bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptome analysis to investigate the high starch accumulation of duckweed (Landoltia punctata) under nutrient starvation
Authors: Tao Xiang , Fang Yang , Xiao Yao , Jin Yan-ling , Ma Xin-rong , Zhao Yun , He Kai-ze , Zhao Hai , Wang Hai-yan 
Published: May 2013

Abstract

Background
Duckweed can thrive on anthropogenic wastewater and produce tremendous biomass production. Due to its relatively high starch and low lignin percentage, duckweed is a good candidate for bioethanol fermentation. Previous studies have observed that water devoid of nutrients is good for starch accumulation, but its molecular mechanism remains unrevealed.

Results
This study globally analyzed the response to nutrient starvation in order to investigate the starch accumulation in duckweed (Landoltia punctata). L. punctata was transferred from nutrient-rich solution to distilled water and sampled at different time points. Physiological measurements demonstrated that the activity of ADP-glucose pyrophosphorylase, the key enzyme of starch synthesis, as well as the starch percentage in duckweed, increased continuously under nutrient starvation. Samples collected at 0 h, 2 h and 24 h time points respectively were used for comparative gene expression analysis using RNA-Seq. A comprehensive transcriptome, comprising of 74,797 contigs, was constructed by a de novo assembly of the RNA-Seq reads. Gene expression profiling results showed that the expression of some transcripts encoding key enzymes involved in starch biosynthesis was up-regulated, while the expression of transcripts encoding enzymes involved in starch consumption were down-regulated, the expression of some photosynthesis-related transcripts were down-regulated during the first 24 h, and the expression of some transporter transcripts were up-regulated within the first 2 h. Very interestingly, most transcripts encoding key enzymes involved in flavonoid biosynthesis were highly expressed regardless of starvation, while transcripts encoding laccase, the last rate-limiting enzyme of lignifications, exhibited very low expression abundance in all three samples.

Conclusion
Our study provides a comprehensive expression profiling of L. punctata under nutrient starvation, which indicates that nutrient starvation down-regulated the global metabolic status, redirects metabolic flux of fixed CO2 into starch synthesis branch resulting in starch accumulation in L. punctata.
Bio-oil based biorefinery strategy for the production of succinic acid
Authors: Wang Caixia , Thygesen Anders , Liu Yilan , Li Qiang , Yang Maohua , Dang Dan , Wang Ze , Wan Yinhua , Lin Weigang , Xing Jianmin 
Published: May 2013

Abstract

Background
Succinic acid is one of the key platform chemicals which can be produced via biotechnology process instead of petrochemical process. Biomass derived bio-oil have been investigated intensively as an alternative of diesel and gasoline fuels. Bio-oil could be fractionized into organic phase and aqueous phase parts. The organic phase bio-oil can be easily upgraded to transport fuel. The aqueous phase bio-oil (AP-bio-oil) is of low value. There is no report for its usage or upgrading via biological methods. In this paper, the use of AP-bio-oil for the production of succinic acid was investigated.

Results
The transgenic E. coli strain could grow in modified M9 medium containing 20 v/v% AP-bio-oil with an increase in OD from 0.25 to 1.09. And 0.38 g/L succinic acid was produced. With the presence of 4 g/L glucose in the medium, succinic acid concentration increased from 1.4 to 2.4 g/L by addition of 20 v/v% AP-bio-oil. When enzymatic hydrolysate of corn stover was used as carbon source, 10.3 g/L succinic acid was produced. The obtained succinic acid concentration increased to 11.5 g/L when 12.5 v/v% AP-bio-oil was added. However, it decreased to 8 g/L when 50 v/v% AP-bio-oil was added. GC-MS analysis revealed that some low molecular carbon compounds in the AP-bio-oil were utilized by E. coli.

Conclusions
The results indicate that AP-bio-oil can be used by E. coli for cell growth and succinic acid production.
Nucleosomal DNA binding drives the recognition of H3K36-methylated nucleosomes by the PSIP1-PWWP domain
Authors: van Nuland Rick , van Schaik Frederik MA , Simonis Marieke , van Heesch Sebastiaan , Cuppen Edwin , Boelens Rolf , Timmers HT Marc , van Ingen Hugo 
Published: May 2013

Abstract

Background
Recognition of histone modifications by specialized protein domains is a key step in the regulation of DNA-mediated processes like gene transcription. The structural basis of these interactions is usually studied using histone peptide models, neglecting the nucleosomal context. Here, we provide the structural and thermodynamic basis for the recognition of H3K36-methylated (H3K36me) nucleosomes by the PSIP1-PWWP domain, based on extensive mutational analysis, advanced nuclear magnetic resonance (NMR), and computational approaches.

Results
The PSIP1-PWWP domain binds H3K36me3 peptide and DNA with low affinity, through distinct, adjacent binding surfaces. PWWP binding to H3K36me nucleosomes is enhanced approximately 10,000-fold compared to a methylated peptide. Based on mutational analyses and NMR data, we derive a structure of the complex showing that the PWWP domain is bound to H3K36me nucleosomes through simultaneous interactions with both methylated histone tail and nucleosomal DNA.

Conclusion
Concerted binding to the methylated histone tail and nucleosomal DNA underlies the high- affinity, specific recognition of H3K36me nucleosomes by the PSIP1-PWWP domain. We propose that this bipartite binding mechanism is a distinctive and general property in the recognition of histone modifications close to the nucleosome core.
Open‐label parallel dose tolerability study of three subcutaneous immunotherapy regimens in house dust mite allergic patients
Authors: Rieker‐Schwienbacher Juliane , Nell Marja J , Diamant Zuzana , van Ree Ronald , Distler Andreas , Boot Johan D , Kleine‐Tebbe Jörg 
Published: May 2013

AbstractBackgroundThe current maintenance dose (10,000 AUeq/monthly) of a subcutaneous allergoid for house dust mite (HDM) immunotherapy has previously shown significant clinical efficacy in patients with HDM induced allergic rhinitis or rhinoconjunctivitis. In order to comply with the 2009 EMA guidelines on immunotherapy products, a study was conducted to evaluate the safety, tolerability and short‐term treatment effects of up‐dosing regimens with high doses (up to 40,000 AUeq) of allergoid HDM immunotherapy.MethodsIn total 48 patients with HDM‐allergic rhinitis or rhinoconjunctivitis (29 M/19 F; 18–53 years) were included and enrolled into one of three up‐dosing regimens (1:4:4): 1) a regular regimen with up‐dosing to 40,000 AUeq followed by two maintenance doses (total duration 17 weeks), 2) an intermediate regimen (14 weeks) or 3) a fast regimen (11 weeks). Safety and tolerability were evaluated by monitoring of early and late local reactions and systemic reactions. In addition, short‐term effects were assessed by conjunctival provocation test (CPT) and levels of serum allergen‐specific IgE, IgG and IgG4.ResultsThirty‐nine patients completed the study according to protocol. No early local reactions occurred. Late local reactions (LLR) were observed in 12% of the injections. In total, 31 systemic reactions, all grade 1, were reported of which two needed oral antihistamine treatment. No grade 2 or higher systemic reactions were observed. Six patients (15%) did not reach the highest dose due to LLR and/or systemic reactions needing antihistamines (20% in the regular regimen, 16% in the intermediate regimen and 13% in the fast regimen). At the end of the study, an improvement in the CPT was observed in 82.1% of patients, indirectly indicating an early treatment effect at the current dose and higher doses. In addition, IgG4 immunoglobulin levels were significantly increased in all groups following treatment.ConclusionsIn this open‐label study, allergoid HDM immunotherapy in doses up to 40,000 AUeq was generally well tolerated and no clinically relevant safety issues were identified. In the safety aspects of the three up‐dosing regimens no clinically relevant differences were encountered. Therefore, these dose ranges and up‐dosing regimens can be safely included in future dose‐finding efficacy studies.
The influence of DNA repair on neurological degeneration, cachexia, skin cancer and internal neoplasms: autopsy report of four xeroderma pigmentosum patients (XP-A, XP-C and XP-D)
Authors: Lai Jin-Ping , Liu Yen-Chun , Alimchandani Meghna , Liu Qingyan , Aung Phyu Phyu , Matsuda Kant , Lee Chyi-Chia R , Tsokos Maria , Hewitt Stephen , Rushing Elisabeth J , Tamura Deborah , Levens David L , DiGiovanna John J , Fine Howard A , Patronas Nicholas , Khan Sikandar G , Kleiner David E , Oberholtzer J Carl , Quezado Martha M , Kraemer Kenneth H 
Published: May 2013

Abstract

Background
To investigate the association of DNA nucleotide excision repair (NER) defects with neurological degeneration, cachexia and cancer, we performed autopsies on 4 adult xeroderma pigmentosum (XP) patients with different clinical features and defects in NER complementation groups XP-A, XP-C or XP-D.

Results
The XP-A (XP12BE) and XP-D (XP18BE) patients exhibited progressive neurological deterioration with sensorineural hearing loss. The clinical spectrum encompassed severe cachexia in the XP-A (XP12BE) patient, numerous skin cancers in the XP-A and two XP-C (XP24BE and XP1BE) patients and only few skin cancers in the XP-D patient. Two XP-C patients developed internal neoplasms including glioblastoma in XP24BE and uterine adenocarcinoma in XP1BE. At autopsy, the brains of the 44 yr XP-A and the 45 yr XP-D patients were profoundly atrophic and characterized microscopically by diffuse neuronal loss, myelin pallor and gliosis. Unlike the XP-A patient, the XP-D patient had a thickened calvarium, and the brain showed vacuolization of the neuropil in the cerebrum, cerebellum and brainstem, and patchy Purkinje cell loss. Axonal neuropathy and chronic denervation atrophy of the skeletal muscles were observed in the XP-A patient, but not in the XP-D patient.

Conclusions
These clinical manifestations and autopsy findings indicate advanced involvement of the central and peripheral nervous system. Despite similar defects in DNA repair, different clinicopathological phenotypes are seen in the four cases, and therefore distinct patterns of neurodegeneration characterize XP-D, XP-A and XP-C patients.
Intrastriatal injection of interleukin-1 beta triggers the formation of neuromyelitis optica-like lesions in NMO-IgG seropositive rats
Authors: Kitic Maja , Hochmeister Sonja , Wimmer Isabella , Bauer Jan , Misu Tatsuro , Mader Simone , Reindl Markus , Fujihara Kazuo , Lassmann Hans , Bradl Monika 
Published: May 2013

AbstractBackgroundNeuromyelitis optica (NMO) is a severe, disabling disease of the central nervous system (CNS) characterized by the formation of astrocyte-destructive, neutrophil-dominated inflammatory lesions in the spinal cord and optic nerves. These lesions are initiated by the binding of pathogenic aquaporin 4 (AQP4)-specific autoantibodies to astrocytes and subsequent complement-mediated lysis of these cells. Typically, these lesions form in a setting of CNS inflammation, where the blood–brain barrier is open for the entry of antibodies and complement. However, it remained unclear to which extent pro-inflammatory cytokines and chemokines contribute to the formation of NMO lesions. To specifically address this question, we injected the cytokines interleukin-1 beta, tumor necrosis factor alpha, interleukin-6, interferon gamma and the chemokine CXCL2 into the striatum of NMO-IgG seropositive rats and analyzed the tissue 24 hours later by immunohistochemistry.ResultsAll injected cytokines and chemokines led to profound leakage of immunoglobulins into the injected hemisphere, but only interleukin-1 beta induced the formation of perivascular, neutrophil-infiltrated lesions with AQP4 loss and complement-mediated astrocyte destruction distant from the needle tract. Treatment of rat brain endothelial cells with interleukin-1 beta, but not with any other cytokine or chemokine applied at the same concentration and over the same period of time, caused profound upregulation of granulocyte-recruiting and supporting molecules. Injection of interleukin-1 beta caused higher numbers of blood vessels with perivascular, cellular C1q reactivity than any other cytokine tested. Finally, the screening of a large sample of CNS lesions from NMO and multiple sclerosis patients revealed large numbers of interleukin-1 beta-reactive macrophages/activated microglial cells in active NMO lesions but not in MS lesions with comparable lesion activity and location.ConclusionsOur data strongly suggest that interleukin-1 beta released in NMO lesions and interleukin-1 beta-induced production/accumulation of complement factors (like C1q) facilitate neutrophil entry and BBB breakdown in the vicinity of NMO lesions, and might thus be an important secondary factor for lesion formation, possibly by paving the ground for rapid lesion growth and amplified immune cell recruitment to this site.
Study on Synergistic Interligand Interactions of Thermally Stable Gold Nanoparticles
Authors: Okumura Atsushi , Yamada Kou , Todori Kenji , Machida Shigeru 
Published: May 2013

Abstract
In order to apply gold nanoparticles to the materials for electronic and optical devices, they are required to be tolerant of heat applied in the fabrication processes. In our previous study, novel gold nanoparticles with excellent thermal stability were developed by introducing an amide bond and a condensed ring into the ligand molecules. On the other hand, particle size is a key factor in determining device performance, gaining control over the size is highly advantageous. In this study, a size-increase reaction of the pyrene-containing gold nanoparticle was carried out. The particle size was successfully increased from 2 to ca. 10 nm, without lowering the thermal stability. Furthermore, their interligand interactions could be probed using fluorescence measurements based on the characteristic excimer emission of pyrene. It is suggested that strong π–π stacking occurred around the particles, even after the size-increase reaction, contributing to maintaining the thermal stability.
Overconfidence in Newsvendor Orders: An Experimental Study
Authors: Ren Yufei , Croson Rachel 
Published: May 2013

Previous studies have shown that individuals make suboptimal decisions in a variety of supply chain and inventory settings. We hypothesize that one cause is that individuals are overconfident (in particular, overprecise) in their estimation of order variation. Previous work has shown theoretically that underestimating the variance of demand causes orders to deviate from optimal in predictable ways. We provide two experiments supporting this theoretical link. In the first, we elicit the precision of each individual's beliefs and demonstrate that overprecision significantly correlates with order bias. We find that overprecision explains almost one-third of the observed ordering mistakes and that the effect of overprecision is robust to learning and other dynamic considerations. In the second, we introduce a new technique to exogenously reduce overprecision. We find that participants randomly assigned to this treatment demonstrate less overprecision and less biased orders than do those in a control group. This paper was accepted by Peter Wakker, decision analysis.
Price Competition with Consumer Confusion
Authors: Chioveanu Ioana , Zhou Jidong 
Published: May 2013

This paper proposes a model in which identical sellers of a homogeneous product compete in both prices and price frames (i.e., ways to present price information). Frame choices affect the comparability of price offers and may cause consumer confusion and lower price sensitivity. In equilibrium, firms randomize their frame choices to obfuscate price comparisons and sustain positive profits. The nature of the equilibrium depends on whether frame differentiation or frame complexity is more confusing. Moreover, an increase in the number of competitors induces firms to rely more on frame complexity, and this may boost industry profits and lower consumer surplus. This paper was accepted by J. Miguel Villas-Boas, marketing.
APLICAÇÃO DO PROCESSO DE RACIOCÍNIO DA TEORIA DAS RESTRIÇÕES EM SISTEMAS ATÍPICOS: UMA ANÁLISE EMPÍRICA DE UMA BATERIA DE ESCOLA DE SAMBA DO CARNAVAL CARIOCA
Authors: Wanderley Carlos Alexandre Nascimento , Cogan Samuel , Silva Anderson Chaves da 
Published: May 2013

ResumoEste artigo mostra a aplicação do Processo de Raciocínio (PR) para identificação dos Efeitos Indesejáveis (EI) e problema-raiz numa bateria de escola de samba. O estudo demonstra a aplicação somente de uma das cinco ferramentas do PR, a ARA. Metodologicamente, a presente pesquisa é classificada como exploratória e bibliográfica. Caracteriza-se como documental, pois examinou o mapa de justificativas dos jurados, utilizando a análise de conteúdo para interpretação sobre o que estava sendo dito sobre o desempenho da bateria. De posse das informações obtidas, foi possível construir a ARA, identificar os EI e visualizar o problema-raiz. Concluiu-se que dos dezessete EI identificados, a disposição dos instrumentos na bateria, prejudicando a percepção auditiva do Diretor de bateria em relação a todos os instrumentos, é o problema-raiz. Ao término da análise são apresentadas questões que podem servir de base para novas pesquisas, utilizando as demais ferramentas do PR não utilizadas neste trabalho. Palavras-chave: processo de raciocínio; teoria das restrições; árvore da realidade atual; escola de samba; bateria.
A Especialização Tecnológica Local como Indutora do Empreendedorismo e do Desenvolvimento Regional: O Caso do Vale da Eletrônica Brasileiro
Authors: Dos Santos Isabel Cristina , Paula Roberta Manfron de 
Published: May 2013

Este trabalho apresenta a percepção dos empreendedores quanto a influência da especialização tecnológica local promovida pelas instituições de ensino superior e seus reflexos no empreendedorismo regional, com base na experiência do Instituto Nacional de Telecomunicações – Inatel, localizado em Santa Rita do Sapucaí, sul de Minas Gerais. O objetivo da pesquisa foi identificar os efeitos tangíveis da transferência de conhecimento de alta tecnologia da universidade para a sociedade produtiva regional. A abordagem metodológica escolhida teve caráter qualitativo, valendo-se de uma pesquisa exploratório-descritiva, que visou ampliar a compreensão do papel dos agentes educacionais locais, especificamente envolvidos no ensino técnico e tecnológico, na geração do desenvolvimento regional. A coleta de dados foi baseada em levantamento documental, bibliográfico e na aplicação de questionários dirigidos aos empreendedores locais, delimitados no escopo geográfico do estudo. Os resultados obtidos permitem concluir que houve evolução nos indicadores socioeconômicos da região.Palavras-chave: especialização tecnológica; empreendorismo regional; incubadoras de negócios; desenvolvimento regional.
A contrastive corpus-based analysis of the frequency of discourse markers in NE and NNE media discourse: Implications for a “universal discourse competence”
Authors: Vaez Dalili Mehdi , Vahid Dastjerdi Hossein 
Published: May 2013

AbstractThis article examines whether there are differences in the frequency of discourse markers (DMs) between Native English (NE) and Non-native English (NNE) corpora of political media discourse. Based on the grammatical-pragmatic perspective of discourse markers (Fraser, 2004), the discourse markers identified in the corpora were divided into four semantic categories: contrastive discourse markers (CDM), elaborative discourse markers (EDM), implicative discourse markers (IDM) and temporal discourse markers (TDM). The results revealed that: (i) in both corpora, implicative discourse markers (IDMs) and elaborative discourse markers (EDMs) have the lowest and highest frequency counts respectively, (ii) there are significant differences across the four types of discourse markers in both corpora, (iii) there is no significant difference in the aggregated frequency of discourse markers across NE and NNE political news discourse, and (iv) there are no relative NE/NNE frequency differences within each category of discourse markers. The findings point to the need for revisiting Kaplan's contrastive rhetoric, and provide evidence for the plausibility of a “ universal discourse competence” in advanced NNE written discourse.
Distance-Based Mapping of Disease Risk
Authors: Jeffery Caroline , Ozonoff Al , White Laura Forsberg , Pagano Marcello 
Published: May 2013

: In this article, we consider the problem of comparing the distribution of observations in a planar region to a pre-specified null distribution. Our motivation is a surveillance setting where we map locations of incident disease, aiming to monitor these data over time, to locate potential areas of high/low incidence so as to direct public health actions.We propose a non-parametric approach to distance-based disease risk mapping inspired by tomographic imaging. We consider several one-dimensional projections via the observed distribution of distances to a chosen fixed point; we then compare this distribution to that expected under the null and average these comparisons across projections to compute a relative-risk-like score at each point in the region. The null distribution can be established from historical data. Scores are displayed on the map using a color scale.In addition, we give a detailed description of the method along with some desirable theoretical properties. To further assess the performance of this method, we compare it to the widely used log ratio of kernel density estimates. As a performance metric, we evaluate the accuracy to locate simulated spatial clusters superimposed on a uniform distribution in the unit disk. Results suggest that both methods can adequately locate this increased risk but each relies on an appropriate choice of parameters. Our proposed method, distance-based mapping (DBM), can also generalize to arbitrary metric spaces and/or high-dimensional data.