bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biochemical and functional characterization of SpdA, a 2′, 3′cyclic nucleotide phosphodiesterase from Sinorhizobium meliloti
Authors: Mathieu-Demazière Céline , Poinsot Véréna , Masson-Boivin Catherine , Garnerone Anne-Marie , Batut Jacques 
Published: November 2013

Abstract

Background
3′, 5′cAMP signaling in Sinorhizobium meliloti was recently shown to contribute to the autoregulation of legume infection. In planta, three adenylate cyclases CyaD1, CyaD2 and CyaK, synthesizing 3′, 5′cAMP, together with the Crp-like transcriptional regulator Clr and smc02178, a gene of unknown function, are involved in controlling plant infection.

Results
Here we report on the characterization of a gene (smc02179, spdA) at the cyaD1 locus that we predicted to encode a class III cytoplasmic phosphodiesterase.
First, we have shown that spdA had a similar pattern of expression as smc02178 in planta but did not require clr nor 3′, 5′cAMP for expression.
Second, biochemical characterization of the purified SpdA protein showed that, contrary to expectation, it had no detectable activity against 3′, 5′cAMP and, instead, high activity against the positional isomers 2′, 3′cAMP and 2′, 3′cGMP.
Third, we provide direct experimental evidence that the purified Clr protein was able to bind both 2′, 3′cAMP and 3′, 5′cAMP in vitro at high concentration. We further showed that Clr is a 3′, 5′cAMP-dependent DNA-binding protein and identified a DNA-binding motif to which Clr binds. In contrast, 2′, 3′cAMP was unable to promote Clr specific-binding to DNA and activate smc02178 target gene expression ex planta.
Fourth, we have shown a negative impact of exogenous 2′, 3′cAMP on 3′, 5′cAMP-mediated signaling in vivo. A spdA null mutant was also partially affected in 3′, 5′cAMP signaling.

Conclusions
SpdA is a nodule-expressed 2′, 3′ specific phosphodiesterase whose biological function remains elusive. Circumstantial evidence suggests that SpdA may contribute insulating 3′, 5′cAMP-based signaling from 2′, 3′ cyclic nucleotides of metabolic origin.
Characterization and co-expression analysis of WRKY orthologs involved in responses to multiple abiotic stresses in Pak-choi (Brassica campestris ssp. chinensis)
Authors: Tang Jun , Wang Feng , Wang Zhen , Huang Zhinan , Xiong Aisheng , Hou Xilin 
Published: November 2013

Abstract

Background
The WRKY transcription factor is an important member of the stress-related transcription factors, which mediate diverse abiotic stresses in many plants. However, up until now, the number of WRKY members, and the regulatory mechanisms involved in abiotic stress responses in Pak-choi (Brassica campestris ssp. chinensis), remained unknown.

Results
We isolated and identified 56 full-length WRKY cDNAs from a Pak-choi stress-induced cDNA library. The 56 putative BcWRKY proteins were divided into three groups based on structural and phylogenetic analyses. A subcellular localization prediction indicated that the putative BcWRKY proteins were enriched in the nuclear region. Experiments involving BcWRKY25 and BcWRKY40 confirmed the prediction. A total of 22 BcWRKYs were differentially expressed in response to at least one stress condition (abscisic acid, cold, salinity, heat, or osmosis) tested on Pak-choi leaves, and a co-expression analysis indicated stress-inducible BcWRKYs co-regulated multiple abiotic stresses. BcWRKY33, BcWRKY40, BcWRKY53, and BcWRKY70 acted as key regulators and played dominant roles within co-regulatory networks of stress-inducible BcWRKYs.

Conclusions
We first isolated and characterized the 56 stress-inducible WRKY transcription factor family members. A total of 22 stress-inducible BcWRKYs found in leaves can co-regulate multiple environmental stresses by integrating the potential mutual interactions of WRKYs in Pak-choi. This information will be valuable when exploring the molecular mechanisms of WRKYs in response to abiotic stresses in plants.
Phenotypic, immunologic, and clinical characteristics of patients with nontuberculous mycobacterial lung disease in Korea
Authors: Lee Ae-Ra , Lee Jinwoo , Choi Sun-Mi , Seong Moon-Woo , Kim Sung A , Kim Myoungsil , Chae Kyung Ok , Lee Ji Sun , Yim Jae-Joon 
Published: November 2013

Abstract

Background
This study aimed to elucidate the phenotypic, immunologic, and clinical characteristics of Korean patients with nontuberculous mycobacterial (NTM) lung disease and compare them with non-NTM bronchiectasis (BE) patients.

Methods
We prospectively recruited patients between 20 and 80 years of age who had nodular BE type NTM lung disease. Phenotypic, immunologic, and clinical characteristics were evaluated through physical examination, laboratory tests, pulmonary function tests, and radiographic examinations. Questionnaires were also answered. The results of the evaluations were compared with the results of non-NTM BE patients.

Results
A total of 84 patients with NTM lung disease and 47 non-NTM BE patients participated in the study. Mycobacterium avium complex lung disease and M. abscessus lung disease were most common. Patients with NTM lung disease had lower body mass index than non-NTM BE patients. Scoliosis was observed more frequently in patients with NTM lung disease than in non-NTM BE patients.

Conclusions
Significant similarities were seen between Korean patients with NTM lung disease and patients from other countries. Differences in phenotypic and clinical characteristics between NTM lung disease and non-NTM BE patients suggest differences in the immunopathogenesis of NTM lung disease and non-NTM BE.

Trial registration information
ClinicalTrials.gov Registration number; NCT01616745
Pharmacoeconomic evaluation of voriconazole vs. liposomal amphotericin B in empiric treatment of invasive fungal infections in Turkey
Authors: Turner Stuart J , Senol Esin , Kara Ates , Al-Badriyeh Daoud , Dinleyici Ener C , Kong David CM 
Published: November 2013

Abstract

Background
Invasive fungal infections (IFI) are associated with considerable expense and mortality on healthcare systems. There is a need to provide evidence of both clinical efficacy and value for money with any health technology. The current pharmacoeconomic evaluation investigated the use of liposomal amphotericin B (LAmB) and voriconazole for the empiric treatment of IFI in the Turkish setting.

Methods
Decision analytic modelling was used to create a pathway for patient treatment with a 5-point composite outcome measure. The data was obtained from a major non-inferiority multicentre randomised controlled study, with an expert panel of clinicians in Turkey providing transition probabilities and cost not available in the literature. Sensitivity analyses were performed on the inputs from the clinical trial and the expert panel.

Results
As per the base case analysis, voriconazole was preferred by Turkish Lira (TL) 2,523 per patient treated and TL2,520 per surviving patient. LAmB was the preferred alternative by TL5,362 per successfully treated patient. Removing fever resolution as part of the composite outcome measure resulted in voriconazole being the preferred alternative per successfully treated patient. Univariate sensitivity analysis highlighted that increasing the duration of voriconazole by >1.2 days or decreasing LAmB by >1.0 days changes the result. Monte Carlo Simulation resulted in 69.4% of simulations favouring voriconazole per patient treated.

Conclusion
There is a strong likelihood that voriconazole is economically more favourable than LAmB in the empiric treatment of IFI in Turkey.
Copy number variations in endoglin locus: mapping of large deletions in Spanish families with hereditary hemorrhagic telangiectasia type 1
Authors: Fontalba Ana , Fernández-Luna Jose L , Zarrabeitia Roberto , Recio-Poveda Lucia , Albiñana Virginia , Ojeda-Fernández Maria L , Bernabéu Carmelo , Alcaraz Luis A , Botella Luisa M 
Published: November 2013

Abstract

Background
The hereditary hemorrhagic telangiectasia syndrome (HHT), also known as the Rendu–Osler-Weber syndrome is a multiorganic vascular disorder inherited as an autosomal dominant trait. Diagnostic clinical criteria include: epistaxis, telangiectases in mucocutaneous and gastrointestinal sites, arteriovenous malformations (AVMs) most commonly found in pulmonary, hepatic and cerebral circulations, and familial inheritance. HHT is transmitted in 90% of the cases as an autosomal dominant condition due to mutations in either endoglin (ENG), or activin receptor-like kinase 1 (ACVRL1/ALK1) genes (HHT type 1 and 2, respectively).

Methods
We have carried out a genetic analysis of four independent Spanish families with HHT clinical criteria, which has permitted the identification of new large deletions in ENG. These mutations were first detected using the MLPA technique and subsequently, the deletion breakpoints were mapped using a customized copy number variation (CNV) microarray. The array was designed to cover the ENG gene and surrounding areas.

Results
All tested families carried large deletions ranging from 3-kb to 100-kb, involving the ENG gene promoter, several ENG exons, and the two downstream genes FGSH and CDK9. Interestingly, common breakpoints coincident with Alu repetitive sequences were found among these families.

Conclusions
The systematic hybridization of DNA from HHT families, with deletions or duplications, to custom designed microarrays, could allow the mapping of breakpoints, coincident with repetitive Alu sequences that might act as “hot spots” in the development of chromosomal anomalies.
Association study of gene polymorphisms and depression with abnormal humor in traditional Uighur medicine
Authors: Yusup Abdiryim , Upur Hanzohra , Abla Ayimgul , Upur Halmurat 
Published: November 2013

Abstract

Background
According to the humor theory of Traditional Uighur Medicine (TUM), a same disease is classified into different abnormal humor types and corresponding methods are applied to treat the diseases according to the type of abnormal humor characteristics. To date the biological foundation of classification of diseases by humor theory has been little studied and the mechanism of action is still unclear. In the present study, we aimed to investigate the association between some related gene polymorphisms and depression with abnormal humor in TUM.

Methods
201 cases of depression patients in a Uighur population were divided into two groups as: 107 cases of depression patients with abnormal black bile (ABB), 94 cases of depression patients with none abnormal black bile (nABB), and 50 healthy people were served as control group. Venous blood was used to isolate DNA samples, and the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique was used for genotyping of single nucleotide polymorphisms (SNPs). Polymorphisms in the serotonin 2A (5-HT2A) receptor gene, brain derived neurotrophic factor (BDNF), serotonin 1A (5-HT1A) receptor gene were investigated in each groups, respectively.

Results
The 5-HT2A A-1438G, 5-HT2A T102C, BDNF Val66Met, and 5-HT1A C-1019G gene polymorphisms showed significant association with ABB. However, no difference between nABB and controls was found for those genotype distribution and allele frequency. Moreover, the T102C and A1438G SNPs in the 5-HT2A receptor gene polymorphisms were in linkage disequilibrium. In addition, the OR associated with the combination of Val66Met-Val/Val genotype plus the presence of -1019C allele was 8.393 for ABB compared with controls (OR 8.393; 95% CI 1.807 ~ 38.991; P= 0.003). Moreover, the OR associated with the presence of -Met plus -1019C alleles was 12.194 for ABB compared with controls (OR 12.194; 95% CI 1.433 ~ 103.776; P= 0.005). The OR associated with the presence of -1438C/C plus Val/Val genotypes was 7.738 for ABB compared with controls (OR 7.738; 95% CI 1.566 ~ 38.241; P= 0.005).

Conclusion
It was concluded that there were significant relationship between the gene polymorphisms and classification of depression with abnormal humor in TUM. The 5-HT2A A-1438G, 5-HT2A T102C, BDNF Val66Met, and 5-HT1A C-1019G gene polymorphisms might predict the incidence of depression with ABB.
Obtaining subjects’ consent to publish identifying personal information: current practices and identifying potential issues
Authors: Yoshida Akiko , Dowa Yuri , Murakami Hiromi , Kosugi Shinji 
Published: November 2013

Abstract

Background
In studies publishing identifying personal information, obtaining consent is regarded as necessary, as it is impossible to ensure complete anonymity. However, current journal practices around specific points to consider when obtaining consent, the contents of consent forms and how consent forms are managed have not yet been fully examined. This study was conducted to identify potential issues surrounding consent to publish identifying personal information.

Methods
Content analysis was carried out on instructions for authors and consent forms developed by academic journals in four fields (as classified by Journal Citation Reports): medicine general and internal, genetics and heredity, pediatrics, and psychiatry. An online questionnaire survey of editors working for journals that require the submission of consent forms was also conducted.

Results
Instructions for authors were reviewed for 491 academic journals (132 for medicine general and internal, 147 for genetics and heredity, 100 for pediatrics, and 112 for psychiatry). Approximately 40% (203: 74 for medicine general and internal, 31 for genetics and heredity, 58 for pediatrics, and 40 for psychiatry) stated that subject consent was necessary. The submission of consent forms was required by 30% (154) of the journals studied, and 10% (50) provided their own consent forms for authors to use. Two journals mentioned that the possible effects of publication on subjects should be considered. Many journal consent forms mentioned the difficulties in ensuring complete anonymity of subjects, but few addressed the study objective, the subjects’ right to refuse consent and the withdrawal of consent. The main reason for requiring the submission of consent forms was to confirm that consent had been obtained.

Conclusion
Approximately 40% of journals required subject consent to be obtained. However, differences were observed depending on the fields. Specific considerations were not always documented. There is a need to address issues around the study objective, subjects’ right to refuse consent and the withdrawal of consent. Whether responsibility for ensuring that the consent form has been signed lies with publishers also needs to be discussed.
The effect of high fiber snacks on digestive function and diet quality in a sample of school-age children
Authors: Brauchla Mary , McCabe George P , Miller Kevin B , Kranz Sibylle 
Published: November 2013

Abstract

Background
Dietary fiber (DF) intake in American children is suboptimal, increasing the risk of GI distress and contributing to poor diet quality. The objective of this study was to determine the effect of introducing two high-fiber snacks per day on gastrointestinal function as well as nutrient and food group intake in healthy children ages 7–11 years old.

Methods
This study was a randomized controlled prospective intervention study of children 7–11 years of age (n = 81) attending a rural Midwestern elementary school. Children were randomized by classroom to consume two high-fiber snacks per day (total of 10-12 g DF) or their usual snacks for 8 weeks. Participants completed two 24-hour dietary recalls and a questionnaire about their GI health at baseline, mid-intervention (week 4), and post-intervention. Dietary data was entered into NDSR 2011 and t-tests utilized to assess changes. Analyses were completed in SAS 9.2.

Results
Children consumed at least half their snack 94% of the time when a snack was chosen (89% of time). Participants in both the intervention and control group had healthy scores on the GI health questionnaire at all time points. The intervention group increased DF (P = 0.0138) and whole grain (WG) intake (P = 0.0010) at mid-intervention but after the intervention returned to their baseline DF intake (P = 0.2205) and decreased their WG intake (P = 0.0420) compared to baseline. Eating high-fiber snacks increased DF intake by 2.5 g per day (21% increase), suggesting displacement of other fiber-rich foods.

Conclusions
Study results indicate that children accept high-fiber foods, thus making these high-fiber foods and snacks consistently available will increase DF intake.
Human tumor necrosis factor (TNF)-alpha-induced protein 8-like 2 suppresses hepatocellular carcinoma metastasis through inhibiting Rac1
Authors: Cao Xuelei , Zhang Li , Shi Yongyu , Sun Yue , Dai Shen , Guo Chun , Zhu Faliang , wang Qun , Wang Jianing , Wang Xiaoyan , Chen Youhai H , Zhang Lining 
Published: November 2013

Abstract

Background
Tumor invasion and metastasis are the major reasons for leading death of patients with hepatocellular carcinoma (HCC). Therefore, to identify molecules that can suppress invasion and metastasis of tumor will provide novel targets for HCC therapies. Tumor necrosis factor (TNF)-alpha-induced protein 8-like 2, TIPE2, is a novel immune negative molecule and an inhibitor of the oncogenic Ras in mice but its function in human is unclear. Our previous research has shown that TIPE2 is downregulated in human primary HCC compared with the paired adjacent non-tumor tissues.

Results
In present study, we provide evidence that TIPE2 inhibits effectively human hepatocellular carcinoma metastasis. The forced expression of TIPE2 in HCC-derived cell lines markedly inhibits tumor cell growth, migration and invasion in vitro and suppresses growth and metastasis of HCC in vivo. Clinical information from a cohort of 112 patients reveals that loss or reduced expression of TIPE2 in primary HCC tissues is significantly associated with tumor metastasis. Mechanically, TIPE2 inhibits the migration and invasion through targeting Rac1 and then reduces F-actin polymerization and expression of matrix metallopeptidase 9 (MMP9) and urokinase plasminogen activator (uPA).

Conclusion
Our results indicate that human TIPE2 is endogenous inhibitor of Rac1 in HCC by which it attenuates invasion and metastasis of HCC. The data suggest that TIPE2 will be a new target for HCC therapy.
Functional tongue reconstruction with the anterolateral thigh flap
Authors: Wang Xue , Yan Guangqi , Zhang Guirong , Li Jiqiang , Liu Jihui , Zhang Yang 
Published: November 2013

Abstract

Background
A retrospective study was conducted to evaluate the advantages of anterolateral thigh (ALT) flap in tongue reconstruction.

Method
From September 2008 to February 2012, patients receiving ALT flap tongue reconstruction were included in the study. Patients undergoing ALT flap were compared with those undergoing similar surgery with radial forearm flap (RFF). The medical records of the included patients were reviewed, and a questionnaire was used to assess acceptability of the surgery.

Results
All flaps (both ALT and RFF) were successful In the ALT group, most patients were satisfied with the appearance of the reconstructed tongue and the intelligibility of their speech, and there were fewer complications with this technique compared with the RFF.

Conclusion
The ALT flap is an ideal method for tongue reconstruction. The thickness and volume of the ALT flap can be adjusted based on the individual extent of the defect, and it can not only provide bulk but also ensure mobility, and it has other advantages also, including a long pedicle and low donor site morbidity.
Highly uniform hole spacing micro brushes based on aligned carbon nanotube arrays
Authors: Yang Zhi , Zhu Xingzhong , Huang Xiaolu , Cheng Yingwu , Liu Yun , Geng Huijuan , Wu Yue , Su Yanjie , Wei Hao , Zhang Yafei 
Published: November 2013

Abstract
Highly uniform hole spacing micro brushes were fabricated based on aligned carbon nanotube (CNT) arrays synthesized by chemical vapor deposition method with the assistance of anodic aluminum oxide (AAO) template. Different micro brushes from CNT arrays were constructed on silicon, glass, and polyimide substrates, respectively. The micro brushes had highly uniform hole spacing originating from the regularly periodic pore structure of AAO template. The CNT arrays, serving as bristles, were firmly grafted on the substrates. The brushes can easily clean particles with scale of micrometer on the surface of silicon wafer and from the narrow spaces between the electrodes in a series of cleaning experiments. The results show the potential application of the CNT micro brushes as a cleaning tool in microelectronics manufacture field.
Hybrid viscosity CQ method for finding a common solution of a variational inequality, a general system of variational inequalities, and a fixed point problem
Authors: Ceng Lu-Chuan , Guu Sy-Ming , Yao Jen-Chih 
Published: November 2013

Abstract
In the literature, various iterative methods have been proposed for finding a common solution of the classical variational inequality problem and a fixed point problem. Research along these lines is performed either by relaxing the assumptions on the mappings in the settings (for instance, commonly seen assumptions for the mapping involved in the fixed point problem are nonexpansive or strictly pseudocontractive) or by adding a general system of variational inequalities into the settings. In this paper, we consider both possible ways in our settings. Specifically, we propose an iterative method for finding a common solution of the classical variational inequality problem, a general system of variational inequalities and a fixed point problem of a uniformly continuous asymptotically strictly pseudocontractive mapping in the intermediate sense. Our iterative method is hybridized by utilizing the well-known extragradient method, the CQ method, the Mann-type iterative method and the viscosity approximation method. The iterates yielded by our method converge strongly to a common solution of these three problems. In addition, we propose a hybridized extragradient-like method to yield iterates converging weakly to a common solution of these three problems.

MSC:49J30, 47H09, 47J20.
On certain hypergeometric identities deducible by using the beta integral method
Authors: Ibrahim Adel K , Rakha Medhat A , Rathie Arjun K 
Published: November 2013

Abstract
The aim of this research paper is to demonstrate how one can obtain eleven new and interesting hypergeometric identities (in the form of a single result) from the old ones by mainly applying the well-known beta integral method which was used successfully and systematically by Krattenthaler and Rao in their well known, very interesting research papers. The results are derived with the help of generalization of a quadratic transformation formula due to Kummer very recently obtained by Kim et al. Several identities, including one obtained earlier by Krattenthaler and Rao, follow special cases of our main findings. The results established in this paper are simple, interesting, easily established and may be potentially useful.

MSC: 33C05, 33C20, 33C70.