bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemical and transcriptional responses of Norway spruce genotypes with different susceptibility to Heterobasidion spp. infection
Authors: Danielsson Marie , Lundén Karl , Elfstrand Malin , Hu Jiang , Zhao Tao , Arnerup Jenny , Ihrmark Katarina , Swedjemark Gunilla , Borg-Karlson Anna-Karin , Stenlid Jan 
Published: November 2011

Abstract

Background
Norway spruce [Picea abies (L.) Karst.] is one of the most important conifer species in Europe. The wood is economically important and infections by wood-rotting fungi cause substantial losses to the industry.
The first line of defence in a Norway spruce tree is the bark. It is a very efficient barrier against infection based on its mechanical and chemical properties. Once an injury or an infection is recognized by the tree, induced defences are activated. In this study we examined transcriptional response, using 454-sequencing, and chemical profiles in bark of Norway spruce trees with different susceptibility to Heterobasidion annosum s.l. infection. The aim was to find associations between the transcriptome and chemical profiles to the level of susceptibility to Heterobasidion spp. in Norway spruce genotypes.

Results
Both terpene and phenol compositions were analysed and at 28 days post inoculation (dpi) high levels of 3-carene was produced in response to H. annosum. However, significant patterns relating to inoculation or to genotypes with higher or lower susceptibility could only be found in the phenol fraction. The levels of the flavonoid catechin, which is polymerized into proanthocyanidins (PA), showed a temporal variation; it accumulated between 5 and 15 dpi in response to H. annosum infection in the less susceptible genotypes. The transcriptome data suggested that the accumulation of free catechin was preceded by an induction of genes in the flavonoid and PA biosynthesis pathway such as leucoanthocyanidin reductase. Quantitative PCR analyses verified the induction of genes in the phenylpropanoid and flavonoid pathway. The qPCR data also highlighted genotype-dependent differences in the transcriptional regulation of these pathways.

Conclusions
The varying dynamics in transcriptional and chemical patterns displayed by the less susceptible genotypes suggest that there is a genotypic variation in successful spruce defence strategies against Heterobasidion. However, both high levels of piceasides and flavonoids in the less susceptible genotypes suggested the importance of the phenolic compounds in the defence. Clearly an extended comparison of the transcriptional responses in the interaction with Heterobasidion between several independent genotypes exhibiting reduced susceptibility is needed to catalogue mechanisms of successful host defence strategies.
Computational analysis of a novel mutation in ETFDH gene highlights its long-range effects on the FAD-binding motif
Authors: Er Tze-Kiong , Chen Chih-Chieh , Liu Yen-Yi , Chang Hui-Chiu , Chien Yin-Hsiu , Chang Jan-Gowth , Hwang Jenn-Kang , Jong Yuh-Jyh 
Published: November 2011

Abstract

Background
Multiple acyl-coenzyme A dehydrogenase deficiency (MADD) is an autosomal recessive disease caused by the defects in the mitochondrial electron transfer system and the metabolism of fatty acids. Recently, mutations in electron transfer flavoprotein dehydrogenase (ETFDH) gene, encoding electron transfer flavoprotein:ubiquinone oxidoreductase (ETF:QO) have been reported to be the major causes of riboflavin-responsive MADD. To date, no studies have been performed to explore the functional impact of these mutations or their mechanism of disrupting enzyme activity.

Results
High resolution melting (HRM) analysis and sequencing of the entire ETFDH gene revealed a novel mutation (p.Phe128Ser) and the hotspot mutation (p.Ala84Thr) from a patient with MADD. According to the predicted 3D structure of ETF:QO, the two mutations are located within the flavin adenine dinucleotide (FAD) binding domain; however, the two residues do not have direct interactions with the FAD ligand. Using molecular dynamics (MD) simulations and normal mode analysis (NMA), we found that the p.Ala84Thr and p.Phe128Ser mutations are most likely to alter the protein structure near the FAD binding site as well as disrupt the stability of the FAD binding required for the activation of ETF:QO. Intriguingly, NMA revealed that several reported disease-causing mutations in the ETF:QO protein show highly correlated motions with the FAD-binding site.

Conclusions
Based on the present findings, we conclude that the changes made to the amino acids in ETF:QO are likely to influence the FAD-binding stability.
Ex vivo susceptibility of Plasmodium falciparum isolates from Dakar, Senegal, to seven standard anti-malarial drugs
Authors: Fall Bécaye , Diawara Silmane , Sow Kowry , Baret Eric , Diatta Bakary , Fall Khadidiatou B , Mbaye Pape S , Fall Fatou , Diémé Yaya , Rogier Christophe , Wade Boubacar , Bercion Raymond , Pradines Bruno 
Published: November 2011

Abstract

Background
As a result of widespread chloroquine and sulphadoxine-pyrimethamine resistance, artemisinin-based combination therapy (ACT) (which includes artemether-lumefantrine and artesunate-amodiaquine) has been recommended as a first-line anti-malarial regimen in Senegal since 2006. Since then, there have been very few reports on the ex vivo susceptibility of Plasmodium falciparum to anti-malarial drugs. To examine whether parasite susceptibility has been affected by the widespread use of ACT, the ex vivo susceptibility of local isolates was assessed at the military hospital of Dakar.

Methods
The ex vivo susceptibility of 93 P. falciparum isolates from Dakar was successfully determined using the Plasmodium lactate dehydrogenase (pLDH) ELISA for the following drugs: chloroquine (CQ), quinine (QN), mefloquine (MQ), monodesethylamodiaquine (MDAQ), lumefantrine (LMF), dihydroartemisinin (DHA) and doxycycline (DOX).

Results
After transformation of the isolate IC50 in ratio of IC50 according to the susceptibility of the 3D7 reference strain (isolate IC50/3D7 IC50), the prevalence of the in vitro resistant isolates with reduced susceptibility was 50% for MQ, 22% for CQ, 12% for DOX, 6% for both QN and MDAQ and 1% for the drugs LMF and DHA. The highest significant positive correlations were shown between responses to CQ and MDAQ (r = 0.569; P < 0.0001), LMF and QN (r = 0.511; P < 0.0001), LMF and DHA (r = 0.428; P = 0.0001), LMF and MQ (r = 0.413; P = 0.0002), QN and DHA (r = 0.402; P = 0.0003) and QN and MQ (r = 0.421; P = 0.0001).

Conclusions
The introduction of ACT in 2002 has not induced a decrease in P. falciparum susceptibility to the drugs DHA, MDAQ and LMF, which are common ACT components. However, the prevalence of P. falciparum isolates with reduced susceptibility has increased for both MQ and DOX. Taken together, these data suggest that intensive surveillance of the P. falciparum in vitro susceptibility to anti-malarial drugs in Senegal is required.
The modified general iterative methods for nonexpansive semigroups in banach spaces†
Authors: Wangkeeree Rabian , Preechasilp Pakkapon 
Published: November 2011

AbstractIn this paper, we introduce the modified general iterative approximation methods for finding a common fixed point of nonexpansive semigroups which is a unique solution of some variational inequalities. The strong convergence theorems are established in the framework of a reflexive Banach space which admits a weakly continuous duality mapping. The main result extends various results existing in the current literature.Mathematics Subject Classification (2000) 47H05, 47H09, 47J25, 65J15
A family of variable step-size affine projection adaptive filter algorithms using statistics of channel impulse response
Authors: Shams Esfand Abadi Mohammad , AbbasZadeh Arani Seyed Ali Asghar 
Published: November 2011

Abstract
This paper extends the recently introduced variable step-size (VSS) approach to the family of adaptive filter algorithms. This method uses prior knowledge of the channel impulse response statistic. Accordingly, optimal step-size vector is obtained by minimizing the mean-square deviation (MSD). The presented algorithms are the VSS affine projection algorithm (VSS-APA), the VSS selective partial update NLMS (VSS-SPU-NLMS), the VSS-SPU-APA, and the VSS selective regressor APA (VSS-SR-APA). In VSS-SPU adaptive algorithms the filter coefficients are partially updated which reduce the computational complexity. In VSS-SR-APA, the optimal selection of input regressors is performed during the adaptation. The presented algorithms have good convergence speed, low steady state mean square error (MSE), and low computational complexity features. We demonstrate the good performance of the proposed algorithms through several simulations in system identification scenario.
Inhibition of p38-MAPK Signaling Pathway Attenuates Breast Cancer Induced Bone Pain and Disease Progression in a Murine Model of Cancer-Induced Bone Pain
Authors: Sukhtankar Devki , Okun Alec , Chandramouli Anupama , Nelson Mark A , Vanderah Todd W , Cress Anne E , Porreca Frank , King Tamara 
Published: November 2011

Background: Mechanisms driving cancer-induced bone pain are poorly understood. A central factor implicated to be a key player in the process of tumorigenesis, osteoclastogenesis and nociception is p38 MAPK. We determined the role of p38 MAPK in a mouse model of breast cancer induced bone pain in which mixed osteolytic and osteoblastic remodeling occurs. Results: In cancer-treated mice, acute as well as chronic inhibition of p38 MAPK with SB203580 blocked flinching and guarding behaviors in a dose-dependent manner whereas no effect on thresholds to tactile stimuli was observed. Radiographic analyses of bones demonstrated that chronic inhibition of p38 MAPK reduced bone loss and incidence of spontaneous fracture in cancer-treated mice. Histological analysis of bones collected from mice treated with the p38 MAPK inhibitor showed complete absence of osteoblastic growth in the intramedullary space as well as significantly reduced tumor burden. Conclusions: Blockade of non-evoked pain behaviors but not hypersensitivity suggests differences in the underlying mechanisms of specific components of the pain syndrome and a possibility to individualize aspects of pain management. While it is not known whether the role of p38 MAPK signaling can be expanded to other cancers, the data suggest a need for understanding molecular mechanisms and cellular events that initiate and maintain cancer-induced bone pain for effective management for both ongoing pain as well as breakthrough pain.
Ethnobotanical investigation of 'wild' food plants used by rice farmers in Kalasin, Northeast Thailand
Authors: Cruz-Garcia Gisella S , Price Lisa L 
Published: November 2011

Abstract
Background
Wild food plants are a critical component in the subsistence system of rice farmers in Northeast Thailand. One of the important characteristics of wild plant foods among farming households is that the main collection locations are increasingly from anthropogenic ecosystems such as agricultural areas rather than pristine ecosystems. This paper provides selected results from a study of wild food conducted in several villages in Northeast Thailand. A complete botanical inventory of wild food plants from these communities and surrounding areas is provided including their diversity of growth forms, the different anthropogenic locations were these species grow and the multiplicity of uses they have.

Methods
Data was collected using focus groups and key informant interviews with women locally recognized as knowledgeable about contemporarily gathered plants. Plant species were identified by local taxonomists.

Results
A total of 87 wild food plants, belonging to 47 families were reported, mainly trees, herbs (terrestrial and aquatic) and climbers. Rice fields constitute the most important growth location where 70% of the plants are found, followed by secondary woody areas and home gardens. The majority of species (80%) can be found in multiple growth locations, which is partly explained by villagers moving selected species from one place to another and engaging in different degrees of management. Wild food plants have multiple edible parts varying from reproductive structures to vegetative organs. More than two thirds of species are reported as having diverse additional uses and more than half of them are also regarded as medicine.

Conclusions
This study shows the remarkable importance of anthropogenic areas in providing wild food plants. This is reflected in the great diversity of species found, contributing to the food and nutritional security of rice farmers in Northeast Thailand.
Coordinated increase of γ-secretase reaction products in the plasma of some female Japanese sporadic Alzheimer's disease patients: quantitative analysis of p3-Alcα with a new ELISA system
Authors: Konno Tomoko , Hata Saori , Hamada Yukiko , Horikoshi-Sakuraba Yuko , Nakaya Tadashi , Saito Yuhki , Yamamoto Tohru , Yamamoto Takayuki , Maeda Masahiro , Ikeuchi Takeshi , Gandy Sam , Akatsu Hiroyasu , Suzuki Toshiharu ,   the Japanese Alzheimer's Disease Neuroimaging Initiative
Published: November 2011

Abstract

Background
Aggregatable amyloid β-peptide (Aβ) and non-aggregatable p3-Alcα are metabolic products of the γ-secretase cleavage of amyloid β-protein precursor (APP) and Alcadeinα (Alcα), respectively. Familial AD (FAD) -linked mutations in the presenilin 1 or 2 (PS1 or PS2) component of γ-secretase can cause alternative intramembranous processing of APP and Alcα, leading to a coordinated generation of variants of both Aβ and p3-Alcα. Variant Alcα peptides have been observed in the cerebrospinal fluid (CSF) of patients with mild cognitive impairment and sporadic Alzheimer's disease (AD). Since, like APP, Alcα is largely expressed in brain, one might predict that alternative processing of Alcα would be reflected in body fluids of some AD patients. These patients with misprocessing of multiple γ-secretase substrates might define an endophenotype of p3-Alcα, in whom AD is due either to dysfunction of γ-secretase or to a disorder of the clearance of hydrophobic peptides such as those derived from transmembrane domains.

Results
We developed a simple procedure for extraction of p3-Alcα from plasma and for analyzing this extract in a sensitive, p3-Alcα-specific sandwich enzyme-linked immunosorbent assay (ELISA) system. Plasma p3-Alcα levels and Aβ40 levels were examined in sporadic AD subjects from two independent Japanese cohorts. In some of these patients, levels of plasma p3-Alcα were significantly higher, and were accompanied by parallel changes in Aβ40 levels. This AD-related difference was more marked in female subjects, but this phenomenon was not observed in subjects with frontotemporal lobar degeneration (FTLD).

Conclusion
Reagents and procedures have been established that enable extraction of p3-Alcα from plasma and for quantification of plasma p3-Alcα levels by ELISA. Some populations of AD subjects apparently show increased levels of both p3-Alcα and Aβ40. Quantification of p3-Alcα level may be useful as a readily accessible biomarker for a population of sporadic AD patients in which disease pathogenesis is associated with either dysfunction of γ-secretase or with a disorder of the clearance of transmembrane domain-derived peptides.
More expressions of BDNF and TrkB in multiple hepatocellular carcinoma and anti-BDNF or K252a induced apoptosis, supressed invasion of HepG2 and HCCLM3 cells
Authors: Guo Dawei , Hou Xuezhong , Zhang Hongbin , Sun Wenyu , Zhu Lei , Liang Jian , Jiang Xiaofeng 
Published: November 2011

AbstractBackgroundBrain-derived neurotrophic factor (BDNF) and its receptor Tropomysin-related kinase B (TrkB) are commonly up-regulated in a variety of human tumors. However, the roles of BDNF/TrkB in hepatocellular carcinoma (HCC) have been poorly investigated.MethodsWe evaluated the expressions of BDNF and TrkB in 65 cases of HCC by immunohistochemical staining. Moreover, in human HCC cell lines of HepG2 and high metastatic HCCLM3, the secretory BDNF in supernatant was measured by ELISA, the effects of BDNF neutralizing antibody or Trk tyrosine kinase inhibitor K252a on apoptosis and invasion were examined by flow cytometry and transwell assay respectively.ResultsHigher expression of BDNF (63.1%) or positive expression of TrkB (55.4%) was found in HCC specimens, which was significantly correlated with multiple and advanced stage of HCC. BDNF secretory level in HCCLM3 was higher than that in HepG2 cells. Both anti-BDNF and K252a effectively induced apoptosis and suppressed invasion of HepG2 and HCCLM3 cells.ConclusionsThese findings suggested that BDNF/TrkB are essential for HCC cells survival and invasion. BDNF/TrkB signaling should probably be an effective target to prevent HCC advancement.
CYP1A1 MspI and exon7 gene polymorphisms and lung cancer risk: An updated meta-analysis and review
Authors: Zhan Ping , Wang Qin , Qian Qian , Wei Shu-Zhen , Yu Li-Ke 
Published: November 2011

Abstract

Background
Many studies have examined the association between the CYP1A1 MspI and exon 7 gene polymorphisms and lung cancer risk in various populations, but their results have been inconsistent.

Methods
To assess this relationship more precisely, a meta-analysis and review were performed. The PubMed, Embase, Web of Science, and CNKI database was searched for case-control studies published up to June 2010. Data were extracted and pooled odds ratios (OR) with 95% confidence intervals (CI) were calculated.

Results
Ultimately, 64 studies, comprising 18,397 subjects from 49 case-control studies of the MspI genotype and 18,518 patients from 40 case-control studies of the exon 7 genotype, were included. A significantly elevated lung cancer risk was associated with 2 MspI genotype variants (for type C vs Type A: OR = 1.26, 95% CI = 1.12-1.42; for types B and C combined vs Type A: OR = 1.20, 95% CI = 1.13-1.28) in overall population. In the stratified analysis, a significant association was found in Asians, Caucasians, lung SCC, lung AC and Male population, not in mixed population, lung SCLC and Female population. However, inconsistent results were observed for CYP1A1 exon7 in our meta-analysis, two variants of the exon 7 polymorphism were associated with a significantly higher risk for lung cancer (for Val/Val vs Ile/Ile: OR = 1.24, 95% CI = 1.09-1.42; for (Ile/Val +Val/Val) vs Ile/Ile: OR = 1.15, 95% CI = 1.07-1.24) in overall population. In the stratified analysis, a significant assocation was found in Asians, Caucasians, lung SCC and Female population, not in mixed population, lung AD, lung SCLC and Male population. Additionally, a significant association was found in smoker population and not found in non-smoker populations for CYP1A1 MspI and exon7 gene.

Conclusions
This meta-analysis suggests that the MspI and exon 7 polymorphisms of CYP1A1 correlate with increased lung cancer susceptibility and there is an interaction between two genotypes of CYP1A1 polymorphism and smoking, but these associations vary in different ethnic populations, histological types of lung caner and gender of case and control population.
Reporting of sex as a variable in cardiovascular studies using cultured cells
Authors: Taylor K Efua , Vallejo-Giraldo Catalina , Schaible Niccole S , Zakeri Rosita , Miller Virginia M 
Published: November 2011

Abstract

Background
Chromosomal complement, including that provided by the sex chromosomes, influences expression of proteins and molecular signaling in every cell. However, less than 50% of the scientific studies published in 2009 using experimental animals reported sex as a biological variable. Because every cell has a sex, we conducted a literature review to determine the extent to which sex is reported as a variable in cardiovascular studies on cultured cells.

Methods
Articles from 10 cardiovascular journals with high impact factors (Circulation, J Am Coll Cardiol, Eur Heart J, Circ Res, Arterioscler Thromb Vasc Biol, Cardiovasc Res, J Mol Cell Cardiol, Am J Physiol Heart Circ Physiol, J Heart Lung Transplant and J Cardiovasc Pharmacol) and published in 2010 were searched using terms 'cultured' and 'cells' in any order to determine if the sex of those cells was reported. Studies using established cell lines were excluded.

Results
Using two separate search strategies, we found that only 25 of 90 articles (28%) and 20 of 101 articles (19.8%) reported the sex of cells. Of those reporting the sex of cells, most (68.9%; n = 31) used only male cells and none used exclusively female cells. In studies reporting the sex of cells of cardiovascular origin, 40% used vascular smooth-muscle cells, and 30% used stem/progenitor cells. In studies using cells of human origin, 35% did not report the sex of those cells. None of the studies using neonatal cardiac myocytes reported the sex of those cells.

Conclusions
The complement of sex chromosomes in cells studied in culture has the potential to affect expression of proteins and 'mechanistic' signaling pathways. Therefore, consistent with scientific excellence, editorial policies should require reporting sex of cells used in in vitro experiments.
Facial emotion processing in major depression: a systematic review of neuroimaging findings
Authors: Stuhrmann Anja , Suslow Thomas , Dannlowski Udo 
Published: November 2011

Abstract

Background
Cognitive models of depression suggest that major depression is characterized by biased facial emotion processing, making facial stimuli particularly valuable for neuroimaging research on the neurobiological correlates of depression. The present review provides an overview of functional neuroimaging studies on abnormal facial emotion processing in major depression. Our main objective was to describe neurobiological differences between depressed patients with major depressive disorder (MDD) and healthy controls (HCs) regarding brain responsiveness to facial expressions and, furthermore, to delineate altered neural activation patterns associated with mood-congruent processing bias and to integrate these data with recent functional connectivity results. We further discuss methodological aspects potentially explaining the heterogeneity of results.

Methods
A Medline search was performed up to August 2011 in order to identify studies on emotional face processing in acutely depressed patients compared with HCs. A total of 25 studies using functional magnetic resonance imaging were reviewed.

Results
The analysis of neural activation data showed abnormalities in MDD patients in a common face processing network, pointing to mood-congruent processing bias (hyperactivation to negative and hypoactivation to positive stimuli) particularly in the amygdala, insula, parahippocampal gyrus, fusiform face area, and putamen. Furthermore, abnormal activation patterns were repeatedly found in parts of the cingulate gyrus and the orbitofrontal cortex, which are extended by investigations implementing functional connectivity analysis. However, despite several converging findings, some inconsistencies are observed, particularly in prefrontal areas, probably caused by heterogeneities in paradigms and patient samples.

Conclusions
Further studies in remitted patients and high-risk samples are required to discern whether the described abnormalities represent state or trait characteristics of depression.