bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-canonical peroxisome targeting signals: identification of novel PTS1 tripeptides and characterization of enhancer elements by computational permutation analysis
Authors: Chowdhary Gopal , Kataya Amr RA , Lingner Thomas , Reumann Sigrun 
Published: August 2012

Abstract

Background
High-accuracy prediction tools are essential in the post-genomic era to define organellar proteomes in their full complexity. We recently applied a discriminative machine learning approach to predict plant proteins carrying peroxisome targeting signals (PTS) type 1 from genome sequences. For Arabidopsis thaliana 392 gene models were predicted to be peroxisome-targeted. The predictions were extensively tested in vivo, resulting in a high experimental verification rate of Arabidopsis proteins previously not known to be peroxisomal.

Results
In this study, we experimentally validated the predictions in greater depth by focusing on the most challenging Arabidopsis proteins with unknown non-canonical PTS1 tripeptides and prediction scores close to the threshold. By in vivo subcellular targeting analysis, three novel PTS1 tripeptides (QRL>, SQM>, and SDL>) and two novel tripeptide residues (Q at position −3 and D at pos. -2) were identified. To understand why, among many Arabidopsis proteins carrying the same C-terminal tripeptides, these proteins were specifically predicted as peroxisomal, the residues upstream of the PTS1 tripeptide were computationally permuted and the changes in prediction scores were analyzed. The newly identified Arabidopsis proteins were found to contain four to five amino acid residues of high predicted targeting enhancing properties at position −4 to −12 in front of the non-canonical PTS1 tripeptide. The identity of the predicted targeting enhancing residues was unexpectedly diverse, comprising besides basic residues also proline, hydroxylated (Ser, Thr), hydrophobic (Ala, Val), and even acidic residues.

Conclusions
Our computational and experimental analyses demonstrate that the plant PTS1 tripeptide motif is more diverse than previously thought, including an increasing number of non-canonical sequences and allowed residues. Specific targeting enhancing elements can be predicted for particular sequences of interest and are far more diverse in amino acid composition and positioning than previously assumed. Machine learning methods become indispensable to predict which specific proteins, among numerous candidate proteins carrying the same non-canonical PTS1 tripeptide, contain sufficient enhancer elements in terms of number, positioning and total strength to cause peroxisome targeting.
Goat milk with and without increased concentrations of lysozyme improves repair of intestinal cell damage induced by enteroaggregative Escherichia coli
Authors: Carvalho Eunice B , Maga Elizabeth A , Quetz Josiane S , Lima Ila FN , Magalhães Hemerson YF , Rodrigues Felipe AR , Silva Antônio VA , Prata Mara MG , Cavalcante Paloma A , Havt Alexandre , Bertolini Marcelo , Bertolini Luciana R , Lima Aldo AM 
Published: August 2012

Abstract

Background
Enteroaggregative Escherichia coli (EAEC) causes diarrhea, malnutrition and poor growth in children. Human breast milk decreases disease-causing bacteria by supplying nutrients and antimicrobial factors such as lysozyme. Goat milk with and without human lysozyme (HLZ) may improve the repair of intestinal barrier function damage induced by EAEC. This work investigates the effect of the milks on intestinal barrier function repair, bacterial adherence in Caco-2 and HEp-2 cells, intestinal cell proliferation, migration, viability and apoptosis in IEC-6 cells in the absence or presence of EAEC.

Methods
Rat intestinal epithelial cells (IEC-6, ATCC, Rockville, MD) were used for proliferation, migration and viability assays and human colon adenocarcinoma (Caco-2, ATCC, Rockville, MD) and human larynx carcinoma (HEp-2, ATCC, Rockville, MD) cells were used for bacterial adhesion assays. Goats expressing HLZ in their milk were generated and express HLZ in milk at concentration of 270 μg/ml . Cells were incubated with pasteurized milk from either transgenic goats expressing HLZ or non-transgenic control goats in the presence and absence of EAEC strain 042 (O44:H18).

Results
Cellular proliferation was significantly greater in the presence of both HLZ transgenic and control goat milk compared to cells with no milk. Cellular migration was significantly decreased in the presence of EAEC alone but was restored in the presence of milk. Milk from HLZ transgenic goats had significantly more migration compared to control milk. Both milks significantly reduced EAEC adhesion to Caco-2 cells and transgenic milk resulted in less colonization than control milk using a HEp-2 assay. Both milks had significantly increased cellular viability as well as less apoptosis in both the absence and presence of EAEC.

Conclusions
These data demonstrated that goat milk is able to repair intestinal barrier function damage induced by EAEC and that goat milk with a higher concentration of lysozyme offers additional protection.
Causes and determinants of inequity in maternal and child health in Vietnam
Authors: Målqvist Mats , Hoa Dinh Thi Phuong , Thomsen Sarah 
Published: August 2012

AbstractBackgroundInequities in health are a major challenge for health care planners and policymakers globally. In Vietnam, rapid societal development presents a considerable risk for disadvantaged populations to be left behind. The aim of this review is to map the known causes and determinants of inequity in maternal and child health in Vietnam in order to promote policy action.MethodsA review was performed through systematic searches of Pubmed and Proquest and manual searches of “grey literature.” A thematic content analysis guided by the conceptual framework suggested by the Commission on Social Determinants of Health was performed.ResultsMore than thirty different causes and determinants of inequity in maternal and child health were identified. Some determinants worth highlighting were the influence of informal fees and the many testimonies of discrimination and negative attitudes from health staff towards women in general and ethnic minorities in particular. Research gaps were identified, such as a lack of studies investigating the influence of education on health care utilization, informal costs of care, and how psychosocial factors mediate inequity.ConclusionsThe evidence of corruption and discrimination as mediators of health inequity in Vietnam calls for attention and indicates a need for more structural interventions such as better governance and anti-discriminatory laws. More research is needed in order to fully understand the pathways of inequities in health in Vietnam and suggest areas for intervention for policy action to reach disadvantaged populations.
Low-temperature synthesis of multilayer graphene/amorphous carbon hybrid films and their potential application in solar cells
Authors: Cui Tongxiang , Lv Ruitao , Huang Zheng-Hong , Zhu Hongwei , Jia Yi , Chen Shuxiao , Wang Kunlin , Wu Dehai , Kang Feiyu 
Published: August 2012

Abstract
The effect of reaction temperature on the synthesis of graphitic thin film on nickel substrate was investigated in the range of 400°C to 1,000°C. Amorphous carbon (a-C) film was obtained at 400°C on nickel foils by chemical vapor deposition; hybrid films of multilayer graphene (MLG) and a-C were synthesized at a temperature of 600°C, while MLG was obtained at temperatures in excess of 800°C. Schottky-junction solar cell devices prepared using films produced at 400°C, 600°C, 800°C, and 1,000°C coupled with n-type Si demonstrate power conversion efficiencies of 0.003%, 0.256%, 0.391%, and 0.586%, respectively. A HNO3 treatment has further improved the efficiencies of the corresponding devices to 0.004%, 1.080%, 0.800%, and 0.820%, respectively. These films are promising materials for application in low-cost and simple carbon-based solar cells.
Infection with street strain rabies virus induces modulation of the microRNA profile of the mouse brain
Authors: Zhao Pingsen , Zhao Lili , Zhang Kun , Feng Hao , Wang Hualei , Wang Tiecheng , Xu Tao , Feng Na , Wang Chengyu , Gao Yuwei , Huang Geng , Qin Chuan , Yang Songtao , Xia Xianzhu 
Published: August 2012

Abstract

Background
Rabies virus (RABV) causes a fatal infection of the central nervous systems (CNS) of warm-blooded animals. Once the clinical symptoms develop, rabies is almost invariably fatal. The mechanism of RABV pathogenesis remains poorly understood. Recent studies have shown that microRNA (miRNA) plays an important role in the pathogenesis of viral infections. Our recent findings have revealed that infection with laboratory-fixed rabies virus strain can induce modulation of the microRNA profile of mouse brains. However, no previous report has evaluated the miRNA expression profile of mouse brains infected with RABV street strain.

Results
The results of microarray analysis show that miRNA expression becomes modulated in the brains of mice infected with street RABV. Quantitative real-time PCR assay of the differentially expressed miRNAs confirmed the results of microarray assay. Functional analysis showed the differentially expressed miRNAs to be involved in many immune-related signaling pathways, such as the Jak-STAT signaling pathway, the MAPK signaling pathway, cytokine-cytokine receptor interactions, and Fc gamma R-mediated phagocytosis. The predicted expression levels of the target genes of these modulated miRNAs were found to be correlated with gene expression as measured by DNA microarray and qRT-PCR.

Conclusion
RABV causes significant changes in the miRNA expression profiles of infected mouse brains. Predicted target genes of the differentially expression miRNAs are associated with host immune response, which may provide important information for investigation of RABV pathogenesis and therapeutic method.
Hemicelluloses negatively affect lignocellulose crystallinity for high biomass digestibility under NaOH and H2SO4 pretreatments in Miscanthus
Authors: Xu Ning , Zhang Wei , Ren Shuangfeng , Liu Fei , Zhao Chunqiao , Liao Haofeng , Xu Zhengdan , Huang Jiangfeng , Li Qing , Tu Yuanyuan , Yu Bin , Wang Yanting , Jiang Jianxiong , Qin Jingping , Peng Liangcai 
Published: August 2012

Abstract

Background
Lignocellulose is the most abundant biomass on earth. However, biomass recalcitrance has become a major factor affecting biofuel production. Although cellulose crystallinity significantly influences biomass saccharification, little is known about the impact of three major wall polymers on cellulose crystallization. In this study, we selected six typical pairs of Miscanthus samples that presented different cell wall compositions, and then compared their cellulose crystallinity and biomass digestibility after various chemical pretreatments.

Results
A Miscanthus sample with a high hemicelluloses level was determined to have a relatively low cellulose crystallinity index (CrI) and enhanced biomass digestibility at similar rates after pretreatments of NaOH and H2SO4 with three concentrations. By contrast, a Miscanthus sample with a high cellulose or lignin level showed increased CrI and low biomass saccharification, particularly after H2SO4 pretreatment. Correlation analysis revealed that the cellulose CrI negatively affected biomass digestion. Increased hemicelluloses level by 25% or decreased cellulose and lignin contents by 31% and 37% were also found to result in increased hexose yields by 1.3-times to 2.2-times released from enzymatic hydrolysis after NaOH or H2SO4 pretreatments. The findings indicated that hemicelluloses were the dominant and positive factor, whereas cellulose and lignin had synergistic and negative effects on biomass digestibility.

Conclusions
Using six pairs of Miscanthus samples with different cell wall compositions, hemicelluloses were revealed to be the dominant factor that positively determined biomass digestibility after pretreatments with NaOH or H2SO4 by negatively affecting cellulose crystallinity. The results suggested potential approaches to the genetic modifications of bioenergy crops.
EasyLCMS: an asynchronous web application for the automated quantification of LC-MS data
Authors: Fructuoso Sergio , Sevilla Ángel , Bernal Cristina , Lozano Ana Belén , Iborra José Luis , Cánovas Manuel 
Published: August 2012

Abstract

Background
Downstream applications in metabolomics, as well as mathematical modelling, require data in a quantitative format, which may also necessitate the automated and simultaneous quantification of numerous metabolites. Although numerous applications have been previously developed for metabolomics data handling, automated calibration and calculation of the concentrations in terms of μmol have not been carried out. Moreover, most of the metabolomics applications are designed for GC-MS, and would not be suitable for LC-MS, since in LC, the deviation in the retention time is not linear, which is not taken into account in these applications. Moreover, only a few are web-based applications, which could improve stand-alone software in terms of compatibility, sharing capabilities and hardware requirements, even though a strong bandwidth is required. Furthermore, none of these incorporate asynchronous communication to allow real-time interaction with pre-processed results.

Findings
Here, we present EasyLCMS (http://www.easylcms.es/), a new application for automated quantification which was validated using more than 1000 concentration comparisons in real samples with manual operation. The results showed that only 1% of the quantifications presented a relative error higher than 15%. Using clustering analysis, the metabolites with the highest relative error distributions were identified and studied to solve recurrent mistakes.

Conclusions
EasyLCMS is a new web application designed to quantify numerous metabolites, simultaneously integrating LC distortions and asynchronous web technology to present a visual interface with dynamic interaction which allows checking and correction of LC-MS raw data pre-processing results. Moreover, quantified data obtained with EasyLCMS are fully compatible with numerous downstream applications, as well as for mathematical modelling in the systems biology field.
Direct detection of nasal Staphylococcus aureus carriage via helicase-dependent isothermal amplification and chip hybridization
Authors: Frech Georges C , Munns Denton , Jenison Robert D , Hicke Brian J 
Published: August 2012

Abstract

Background
The bacterium Staphylococcus aureus constitutes one of the most important causes of nosocomial infections. One out of every three individuals naturally carries S. aureus in their anterior nares, and nasal carriage is associated with a significantly higher infection rate in hospital settings. Nasal carriage can be either persistent or intermittent, and it is the persistent carriers who, as a group, are at the highest risk of infection and who have the highest nasal S. aureus cell counts. Prophylactic decolonization of S. aureus from patients’ noses is known to reduce the incidence of postsurgical infections, and there is a clear rationale for rapid identification of nasal S. aureus carriers among hospital patients.

Findings
A molecular diagnostic assay was developed which is based on helicase-dependent target amplification and amplicon detection by chip hybridization to a chip surface, producing a visible readout. Nasal swabs from 70 subjects were used to compare the molecular assay against culturing on “CHROMagar Staph aureus” agar plates. The overall relative sensitivity was 89%, and the relative specificity was 94%. The sensitivity rose to 100% when excluding low-count subjects (<100 S. aureus colony-forming units per swab).

Conclusions
This molecular assay is much faster than direct culture and has sensitivity that is appropriate for identification of high-count (>100 S. aureus colony-forming units per swab) nasal S. aureus carriers who are at greatest risk for nosocomial infections.
Applying the Electronic Commerce Technology Acceptance (ECTA) Framework to Overcome Challenges Facing Governmental Institutions' E-mailing Systems Technology Adoption in Jordan
Authors: Al-Haraizah Ahed S , Choudhury Islam 
Published: August 2012

Insight into the reasons why people adopt or reject technology is one of the most challenging issues in information technology research. This paper draws on the Electronic Commerce Technology Acceptance (ECTA) framework [1], which is in turn based on Technology Acceptance Model (TAM) [2–3], and examines Jordan government's employees' attitudes towards adopting and use Electronic Mailing systems within their job. A quantitative survey is used to establish and illustrates employee's behavioural intention and decision to e-mailing systems. The main influencing issues that are discussed in this paper affect these employees imply perceived usefulness, perceived ease of use, employees' attitudes towards new technologies, and behavioural intention to use. These various issues suggested in the Technology Acceptance Model (TAM) [3–4]. Whereas the extended Technology Acceptance Model (TAM) has been made to include the external social factors proposed in this paper such as trust, cultural beliefs, and sociology of technology. Eventually, the significant insight emanated from the findings identifies ways of assisting and spurring employees to make use of technology effectively.
Automating Reuse of Online Semantic Resources by Concept Extraction Using Word Sense Disambiguation
Authors: Imdadi Nadia , Rizvi Syed A.M. 
Published: August 2012

Several dimensions have been added since the idea of Semantic web was conceived by Tim B. Lee, to the previously linear representation of the World Wide Web that consisted of web resources like web pages and hyperlinks. These dimensions allow for software agents/machines to make knowledgeable decisions and retrieve relevant resources which are related in meaning and not only by named links. The new infrastructure consists of semantic repositories like network of ontologies, also called semantic networks. Some interesting research issues have emerged in the context of these semantic repositories and these are their creation, bootstrapping and interoperability to make semantic web a reality. A novel approach is proposed to deal with the issue of creation of ontologies from existing online semantic repositories by using Swoogle API. The aim is to discover concepts from online resources indexed by the Swoogle Search Engine by using advanced techniques of Word Sense Disambiguation in Computational Linguistics Techniques.
Vibrant Ambient Intelligence with Agents Based Service Oriented Approach
Authors: Bhuvaneshwari N. Sudha , Sujatha S. 
Published: August 2012

Ambient Intelligence (AmI) refers to electronic environments that are sensitive and responsive to the presence of people. Ambient intelligence is closely related to the long term vision of an intelligent service system in which technologies are able to automate a platform embedding the required devices for powering context aware, personalized, adaptive and anticipatory services. Ambient intelligence is a vision on the future of consumer electronics, telecommunications and computing that was originally developed in the late 1990s for the time frame 2010–2020. This paper on Vibrant Ambient Intelligence with Agents based Service Oriented Approach focuses on the ambient intelligence environment of managing the traffic congestion control in Coimbatore city through VAISTC4 proposal without crippling the mobility of users using Mobile Internet Protocol Version 6(IPV6). It also discusses on the benefit of coupling service-oriented approach and multi-agent systems towards more appropriate interactions with users. With the advancement in Mobile Computing Technology the number and diversity of sensors being carried by people have increased that has made humans to behave like computers in their social context where privacy poses a greater issue. This paper also provides a solution on how the privacy context of an individual can be cherished using privacy mapping approach.
Pavement Performance: Current Trends, Advances, and Challenges
Authors: Choubane Bouzid 
Published: August 2012

Description
Sixteen peer-reviewed papers cover the latest research on pavement condition assessment and surface characteristics measurements used in evaluating the performance and management of roadway systems.
This new publication provides critical information for making informed decisions, including determining cost-effective rehabilitation and preservation strategies, identifying potentially hazardous conditions, and monitoring the condition and surface characteristics of the various in-service pavements.
Psychiatric Consultation after Kidney Transplantation: A 10-Year Single-Center Study Including Outpatients in Japan
Authors: Nishimura Katsuji , Kobayashi Sayaka , Sugawara Hiroko , Nakajima Ichiro , Ishida Hideki , Fuchinoue Shohei , Tanabe Kazunari , Ishigooka Jun 
Published: August 2012

Background: The aim of this study was to elucidate the clinical characteristics and frequency of psychiatric consultation in a routine clinical setting after kidney transplantation. Methods: Subjects were 1,139 consecutive recipients who received kidney transplantation at our hospital between January 1997 and September 2006. The hospital patient database was searched to determine whether these recipients received psychiatric consultation after their transplantation during this period. Results: Among 1,139 recipients, 118 (10%) received psychiatric consultation after their transplantation. There were significantly more women among these recipients ( p = 0.036). Many of the recipients had received psychiatric consultation before transplantation ( p < 0.0001) and had received dialysis for a long time ( p = 0.018). There were three main psychiatric diagnoses according to ICD-10 diagnostic criteria in these 118 recipients: 42 (36%) had neurotic, stress-related, and somatoform disorders (F4); 35 (30%) had organic, including symptomatic, mental disorders (F0); and 27 (23%) had mood (affective) disorders (F3). The median length of time between kidney transplantation and initial psychiatric consultation was 57 days (interquartile range: 10–650 days). The lengths were 7 days (6–17 days) for F0, 75 days (18–650 days) for F4, 243 days (35–1,004 days) for F3, and 253 days (10–1,393 days) for other diagnostic groups. Significant differences were observed among these four groups (Jonckheere-Terpstra test, p < 0.001). Conclusion: Our results show that appropriate psychiatric intervention is necessary not only in early stages after kidney transplantation but also over the long term.
Is the Cognitive-Behavioral Therapy an Effective Intervention to Prevent the Postnatal Depression? A Critical Review
Authors: Nardi Bernardo , Laurenzi Sabrina , Di Nicolò Marzia , Bellantuono Cesario 
Published: August 2012

Objective: The aim of this article is to review and discuss the efficacy of the Cognitive-Behavioral Therapy (CBT), in the prevention of postnatal depression (PD) in pregnant women at risk. Method: PubMed, Medline, PsychInfo, Embase, and the Cochrane Library databases were searched from February 1991 to February 2011. Method: Eight Randomized Controlled Trials (RCT) on the prevention of PD with the CBT were selected and their data were analyzed. The literature analyzed recommends that depression in pregnancy requires an efficient management to provide mother's symptoms relief as well as to prevent the PD. While several studies demonstrated the efficacy of the CBT in the treatment of PD, the efficacy of the CBT in preventing PD in pregnant women at risk has been investigated only by a few studies, presenting a number of methodological flaws. Conclusions: Better designed RCT are needed to support the efficacy of such psycho-therapeutic preventive strategy in women at risk for PD.