bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of approaches for estimating the accuracy of genomic prediction in plant breeding
Authors: Ould Estaghvirou Sidi Boubacar , Ogutu Joseph O , Schulz-Streeck Torben , Knaak Carsten , Ouzunova Milena , Gordillo Andres , Piepho Hans-Peter 
Published: December 2013

AbstractBackgroundIn genomic prediction, an important measure of accuracy is the correlation between the predicted and the true breeding values. Direct computation of this quantity for real datasets is not possible, because the true breeding value is unknown. Instead, the correlation between the predicted breeding values and the observed phenotypic values, called predictive ability, is often computed. In order to indirectly estimate predictive accuracy, this latter correlation is usually divided by an estimate of the square root of heritability. In this study we use simulation to evaluate estimates of predictive accuracy for seven methods, four (1 to 4) of which use an estimate of heritability to divide predictive ability computed by cross-validation. Between them the seven methods cover balanced and unbalanced datasets as well as correlated and uncorrelated genotypes. We propose one new indirect method (4) and two direct methods (5 and 6) for estimating predictive accuracy and compare their performances and those of four other existing approaches (three indirect (1 to 3) and one direct (7)) with simulated true predictive accuracy as the benchmark and with each other.ResultsThe size of the estimated genetic variance and hence heritability exerted the strongest influence on the variation in the estimated predictive accuracy. Increasing the number of genotypes considerably increases the time required to compute predictive accuracy by all the seven methods, most notably for the five methods that require cross-validation (Methods 1, 2, 3, 4 and 6). A new method that we propose (Method 5) and an existing method (Method 7) used in animal breeding programs were the fastest and gave the least biased, most precise and stable estimates of predictive accuracy. Of the methods that use cross-validation Methods 4 and 6 were often the best.ConclusionsThe estimated genetic variance and the number of genotypes had the greatest influence on predictive accuracy. Methods 5 and 7 were the fastest and produced the least biased, the most precise, robust and stable estimates of predictive accuracy. These properties argue for routinely using Methods 5 and 7 to assess predictive accuracy in genomic selection studies.
TcNPR3 from Theobroma cacao functions as a repressor of the pathogen defense response
Authors: Shi Zi , Zhang Yufan , Maximova Siela N , Guiltinan Mark J 
Published: December 2013

Abstract

Background

Arabidopsis thaliana (Arabidopsis) NON-EXPRESSOR OF PR1 (NPR1) is a transcription coactivator that plays a central role in regulating the transcriptional response to plant pathogens. Developing flowers of homozygous npr3 mutants are dramatically more resistant to infection by the pathogenic bacterium Pseudomonas syringae, suggesting a role of NPR3 as a repressor of NPR1-mediated defense response with a novel role in flower development.

Results
We report here the characterization of a putative NPR3 gene from the tropical tree species Theobroma cacao (TcNPR3). Like in Arabidopsis, TcNPR3 was constitutively expressed across a wide range of tissue types and developmental stages but with some differences in relative levels compared to Arabidopsis. To test the function of TcNPR3, we performed transgenic complementation analysis by introducing a constitutively expressing putative TcNPR3 transgene into an Arabidopsis npr3 mutant. TcNPR3 expressing Arabidopsis plants were partially restored to the WT pathogen phenotype (immature flowers susceptible to bacterial infection). To test TcNPR3 function directly in cacao tissues, a synthetic microRNA targeting TcNPR3 mRNA was transiently expressed in cacao leaves using an Agrobacterium-infiltration method. TcNPR3 knock down leaf tissues were dramatically more resistance to infection with Phytophthora capsici in a leaf bioassay, showing smaller lesion sizes and reduced pathogen replication.

Conclusions
We conclude that TcNPR3 functions similar to the Arabidopsis NPR3 gene in the regulation of the cacao defense response. Since TcNPR3 did not show a perfect complementation of the Arabidopsis NPR3 mutation, the possibility remains that other functions of TcNPR3 remain to be found. This novel knowledge can contribute to the breeding of resistant cacao varieties against pathogens through molecular markers based approaches or biotechnological strategies.
Postpartum fever in the presence of a fibroid: Sphingomonas paucimobilissepsis associated with pyomyoma
Authors: Del Borgo Cosmo , Maneschi Francesco , Belvisi Valeria , Morelli Francesca , Vetica Angelo , Marocco Raffaella , Tieghi Tiziana , Lichtner Miriam , Mastroianni Claudio M 
Published: December 2013

AbstractBackgroundPyomyoma is a life-threatening complication of uterine leiomyoma. It may occur in post- menopausal women, during pregnancy and in the postpartum period. Fever may be the only manifestation during the early stages of the disease. We detail the first reported case of postpartum pyomyoma-related sepsis due toSphingomonas paucimobilis,a Gram-negative bacillus that is gaining recognition as an important human pathogen.Case presentationA woman presented with an asymptomatic uterine fibroid and a two-week history of fever during the postpartum period. Suppurative uterine leiomyoma was diagnosed, and blood cultures grewSphingomonas paucimobilis.The myoma was surgically removed from the uterus without hysterectomy. Intravenous antimicrobial therapy was given for fifteen days, and the patient was discharged from hospital in good condition.ConclusionPyomyoma should be considered in broad differential diagnosis of postpartum fever. This case highlights a unique disease manifestation ofS. paucimobilis, an emerging opportunistic pathogen with increasing significance in the nosocomial setting.
Effect of low frequency magnetic fields on melanoma: tumor inhibition and immune modulation
Authors: Nie Yunzhong , Du Leilei , Mou Yongbin , Xu Zhenjun , Weng Leihua , Du Youwei , Zhu Yanan , Hou Yayi , Wang Tingting 
Published: December 2013

Abstract

Background
We previously found that the low frequency magnetic fields (LF-MF) inhibited gastric and lung cancer cell growth. We suppose that exposure to LF-MF may modulate immune function so as to inhibit tumor. We here investigated whether LF-MF can inhibit the proliferation and metastasis of melanoma and influence immune function.

Methods
The effect of MF on the proliferation, cell cycle and ultrastracture of B16-F10 in vitro was detected by cell counting Kit-8 assay, flow cytometry, and transmission electron microscopy. Lung metastasis mice were prepared by injection of 2 × 105 B16-F10 melanoma cells into the tail vein in C57BL/6 mice. The mice were then exposed to an LF-MF (0.4 T, 7.5 Hz) for 43 days. Survival rate, tumor markers and the innate and adaptive immune parameters were measured.

Results
The growth of B16-F10 cells was inhibited after exposure to the LF-MF. The inhibition was related to induction of cell cycle arrest and decomposition of chromatins. Moreover, the LF-MF prolonged the mouse survival rate and inhibited the proliferation of B16-F10 in melanoma metastasis mice model. Furthermore, the LF-MF modulated the immune response via regulation of immune cells and cytokine production. In addition, the number of Treg cells was decreased in mice with the LF-MF exposure, while the numbers of T cells as well as dendritic cells were significantly increased.

Conclusion
LF-MF inhibited the growth and metastasis of melanoma cancer cells and improved immune function of tumor-bearing mice. This suggests that the inhibition may be attributed to modulation of LF-MF on immune function and LF-MF may be a potential therapy for treatment of melanoma.
Assessment of knowledge on sexually transmitted infections and sexual risk behaviour in two rural districts of Bhutan
Authors: Norbu Kunzang , Mukhia Sontosh , Tshokey  
Published: December 2013

Abstract

Background
The incidence of STI is high and increasing in Bhutan. Poor understanding of risky sexual behavior could be a cause. Comprehensive community surveys have not been previously done. This study was conducted to assess local knowledge on STIs and sexual risk behaviour in two rural districts of Bhutan: Gasa and Zhemgang.

Methods
The study population included residents aged 15–49 years in the two districts. Health Assistants (HAs) visited all households to distribute questionnaires assessing understanding of knowledge on STIs and risk behaviour. Questionnaires were scored and analyzed.

Results
The average score was 61.6%. Respondents had highest knowledge about prevention and lowest about disease and complications. There was a positive correlation between level of education and knowledge on STI (P < 0.05). Almost 37% of students scored low. Nearly one-third of the study population was practicing risky sexual behavior with 31.2% having sexual relationships with non-regular partners and 10.9% had extramarital sexual contacts. Regular use of condoms with non-regular partners was 49.1%. The most common reason for not using condom was unavailability during the sexual encounter. The study showed that despite increasing knowledge there was no reduction in risky sexual behaviour (p > 0.05).

Conclusions
The study population had variable understanding of STIs and their complications. One in three persons practiced risky sexual behaviour, higher in men. Condom use was low. There was no reduction of risky sexual behaviour with increasing level of knowledge indicating that increasing level of knowledge does not necessarily reduce risky sexual behaviour.
Evaluating performance of dental caries detection methods among third-year dental students
Authors: Parviainen Heini , Vähänikkilä Hannu , Laitala Marja-Liisa , Tjäderhane Leo , Anttonen Vuokko 
Published: December 2013

Abstract

Background
Reliable caries detection is a cornerstone in the modern caries treatment schema. This study aimed to evaluate adopting traditional and new caries detection methods by third-year dental students.

Methods
Fifty-seven students were given lectures on caries detection, after which they evaluated 27 extracted carious teeth using traditional clinical assessment (CE), Nyvad’s, and ICDAS methods. On three teeth they also performed DIAGNOdent pen® (LF) scanning. Histological scores of the sectioned teeth (ICDAS, LF) and activity estimations of the lesions by the supervisors were used as golden standards (Nyvad, CE). For the ICDAS method , sensitivity and specificity were calculated using dentine caries (D3) as a cut-off point. Mean ICC and kappa values were calculated to evaluate interexaminer agreement for all lesions and methods. Spearman’s correlation coefficient evaluated LF scanning.

Results
ICDAS method presented good sensitivity ( 0.78) and specificity (0.87). The inter-examiner agreement for different methods was fair or good (CE ICC = 0.69, κ = 0.53; Nyvad’s method ICC = 0.68, κ = 0.48, ICDAS ICC = 0.66, κ = 0.47). Variation in LF values was the greatest with lesions extending to middle third of dentin. In that case, the Spearman’s correlation coefficient was also the weakest.

Conclusions
To follow the guidelines by the European Core Curriculum on Cariology, the third year dental students are introduced to methods for detecting lesion depth and assessing lesion activity as well as using new caries detection methods. Their performance in estimating lesion depth is good, and fair to good in estimating lesion activity even after basic training only.
Fermentation stage-dependent adaptations of Bacillus licheniformis during enzyme production
Authors: Wiegand Sandra , Voigt Birgit , Albrecht Dirk , Bongaerts Johannes , Evers Stefan , Hecker Michael , Daniel Rolf , Liesegang Heiko 
Published: December 2013

Abstract

Background
Industrial fermentations can generally be described as dynamic biotransformation processes in which microorganisms convert energy rich substrates into a desired product. The knowledge of active physiological pathways, reflected by corresponding gene activities, allows the identification of beneficial or disadvantageous performances of the microbial host. Whole transcriptome RNA-Seq is a powerful tool to accomplish in-depth quantification of these gene activities, since the low background noise and the absence of an upper limit of quantification allow the detection of transcripts with high dynamic ranges. Such data enable the identification of potential bottlenecks and futile energetic cycles, which in turn can lead to targets for rational approaches to productivity improvement. Here we present an overview of the dynamics of gene activity during an industrial-oriented fermentation process with Bacillus licheniformis, an important industrial enzyme producer. Thereby, valuable insights which help to understand the complex interactions during such processes are provided.

Results
Whole transcriptome RNA-Seq has been performed to study the gene expression at five selected growth stages of an industrial-oriented protease production process employing a germination deficient derivative of B. licheniformis DSM13. Since a significant amount of genes in Bacillus strains are regulated posttranscriptionally, the generated data have been confirmed by 2D gel-based proteomics. Regulatory events affecting the coordinated activity of hundreds of genes have been analyzed. The data enabled the identification of genes involved in the adaptations to changing environmental conditions during the fermentation process. A special focus of the analyses was on genes contributing to central carbon metabolism, amino acid transport and metabolism, starvation and stress responses and protein secretion. Genes contributing to lantibiotics production and Tat-dependent protein secretion have been pointed out as potential optimization targets.

Conclusions
The presented data give unprecedented insights into the complex adaptations of bacterial production strains to the changing physiological demands during an industrial-oriented fermentation. These are, to our knowledge, the first publicly available data that document quantifiable transcriptional responses of the commonly employed production strain B. licheniformis to changing conditions over the course of a typical fermentation process in such extensive depth.
N-dimensional N-microphone sound source localization
Authors: Parsayan Ali , Ahadi Seyed Mohammad 
Published: December 2013

AbstractThis paper investigates real-time N-dimensional wideband sound source localization in outdoor (far-field) and low-degree reverberation cases, using a simple N-microphone arrangement. Outdoor sound source localization in different climates needs highly sensitive and high-performance microphones, which are very expensive. Reduction of the microphone count is our goal. Time delay estimation (TDE)-based methods are common for N-dimensional wideband sound source localization in outdoor cases using at least N + 1 microphones. These methods need numerical analysis to solve closed-form non-linear equations leading to large computational overheads and a good initial guess to avoid local minima. Combined TDE and intensity level difference or interaural level difference (ILD) methods can reduce microphone counts to two for indoor two-dimensional cases. However, ILD-based methods need only one dominant source for accurate localization. Also, using a linear array, two mirror points are produced simultaneously (half-plane localization). We apply this method to outdoor cases and propose a novel approach for N-dimensional entire-space outdoor far-field and low reverberation localization of a dominant wideband sound source using TDE, ILD, and head-related transfer function (HRTF) simultaneously and only N microphones. Our proposed TDE-ILD-HRTF method tries to solve the mentioned problems using source counting, noise reduction using spectral subtraction, and HRTF. A special reflector is designed to avoid mirror points and source counting used to make sure that only one dominant source is active in the localization area. The simple microphone arrangement used leads to linearization of the non-linear closed-form equations as well as no need for initial guess. Experimental results indicate that our implemented method features less than 0.2 degree error for angle of arrival and less than 10% error for three-dimensional location finding as well as less than 150-ms processing time for localization of a typical wideband sound source such as a flying object (helicopter).
Prevalence of active hepatitis C virus infections among general public of Lahore, Pakistan
Authors: Anwar Muhammad Ikram , Rahman Moazur , Hassan Mahmood Ul , Iqbal Mazhar 
Published: December 2013

Abstract

Background
To find out the prevalence of active hepatitis C virus (HCV) infections among general public in Lahore city, since data concerning the prevalence of active HCV in this city is currently unavailable.

Methods
Blood samples were collected randomly from individuals visiting different clinical laboratories in Lahore. Serum was separated and processed by nested PCR qualitative assay for the detection of HCV RNA. The samples were categorized into different age groups on the basis of pre-test questionnaires in order to record the age-wise differences regarding the prevalence of active HCV. Data were analyzed statistically using Chi-Square test.

Results
Out of the 4246 blood samples analyzed in this study, 210 were confirmed to be positive for active HCV infection. Gender-wise active HCV prevalence revealed no significant difference [OR = 1.10 CI = (0.83-1.46), p > 0.05]. However, among the age groups the highest prevalence was observed in the age groups 20–29 (7.7%) and 30–39 years (6.4%) with odds of prevalence of 14.8% (OR = 2.48, CI = (1.40-4.38), p < 0.05) and 10.3% (OR = 2.03, CI = (1.10-3.71), respectively. In age groups above 40 years (40–49, 50–59 and >59 years), a decrease in levels of active HCV prevalence was observed.

Conclusions
Among tested samples, 4.9% of the subjects were confirmed to harbour active HCV infections and the “middle aged” population in Lahore was found to be at a higher risk of the HCV ailments compared to both their younger and older peers.
Reduced self-control leads to disregard of an unfamiliar behavioral option: an experimental approach to the study of neuroenhancement
Authors: Wolff Wanja , Baumgarten Franz , Brand Ralf 
Published: December 2013

AbstractBackgroundNeuroenhancement (NE), the use of psychoactive substances in order to enhance a healthy individual’s cognitive functioning from a proficient to an even higher level, is prevalent in student populations. According to the strength model of self-control, people fail to self-regulate and fall back on their dominant behavioral response when finite self-control resources are depleted. An experiment was conducted to test the hypothesis that ego-depletion will prevent students who are unfamiliar with NE from trying it.Findings130 undergraduates, who denied having tried NE before (43% female, mean age = 22.76 ± 4.15 years old), were randomly assigned to either an ego-depletion or a control condition. The dependent variable was taking an “energy-stick” (a legal nutritional supplement, containing low doses of caffeine, taurine and vitamin B), offered as a potential means of enhancing performance on the bogus concentration task that followed. Logistic regression analysis showed that ego-depleted participants were three times less likely to take the substance,OR = 0.37,p = .01.ConclusionThis experiment found that trying NE for the first time was more likely if an individual’s cognitive capacities were not depleted. This means that mental exhaustion is not predictive for NE in students for whom NE is not the dominant response. Trying NE for the first time is therefore more likely to occur as a thoughtful attempt at self-regulation than as an automatic behavioral response in stressful situations. We therefore recommend targeting interventions at this inter-individual difference. Students without previous reinforcing NE experience should be provided with information about the possible negative health outcomes of NE. Reconfiguring structural aspects in the academic environment (e.g. lessening workloads) might help to deter current users.
Predictive diagnosis of endometrial hyperplasia and personalized therapeutic strategy in women of fertile age
Authors: Goncharenko Vadym M , Beniuk Vasyl A , Kalenska Olga V , Demchenko Olga M , Spivak Mykola Ya , Bubnov Rostyslav V 
Published: December 2013

Abstract

Introduction
Endometrial hyperplasia has a high risk for malignant transformation and relapses; existing mini-invasive treatments may lead to irrevocable endometrium destruction. The aims were to analyze receptor systems in endometrial hyperplasia, to evaluate the capabilities of ultrasonography, sonoelastography for diagnosis and treatment control, and to develop treatment algorithm.

Materials and methods
We included 313 women (20–45 years), assessed into the following: group 1 (n = 112) with glandular cystic hyperplasia, group 2 (n = 98) endometrial polyps, and group 3 (n = 103) atypical hyperplasia; and 82 controls who have undergone hysteroscopy before in vitro fertilization in tubal origin infertility were also included. Patients underwent clinical examination, transvaginal ultrasound, immunohistochemical study, and hormonal therapy/hysteroresectoscopy.

Results
In patients with glandular hyperplasia, we registered increase of endometrium estrogen receptors (75.6% in the epithelium and 30.9% in the stroma; in controls, 43.3% and 29.6%, respectively); in polyps, there was a significant estrogen receptor increase in the stroma (48.2% vs 29.6% in controls), and in atypical hyperplasia, progesterone receptors significantly increased in the stroma. Ki-67 increased (40% to 50%) in the epithelium without changes in the stroma. Ultrasound has a sensitivity of 96% and a specificity of 85% for early detection of endometrial pathology and prediction outcome of intervention, and sonoelastography has a sensitivity of 91% and a specificity of 83% for polyp diagnosis. Personalized treatment was effective in 88.8%, relapse was diagnosed in 11.2% after 6 months, and conservative treatment of atypical hyperplasia was effective in 45%: in 25.8%, ablative hysteroresectoscopy was performed, while in 22.6% with comorbidities, hystero/oophorectomies were performed.

Conclusions
The evaluation of receptor status with ultrasound data in patients with endometrial hyperplasia allows for a clear definition of the treatment policy, avoidance of relapse, treatment optimization, and observation of such patients.