schemes that relocated the residents elsewhere, 2) formally employing some of the residents for the stage of construction, as opposed to “self-help” housing projects in which the residents contributed with unpaid labor, and 3) including them in the urban and architectural design of the of the new housing.

This paper will examine the context in which the Pilot Plan was conceived of as a way of re-assessing the roles of the state, the user, and housing-related professionals, often seen as antagonistic. The paper argues that residents’ fair participation and state intervention in housing schemes are not necessarily incompatible, and can function in specific social and political contexts through multi-actor proposals backed by a political will that prioritizes grassroots agency.
Effect of Acid on Natural Zeolite Dealumination on Indigo Carmine Adsorption Capability
Authors: Sulistyowati Nanik , Sriyanti Sriyanti , Darmawan Adi
Published: May 2018

Modifying natural zeolite with dealumination using H2SO4 and HCl, and its application to adsorb indigo carmine has been performed. Dealumination was carried out by reacting a natural zeolite with a mixture of KMnO4-H2SO4 and a mixture of KMnO4-HCl then refluxed for 5 hours followed by washing with demineralized water until a neutral pH was obtained and dried for 12 hours at 80°C. Dealuminated zeolites were then characterized by XRD, FTIR and Si/Al ratio measurements. Dealuminated zeolite was then used to adsorb indigo carmine in a batch-shaker system for 30 min with concentration variation XRD diffraction shows that natural zeolite and dealuminated zeolite contain modernit minerals. Dealumination increased the Si/Al ratio from 0.935 to 2.075 and 7.912 which meant that dealumination was successful. The indigo carmine adsorption result showed that zeolite adsorption capacity II> zeolite I> natural zeolite. FTIR data showed that there was no change of zeolite structure before and after adsorption
Decolorization of Remazol Black B Solution by PbO2 Modified Fenton Method in a Scaled Up Reactor
Authors: Hasibuan Muhamad Abduh , Widodo Didik Setiyo , Lusiana Retno Ariadi
Published: May 2018

Study on decolourization of remazol black B (RBB) solution has been performed in a scale up reactor. As an artificial waste, the dye sample that contains azo groups is difficult to decompose under ordinary environmental conditions so it requires further treatment before discharging to open aquatic system. Many efforts have been reported and further developed toward other azo dyes. One of an outstanding approach is Fenton method. This study modified the method with PbO2 rather than Fe2+. In this modification, the dyestuff was degraded by radical •OH resulting from reaction between H2O2 and Pb2+ ion generated from PbO2. In Preliminary works, decolourization was performed and optimized in lab-scaled. Analysis were conducted and the best condition was applied to decolorize the sample in a scale-up size. Characteristics of the reactor was also determined. Results showed that at optimum condition, 100 mL of 50 ppm remazol black B was decolorized up to 98.82 % within 15 minutes. On scale up to 1 L-sized reactor, within the time highest percentages of remazol black B decolourization was reached 82.02 % by addition of 10 % H2O2 and COD decrease to 98.96 %. In the 1 L reactor, RBB sample with concentration of 50 ppm, PbO2 1 gram and H2O2 10 % obey the proposed decolourization equation of D = -0,0011x2 + 0.5705x – 0.6788 with x = volume peroxide (in mL), D = percent of decolourization.
Synthesis of Nano Chitosan as Carrier Material of Cinnamon’s Active Component
Authors: Ngadiwiyana Ngadiwiyana , Fachriyah Enny , Sarjono Purbowatiningrum Ria , Prasetya Nor Basid Adiwibawa , Ismiyarto Ismiyarto , Subagio Agus
Published: May 2018

Development and innovation to improve the efficacy of active ingredients of a plant can be done by using nanoparticle encapsulation of chitosan, which has dual function of protecting natural extracts degradation and delivering natural extracts to the target site. Chitosan is a natural polymer that is nontoxic, mucoadhesive, biodegradable, and biocompatible. This polymer also has a low level of immunogenicity and can be prepared into nanoparticles in mild conditions that make it suitable for natural extracts delivery systems. This paper reported synthesis of chitosan nanoparticles for cinnamon’s natural extract delivery. Chitosan synthesis was carried out by chitin deacetylation isolated from shrimp shells. Chitosan characterization was done by measuring deacetylation degree by FTIR. Chitosan nanoparticles were prepared by ionic gelation method using tripolyphosphate as crosslinker. Morphology and particle size of nano chitosan were characterized using a scanning electron microscope (SEM) and a transmission electron microscope (TEM). The result found that the yield of deproteinated chitin was 62.60%. Further process of demineralization resulted a yield of 52.60%, then depigmentation with a yield of 75.56%, and deacetylation with a yield of 79.02%. FTIR analysis showed that deacetylation degree of chitin into chitosan was found of 87.78%. Characterization by SEM found that nano chitosan has a particle size of 87 nm. While TEM images showed that the nano chitosan has a uniform shape and a lower physical aggregation.
Advances in mechanism and treatment strategy of cancer
Authors: Zeng Ye
Published: May 2018

Cancer is one of the most serious diseases with high incidence and high mortality rate threaten human health and quality of life. The researches on mechanisms of cancer development and metastasis, and effective and reasonable treatment strategies are of great significance. The traditional treatments for tumors such as surgery, radiotherapy, and chemotherapy have some benefits, but many drawbacks such as drug-resistance and side-effects. With the emergence of new therapeutic methods such as tumor-targeted drugs and immune drugs, the survival of cancer patients is improved, but reports on cardiac damage caused by therapeutic drugs are increasing.
Influence of the vaccinating density of A549 cells on tumorigenesis and distant organ metastasis in a lung cancer mice model
Authors: Zhang Xiaomei , Liu Yan , Peng Xu , Zeng Ye , Li Liang , Wang Jingge , He Xueling
Published: May 2018

Lung metastasis of malignant tumors, such as lung carcinoma, is a major cause of cancer-related deaths worldwide. The commonly used lung tumor models were established by subcutaneous or intravenous injection of the non-small cell lung cancer cell line A549 in mice. However, the influence of cell densities on tumorigenesis and distant organ metastasis remains poorly investigated. In this study, A549 cells were subcutaneously injected into mice at 1 í— 107 cells/mL, 5 í— 106 cells/mL, and 1 í— 106 cells/mL or intravenously at 1 í— 106 cells/mL, 5 í— 106 cells/mL, and 1 í— 106 cells/mL. Then, histology analysis, immunohistochemistry staining, and in-situ TUNEL assay were performed to evaluate tumor growth and metastasis. Results showed that subcutaneously injecting the A549 cells could develop tumors and that fewer apoptotic cells were found in the 5 í— 106 cells/mL group than in the other two groups. In groups intravenously injected with A549 cells, there were tumor nodules in all groups, and the 1 í— 105 cells/mL group showed longer survival time than the other two groups without any distant organ metastasis. There were tumor nodules formed in the liver in the 1 í— 106 cells/mL group at 14 d. Together, our results demonstrated that 5 í— 106 cells/mL and 1 í— 105 cells/mL are the optimal cell concentrations for the subcutaneous and experimental metastatic models, respectively.
Flavored Guilu Erxian decoction inhibits the injury of human bone marrow mesenchymal stem cells induced by cisplatin
Authors: Ke Bin , Shi Lin , Xu Zhaozhong , Wu Gang , Gong Yuxin , Zhu Lixia , Wang Yanjing , Ouyang Huailiang , Wang Xilong
Published: May 2018

To examine the exact role of flavored Guilu Erxian decoction, a Traditional Chinese Medicine (TCM) in the treatment of cisplatin-induced side-effects in bone marrow mesenchymal stem cells (BM-MSCs). BM-MSCs were isolated from bone marrow collected from SD rats and identified by flow cytometry. Cells were cultivated in MEM alpha medium containing 5% (TCM-L), 10% (TCM-M) and 20% (TCM-H) dosages of flavored Guilu Erxian decoction with or without cisplatin. Cell viability was determined through CCK-8 and thymidine analog 5-ethynyl-2"²-deoxyuridine (EdU) staining assay. Flow cytometry was used to determine cell cycle and apoptosis. The expression of p21 and cleaved-caspase-3 were examined using Western blot assay. The PI3K-AKT-mTOR pathway associated proteins, including p-PI3K, p-AKT and p-mTOR, were also examined by Western blot assay. CCK-8 and EdU staining assay demonstrated that cisplatin could inhibit cell proliferation in BM-MSCs in a dose and time dependent manner. Further, cisplatin could induce apoptosis through increasing G0/G1 cell cycle arrest, p21 and cleaved-caspase-3 expression. However, these phenomena would be significantly alleviated when adding the serum containing flavored Guilu Erxian decoction. Furthermore, the PI3K-AKT-mTOR pathway activation could be inhibited by cisplatin in BM-MSCs, while flavored Guilu Erxian decoction treatment successfully abrogated this effect. Combination of flavored Guilu Erxian decoction and cisplatin could reduce the damage to BM-MSCs. This indicates that the flavored Guilu Erxian decoction can enhance the possibility of BM-MSCs repairing and rehabilitating the normal function of injured tissues induced by cisplatin, which could provide a new direction for therapeutic applications.
Levels of serum bilirubin in small cell lung cancer and non-small cell lung cancer patients
Authors: Jiang Da , Shi Jian , Yuan Meng , Duan Xiaoyang , Li Lihua , Li Qian
Published: May 2018

Elevated bilirubin has been associated with protection of cardiovascular and kidney systems, whereas decreased bilirubin may predispose respiratory diseases. However, whether serum bilirubin levels are associated with lung cancer remains unclear. Here, clinical and pathologic data of a cohort of 363 lung cancer patients along with 363 age-and gender-matched healthy subjects were collected. The association of serum bilirubin levels with lung cancer was analyzed. The levels of serum bilirubin were significantly lower in lung cancer patients. The aspartate transaminase and alkaline phosphatase levels were significantly higher in lung cancer. Multi-classification logistics regression analysis revealed low total bilirubin level [OR (95%CI), 1.12 (1.02-1.23)], aspartate transaminase [OR (95%CI), 1.12 (1.02-1.23)], and alanine transaminase [OR (95%CI), 1.12 (1.02-1.23)] were risk factors in lung cancer. Serum bilirubin levels were significantly changed among small cell lung cancer (SCLC), lung adenocarcinoma (LAC) and lung squamous cell carcinoma (LSC). Total bilirubin level, smoke history and heart disease were risk factors for subtypes. Compared with LSC, patients with smoke history had significant higher risk in LAC [OR (95% Confidence Interval, CI), 4.49 (1.70, 11.96)]. Compared with LSC, patients with smoke history [OR (95%CI), 4.49 (1.70, 11.96)] and heart disease [OR (95%CI), 4.49 (1.70, 11.96)] had significant higher risk in SCLC. Compared with SCLC, patients with low total bilirubin [OR (95%CI), 1.12 (1.02-1.23)] and heart disease [OR (95%CI), 3.52 (1.01-12.23)] had significant higher risk in LAC. Taken together, these results suggested low serum bilirubin levels are tightly associated with lung cancer, especially with LAC. Serum bilirubin levels might serve as a predictor for lung cancer patients clinically.
The regulatory effect of Xiaoyao San on glucocorticoid receptors under the condition of chronic stress
Authors: Lu Jiandong , Fu Lijun , Qin Guozhong , Shi Pengliang , Fu Wenjun
Published: May 2018

In modern society, fierce competitions cause yearly increase of depression and anxiety. Xiaoyao San is a traditional Chinese medicine which relieves depression and nourishes liver. The active ingredients contain saikoside A, saikoside C, saikoside D, ferulic acid, ligustilide, Atractylenolide I, Atractylenolide II, Atractylenolide â…¢, paeoniflorin, Albiflorin, liquiritin, glycyrrhizic acid and pachymic acid. In stress condition, glucocorticoid receptors participate in the hypothalamus-pituitarium-adrenal gland (HPA) axis to regulate the balance of organism. In response to stress, the HPA axis (hypothalamus-pituitarium-adrenal gland) is activated and the levels of glucocorticoid (GC) and catecholamine (CA) are increased to enhance neuroendocrine reactions. Chronic stress activates HPA axis and sustaining increase of GC, reduces the expression amount of GR and inhibits the mechanism of negative feedback on HPA. The lower negative feedback on HPA could lead to ketonemia. Several active ingredients of Xiaoyao San can raise the expression of GR and recover the negative feedback of HPA axis to relieve depression and illness state. In spite of the poor understanding of the current effective components in Xiaoyao San, this will be the focus of our further research. The study of Xiaoyao San could help us better understand its anti-depression mechanism and cure the patients.
Adenovirus-mediated overexpression FADD induces a significant antitumor effect on human colorectal cancer cells both in vitro and in vivo
Authors: He Xueling , Peng Xu , Liu Yan , Zhang Xiaomei , Li Hualing , Yin Hailin
Published: May 2018

The Wnt/Î²-catenin signaling pathway plays important roles in cancers such as colorectal cancer. Colon cancer cells secrete and express high levels of Î²-catenin, which may stimulate autocrine signaling and further enhance activities of the canonical Wnt signaling pathway. Free Î²-catenin in the cytoplasm and nucleus leads to its association with T cell factor (TCF)/lymphocyte enhancing factor (Lef) transcription factors, and subsequent transcriptional activation of downstream target genes. FADD plays a key role in cellular apoptosis in many different types of cancer. Therefore, a recombinant adenovirus is constructed, in which an apoptosis gene FADD is placed under control of a promoter containing Tcf-responsive elements. It is observed that FADD overexpression can suppress cell growth and enhance apoptosis of SW480 cells in vitro. In addition, Ad-FADD can also suppress the growth of subcutaneous xenografts in the nude mice. Together, these results suggest that Ad-FADD has anti-proliferative and pro-apoptotic effects in colon cancer cells, which provides a novel strategy for treatment of colorectal cancer.
Hyperlocals and Legacy Media
Authors: Nygren Gunnar , Leckner Sara , Tenor Carina
Published: May 2018

Declining legacy media seriously affects local journalism in Sweden. Since 2004, nearly every second local office for local newspapers has been closed, and local coverage is diminishing. In a parallel development, new types of hyperlocal media are growing, according to a national mapping of local media ecologies. The study presented here is based on two surveys: one of local municipalities and one of independent hyperlocals. The key question is: are hyperlocals filling the gap? In many cases, the motivation behind new hyperlocal media has been discontent with declining media coverage from legacy media. In general, however, the pattern is more complicated; most hyperlocals grow in places where legacy media is also present. The main conclusion is that hyperlocals are only partly filling the gaps from declining legacy media, while parts of Sweden are becoming “news deserts.” Another important result is that hyperlocals are developing both in print and online, often in combination, to create a sustainable business model.
Genetic Variability, Heritability, and Correlation of Some Agronomical Characters of Soybean Varieties
Authors: Kuswantoro Heru , Artari Rina , Rahajeng Wiwit , Ginting Erliana , Supeno Agus
Published: May 2018

Genetic diversity and inheritance of the traits determine the success of the breeding program. Analysis of genetic variability and heritability assist breeders to decide a strategy and appropriate selection criteria that will be used to repair the desired character. The purpose of this study was to obtain information about genetic diversity, heritability and correlation of nine agronomic characters of soybean varieties. The materials were 16 soybean varieties that arranged in a randomized block design with three replications. The results showed that days to flowering, number of branches per plant, number of reproductive nodes, number of unfilled pods per plant, weight of 100 seeds, and grain yield revealed broad CVG (Genetic Coeffiecient of Variance), whereas the days to maturity, plant height, number of pods per plant had a narrow CVG. CVP (Phenotypic Coeffiecient of Variance) value higher than the value of CVG on all the observed characters with a slight difference, except for grain yield. The broad sense heritability varied from low (seed yield), medium (the number of branches, number of reproductive nodes, number of pods and the number of unfilled pods), and high (days to flowering, days to maturity, plant height, and weight of 100 seeds). Characters of days to flowering and weight of 100 seeds are effectively used as selection criteria because they had a broad CVG and high heritability. Correlation of all yield components to the seed yield was not significant, and negatively correlated to weight of 100 seeds. Variety with higher plant height tended to have a higher number of branches, reproductive nodes and filled pod per plant.
In Vitro Propagation of Bambusa balcooa as Alternative Material of Wood
Authors: Nurhayani Siti , Megia Rita , Purnamaningsih Ragapadmi
Published: May 2018

A diversion of raw material from wood to bamboo is necessary. In vitro culture of bamboo can be used to provide a high number of seedling. The aim of this study was to increase the multiplication of a high quality Bambusa balcooa as a wood alternative material. Part of plants used was the sterile axillary shoot. The explants were planted on MS0 medium for 2 weeks and later on multiplication medium MS+0.3 mg/l BAP + 0.3mg/l TDZ. The shoots obtained were fragmented into clusters (3-5 shoots) used for the next multiplication stage using five different medium formulas: (1) MS0; MS containing: (2) 0.1 mg/l BAP, (3) 0.3 mg/l BAP, (4) 0.1 mg/l BAP + 0.1 mg/l TDZ and (5) 0.3 mg/l BAP + 0.1 mg/l TDZ. The results showed that MS medium containing 0.1 mg/l BAP + 0.1mg/l TDZ was the best medium for B. balcooa propagation. The shoots produced from aforementioned medium had a better quality compared to the other medium. Forty days after planting, the average number of shoots in this medium was 14.25. MS medium containing 0.3 mg/l BAP + 0.1 mg/l TDZ produced the highest number of shoot but in lower quality. Rooting medium containing 10 mg/l IBA + 5 mg/l NAA produced 9-16 root in 8 weeks. Vermicompost was more prevalent for the acclimatization of B. balcooa compared to compost. The use of B.balcooa resulted in in vitro propagation as a substitute alternative for wood is expected to save the environment from illegal logging.
High Connectivity Among Synedrella nodiflora Populations in Java Island Based on Intergenic Spacer atpB-rbcL
Authors: Susanto Agus Hery , Nuryanto Agus , Daryono Budi Setiadi
Published: May 2018

Synedrella nodiflora (L.) Gaertn has taxonomically been the only species of genus Synedrella, which spreads over many tropical countries. In spite of its wide range of distribution, the genus remains monospecific. This leads to assumption of the very low genetic diversity among S. nodiflora populations worldwide. It may also be the case in Java Island, though rapid changes in ecosystem condition occurs. Here we report our study on S. nodiflora population genetics in Java Island using intergenic spacer (IGS) atpB –  rbcL as a molecular marker, since it has been well known as one of the most variable chloroplast genome regions in a wide range of plant species so far. As many as 58 individuals were collected randomly from ten different locations in the island. Based on IGS atpB – rbcL sequences of 860 bp length, only two haplotypes were observed. Both show only one polymorphic site (0.12%) and one transversion, where T is substituted by G at position 790, indicating that high connectivity among populations of S. nodiflora in Java Island is observed. This results in a low genetic differences among the populations, which at the same time provides a fact of nearly no variation among the IGS atpB – rbcL sequences.
The Structural Resistance’s Anatomy of Sweet Potato Leaves to Fungal Pathogen Sphaceloma batatas
Authors: Samiyarsih Siti , Juwarno Juwarno , Muljowati Juni Safitri
Published: May 2018

Anatomical characters can be used as instructions to the structural resistance of plants to pathogen attack. Various pathogens attack sweet potato plants, such as the Sphaceloma batatas fungus that causes scurvy disease (scab). The aims of this research t test the structural resistance of sweet potato plants based on leaf anatomical character and intensity of disease attack due to the inoculated of S. batatas. The research was conducted from June to November 2016, using the Completely Randomized Design Experimental (RAL) method with a factorial pattern. The first factor was ten sweet potato cultivars and the second factor was the inoculum of S. batatas fungus each treatment with five replications. The character of leaf anatomy observed was thick of cuticle, thick of mesophyll, size and number of stomata and number of trichomes per 1 mm2 leaf area. Based on the research result, it was concluded that the inoculation of the fungus of S. batatas caused the decrease of stomata length and width on ten sweet potato cultivars. The highest intensity of disease attack was 14.33% and correlated with stomata length (r = 0.49). The anatomical structural resistance to scurvy can be used as a basis for determining crosses for obtaining superior sweet potato cultivars. The benefit of the research is to advise the community to cultivate sweet potatoes that have structural resistance to scurvy, such as cuticle and thick mesophyll, high trichomata density.
Nutrient Limiting Factor for Enabling Algae Growth of Rawapening Lake, Indonesia
Authors: Piranti Agatha Sih , Rahayu Diana Retna Utarini Suci , Waluyo Gentur
Published: May 2018

Two important issues for establishment of nutrient criteria are identifying which nutrient limits algal growth and determining the concentration of that nutrient enabling nuisance growths. The purposes of this research were: 1) to examine the nutrient (TN, TP, ratio of TN/TP) dynamic in Rawapening Lake spatially and temporally, 2) to identify Nutrient Limiting of Algal Growth in Rawapening Lake, and 2) to determine the nutrient criteria for enabling algae growth in Rawapening Lake. The research was conducted using a survey method in 7 sites from February to August 2016. The result showed that spatially Total Nitrogen (TN) and Total Phosphor (TP) in the lake were not evenly distributed and temporally influenced by the inflow. The development of algae biomass in Rawapening Lake determined ratio of TN/TP. Nutrient criteria as follow: oligotrophic was 5.96 - 14.39, mesotrophic was 14.39 - 42.15, eutrophic 42.15 - 51.65, and hyper-eutrophic > 51.65. These criteria could be used in designing controlling eutrophication problem by arranging nutrient input from both external and internal sources in order to meet those limit. The benefits of research contributes to the development of environmental monitoring methods to assess the trophic status using more appropriate in accordance with the conditions of the tropics region. It also could be used for consideration in policy direction and orientation of land use in catchment areas in relation to water quality of the lake.
Biodiversity of Termites and Damage Building in Semarang, Indonesia
Authors: Subekti Niken , Priyono Bambang , Aisyah Afrin Nur
Published: May 2018

Termites cause a lot of damage and big losses for building components, especially those made of wood. High population growth and rapid infrastructure development in Semarang city affect the natural habitats of termites. This phenomenon changes the termites' behavior of foraging in buildings. Semarang city has humidity, temperature, and altitude that allows termites to live and breed well. The purpose of this study was to determine the types of termites living in housing in Semarang city as well as the level of attacks on housing. This research was conducted in nine housing in Semarang City. The research was carried out with two methods: building inspection and wood-feeding method by using Pinus mercusii wood measures 2 cm x 2 cm x 46 cm. The results found four types of termites that attack wood feeds namely Macrotermes gilvus, Microtermes inspiratus, Odontotermes javanicus, Coptotermes curvignathus and Cryptotermes sp.. Based on interviews and building inspection, it was known that the condition of the building in the category of "moderate" was occupying the most position (74.44%), good (17.78%) and lightly damaged (7.78%). From the causes of damage to building components, it can be concluded that the level of termite attack against damage to recidential buildings in Semarang city 44.58%. Cross-tabulation analysis of Chi-Square shows that there is a correlation between age and treatment with damage to the building. Futher, the finding can be used as baseline information for further scientific investigation for effective termites control on residential building components.