bluuebunny/crossref_metadata_2025_split huggingface dataset:
Irrigation Development: A Process of Land Degradation and Marginalisation of the Land Poor
Authors: Rizvi Firdaus Fatima 
Published: May 2012

This article looks into the instances of growing waterlogging, which is a negative externality of the developmental process (canal irrigation) that has affected the marginalised sections to a greater extent, who mostly depend on land for livelihood and self-sustenance. Land-use pattern has undergone a tremendous transformation due to irrigation development in terms of increase in fallow and culturable waste lands. Fertility of the land has considerably been reduced: agricultural production has gone down, animals and trees have been diminished, livelihood and employment opportunities have declined, largely affecting the Other Backward Castes and Scheduled Castes living in its lower catchments that have sub-marginal landholdings and are historically marginalised, thus leading to higher incidence of migration among the local inhabitants of the basin. The study recommends how integrated land and water development programmes at village level could improve land utilisation pattern. These changes would indirectly increase agricultural productivity, enhance livelihood of the farmers and the local communities by increasing employment and livelihood activities at village level. The employment scheme National Rural Employment Guarantee Scheme (NREGS) would be of crucial importance in managing water resources and enhancing land development simultaneously.
Cognitive deficit in first-time coronary artery bypass graft patients: a randomized clinical trial of lidocaine versus procaine hydrochloride
Authors: Ghafari R , Baradari A Gholipour , Firouzian A , Nouraei M , Aarabi M , Zamani A , Zeydi A Emami 
Published: May 2012

Introduction: Cognitive dysfunction increasingly has been recognized as a complication after cardiac surgery. Different methods have been considered for the reduction of cognitive dysfunction after cardiac surgery. One of these methods is by using lidocaine during surgery. The aim of this study was to determine the effects of adding lidocaine to the cardioplegia solution on cognitive impairment after coronary artery surgery. Design and methods: In a prospective, randomized, double-blind trial, 110 patients aged between 20-70 years, scheduled for elective CABG surgery using cardiopulmonary bypass, were recruited into the study. They were randomized into two groups who received either cardioplegia solution containing lidocaine 2 mg/kg or procaine hydrochloride 5 mg/kg. The neurocognitive test used in this study was the Mini Mental State Examination (MMSE) or Folstein test. The test was done on the day before and 10 days and 2 months after the operation. Results: In the procaine group, the total score after 10 days decreased significantly compared to the preoperative score (mean difference 0.68; 95% CI: 0.20 to 1.17, p=0.006). Comparison between mean differences after 10 and 60 days of operation between the lidocaine and procaine groups were statistically significant, p-value 0.017 and 0.013, respectively. There was no cognitive impairment in the lidocaine group, but, in the procaine group, four patients (7.7%) after 10 days and one patient (1.9%) after both 10 and 60 days had cognitive impairment, p=0.051. Conclusions: Administration of lidocaine compared to that of procaine through the cardioplegia solution had a better effect on cognitive function after coronary artery bypass graft surgery.
Synthesis and characterization of organo-soluble polyimides containing phthalazinone and bicarbazole moieties in the main chain
Authors: Wang Jianyan , Liu Cheng , Su Guixian , Jian Xigao 
Published: May 2012

Organo-soluble aromatic polyimides with good comprehensive properties are favorable for insulating layer material applications in flexible copper-clad laminates. A novel aromatic diamine, bis( N-4-amine-phenyl)-3,3′-bicarbazole (BCZDA) was firstly successfully synthesized. The structure of BCZDA was definitely confirmed via Fourier transform infrared and 1H-NMR spectroscopy and elemental analysis. Then a series of soluble polyimides were prepared from BCZDA and the diamine containing phthalazinone moiety as coreactant by one-pot solution copolycondensation with two kinds of anhydrides, 3,3′,4,4′-benzophenonetetracarboxylic dianhydride and 2-bis[4-(3,4- dicarboxyphenoxy) phenyl] propane dianhydride in sulfolane. Experimental results indicated that all the copolyimides having the glass transition temperature in range of 295 to 304 °C exhibited good solubility in N-methyl-2-pyrrolidinone (NMP), m-cresol, and N, N-dimethyl acetamide (DMAc). Their onset temperatures at 5% weight loss were all higher than 505 °C in nitrogen. Their flexible films cast in NMP exhibited good adhesive property (2.32–3.42 N mm−1) to copper foil and had good mechanical properties with the tensile strength of 69.5–79.3 MPa, elongation to break of 16–23% , and tensile modulus of 1.2–1.5 GPa. The copolyimides possessed dielectric constants of 3.08–3.26 (100 kHz) and low water absorption in the range of 0.92–1.06%, indicating that these obtained copolyimides are good candidates for the fields of microelectronics.
Client Satisfaction with HIV Counseling Services
Authors: Papanna Mohan K. , Kumar Pawan , Shetty Avinash , Kamath Asha , Bhaskaran Unnikrishnan , Saddichha Sahoo 
Published: May 2012

Background: Client satisfaction is a good predictor of performance of health programs. Hence, clients’ perception and satisfaction studies provide insight to improve the program. Purpose: To assess clients’ perception and satisfaction with Integrated Counselling and Testing Centres (ICTCs) for HIV in an operational setting. Methods: A total of 191 client exit interviews from 12 ICTCs. The clients were stratified into general and antenatal clients. A systematic random sampling was done at high client load centers. Results: Cumulative client satisfaction was found to be 60% (±24%). Most of the clients (76%) agreed that counseling cleared doubts about HIV and found counseling beneficial (71%). Only 32% of the clients could recall issues discussed during the sessions. However, 92.5% were satisfied with ICTC facilities. Conclusions: Poor perception and low satisfaction with ICTCs needs to be addressed as this could have a direct bearing on the program.
Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures
Authors: Hayes Michael L , Giang Karolyn , Mulligan R Michael 
Published: May 2012

Abstract

Background
Pentatricopeptide repeat (PPR) proteins are required for numerous RNA processing events in plant organelles including C-to-U editing, splicing, stabilization, and cleavage. Fifteen PPR proteins are known to be required for RNA editing at 21 sites in Arabidopsis chloroplasts, and belong to the PLS class of PPR proteins. In this study, we investigate the co-evolution of four PPR genes (CRR4, CRR21, CLB19, and OTP82) and their six editing targets in Brassicaceae species. PPR genes are composed of approximately 10 to 20 tandem repeats and each repeat has two α-helical regions, helix A and helix B, that are separated by short coil regions. Each repeat and structural feature was examined to determine the selective pressures on these regions.

Results
All of the PPR genes examined are under strong negative selection. Multiple independent losses of editing site targets are observed for both CRR21 and OTP82. In several species lacking the known editing target for CRR21, PPR genes are truncated near the 17th PPR repeat. The coding sequences of the truncated CRR21 genes are maintained under strong negative selection; however, the 3’ UTR sequences beyond the truncation site have substantially diverged. Phylogenetic analyses of four PPR genes show that sequences corresponding to helix A are high compared to helix B sequences. Differential evolutionary selection of helix A versus helix B is observed in both plant and mammalian PPR genes.

Conclusion
PPR genes and their cognate editing sites are mutually constrained in evolution. Editing sites are frequently lost by replacement of an edited C with a genomic T. After the loss of an editing site, the PPR genes are observed with three outcomes: first, few changes are detected in some cases; second, the PPR gene is present as a pseudogene; and third, the PPR gene is present but truncated in the C-terminal region. The retention of truncated forms of CRR21 that are maintained under strong negative selection even in the absence of an editing site target suggests that unrecognized function(s) might exist for this PPR protein. PPR gene sequences that encode helix A are under strong selection, and could be involved in RNA substrate recognition.
Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)
Authors: Stoffel Kevin , van Leeuwen Hans , Kozik Alexander , Caldwell David , Ashrafi Hamid , Cui Xinping , Tan Xiaoping , Hill Theresa , Reyes-Chin-Wo Sebastian , Truco Maria-Jose , Michelmore Richard W , Van Deynze Allen 
Published: May 2012

AbstractBackgroundHigh-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa).ResultsWe developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola,L. saligna,L. virosaandL. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types.ConclusionBy hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously.
miRFANs: an integrated database for Arabidopsis thalianamicroRNA function annotations
Authors: Liu Hui , Jin Ting , Liao Ruiqi , Wan Linxia , Xu Bin , Zhou Shuigeng , Guan Jihong 
Published: May 2012

Abstract

Background
Plant microRNAs (miRNAs) have been revealed to play important roles in developmental control, hormone secretion, cell differentiation and proliferation, and response to environmental stresses. However, our knowledge about the regulatory mechanisms and functions of miRNAs remains very limited. The main difficulties lie in two aspects. On one hand, the number of experimentally validated miRNA targets is very limited and the predicted targets often include many false positives, which constrains us to reveal the functions of miRNAs. On the other hand, the regulation of miRNAs is known to be spatio-temporally specific, which increases the difficulty for us to understand the regulatory mechanisms of miRNAs.

Description
In this paper we present miRFANs, an online database for Arabidopsis thaliana
miRNA function annotations. We integrated various type of datasets, including miRNA-target interactions, transcription factor (TF) and their targets, expression profiles, genomic annotations and pathways, into a comprehensive database, and developed various statistical and mining tools, together with a user-friendly web interface. For each miRNA target predicted by psRNATarget, TargetAlign and UEA target-finder, or recorded in TarBase and miRTarBase, the effect of its up-regulated or down-regulated miRNA on the expression level of the target gene is evaluated by carrying out differential expression analysis of both miRNA and targets expression profiles acquired under the same (or similar) experimental condition and in the same tissue. Moreover, each miRNA target is associated with gene ontology and pathway terms, together with the target site information and regulating miRNAs predicted by different computational methods. These associated terms may provide valuable insight for the functions of each miRNA.

Conclusion
First, a comprehensive collection of miRNA targets for Arabidopsis thaliana provides valuable information about the functions of plant miRNAs. Second, a highly informative miRNA-mediated genetic regulatory network is extracted from our integrative database. Third, a set of statistical and mining tools is equipped for analyzing and mining the database. And fourth, a user-friendly web interface is developed to facilitate the browsing and analysis of the collected data.
Current practices of partner notification among MSM with HIV, gonorrhoea and syphilis in the Netherlands: an urgent need for improvement
Authors: van Aar Fleur , Schreuder Imke , van Weert Yolanda , Spijker Ralph , Götz Hannelore , Op de Coul Eline ,   the Partner Notification Group
Published: May 2012

Abstract

Background
Partner notification (PN) among individuals newly diagnosed with HIV/STI is seen as a vital tool to identify others at risk of infection. However, hardly any data are available on the effectiveness of PN on HIV/STI transmission in the Netherlands. This study aims to fill this gap by assessing current PN practices, case-finding effectiveness, and determinants of being notified among men having sex with men (MSM) in the Netherlands.

Methods
Nurses from five STI centers participated in a prospective pilot study on PN outcomes (partners being: at risk, notifiable, notified, and tested) for HIV/STI, by completing a newly developed PN registration form (PN database). PN outcomes including case-finding effectiveness (number of newly diagnosed cases in partners/number of partners being tested) for HIV, syphilis, and gonorrhoea were studied among MSM. Furthermore, the national STI database was analyzed to identify determinants of being notified. The number of infections that remained undetected was estimated based on these two databases.

Results
In total 105 MSM, newly diagnosed with HIV/STI, reported 612 sexual partners at risk of whom 41% were notifiable and 31% were notified. Patient referral was the predominant PN method (90%). The overall case-finding percentage was 36% (HIV: 15-33%, gonorrhoea: 17-50% and syphilis: 4-11%). Case-finding percentages were lower in the national STI database: 21% (5%, 28%, 12%). Persons with one or more sexual partners, known HIV positives, and IDU were more likely to be notified to the STI clinic. Notified clients were more likely to have HIV/STI than unnotified clients (OR 1.7-2.5). Based on these two databases, an estimated 75 to 133 infections remained undetected (HIV: 12–90; gonorrhoea: 28–97; syphilis: 5–12 infections).

Conclusions
Partner notification among MSM in the Netherlands is suboptimal; an extensive number of STI/HIV infections remained undetected mainly due to unnotifiable partners. To enhance PN practices, combined and innovative PN interventions such as Internet-based PN will be implemented for hard-to-reach MSM and other risk groups.
“Blind periods” in screening for toxoplasmosis in pregnancy in Austria – a debate
Authors: Sagel Ulrich , Krämer Alexander , Mikolajczyk Rafael T 
Published: May 2012

Abstract
Recent studies from Austria, France and Italy have shown that there is a poor adherence to the screening scheme for maternal Toxoplasma infections in pregnancy demonstrated by the fact that many recommended examinations are missed. This leads to undetected infections and limits our knowledge of incidence of the disease. We discuss the negative consequences of this situation on research on treatment effectiveness and the outcomes of congenital toxoplasmosis. The responsible public health institutions should assume responsibility for appropriate surveillance of the screening programme and take measures to improve screening adherence during pregnancy. Screening should start as early as possible in pregnancy and the latest test should be done at delivery. Screening schedule should allow distinguishing infections from the first, second and third trimester of pregnancy, as the risk of materno-foetal transmission and outcomes in case of foetal infections varies by time.
Factors associated with attention deficit/hyperactivity disorder among US children: Results from a national survey
Authors: Lingineni Ravi K , Biswas Swati , Ahmad Naveed , Jackson Bradford E , Bae Sejong , Singh Karan P 
Published: May 2012

Abstract

Background
The purpose of this study was to investigate the association between Attention Deficit/Hyperactivity Disorder (ADHD) and various factors using a representative sample of US children in a comprehensive manner. This includes variables that have not been previously studied such as watching TV/playing video games, computer usage, family member’s smoking, and participation in sports.

Methods
This was a cross-sectional study of 68,634 children, 5–17 years old, from the National Survey of Children’s Health (NSCH, 2007–2008). We performed bivariate and multivariate logistic regression analyses with ADHD classification as the response variable and the following explanatory variables: sex, race, depression, anxiety, body mass index, healthcare coverage, family structure, socio-economic status, family members’ smoking status, education, computer usage, watching television (TV)/playing video games, participation in sports, and participation in clubs/organizations.

Results
Approximately 10% of the sample was classified as having ADHD. We found depression, anxiety, healthcare coverage, and male sex of child to have increased odds of being diagnosed with ADHD. One of the salient features of this study was observing a significant association between ADHD and variables such as TV usage, participation in sports, two-parent family structure, and family members’ smoking status. Obesity was not found to be significantly associated with ADHD, contrary to some previous studies.

Conclusions
The current study uncovered several factors associated with ADHD at the national level, including some that have not been studied earlier in such a setting. However, we caution that due to the cross-sectional and observational nature of the data, a cause and effect relationship between ADHD and the associated factors can not be deduced from this study. Future research on ADHD should take into consideration these factors, preferably through a longitudinal study design.
Is the process of delivery of an individually tailored lifestyle intervention associated with improvements in LDL cholesterol and multiple lifestyle behaviours in people with Familial Hypercholesterolemia?
Authors: Broekhuizen Karen , Jelsma GM Judith , van PoppelNM Mireille , Koppes LJ Lando , Brug Johannes , van Mechelen Willem 
Published: May 2012

Abstract

Background
More insight in the association between reach, dose and fidelity of intervention components and effects is needed. In the current study, we aimed to evaluate reach, dose and fidelity of an individually tailored lifestyle intervention in people with Familial Hypercholesterolemia (FH) and the association between intervention dose and changes in LDL-Cholesterol (LDL-C), and multiple lifestyle behaviours at 12-months follow-up.

Methods
Participants (n = 181) randomly allocated to the intervention group received the PRO-FIT intervention consisting of computer-tailored lifestyle advice (PRO-FIT*advice) and counselling (face-to-face and telephone booster calls) using Motivational Interviewing (MI). According to a process evaluation plan, intervention reach, dose delivered and received, and MI fidelity were assessed using the recruitment database, website/counselling logs and the Motivational Interviewing Treatment Integrity (MITI 3.1.1.) code. Regression analyses were conducted to explore differences between participant and non-participant characteristics, and the association between intervention dose and change in LDL-C, and multiple lifestyle behaviours.

Results
A 34% (n = 181) representative proportion of the intended intervention group was reached during the recruitment phase; participants did not differ from non-participants (n = 623) on age, gender and LDL-C levels. Of the participants, 95% received a PRO-FIT*advice log on account, of which 49% actually logged on and completed at least one advice module. Nearly all participants received a face-to-face counselling session and on average, 4.2 telephone booster calls were delivered. None of the face-to-face sessions were implemented according to MI guidelines. Overall, weak non-significant positive associations were found between intervention dose and LDL-C and lifestyle behaviours.

Conclusions
Implementation of the PRO-FIT intervention in practice appears feasible, particularly PRO-FIT*advice, since it can be relative easily implemented with a high dose delivered. However, only less than half of the intervention group received the complete intervention-package as intended. Strategies to let participants optimally engage in using web-based computer-tailored interventions like PRO-FIT*advice are needed. Further, more emphasis should be put on more extensive MI training and monitoring/supervision.

Trial registration
NTR1899 at ww.trialregister.nl.
Identification Of Small Molecule TRABID Deubiquitinase Inhibitors By Computation-Based Virtual Screen
Authors: Shi Tong , Bao Ju , Wang Nick X , Zheng Jie , Wu Dianqing 
Published: May 2012

Abstract

Background
Wnt/β-catenin-mediated gene transcription plays important roles in a wide range of biological and pathophysiological processes including tumorigenesis where β-catenin-mediated transcription activity frequently elevates. TRABID, a deubiquitinase, was shown to have a positive Wnt/β-catenin-mediated gene transcription and hence holds a promise as a putative anti-cancer target.

Results
In this study, we used a combination of structure based virtual screening and an in vitro deubiquitinase (DUB) assay to identify several small molecules that inhibit TRABID DUB activity. However, these inhibitors failed to show inhibitory effects on β-catenin-mediated gene transcription. In addition, expression of TRABID shRNAs, wildtype TRABID, or the DUB activity-deficient mutant showed little effects on β-catenin-mediated gene transcription.

Conclusions
TRABID may not be a critical component in canonical Wnt/β-catenin signal transduction or that a minute amount of this protein is sufficient for its role in regulating Wnt activity.