bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing
Authors: Li Xuehui , Acharya Ananta , Farmer Andrew D , Crow John A , Bharti Arvind K , Kramer Robin S , Wei Yanling , Han Yuanhong , Gou Jiqing , May Gregory D , Monteros Maria J , Brummer E Charles 
Published: October 2012

AbstractBackgroundAlfalfa, a perennial, outcrossing species, is a widely planted forage legume producing highly nutritious biomass. Currently, improvement of cultivated alfalfa mainly relies on recurrent phenotypic selection. Marker assisted breeding strategies can enhance alfalfa improvement efforts, particularly if many genome-wide markers are available. Transcriptome sequencing enables efficient high-throughput discovery of single nucleotide polymorphism (SNP) markers for a complex polyploid species.ResultThe transcriptomes of 27 alfalfa genotypes, including elite breeding genotypes, parents of mapping populations, and unimproved wild genotypes, were sequenced using an Illumina Genome Analyzer IIx.De novoassembly of quality-filtered 72-bp reads generated 25,183 contigs with a total length of 26.8 Mbp and an average length of 1,065 bp, with an average read depth of 55.9-fold for each genotype. Overall, 21,954 (87.2%) of the 25,183 contigs represented 14,878 unique protein accessions. Gene ontology (GO) analysis suggested that a broad diversity of genes was represented in the resulting sequences. The realignment of individual reads to the contigs enabled the detection of 872,384 SNPs and 31,760 InDels. High resolution melting (HRM) analysis was used to validate 91% of 192 putative SNPs identified by sequencing. Both allelic variants at about 95% of SNP sites identified among five wild, unimproved genotypes are still present in cultivated alfalfa, and all four US breeding programs also contain a high proportion of these SNPs. Thus, little evidence exists among this dataset for loss of significant DNA sequence diversity from either domestication or breeding of alfalfa. Structure analysis indicated that individuals from the subspeciesfalcata, the diploid subspeciescaerulea, and the tetraploid subspeciessativa(cultivated tetraploid alfalfa) were clearly separated.ConclusionWe used transcriptome sequencing to discover large numbers of SNPs segregating in elite breeding populations of alfalfa. Little loss of SNP diversity was evident between unimproved and elite alfalfa germplasm. The EST and SNP markers generated from this study are publicly available at the Legume Information System (http://medsa.comparative-legumes.org/) and can contribute to future alfalfa research and breeding applications.
An inventory of Canadian pregnancy and birth cohort studies: research in progress
Authors: Joly Marie-Pier , Boivin Michel , Junker Anne , Bocking Alan , Kramer Michael S , Atkinson Stephanie A 
Published: October 2012

Abstract

Background
A web-based inventory was developed as a voluntary registry of Canadian pregnancy and birth cohort studies, with the objective to foster collaboration and sharing of research tools among cohort study groups as a means to enrich research in maternal and child health across Canada.

Description
Information on existing birth cohort studies conducted in Canada exclusively or as part of broader international initiatives was accessed by searching the literature in PubMed and PsychInfo databases. Additional studies were identified by enquiring about the research activities of researchers at Canadian universities or working in affiliated hospitals or research centres or institutes. Of the fifty-eight birth cohort studies initially identified, forty-six were incorporated into the inventory if they were of a retrospective and/or prospective longitudinal design and with a minimum of two phases of data collection, with the first period having occurred before, during, or shortly after pregnancy and had an initial study sample size of a minimum of 200 participants.
Information collected from each study was organized into four main categories: basic information, data source and period of collection, exposures, and outcome measures and was coded and entered into an Excel spreadsheet. The information incorporated into the Excel spreadsheet was double checked, completed when necessary, and verified for completeness and accuracy by contacting the principal investigator or research coordinator. All data collected were then uploaded onto the website of the Institute of Human Development Child and Youth Health of the Canadian Institutes of Health Research. Subsequently, the database was updated and developed as an online searchable inventory on the website of the Maternal, Infant, Child and Youth Research Network.

Conclusions
This inventory is unique, as it represents detailed information assembled for the first time on a large number of Canadian birth cohort studies. Such information provides a valuable resource for investigators in the planning stages of cohort studies and identifying current research gaps.
“Expectant Parents”: Study protocol of a longitudinal study concerning prenatal (risk) factors and postnatal infant development, parenting, and parent-infant relationships
Authors: Maas A Janneke BM , Vreeswijk Charlotte MJM , de Cock Evi SA , Rijk Catharina HAM , van Bakel Hedwig JA 
Published: October 2012

Abstract

Background
While the importance of the infant-parent relationship from the child’s perspective is acknowledged worldwide, there is still a lack of knowledge about predictors and long-term benefits or consequences of the quality of parent-infant relationships from the parent’s perspective. The purpose of this prospective study is to investigate the quality of parent-infant relationships from parents’ perspectives, both in the prenatal and postpartum period. This study therefore focuses on prenatal (risk) factors that may influence the quality of pre- and postnatal bonding, the transition to parenthood, and bonding as a process within families with young children. In contrast to most research concerning pregnancy and infant development, not only the roles and experiences of mothers during pregnancy and the first two years of infants’ lives are studied, but also those of fathers.

Methods/design
The present study is a prospective longitudinal cohort study, in which pregnant women (N = 466) and their partners (N = 319) are followed from 15 weeks gestation until their child is 24 months old. During pregnancy, midwives register the presence of prenatal risk factors and provide obstetric information after the child’s birth. Parental characteristics are investigated using self-report questionnaires at 15, 26, and 36 weeks gestational age and at 4, 6, 12, and 24 months postpartum. At 26 weeks of pregnancy and at 6 months postpartum, parents are interviewed concerning their representations of the (unborn) child. At 6 months postpartum, the mother-child interaction is observed in several situations within the home setting. When children are 4, 6, 12, and 24 months old, parents also completed questionnaires concerning the child’s (social-emotional) development and the parent-child relationship. Additionally, at 12 months information about the child’s physical development and well-being during the first year of life is retrieved from National Health Care Centres.

Discussion
The results of this study may contribute to early identification of families at risk for adverse parent-infant relationships, infant development, or parenting. Thereby this study will be relevant for the development of policy, practice, and theory concerning infant mental health.
ORCHIDS: an Observational Randomized Controlled Trial on Childhood Differential Susceptibility
Authors: Chhangur Rabia R , Weeland Joyce , Overbeek Geertjan , Matthys WalterCHJ , Orobio de Castro Bram 
Published: October 2012

Abstract

Background
A central tenet in developmental psychopathology is that childhood rearing experiences have a major impact on children’s development. Recently, candidate genes have been identified that may cause children to be differentially susceptible to these experiences (i.e., susceptibility genes). However, our understanding of the differential impact of parenting is limited at best. Specifically, more experimental research is needed. The ORCHIDS study will investigate gene-(gene-)environment interactions to obtain more insight into a) moderating effects of polymorphisms on the link between parenting and child behavior, and b) behavioral mechanisms that underlie these gene-(gene-)environment interactions in an experimental design.

Methods/Design
The ORCHIDS study is a randomized controlled trial, in which the environment will be manipulated with an intervention (i.e., Incredible Years parent training). In a screening, families with children aged 4–8 who show mild to (sub)clinical behavior problems will be targeted through community records via two Dutch regional healthcare organizations. Assessments in both the intervention and control condition will be conducted at baseline (i.e., pretest), after 6 months (i.e., posttest), and after 10 months (i.e., follow-up).

Discussion
This study protocol describes the design of a randomized controlled trial that investigates gene-(gene-)environment interactions in the development of child behavior. Two hypotheses will be tested. First, we expect that children in the intervention condition who carry one or more susceptibility genes will show significantly lower levels of problem behavior and higher levels of prosocial behavior after their parent(s) received the Incredible Years training, compared to children without these genes, or children in the control group. Second, we expect that children carrying one or more susceptibility genes will show a heightened sensitivity to changes in parenting behaviors, and will manifest higher emotional synchronization in dyadic interchanges with their parents. This may lead to either more prosocial behavior or antisocial behavior depending on their parents’ behavior.

Trial registration
Dutch Trial Register (NTR3594)
Quantification of multiple infections of Plasmodium falciparum in vitro
Authors: Wacker Mark A , Turnbull Lindsey B , Walker Leah A , Mount Michael C , Ferdig Michael T 
Published: October 2012

Abstract

Background
Human malaria infections caused by the parasite Plasmodium falciparum often contain more than one genetically distinct parasite. Despite this fact, nearly all studies of multiple strain P. falciparum infections have been limited to determining relative densities of each parasite within an infection. In light of this, new methods are needed that can quantify the absolute number of parasites within a single infection.

Methods
A quantitative PCR (qPCR) method was developed to track the dynamic interaction of P. falciparum infections containing genetically distinct parasite clones in cultured red blood cells. Allele-specific primers were used to generate a standard curve and to quantify the absolute concentration of parasite DNA within multi-clonal infections. Effects on dynamic growth relationships between parasites under drug pressure were examined by treating mixed cultures of drug sensitive and drug resistant parasites with the anti-malarial drug chloroquine at different dosing schedules.

Results
An absolute quantification method was developed to monitor the dynamics of P. falciparum cultures in vitro. This method allowed for the observation of competitive suppression, the reduction of parasites numbers due to the presence of another parasite, and competitive release, the improved performance of a parasite after the removal of a competitor. These studies demonstrated that the presence of two parasites led to the reduction in density of at least one parasite. The introduction of drug to a mixed culture containing both a drug resistant and drug sensitive parasites resulted in an increased proportion of the drug resistant parasite. Moreover, following drug treatment, the resistant parasite experienced competitive release by exhibiting a fitness benefit greater than simply surviving drug treatment, due to the removal of competitive suppression by the sensitive parasite.

Conclusions
The newly developed assay allowed for the examination of the dynamics of two distinct clones in vitro; both competitive suppression and release were observed. A deeper understanding of the dynamic growth responses of multiple strain P. falciparum infections, with and without drug pressure, can improve the understanding of the role of parasite interactions in the spread of drug resistant parasites, perhaps suggesting different treatment strategies.
Evaluation of the malaria rapid diagnostic test SDFK90: detection of both PfHRP2 and Pf-pLDH
Authors: Heutmekers Marloes , Gillet Philippe , Cnops Lieselotte , Bottieau Emmanuel , Van Esbroeck Marjan , Maltha Jessica , Jacobs Jan 
Published: October 2012

Abstract

Background
Rapid diagnosis of Plasmodium falciparum infections is important because of the potentially fatal complications. SDFK90 is a recently marketed malaria rapid diagnostic test (RDT) targeting both histidine-rich protein 2 (PfHRP2) and P. falciparum-specific Plasmodium lactate dehydrogenase (Pf-pLDH). The present study evaluated its diagnostic accuracy.

Methods
SDFK90 was tested against a panel of stored whole blood samples (n= 591) obtained from international travellers suspected of malaria, including the four human Plasmodium species and Plasmodium negative samples. Microscopy was used as a reference method, corrected by PCR for species diagnosis. In addition, SDFK90 was challenged against 59 P. falciparum samples with parasite density ≥4% to assess the prozone effect (no or weak visible line on initial testing and a higher intensity upon 10-fold dilution).

Results
Overall sensitivity for the detection of P. falciparum was 98.5% and reached 99.3% at parasite densities >100/μl. There were significantly more PfHRP2 lines visible compared to Pf-pLDH (97.3% vs 86.9%), which was mainly absent at parasite densities <100/μl. Specificity of SDFK90 was 98.8%. No lot-to-lot variability was observed (p = 1.00) and test results were reproducible. A prozone effect was seen for the PfHRP2 line in 14/59 (23.7%) P. falciparum samples tested, but not for the Pf-pLDH line. Few minor shortcomings were observed in the kit’s packaging and information insert.

Conclusions
SDFK90 performed excellent for P. falciparum diagnosis. The combination of PfHRP2 and Pf-pLDH ensures a low detection threshold and counters potential problems of PfHRP2 detection such as gene deletions and the prozone effect.
Long-term survival of patients suffering from glioblastoma multiforme treated with tumor-treating fields
Authors: Rulseh Aaron Michael , Keller Jiří , Klener Jan , Šroubek Jan , Dbalý Vladimír , Syrůček Martin , Tovaryš František , Vymazal Josef 
Published: October 2012

Abstract
Glioblastoma multiforme (GBM) is the most common and malignant primary intracranial tumor, and has a median survival of only 10 to 14 months with only 3 to 5% of patients surviving more than three years. Recurrence (RGBM) is nearly universal, and further decreases the median survival to only five to seven months with optimal therapy. Tumor-treating fields (TTField) therapy is a novel treatment technique that has recently received CE and FDA approval for the treatment of RGBM, and is based on the principle that low intensity, intermediate frequency electric fields (100 to 300 kHz) may induce apoptosis in specific cell types. Our center was the first to apply TTField treatment to histologically proven GBM in a small pilot study of 20 individuals in 2004 and 2005, and four of those original 20 patients are still alive today. We report two cases of GBM and two cases of RGBM treated by TTField therapy, all in good health and no longer receiving any treatment more than seven years after initiating TTField therapy, with no clinical or radiological evidence of recurrence.
Decreased expression of microRNA let-7i and its association with chemotherapeutic response in human gastric cancer
Authors: Liu Kun , Qian Tao , Tang Liming , Wang Jie , Yang Haohua , Ren Jun 
Published: October 2012

Abstract

Background
MicroRNA let-7i has been proven to be down-regulated in many human malignancies and correlated with tumor progression and anticancer drug resistance. Our study aims to characterize the contribution of miRNA let-7i to the initiation and malignant progression of locally advanced gastric cancer (LAGC), and evaluate its possible value in neoadjuvant chemotherapeutic efficacy prediction.

Methods
Eighty-six previously untreated LAGC patients who underwent preoperative chemotherapy and radical resection were included in our study. Let-7i expression was examined for pairs of cancer tissues and corresponding normal adjacent tissues (NATs), using quantitative RT-PCR. The relationship of let-7i level to clinicopathological characteristics, pathologic tumor regression grades after chemotherapy, and overall survival (OS) was also investigated.

Results
Let-7i was significantly down-regulated in most tumor tissues (78/86: 91%) compared with paired NATs (P < 0.001), and low levels of let-7i were significantly correlated with local invasion, lymphatic metastasis, and poor pathologic tumor response. Multivariate Cox regression analysis revealed that low let-7i expression was an unfavorable prognostic factor of OS (hazard ratio (HR) = 2.316, P =0.024) independently of other clinicopathological factors, including tumor node metastasis (TNM) stage (HR = 3.226, P = 0.013), depth of infiltration (HR = 4.167, P < 0.001), and lymph node status (HR = 2.245, P = 0.037).

Conclusions
These findings indicate that let-7i may be a good candidate for use a therapeutic target and a potential tissue marker for the prediction of chemotherapeutic sensitivity and prognosis in LAGC patients.
Seroepidemiology of human enterovirus71 and coxsackievirusA16 in Jiangsu province, China
Authors: Ji Hong , Li Liang , Liu YanMing , Ge HengMing , Wang XuShan , Hu JianLi , Wu Bin , Fu JianGuang , Zhang ZhenYu , Chen XiaoQin , Zhang MingLei , Ding Qiang , Xu WenBo , Tang FenYang , Zhou MingHao , Wang Hua , Zhu FengCai 
Published: October 2012

AbstractBackgroundThe major etiology of hand, foot and mouth disease (HFMD) is infection with human enterovirus A (HEV-A). Among subtypes of HEV-A, coxsackievirusA16 (CoxA16) and enterovirus 71 (EV71) are major causes for recurrent HFMD among infants and children in Jiangsu Province, mainland China. Here, we analyzed maternal antibodies between prenatal women and their neonates, to determine age-specific seroprevalence of human EV71 and CoxA16 infections in infants and children aged 0 to 15 years. The results may facilitate the development of immunization against HFMD.MethodsThis study used cross-section of 40 pairs of pregnant women and neonates and 800 subjects aged 1 month to 15 years old. Micro-dose cytopathogenic effects measured neutralizing antibodies against EV71 and CoxA16. Chi-square test compared seroprevalence rates between age groups and McNemar test, paired-Samples t-test and independent-samples t-test analyzed differences of geometric mean titers.ResultsA strong correlation between titers of neutralizing antibody against EV71 and CoxA16 in prenatal women and neonates was observed (rEV71 = 0.67, rCoxA16 = 0.56, respectively,p < 0.05). Seroprevalence rates of anti-EV71 antibody gradually decreased with age between 0 to 6 months old, remained low between 7 to 11 months (5.0–10.0%), and increased between 1 and 4 years (22.5–87.5%). Age-specific seroprevalence rates of anti-EV71 antibody stabilized in >80% of children between 5 to 15 years of age. However, seroprevalence rates of anti-CoxA16 antibody were very low (0.0–13.0%) between 0 to 6 months of age, gradually increased between 7 months to 4 years (15.0–70.0%), and stabilized at 54.0% (108/200) between 5 to 15 years. Seroprevalence rates against EV71 and CoxA16 were low under 1 year (0.0–10.0%), and showed an age dependent increase with high seroprevalence (52.5–62.5%) between 4 and10 years of age.ConclusionsConcomitant infection of EV71 and CoxA16 was common in Jiangsu Province. Therefore, development of bivalent vaccine against both EV71 and CoxA16 is critical. The optimal schedule for vaccination may be 4 to11 months of age.
High diversity of genetic lineages and virulence genes in nasal Staphylococcus aureusisolates from donkeys destined to food consumption in Tunisia with predominance of the ruminant associated CC133 lineage
Authors: Gharsa Haythem , Ben Sallem Rym , Ben Slama Karim , Gómez-Sanz Elena , Lozano Carmen , Jouini Ahlem , Klibi Naouel , Zarazaga Myriam , Boudabous Abdellatif , Torres Carmen 
Published: October 2012

Abstract

Background
The objective of this study was to determine the genetic lineages and the incidence of antibiotic resistance and virulence determinants of nasal Staphylococcus aureus isolates of healthy donkeys destined to food consumption in Tunisia.

Results
Nasal swabs of 100 donkeys obtained in a large slaughterhouse in 2010 were inoculated in specific media for S. aureus and methicillin-resistant S. aureus (MRSA) recovery. S. aureus was obtained in 50% of the samples, being all of isolates methicillin-susceptible (MSSA). Genetic lineages, toxin gene profile, and antibiotic resistance mechanisms were determined in recovered isolates. Twenty-five different spa-types were detected among the 50 MSSA with 9 novel spa-types. S. aureus isolates were ascribed to agr type I (37 isolates), III (7), II (4), and IV (2). Sixteen different sequence-types (STs) were revealed by MLST, with seven new ones. STs belonging to clonal clomplex CC133 were majority. The gene tst was detected in 6 isolates and the gene etb in one isolate. Different combinations of enterotoxin, leukocidin and haemolysin genes were identified among S. aureus isolates. The egc-cluster-like and an incomplete egc-cluster-like were detected. Isolates resistant to penicillin, erythromycin, fusidic acid, streptomycin, ciprofloxacin, clindamycin, tetracycline, or chloramphenicol were found and the genes blaZ, erm(A), erm(C), tet(M), fusC were identified.

Conclusions
The nares of donkeys frequently harbor MSSA. They could be reservoirs of the ruminant-associated CC133 lineage and of toxin genes encoding TSST-1 and other virulence traits with potential implications in public health. CC133 seems to have a broader host distribution than expected.