bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autotoxicity mechanism of Oryza sativa: transcriptome response in rice roots exposed to ferulic acid
Authors: Chi Wen-Chang , Chen Yun-An , Hsiung Yu-Chywan , Fu Shih-Feng , Chou Chang-Hung , Trinh Ngoc Nam , Chen Ying-Chih , Huang Hao-Jen 
Published: May 2013

Abstract

Background
Autotoxicity plays an important role in regulating crop yield and quality. To help characterize the autotoxicity mechanism of rice, we performed a large-scale, transcriptomic analysis of the rice root response to ferulic acid, an autotoxin from rice straw.

Results
Root growth rate was decreased and reactive oxygen species, calcium content and lipoxygenase activity were increased with increasing ferulic acid concentration in roots. Transcriptome analysis revealed more transcripts responsive to short ferulic-acid exposure (1- and 3-h treatments, 1,204 genes) than long exposure (24 h, 176 genes). Induced genes were involved in cell wall formation, chemical detoxification, secondary metabolism, signal transduction, and abiotic stress response. Genes associated with signaling and biosynthesis for ethylene and jasmonic acid were upregulated with ferulic acid. Ferulic acid upregulated ATP-binding cassette and amino acid/auxin permease transporters as well as genes encoding signaling components such as leucine-rich repeat VIII and receptor-like cytoplasmic kinases VII protein kinases, APETALA2/ethylene response factor, WRKY, MYB and Zinc-finger protein expressed in inflorescence meristem transcription factors.

Conclusions
The results of a transcriptome analysis suggest the molecular mechanisms of plants in response to FA, including toxicity, detoxicification and signaling machinery. FA may have a significant effect on inhibiting rice root elongation through modulating ET and JA hormone homeostasis. FA-induced gene expression of AAAP transporters may contribute to detoxicification of the autotoxin. Moreover, the WRKY and Myb TFs and LRR-VIII and SD-2b kinases might regulate downstream genes under FA stress but not general allelochemical stress. This comprehensive description of gene expression information could greatly facilitate our understanding of the mechanisms of autotoxicity in plants.
Extracellular DNA-induced antimicrobial peptide resistance in Salmonella enterica serovar Typhimurium
Authors: Johnson Lori , Horsman Shawn R , Charron-Mazenod Laetitia , Turnbull Amy L , Mulcahy Heidi , Surette Michael G , Lewenza Shawn 
Published: May 2013

Abstract

Background
The Salmonella enterica serovar Typhimurium PhoPQ two component system (TCS) is activated by low Mg2+ levels, low pH and by antimicrobial peptides (AP). Under Mg2+ limitation, the PhoPQ system induces pmrD expression, which post-translationally activates the PmrAB TCS. PhoPQ and PmrAB control many genes required for intracellular survival and pathogenesis. These include the polymyxin resistance (pmr) operon, which is required for aminoarabinose modification of LPS and protecting the outer membrane from antimicrobial peptide disruption and killing. Extracellular DNA is a ubiquitous polymer in the matrix of biofilms and accumulates in some infection sites. Extracellular DNA chelates cations and thus activates the Pseudomonas aeruginosa PhoPQ/PmrAB systems, leading to expression of the orthologous arn (pmr) operon.

Results
Here we show that extracellular DNA induces expression of the S. Typhimurium pmr antimicrobial peptide resistance operon in a PhoPQ and PmrAB-dependent manner. Induction of the pmr genes by DNA was blocked when present with excess Mg2+. Exogenous DNA led to increased resistance of planktonic cultures to aminoglycosides, antimicrobial peptides (AP) and ciprofloxacin, but only AP resistance was PhoPQ/PmrAB-dependent. Extracellular DNA was shown to be a matrix component of S. Typhimurium biofilms cultivated in flow chambers and on glass surfaces. A pmrH-gfp fusion was highly expressed in flow chamber biofilms cultivated in medium with repressing levels of 10 mM Mg2+ and co-localized with eDNA. Expression of pmrH-lux was monitored in plastic peg biofilms and shown to require PhoPQ and PmrAB. Biofilms had higher levels of pmrH expression compared to planktonic cultures. We propose that DNA accumulation in biofilms contributes to the increased pmrH-lux expression in biofilms.

Conclusions
The Salmonella PhoPQ/PmrAB systems and antimicrobial peptide resistance are activated by the cation chelating properties of extracellular DNA. DNA-induced AP resistance may allow immune evasion and increased survival of S. Typhimurium biofilms formed during extracellular growth stages of an infection or outside the host.
A cross-sectional study to compare care needs of individuals with and without dementia in residential homes in the Netherlands
Authors: van der Ploeg Eva S , Bax Dieuwertje , Boorsma Marijke , Nijpels Giel , van Hout Hein PJ 
Published: May 2013

Abstract

Background
Little is known about met and unmet needs of individuals in residential care, many of whom suffer from dementia. Unmet needs are associated with a decreased quality of life, worse mental health, dissatisfaction with services, and increased costs of care. The aim of this study was to compare the number and type of (unmet) needs of people with and without dementia in residential care in the Netherlands.

Methods
187 individuals in residents care or their relatives were interviewed to identify their care needs on 24 topics using the Camberwell Assessment of Needs for the Elderly (CANE) interview.

Results
Individuals diagnosed with probable dementia reported more needs in total and more unmet needs in comparison with individuals without this diagnosis. More specifically, differences were found for the topics “accommodation”, “money”, “benefits”, “medication management”, “incontinence”, “memory problems”, “inadvertent self-harm”, “company” and “daytime activities”.

Conclusions
It seems that the differences in care needs between individuals with and without dementia can be attributed to actual differences in physical and cognitive functioning. Residents with dementia reported more often unmet needs which might imply that care for people with dementia can still be better attuned to their needs.
Analysis of S. Epidermidis icaA and icaD genes by polymerase chain reaction and slime production: a case control study
Authors: Zhou Shusheng , Chao Xiaoguang , Fei Mingming , Dai Yuanyuan , Liu Bao 
Published: May 2013

Abstract

Background

Staphylococcus epidermidis is a common pathogen in medical device-associated infections and have an ability to form adherent slime. We aimed to study the effects of icaA and icaD genes on the slime formation of Staphylococcus epidermidis associated with catheter-associated infections.

Methods

S. epidermidis isolates from the central venous catheter blood of patients with catheter-associated infections, and from the nasal vestibules of healthy volunteers, intensive care unit hospital staff, and patients, were collected. Slime phenotype was determined by Congo red agar test. The icaA/D was detected by polymerase chain reaction. Slime was examined using scanning electron microscopy.

Results
A total of 82 S. epidermidis isolates were collected. We found a statistically significant difference with regards to slime production between the clinical isolates from the catheter blood specimens and those from the nasal vestibules (p<0.05). All S. epidermidis slime positive strains isolated were icaA positive. There was a greater correlation between the presence of both icaA and icaD and the slime production than the single expression of icaA or icaD and the presence of slime in all groups. The co-expression of mecA and icaD was associated with enhanced resistance to antibiotics.

Conclusion

S. epidermidis bacteria are significant nosocomial pathogens, and icaA/D can clarify the adhesion mechanism in the pathogenesis of infections associated with medical devices. This study result could be useful for the development of rapid diagnosis for slime producing and methicillin resistant S. epidermidis strains.
Polymorphism of A133S and promoter hypermethylation in Ras association domain family 1A gene (RASSF1A) is associated with risk of esophageal and gastric cardia cancers in Chinese population from high incidence area in northern China
Authors: Zhou Sheng Li , Cui Juan , Fan Zong Min , Li Xue Min , Li Ji Lin , Liu Bao Chi , Zhang Dong Yun , Liu Hong Yan , Zhao Xue Ke , Song Xin , Wang Ran , Yan Ze Chen , Yi Hui Xing , Wang Li Dong 
Published: May 2013

Abstract

Background
The role of tumor suppressor gene RASSF1A in the esophageal and gastric cardia carcinogenesis is still inconclusive. In this study, the polymorphism, promoter methylation and gene expression of RASSF1A were characterized in esophageal squamous cell carcinoma (ESCC) and gastric cardia adenocarcinoma (GCA).

Methods
We firstly analyzed the prevalence of RASSF1A A133S in a total of 228 cancer patients with ESCC (n=112) and GCA (n=116) and 235 normal controls by polymerase chain reaction (PCR) and restriction enzyme-digestion assay. Then, the promoter methylation status of the RASSF1A in ESCC (n=143), GCA (n=92) and corresponding adjacent normal tissues were further investigated using methylation-specific PCR (MSP) approach. Finally, the RASSF1A protein expression were determined in ESCC (n=27), GCA (n=24) and the matched adjacent normal tissues by immunohistochemical method.

Results
The frequency of 133Ala/Se and Ser/Ser genotype was significantly higher in GCA patients than in normal controls (19.0% vs. 10.2%, P=0.02). Compared with Ala/Ala genotype, Ala/Se and Ser/Ser genotype significantly increased susceptibility to GCA (OR=2.06, 95% CI=1.09–3.97). However, this polymorphism had no association with ESCC (P=0.69). The promoter methylation of RASSF1A gene was significantly increased the risk to both ESCC (OR=5.90, 95% CI=2.78–12.52) and GCA (OR=7.50, 95% CI= 2.78–20.23). Promoter methylation of RASSF1A gene in ESCC was also associated with age and cancer cell differentiation (for age: OR=3.11, 95% CI=1.10–8.73; for differentiation: OR=0.29, 95% CI=0.12–0.69). RASSF1A positive expression was significantly decreased the risk of GCA (OR=0.16, 95% CI=0.03–0.83). In contrast, there was no statistical significance between RASSF1A positive expression and ESCC. The expression of RASSF1A protein trend to be positively related with older GCA patients (OR=16.20, 95% CI=1.57–167.74).

Conclusions
The present findings suggest that alterations of RASSF1A may play an important role in gastric cardia carcinogenesis in terms of polymorphism, promoter hypermethylation and protein expression. Whereas, RASSF1A hypermethylation may probably also be involved in esophageal squamous cell carcinogenesis.
Effects of a Brief Qigong-based Stress Reduction Program (BQSRP) in a distressed Korean population: a randomized trial
Authors: Hwang Eun-Young , Chung Sun-Yong , Cho Jae-Heung , Song Mi-Yeon , Kim Sehyun , Kim Jong-Woo 
Published: May 2013

Abstract

Background
Distressed individuals in Korea may benefit from the practice of mind–body exercises such as Qigong. However, the effectiveness of such techniques needs to be investigated.

Methods
Fifty participants who were eligible to this study were randomized into a group receiving a 4-week intervention of a brief Qigong-based stress reduction program (BQSRP) or a wait-list control group. Before and after the intervention period, saliva samples were collected and questionnaires were completed on perceived stress, anxiety, “Hwa-Byung” (anger syndrome), and quality of life. Salivary cortisol has emerged in mind-body therapy research as an easy-to-collect, relatively inexpensive, biologic marker of stress. Salivary corisol were collected to evaluate physiological effect of BQSRP. Between-group comparisons of change from baseline to study completion were analyzed by analysis of covariance for the Perceived Stress Scale and independent two sample t- tests for other measures.

Results
Compared with the control group, the BQSRP intervention group displayed significantly larger decreases in Perceived Stress Scale scores (p = 0.0006), State Anxiety scores (p = 0.0028), Trait Anxiety scores (p < 0.0001), personality subscale scores of the Hwa-Byung Scale (p = 0.0321), symptoms scores of the Hwa-Byung Scale (p = 0.0196), and a significantly larger increase in World Health Organization Quality of Life Abbreviated version scores (p s < .05). Salivary cortisol levels were not changed.

Conclusions
The BQSRP appears to be effective in reducing stress perception, anxiety, anger, and improving quality of life (KCT0000056).
3,4-dihydroxyphenyl acetic acid and (+)-epoxydon isolated from marine algae-derived microorganisms induce down regulation of epidermal growth factor activated mitogenic signaling cascade in Hela cells
Authors: Jo Mi Jeong , Bae Seong Ja , Son Byeng Wha , Kim Chi Yeon , Kim Gun Do 
Published: May 2013

Abstract

Background
Epidermal growth factor receptor (EGFR) is a member of the receptor tyrosine kinase (RTK) family. Epidermal growth factor induces its dimerization and stimulates phosphorylation of intracellular tyrosine residues. Phosphorylation of EGFR is studied for cancer therapy because EGFR regulates many cellular processes including cell proliferation, differentiation, and survival. Hence, down-regulation of EGFR kinase activity results in inhibition of signaling cascades amenable for proliferation and progression of cell cycle.

Methods
In the study, we purified 3,4-dihydroxyphenyl acetic acid and (+)-epoxydon from Aspergillus sp. isolated from marine brown alga Ishige okamurae and Phoma herbarum isolated from marine red alga Hypnea saidana respectively and determined its anti-tumor activities against HeLa human cervical cancer cells.

Results
Two compounds suppressed EGFR activity in vitro with IC50 values for 3,4-dihydroxyphenyl acetic acid and (+)-epoxydon were 2.8 and 0.6 μg/mL respectively and reduced the viable numbers of HeLa cells. Immunoblotting analysis exhibited that the compounds induced inhibition of cell growth by causing downregulation of the mitogenic signaling cascade, inactivation of p90RSK, and release of cytochrome c from mitochondria.

Conclusions
Results suggest that decreased expression of active EGFR and EGFR-related downstream molecules by treatment with the compounds may results in the inhibition of cell growth and inducement of apoptosis.
Epidemiology of Plasmodium infections in Flores Island, Indonesia using real-time PCR
Authors: Kaisar Maria MM , Supali Taniawati , Wiria Aprilianto E , Hamid Firdaus , Wammes Linda J , Sartono Erliyani , Luty Adrian JF , Brienen Eric AT , Yazdanbakhsh Maria , van Lieshout Lisette , Verweij Jaco J 
Published: May 2013

Abstract

Background
DNA-based diagnostic methods have been shown to be highly sensitive and specific for the detection of malaria. An 18S-rRNA-based, real-time polymerase chain reaction (PCR) was used to determine the prevalence and intensity of Plasmodium infections on Flores Island, Indonesia.

Methods
Microscopy and real-time multiplex PCR for the detection of Plasmodium species was performed on blood samples collected in a population-based study in Nangapanda Flores Island, Indonesia.

Results
A total 1,509 blood samples were analysed. Real-time PCR revealed prevalence for Plasmodium falciparum, Plasmodium vivax, and Plasmodium malariae to be 14.5%, 13.2%, and 1.9% respectively. Sub-microscopic parasitaemia were found in more than 80% of all positive cases. The prevalence of P. falciparum and P. vivax was significantly higher in subjects younger than 20 years (p ≤ 0.01). In the present study, among non-symptomatic healthy individuals, anaemia was strongly correlated with the prevalence and load of P. falciparum infections (p ≤ 0.01; p = 0.02) and with the load of P. vivax infections (p = 0.01) as detected with real-time PCR. Subjects with AB blood group tend to have a higher risk of being infected with P. falciparum and P. vivax when compared to other blood groups.

Conclusion
The present study has shown that real-time PCR provides more insight in the epidemiology of Plasmodium infections and can be used as a monitoring tool in the battle against malaria. The unsurpassed sensitivity of real-time PCR reveals that sub microscopic infections are common in this area, which are likely to play an important role in transmission and control.

Trial registration
Trials number http://www.controlled-trials.com/ISRCTN83830814
Novel mechanism of regulation of fibrosis in kidney tumor with tuberous sclerosis
Authors: Liang Sitai , Cuevas Gabriela , Tizani Shaza , Salas Tiffanie , Liu Huijuan , Li Baojie , Habib Samy L 
Published: May 2013

Abstract

Background
Deficiency in tuberin results in activation the mTOR pathway and leads to accumulation of cell matrix proteins. The mechanisms by which tuberin regulates fibrosis in kidney angiomyolipomas (AMLs) of tuberous sclerosis patients are not fully known.

Method
In the present study, we investigated the potential role of tuberin/mTOR pathway in the regulation of cell fibrosis in AML cells and kidney tumor tissue from tuberous sclerosis complex (TSC) patients.

Results
AML cells treated with rapamycin shows a significant decrease in mRNA and protein expression as well as in promoter transcriptional activity of alpha-smooth muscle actin (α-SMA) compared to untreated cells. In addition, cells treated with rapamycin significantly decreased the protein expression of the transcription factor YY1. Rapamycin treatment also results in the redistribution of YY1 from the nucleus to cytoplasm in AML cells. Moreover, cells treated with rapamycin resulted in a significant reduce of binding of YY1 to the αSMA promoter element in nuclear extracts of AML cells. Kidney angiomyolipoma tissues from TSC patients showed lower levels of tuberin and higher levels of phospho-p70S6K that resulted in higher levels of mRNA and protein of αSMA expression compared to control kidney tissues. In addition, most of the α-SMA staining was identified in the smooth muscle cells of AML tissues. YY1 was also significantly increased in tumor tissue of AMLs compared to control kidney tissue suggesting that YY1 plays a major role in the regulation of αSMA.

Conclusions
These data comprise the first report to provide one mechanism whereby rapamycin might inhibit the cell fibrosis in kidney tumor of TSC patients.
Effects of a commercial product containing guaraná on psychological well-being, anxiety and mood: a single-blind, placebo-controlled study in healthy subjects
Authors: Silvestrini Gianluca Ivan , Marino Franca , Cosentino Marco 
Published: May 2013

Abstract

Background
Guaranà (Paulinia cupana) seed extracts are increasingly popular worldwide for their stimulant, cognitive and behavioral effects. To assess the effects on psychological well-being, anxiety and mood of a commercially available guaranà preparation taken regularly over several days according to the labelled dosages and instructions, 27 healthy volunteers were enrolled in a prospective, randomized, single-blind, placebo-controlled, crossover study.

Results
Guaranà 350 mg × 3 daily just after breakfast or placebo were given for 5 consecutive days. Assessment was performed one day after the last intake and included the psychological well-being (PWB) scales, the self-rating anxiety state scale (SAS), and the Bond–Lader mood scales. There were no significant differences between guaranà and placebo in any of the 6 areas of PWB, in SAS, as well as in any of the 16 mood scales.

Conclusions
In healthy subjects a 5-day treatment with a commercial preparation of guaranà used according to labelled instructions provided no evidence for any major effects on psychological well-being, anxiety and mood. Considering the increasing popularity of guaranà-containing products sold as dietary supplements for fitness purposes, controlled studies are strongly warranted to assess their benefits in comparison to the labelled claims.
Passivation mechanism of thermal atomic layer-deposited Al2O3 films on silicon at different annealing temperatures
Authors: Zhao Yan , Zhou Chunlan , Zhang Xiang , Zhang Peng , Dou Yanan , Wang Wenjing , Cao Xingzhong , Wang Baoyi , Tang Yehua , Zhou Su 
Published: May 2013

Abstract
Thermal atomic layer-deposited (ALD) aluminum oxide (Al2O3) acquires high negative fixed charge density (Q
f) and sufficiently low interface trap density after annealing, which enables excellent surface passivation for crystalline silicon. Q
f can be controlled by varying the annealing temperatures. In this study, the effect of the annealing temperature of thermal ALD Al2O3 films on p-type Czochralski silicon wafers was investigated. Corona charging measurements revealed that the Q
f obtained at 300°C did not significantly affect passivation. The interface-trapping density markedly increased at high annealing temperature (>600°C) and degraded the surface passivation even at a high Q
f. Negatively charged or neutral vacancies were found in the samples annealed at 300°C, 500°C, and 750°C using positron annihilation techniques. The Al defect density in the bulk film and the vacancy density near the SiO
x
/Si interface region decreased with increased temperature. Measurement results of Q
f proved that the Al vacancy of the bulk film may not be related to Q
f. The defect density in the SiO
x
region affected the chemical passivation, but other factors may dominantly influence chemical passivation at 750°C.
Discretionary bandwidth granting scheme for homogenous real-time applications
Authors: Wee Kuokkwee , R Mardeni , Tan S W , Lee S W 
Published: May 2013

Abstract
IEEE 802.16e is an advanced wireless access technology that provides high-speed data transmission in long distance and offers quality of service (QoS) to subscribers. The provisioning of QoS is one of the great features by IEEE 802.16 to support both real-time and non-real-time applications. In IEEE 802.16, the common part sublayer in the MAC layer is responsible for maintaining the QoS services. There are many functions in the common part sublayer; the most popular topics discussed by researchers are the uplink and downlink scheduling algorithms. Many discussions had been made and focused on these two classes of schedulers. Another equally important component but overlooked so far is the bandwidth request and grant module. Bandwidth request and grant module arbitrates the amount of bandwidth to be granted, besides handling the bandwidth requests. This bandwidth request and grant process has always been developed in a conventional way, and its importance has been underestimated. In addition, the bandwidth distribution within a same service class or category also attracted little attention thus far. Many algorithms for interclass scheduling have been studied and proposed but not as much for intraclass scheduling. However, in bandwidth request and grant process, constraints on the required knowledge by the schedulers limit the intraclass scheduling algorithms to be applied onto them. We view the bandwidth request and grant process as an important part of the QoS architecture. In this paper, we proposed a new bandwidth granting scheme for the bandwidth request and granting process, which enables bandwidth to be fairly granted based on the necessity to all the requests from the same service class or category. By applying our scheme, significant improvements have been observed and recorded. Experiment results have proven and confirmed the effectiveness of our proposed scheme as compared to the conventional scheme.