bluuebunny/crossref_metadata_2025 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

Background

In 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.

Results

The 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.

Conclusions

The 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

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

Background

Pyomyoma 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 presentation

A 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.

Conclusion

Pyomyoma 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

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

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

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

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

This 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

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

Background

Neuroenhancement (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.

Findings

130 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.

Conclusion

This 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

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.
The neurological disease ontology
Authors: Jensen Mark , Cox Alexander P , Chaudhry Naveed , Ng Marcus , Sule Donat , Duncan William , Ray Patrick , Weinstock-Guttman Bianca , Smith Barry , Ruttenberg Alan , Szigeti Kinga , Diehl Alexander D
Published: December 2013

Background

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke.

Description

ND is implemented in OWL 2 and currently has more than 450 terms that refer to and describe various aspects of neurological diseases. ND directly imports the development version of OGMS, which uses BFO 2. Term development in ND has primarily extended the OGMS terms ‘disease’, ‘diagnosis’, ‘disease course’, and ‘disorder’. We have imported and utilize over 700 classes from related ontology efforts including the Foundational Model of Anatomy, Ontology for Biomedical Investigations, and Protein Ontology. ND terms are annotated with ontology metadata such as a label (term name), term editors, textual definition, definition source, curation status, and alternative terms (synonyms). Many terms have logical definitions in addition to these annotations. Current development has focused on the establishment of the upper-level structure of the ND hierarchy, as well as on the representation of Alzheimer’s disease, multiple sclerosis, and stroke. The ontology is available as a version-controlled file athttp://code.google.com/p/neurological-disease-ontology along with a discussion list and an issue tracker.

Conclusion

ND seeks to provide a formal foundation for the representation of clinical and research data pertaining to neurological diseases. ND will enable its users to connect data in a robust way with related data that is annotated using other terminologies and ontologies in the biomedical domain.
A novel promising Trichoderma harzianum strain for the production of a cellulolytic complex using sugarcane bagasse in natura
Authors: Benoliel Bruno , Torres Fernando Araripe Gonçalves , de Moraes Lidia Maria Pepe
Published: December 2013

Brazil is a major producer of agro-industrial residues, such as sugarcane bagasse, which could be used as raw material for microbial production of cellulases as an important strategy for the development of sustainable processes of second generation ethanol production. For this purpose, this work aimed at screening for glycosyl hydrolase activities of fungal strains isolated from the Brazilian Cerrado. Among 13 isolates, a Trichoderma harzianum strain (L04) was identified as a promising candidate for cellulase production when cultured on in natura sugarcane bagasse. Strain L04 revealed a well-balanced cellulolytic complex, presenting fast kinetic production of endoglucanases, exoglucanases and β-glucosidases, achieving 4,022, U.L-1 (72 h), 1,228 U.L-1 (120 h) and 1,968 U.L-1 (48 h) as the highest activities, respectively. About 60% glucose yields were obtained from sugarcane bagasse after 18 hours hydrolysis. This new strain represents a potential candidate for on-site enzyme production using sugarcane bagasse as carbon source.
Moderators of remission with interpersonal counselling or drug treatment in primary care patients with depression: randomised controlled trial
Authors: Menchetti Marco , Rucci Paola , Bortolotti Biancamaria , Bombi Annarosa , Scocco Paolo , Kraemer Helena Chmura , Berardi Domenico ,   the DEPICS group
Published: December 2013

Background

Despite depressive disorders being very common there has been little research to guide primary care physicians on the choice of treatment for patients with mild to moderate depression.

Aims

To evaluate the efficacy of interpersonal counselling compared with selective serotonin reuptake inhibitors (SSRIs), in primary care attenders with major depression and to identify moderators of treatment outcome.

Method

A randomised controlled trial in nine centres (DEPICS, Australian New Zealand Clinical Trials Registry number: ACTRN12608000479303). The primary outcome was remission of the depressive episode (defined as a Hamilton Rating Scale for Depression score 7 at 2 months). Daily functioning was assessed using the Work and Social Adjustment Scale. Logistic regression models were used to identify moderators of treatment outcome.

Results

The percentage of patients who achieved remission at 2 months was significantly higher in the interpersonal counselling group compared with the SSRI group (58.7%v.45.1%,P= 0.021). Five moderators of treatment outcome were found: depression severity, functional impairment, anxiety comorbidity, previous depressive episodes and smoking habit.

Conclusions

We identified some patient characteristics predicting a differential outcome with pharmacological and psychological interventions. Should our results be confirmed in future studies, these characteristics will help clinicians to define criteria for first-line treatment of depression targeted to patients' characteristics.
Cortisol awakening response and subsequent depression: prospective longitudinal study
Authors: Carnegie Rebecca , Araya Ricardo , Ben-Shlomo Yoav , Glover Vivette , O'Connor Thomas G. , O'Donnell Kieran J. , Pearson Rebecca , Lewis Glyn
Published: December 2013

Background

Some studies have found an association between elevated cortisol and subsequent depression, but findings are inconsistent. The cortisol awakening response may be a more stable measure of hypothalamic–pituitary–adrenal function and potentially of stress reactivity.

Aims

To investigate whether salivary cortisol, particularly the cortisol awakening response, is associated with subsequent depression in a large population cohort.

Method

Young people (aged 15 years,n= 841) from the Avon Longitudinal Study of Parents and Children (ALSPAC) collected salivary cortisol at four time points for 3 school days. Logistic regression was used to calculate odds ratios for developing depression meeting ICD-10 criteria at 18 years.

Results

We found no evidence for an association between salivary cortisol and subsequent depression. Odds ratios for the cortisol awakening response were 1.24 per standard deviation (95% CI 0.93–1.66,P= 0.14) before and 1.12 (95% CI 0.73–1.72,P= 0.61) after adjustment for confounding factors. There was no evidence that the other cortisol measures, including cortisol at each time point, diurnal drop and area under the curve, were associated with subsequent depression.

Conclusions

Our findings do not support the hypothesis that elevated salivary cortisol increases the short-term risk of subsequent depressive illness. The results suggest that if an association does exist, it is small and unlikely to be of clinical significance.
Deliberation and Precipitation
Authors: Richmond Colin
Published: December 2013

In an issue of Common Knowledge given over to experiments in scholarly form and to the discussion of them, this piece is one of three on the genre of microhistory. The other two (by Natalie Zemon Davis and Sir Keith Thomas) argue the merits and demerits of the genre, while this piece seeks to exemplify both its virtues and its risks. To show how microhistory offers intense deliberation on a narrowly defined topic, yet also a kind of hastiness — an impatience with demands for broader scope — Colin Richmond examines one limited facet of the relationship between two Americans resident in England at the turn of the last century: the novelist Henry James and the painter Edwin Austin Abbey. Detailed evidence is mustered to document James's love of fresh hens' eggs and of the undignified lengths he would go to obtain them through the agency of Abbey and his wife. This short piece is written as if a parable, and while its moral goes unstated, the reader's attention is drawn to the unsettled question of whether James exerted maximal effort for minimal results, or whether he knew something about the value of freshness undreamed of by those more patient and dignified in pursuing their desires.
Imagination and the Good Life
Authors: Zwicky Jan
Published: December 2013

In this essay, part of a cluster of pieces on her concept of “lyric philosophy,” the author explores connections between imagination, understood as the capacity to think in images, and what Wittgenstein called “seeing-as.” In seeing-as, we focus on what Wittgenstein identifies as inner structural relations. This is a term that Max Wertheimer, one of the founders of gestalt philosophical psychology, used independently to describe how seeing-as involves seeing into a thing or situation. The present essay suggests that both seeing-as and seeing-into depend on, and develop, sensitivity to ontological resonance, the attunement of things with one another, the deep analogies that constitute the underlying structure of the world. Imagination is thus fundamental to the good, or ethical, life. For its disciplined exercise relieves us of what Simone Weil calls the “Ring of Gyges”: the refusal to perceive significant analogies between ourselves and other beings, which is the root of injustice.
Fighting Words
Authors: Spellmeyer Kurt
Published: December 2013

In a university increasingly shaped by commercial interests promoting “skills” at the expense of knowledge, composition has the opportunity to cooperate with the new order. But the field might choose to play an opposing role, revitalizing the humanities by placing politics where it belongs—at the very center of learning.
Reading Yourself
Authors: Sutherland Stephen
Published: December 2013

Drawing on the notion that revision involves the performance of a writer’s identity in a conversation with herself, this article argues for conceptualizing revision as ecstasis and ventriloquism. By using the metaphor of ventriloquism to translate theory into heuristics for teaching revision, it enacts an underlying argument that pedagogy is metaphor. In doing so, it offers four practical strategies for teaching students to revise.
“Odd Topics” And Open Minds
Authors: Heiman James
Published: December 2013

Teaching nontraditional themes in first-year writing courses sometimes confuses students and frustrates instructors. This article shows how using a transformative, critical-thinking pedagogy challenges the content and purpose of “English” courses—making such themes more accessible while improving students’ use of rhetorical inquiry to both analyze and compose texts.
Reduction of blood oxygen levels enhances postprandial cardiac hypertrophy in Burmese python (Python molurus)
Authors: Slay Chris , Enok Sanne , Hicks James , Wang Tobias
Published: December 2013

Physiological cardiac hypertrophy is characterized by reversible enlargement of cardiomyocytes and changes in chamber architecture, which increase stroke volume and VO2 max via augmented convective oxygen transport. Cardiac hypertrophy is known to occur in response to repeated elevations of O2 demand and/or reduced O2 supply in several species of vertebrate ectotherms, including postprandial Burmese pythons (Python molurus). Recent data suggest postprandial cardiac hypertrophy in P. molurus is a facultative rather than obligatory response to digestion, though the triggers of this response are unknown. Here we hypothesize that an O2 supply-demand mismatch stimulates postprandial cardiac enlargement in Burmese pythons. To test this hypothesis, we rendered animals anemic prior to feeding, essentially halving blood oxygen content during the postprandial period. Fed anemic animals had heart rates 126% higher than fasted controls, which, coupled with a 71% increase in mean arterial pressure suggests fed anemic animals were experiencing significantly elevated cardiac work. We found significant cardiac hypertrophy in fed anemic animals, which exhibited ventricles 39% larger than fasted controls and 28% larger than fed controls. These findings support our hypothesis that those animals with a greater magnitude of O2 supply-demand mismatch exhibit the largest hearts. The "low O2 signal" stimulating postprandial cardiac hypertrophy is likely mediated by elevated ventricular wall stress associated with postprandial hemodynamics.
Are torpid bats immune to anthropogenic noise?
Authors: Luo Jinhong , Clarin B.-Markus , Borissov Ivailo M. , Siemers Björn M.
Published: December 2013

Anthropogenic noise has a negative impact on a variety of animals. However, many bat species roost in places with high levels of anthropogenic noise. Here we test the hypothesis that torpid bats are insensitive to anthropogenic noise. In a laboratory experiment, we recorded skin temperature (Tsk) of bats roosting individually that were subjected to playbacks of different types of noise. We found that torpid bats with Tsk ~10°C lower than their active Tsk, responded to all types of noise by elevating Tsk. Bats responded most strongly to colony and vegetation noise, and most weakly to traffic noise. The time of day when torpid bats were exposed to noise had a pronounced effect on responses. Torpid bats showed increasing responses from morning towards evening, i.e. towards the onset of the active phase. Skin temperature at the onset of noise exposure (Tsk-start, 17 ~ 29°C) was not related to the response. Moreover, we found evidence that torpid bats rapidly habituated to repeated and prolonged noise exposure.
Biomechanical strategies for mitigating collision damage in insect wings: structural design versus embedded elastic materials
Authors: Mountcastle Andrew M. , Combes Stacey A.
Published: December 2013

The wings of many insects accumulate considerable wear and tear during their lifespan, and this irreversible structural damage can impose significant costs on insect flight performance and survivability. Wing wear in foraging bumblebees (and likely many other species) is caused by inadvertent, repeated collisions with vegetation during flight, suggesting the possibility that insect wings may display biomechanical adaptations to mitigate the damage associated with collisions. We used a novel experimental technique to artificially induce wing wear in bumblebees and yellowjacket wasps, closely related species with similar life histories but distinct wing morphologies. Wasps have a flexible resilin joint (the costal break) positioned distally along the leading edge of the wing, which allows the wing tip to crumple reversibly when it hits an obstacle, whereas bumblebees lack an analogous joint. Through experimental manipulation of its stiffness, we found that the costal break plays a critical role in mitigating collision damage in yellowjacket wings. However, bumblebee wings do not experience as much damage as would be expected based on their lack of a costal break, possibly due to differences in the spatial arrangement of supporting wing veins. Our results indicate that these two species utilize different wing design strategies for mitigating damage resulting from collisions. A simple inertial model of a flapping wing reveals the biomechanical constraints acting on the costal break, which may help explain its absence in bumblebee wings.
Antimicrobial properties of a nanostructured eggshell from a compost-nesting bird
Authors: D'Alba Liliana , Jones Darryl N. , Eliason Chad , Badawy Hope T. , Shawkey Matthew D.
Published: December 2013

Infection is an important source of mortality for avian embryos but parental behaviors and eggs themselves can provide a network of antimicrobial defenses. Mound builders (Aves: Megapodiidae) are unique among birds in that they produce heat for developing embryos not by sitting on eggs but by burying them in carefully tended mounds of soil and microbially decomposing vegetation. The low infection rate of eggs of one species in particular, the Australian brush-turkey (Alectura lathami) suggests that they possess strong defensive mechanisms. To identify some of these mechanisms we first quantified antimicrobial albumen proteins and characterized eggshell structure, finding that albumen was not unusually antimicrobial, but that eggshell cuticle was composed of nanometer-sized calcite spheres. Experimental tests revealed that these modified eggshells were significantly more hydrophobic and better at preventing bacterial attachment and penetration into the egg contents than chicken eggs. Our results suggest that these mechanisms may contribute to the antimicrobial defense system of these eggs, and may provide inspiration for new biomimetic anti-fouling surfaces.
Ectoparasite performance when feeding on reproducing mammalian females: an unexpected decrease when on pregnant hosts
Authors: Dlugosz Elizabeth M. , Downs Cynthia J. , Khokhlova Irina , Degen Allan , Krasnov Boris R.
Published: December 2013

Reproduction is an energy-demanding activity in mammalian females, with increased energy requirements during pregnancy and, especially, during lactation. To better understand the interactions between parasitism and host reproduction, we investigated feeding and reproductive performance of fleas (Xenopsylla ramesis) parasitizing non-reproducing, pregnant, or lactating gerbilline rodents (Meriones crassus). Based on energetic considerations, we predicted that feeding and reproductive performance of fleas would be lowest on non-breeding females, moderate on pregnant females, and highest on lactating females. We estimated feeding performance of the fleas via absolute and mass-specific bloodmeal size and reproductive performance via egg production and latency to peak oviposition. Host reproductive status had no effect on either absolute or mass-specific bloodmeal size or the day of peak oviposition, but significantly affected the daily number of eggs produced by a female flea. Surprisingly, and contrary to our predictions, egg production of fleas fed on pregnant rodents was significantly lower than that on non-reproducing and lactating rodents, while no difference in egg production between fleas feeding on non-reproducing and lactating hosts was found. Our results suggest that differences in parasite reproduction when feeding on hosts of different reproductive status are not associated with the different energy requirements of the hosts at non-breeding, pregnancy and lactation but rather with variation in hormonal and/or immune status during these periods.
Bacterial RNA motif in the 5′ UTR of rpsF interacts with an S6:S18 complex
Authors: Fu Yang , Deiorio-Haggar Kaila , Soo Mark W. , Meyer Michelle M.
Published: December 2013

Approximately half the transcripts encoding ribosomal proteins in Escherichia coli include a structured RNA motif that interacts with a specific ribosomal protein to inhibit gene expression, thus allowing stoichiometric production of ribosome components. However, many of these RNA structures are not widely distributed across bacterial phyla. It is increasingly common for RNA motifs associated with ribosomal protein genes to be identified using comparative genomic methods, yet these are rarely experimentally validated. In this work, we characterize one such motif that precedes operons containing rpsF and rpsR, which encode ribosomal proteins S6 and S18. This RNA structure is widely distributed across many phyla of bacteria despite differences within the downstream operon, and examples are present in both E. coli and Bacillus subtilis. We demonstrate a direct interaction between an example of the RNA from B. subtilis and an S6:S18 complex using in vitro binding assays, verify our predicted secondary structure, and identify a putative protein-binding site. The proposed binding site bears a strong resemblance to the S18 binding site within the 16S rRNA, suggesting molecular mimicry. This interaction is a valuable addition to the canon of ribosomal protein mRNA interactions. This work shows how experimental verification translates computational results into concrete knowledge of biological systems.
Cancer quasispecies and stem-like adaptive aneuploidy
Authors: Napoletani Domenico , Signore Michele , Struppa Daniele C
Published: December 2013

In this paper we develop a theoretical frame to understand self-regulation of aneuploidy rate in cancer and stem cells. This is accomplished building upon quasispecies theory, by leaving its formal mathematical structure intact, but by drastically changing the meaning of its objects. In particular, we propose a novel definition of chromosomal master sequence, as a sequence of physically distinct whole or fragmented chromosomes, whose length is taken to be the sum of the copy numbers of each whole or fragmented chromosome. This fundamental change in the functional objects of quasispecies theory allows us to show that previously measured aneuploidy rates in cancer populations are already close to a formally derived aneuploid error threshold, and that any value of aneuploidy rate larger than the aneuploid error threshold would lead to a loss of fitness of a tumor population. Finally, we make a phenomenological analysis of existing experimental evidence to argue that single clone cancer cells, derived from an aneuploid cancer subpopulation, are capable of self-regulating their aneuploidy rate and of adapting it to distinct environments, namely primary and metastatic microenvironments. We also discuss the potential origin of this self-regulatory ability in the wider context of developmental and comparative biology and we hypothesize the existence of a diversification factor, i.e. a cellular mechanism that regulates adaptation of aneuploidy rates, active in all embryo, adult and cancer stem cells.
Mutual insurance of property in prerevolutionary Russia
Authors: Краюшкина  , Krayushkina Elena
Published: December 2013

The system of mutual property insurance in the Russian Empire is considered.

It is shown how mutual property insurance affected the economic development

of Russia, strengths and weaknesses in the activities of various insurance

establishments are explored. Positive pieces of historical experience in the field

of insurance is proposed to use in the course of reforming the modern insurance

legislation.
Ways of increase the overall performance of russian industrial enterprises vsovremennyh conditions
Authors: Сизов  , Sizov L.
Published: December 2013

In given article problems of increase of an overall performance and innovative

activity of the Russian industrial enterprises are considered. On the basis of

application synergetic the approach to the organization of activity of creation of

the innovative infrastructure giving synergetic effect, introduction of innovative

loans and realization of the concept of macro logistical platforms it is possible

to achieve competitiveness of the Russian industrial enterprises.
Problems of the institute of households in contemporary russian economy
Authors: Хадиуллина  , Khadiullina G. , Хасанова  , Khasanova A. , Нугуманова  , Nugumanova L.
Published: December 2013

In the clause presented methodological principles, methodical provisions and practical offers on formation and development of institutes of household in modern Russian economy, justified treatment of households as subject of contract relations concerning assets of various level of specificity (production factors), formulated contradictions in system of contract relations with participation of house farms, defined models of behavior house farms on a labor market, defined maintenance of institutional trap of poverty (QWERTY effect), presented role of house farms in achievement of institutional balance in modern Russian economy.
The system of program management of the innovation component of industrial production in the regional economic complex
Authors: Шишкин  , Shishkin Andrey
Published: December 2013

It considers the concepts associated with the system software of management

of innovative projects. Analyzed different approaches, management at different

levels. The characteristic of a program-target approach in project management.

Given the characteristics of the stages of the project. A scheme of the decision

on implementation of the innovation project. Analyzed in a quantitative method

of identification of investments for realization of the innovative project.

Characterized separate stages of the business plan of the innovative project.

Formed table of indicators of efficiency of the innovative project.

Recommendations on the formation of a formal model of the decision on the

implementation of the innovation project.
Practice Summary: Flight Trajectory Optimization
Authors: Bollapragada Srinivas , Klooster Joel , Cumings MacKenzie
Published: December 2013

We developed and implemented a novel algorithm to control the trajectory of an aircraft flight to reduce the costs it incurs. Our algorithm computes the values for the parameters to be entered into the aircraft’s flight management system to minimize the fuel and schedule-adherence costs incurred on the flight. We implemented it in a prototype software system that is currently in use at GE Aviation Services.