bluuebunny/crossref_metadata_2025 huggingface dataset:
High-temperature strain measurement using active imaging digital image correlation and infrared radiation heating
Authors: Pan Bing , Wu Dafang , Gao Jianxin
Published: September 2013

A technique for non-contact and full-field high-temperature strain measurement of a sample subjected to radiation heating using active imaging digital image correlation is described in this work. A high-performance quartz lamp heater system was designed to reproduce transient thermal environments experienced by hypersonic vehicles. The digital images of the test sample surface at various temperatures are captured using a novel active imaging optical system based on a combination of monochromatic light illumination and bandpass filter imaging. Subsequently, the captured images are processed by a robust reliability-guided displacement tracking algorithm with an automatic reference image updating scheme to extract full-field thermal deformation. With the improvements made in both the imaging system and correlation algorithm, the de-correlation problem of speckle patterns caused by the thermal radiation and surface oxidation of the heated test object are effectively addressed, enabling reliable deformation measurement in extremely high temperature environments. The performance of the proposed active imaging digital image correlation technique is verified by two experiments: (1) measurement of the uniform thermal strains of a chromium–nickel austenite stainless steel sample which is heated from room temperature to 1300 °C, and (2) measurement of the non-uniform thermal strain fields of a woven C/SiC composite at 1550 °C. The test results show that the active imaging digital image correlation is an easy-to-implement yet effective optical technique for high-temperature strain measurement, and has great potential in characterizing thermo-mechanical behaviour of materials and structures for hypersonic vehicles. Limitations and potential improvements of the present technique are also discussed.
Does third-party trade reduce conflict? Credible signaling versus opportunity costs
Authors: Kinne Brandon J
Published: September 2013

The study of trade and conflict has largely focused on dyadic interdependence, or trade within discrete pairs of states. Yet, states may also be indirectly interdependent, by way of trade to third parties. This paper examines the influence of third-party trade on dyadic conflict initiation. I argue that certain structures of trade provide economically invested third parties with (1) an incentive to discourage dyadic conflict between a potential initiator and a potential target, and (2) the means to show disapproval of conflict by sending trade-based signals of resolve. The argument thus emphasizes the ability of third parties to introduce novel ex post information into bargaining dynamics, causing potential aggressors to reconsider their conflict strategies. Empirical analysis shows that, in fact, when a given dyad shares the sort of trade structures that enable costly signaling by third parties, the probability of conflict initiation declines substantially. In contrast, when third-party trade merely increases a potential initiator’s opportunity costs for conflict, conflict behavior remains unchanged.
Negotiating Courtship
Authors: Lamont Ellen
Published: September 2013

Traditional courtship norms delineate distinct gendered behaviors for men and women based on the model of a dominant, breadwinning male and a passive, dependent female. Previous research shows, however, that as women have increased their access to earned income, there has been a rising ideological and behavioral commitment to egalitarian relationships. Drawing on in-depth interviews with 38 college-educated women, this article explores how women negotiate these seemingly contradictory beliefs in order to understand how and why gendered courtship conventions persist even as heterosexual romantic relationships become more egalitarian. My findings show that while the women reference essentialist beliefs about men’s “nature” to explain their commitment to courtship conventions, they draw on narratives of choice, individualism, and personal autonomy to assert that the symbolic gendering of courtship will not interfere with their desire for an egalitarian marriage. However, women’s behaviors and narratives reinforce notions of gender difference, potentially providing support for other forms of gender inequality.
Gay Bullying and Online Opinion Expression
Authors: Gearhart Sherice , Zhang Weiwu
Published: September 2013

Social network sites (SNSs) such as Facebook, Twitter, YouTube, and LinkedIn have recently attracted the attention of public opinion scholars. However, research testing existing public opinion theories in a social media context is scarce. This study represents arguably the first empirical examination of the spiral of silence theory in the social media environment. Through an experimental manipulation embedded in an Internet survey, respondents ( N = 760) were presented with a hypothetical scenario (i.e., friendly or hostile) concerning gay bullying, an issue suited for investigation due to its moral components. Willingness to self-censor and to some extent, congruency with the national opinion climate were significant predictors of various online opinion response strategies, indicating the presence of the spiral of silence phenomenon in the social media environment. However, individual characteristics such as issue importance were related to willingness to communicate about the issue, suggesting a liberating effect on opinion expression.
Role of Fidaxomicin for the Treatment of Clostridium difficile Infection
Authors: Juang Paul , Hardesty Jennifer S.
Published: September 2013

Clostridium difficile is a gram-negative, anaerobic, spore-forming emerging pathogen within health care systems and community-based populations that has a high associated morbidity and mortality as well as cost for the health care system. Recent studies reported high rates of recurrence thus a need for new pharmacological agents to treat C difficile infections (CDIs). Fidaxomicin is a novel macrocyclic antibiotic, originally isolated from fermentation broth of Dactylosporangium aurantiacum spp Hamdenensis, with selective spectrum, unique pharmacokinetic and pharmacodynamics profile, adverse effect profile, efficacy, and role in the treatment of and time to recurrent CDI. Fidaxomicin data have similar clinical cure, when compared to vancomycin, with lower recurrence rates and higher global cure rates in non-BI/NAP1/027 strains. Fidaxomicin also lacks activity against gram-negative bacteria; hence, its potential effect on resistance development among enteric bacteria appears to be low. It appears to have minimal need for renal or hepatic adjustments and minimal concerns for drug–drug interactions. Overall, fidaxomicin has been generally well tolerated with the most common adverse effects reported as mild gastrointestinal complaints. Fidaxomicin appears to have a role in the treatment of CDI with potential lower rates of recurrence, especially in patients with severe disease or risk factors for recurrent CDI.
Synthesis and characterization of new thermally stable polymers as new high-performance engineering plastics
Authors: Al-Hussaini Ayman S.
Published: September 2013

A series of new poly(imino ether)s (PIEs) have been synthesized via palladium-catalyzed polycondensation of 4,4′-dibromodiphenyl ether with various aromatic diamines. All PIEs were fully characterized by Fourier transform infrared spectroscopy, elemental analyses, differential scanning calorimetry, thermogravimetric analysis, gel permeation chromatography, and x-ray diffraction. These polymers show high thermal stability and high decomposition temperatures. A model compound was synthesized and characterized by standard spectroscopic methods in order to confirm the proposed structure and to assist in the structure proof of the polymer.
Incarceration and unstable housing interact to predict sexual risk behaviours among African American STD clinic patients
Authors: Widman Laura , Noar Seth M , Golin Carol E , Willoughby Jessica F , Crosby Richard
Published: September 2013

Given the dramatic racial disparities in the rates of HIV/sexually transmitted infections (STIs) among African Americans, understanding broader structural factors that increase the risk for HIV/STIs is crucial. This study investigated incarceration history and unstable housing as two structural predictors of HIV risk behaviour among 293 African Americans (159 men/134 women, mean age = 27). Participants were recruited from an urban sexually transmitted disease (STD) clinic in the southeastern U.S. Approximately half the sample had been incarcerated in their lifetime (54%), and 43% had been unstably housed in the past six months. Incarceration was independently associated with the number of sex partners and the frequency of unprotected sex. Unstable housing was independently associated with the frequency of unprotected sex. However, these main effects were qualified by significant interactions: individuals with a history of incarceration and more unstable housing had more sex partners and more unprotected sex in the past three months than individuals without these structural barriers. Implications for structural-level interventions are discussed.
Design and optimization of a cascade thermoacoustic Stirling engine
Authors: Karimi M , Ghorbanian K
Published: September 2013

This article deals with the design and optimization of a cascade thermoacoustic Stirling engine. Different configurations for cascade thermoacoustic Stirling heat engine are investigated. A simplified model is proposed to enable initial design guidelines. The most important characteristics of the cascade system are examined. The results indicate that the thermoacoustic engines in cascade configuration may achieve very low onset temperatures. A suitable configuration is selected and the locations and dimensions of different thermoacoustic units are optimized to achieve low onset temperatures as well as high values for the acoustic power output and efficiency. The results support the employment of cascade engine systems.
Numerical investigation on effect of inlet nozzle size on efficiency and flow pattern in squirrel cage fans
Authors: Gholamian Mojtaba , Rao Gurram K Mohan , Bhramara Panitapu
Published: September 2013

Squirrel cage fan is a special type of turbo machines commonly used in industries and buildings (as a part of heating, ventilation and air conditioning (HVAC) systems). There are lots of important parameters that can affect the performance and efficiency (energy consuming). Experiments have shown that there are some turbulent areas in volute and impeller, and also in few cases, the relationships between the fan parameters, geometry and nondimensional parameters, and turbulent areas or performances were defined.

In this paper, the effect of inlet-nozzle diameter on performance and flow pattern is considered. Three inlet nozzle sizes with respect to impeller size were chosen (smaller, nearly same, and bigger than inner impeller diameter), and numerical simulations with different turbulence models were performed to find the effect of inlet size on flow pattern, performance, and efficiency. For the validation of numerical results, some experiments were done, and all the performance parameters were compared to that of numerical results. These results showed good matching between experimental and numerical results. From each case study, flow pattern and its mechanism and the reasons of low efficiency are studied and presented.
The reaction of rural families in Kenya to technology changes
Authors: Okello Vincent , Owala Hellen , Sanchez Teodoro
Published: September 2013

Energy as a service is central to livelihoods. Services such as lighting, cooking and heating of water, space heating, cooling, information, communication, and earning a living are not always accessible without grid electricity and are critical to sustainable development. The acceptability of any new energy technology is very important if it has to be usable by the target group it is designed for. This paper documents a case study undertaken in rural areas of Kisumu, Kenya, to understand the behaviour of communities to technology changes, particularly solar photovoltaic for lighting and a high-efficiency wood stove. It shows the research methods used and the findings. The participating households were selected from a peri-urban community near Kisumu town, the third largest city in Kenya. The selected households were using kerosene tin lamps and open three-stone fire for lighting and cooking, respectively. This study shows that new technologies have a better chance of sustained adoption if they comply with some attributes that match with broad needs – a cleaner kitchen, reduced firewood costs, better quality air in the kitchen, durability of the product and others. The installers need to communicate to the users that their broader needs are being met, and that their main interest is not just to sell the stoves. At the time the study was initiated, there were relatively few clean burning stoves available on the local markets. The relative success enjoyed by the project activities indicated a high user acceptance, and by the retention experienced beyond the study period, by both the lighting systems and the highly efficient stoves.
Theoretical and experimental studies of a switched inertance hydraulic system
Authors: Pan Min , Johnston Nigel , Plummer Andrew , Kudzma Sylwester , Hillis Andrew
Published: September 2013

A switched inertance hydraulic system uses a fast switching valve to control flow or pressure and is potentially very efficient as it does not rely on dissipation of power by throttling. This article studies its performance using an analytical method which efficiently describes the system in the time domain and frequency domain. A lumped parameter model and a distributed parameter model have been used for investigation using different parameters and conditions. The analytical models have been validated in experiments and the results on a prototype device show a very promising performance. The proposed analytical models are effective for understanding, analysing and optimizing the characteristics and performance of a switched inertance hydraulic system.
The Effect of a Cultural Competence Educational Intervention for First-Year Nursing Students in Israel
Authors: Noble Anita , Nuszen Evelyn , Rom Miriam , Noble Lawrence M.
Published: September 2013

Purpose: To evaluate the effectiveness of an educational intervention to increase general cultural competence of first-year nursing students. Design: This was a quasi-experimental study that used a convenience sample with an experimental group and a control group and pre- and posttesting. The sample comprised 146 first-year nursing students enrolled in the Introduction to Nursing course divided into an intervention group ( n = 58) of students from one school and a control group ( n = 88) including students from two schools. The intervention group received a 2-hour faculty lecture on cultural competence, and students prepared and delivered a student group presentation about a cultural group in Israel, basing the presentation on Campinha-Bacote’s five constructs. A demographic data instrument and Campinha-Bacote’s Inventory for Assessing the Process of Cultural Competence Among Healthcare Professional–Revised© were used for pre- and posttesting. Findings: Students who received the educational intervention increased scores significantly (68 ± 6 to 73 ± 6, p = .000), students who did not receive the educational intervention had no significant increase (67 ± 6 to 66 ± 6). Discussion/Conclusions: Introducing the topic of cultural competence for nursing students in the first-year Introduction to Nursing course as an integrative learning strategy revealed significant increases in cultural competence scores. Implications for Practice: Recommendations are to include evidence-based cultural competence teaching strategies into the nursing curriculum.
Promoting an Equal and Healthy Environment
Authors: Warne Maria , Snyder Kristen , Gillander Gådin Katja
Published: September 2013

Education is an important factor in health equity, but many students still do not complete high school. A focus on the school context rather than on individual problems might help to create a supportive environment for health and learning. In this study we explored factors that promote health and learning from the perspective of vocational and low-achieving high school students in Sweden. We used grounded theory with a constructivist orientation, informed and sensitized by the concept of salutogenesis. Students from a school in a mid-sized municipality in Sweden participated, and we collected data using the photovoice method and interviews. Students identified general factors as significant to their well-being and success in school. The main theme, “promoting driving forces for health and learning,” emerged from the categories “longing to be seen by teachers,” “longing for support,” and “longing for recuperation.”
Parental Advocacy Styles for Special Education Students During the Transition to Adulthood
Authors: Rehm Roberta S. , Fisher Lucille T. , Fuentes-Afflick Elena , Chesla Catherine A.
Published: September 2013

In an ethnographic study of planning for the transition to adulthood, we explored parental advocacy styles in special education settings for youth and young adults with chronic health conditions and developmental disabilities. Of 61 parents, 43 were satisfied with outcomes in negotiations for school services for their children. We identified three parental advocacy styles for these parents: (a) high-profile parents, who insisted on specific, wide-ranging services for their children that often resulted in conflict with educators; (b) strategic parents, who negotiated for selected goals and were willing to compromise, and (c) grateful-gratifier parents, who formed close relationships with educators and trusted them to make appropriate decisions. Eighteen parents were overwhelmed, burned out, or unfocused, and generally dissatisfied with outcomes of educational planning meetings. Professional efforts to enhance parental advocacy can target development of skills and strategies that have worked for successful negotiators.
Recognizing and Overcoming Challenges of Couple Interview Research
Authors: Mellor Ruth M. , Slaymaker Emma , Cleland John
Published: September 2013

In this article we discuss some methodological and ethical challenges we faced when conducting a couple-based study on men’s role in contraceptive switching, and how we overcame them. The challenges we discuss include recruiting couples with a range of experiences, ensuring informed consent of participants, maintaining confidentiality within interviews, and participants discussing interview content between interviews. As appropriate, we have drawn on study participants’ views of these challenges. We conclude that although couple research poses challenges, they can be overcome or minimized, and that for certain research questions this methodology is well worth using.
Working in Partnership With Interpreters
Authors: Maradik Harris Lesley , Boggiano Victoria , Nguyen Duy Thang , Pham Le Hoang Linh
Published: September 2013

This article brings together two American qualitative researchers and two Vietnamese interpreters who investigated the social impacts of HIV/AIDS in Vietnam from the standpoint of the local community. As cultural outsiders with limited Vietnamese language skills, the researchers relied on the insights and expertise of the interpreters to the extent that interpreter roles expanded to become coresearchers. We explain the guidelines we used to work in partnership in the field. We then describe how the relationship between researcher and interpreter developed into coresearching, and how we utilized this relationship to respond to challenges in the work. Despite an increasing number of international qualitative studies, little research has focused on the nuances of a working partnership between researcher and interpreter, and few studies include interpreters as coresearchers. This article contributes to an understanding of how the researcher–interpreter relationship impacts the voice of the participant and, ultimately, the final outcomes of the project.
Recognition and Treatment of Anaphylaxis in the School Setting
Authors: Schoessler Sally , White Martha V.
Published: September 2013

Since anaphylaxis is unpredictable, rapid in onset, and potentially life threatening, it is critical for school staff to recognize and respond to its symptoms quickly. The symptoms of anaphylaxis can be challenging to differentiate, particularly in school-age children who may have trouble explaining what they are experiencing. School staff must understand the distinctive ways in which children describe and manifest anaphylactic symptoms, and the school nurse has a key leadership role in providing this training. The school nurse should create and coordinate individualized emergency care/action plans for students with known allergies, as well as a comprehensive care plan for all students, to ensure a safe environment and a rapid response to any life-threatening allergic reaction. This should include having epinephrine stocked and readily accessible so that it can be given promptly in the case of an anaphylactic emergency.
On the elasticities of quartz across the α–β phase transformation
Authors: Pitteri Mario
Published: September 2013

The purpose of this paper is to describe the behavior of the elasticities of quartz across the α– β phase transformation at room pressure. In spite of the known dynamic behavior of quartz, we adhere to the prejudice that an equilibrium theory is sufficient for this task, and propose a Landau model based on a three-phase, two-order-parameter polynomial free energy. One of the order parameters, describing a suitable displacement of the oxygen atoms, produces an isostructural transition just above the temperature of the α– β phase transformation. Subsequently, the latter takes place with the joint contribution of the second structural order parameter, associated with another displacement of the oxygens. The free energy consists of the minimal number of monomials necessary to produce the two mentioned transitions and only those; in spite of this minimality, the results from theory appear to reasonably agree with the experimental data. A posteriori, we reconstruct the phase diagram in the plane of the coefficients of the quadratic monomials.
A Review of Peer Relationships and Friendships in Youth With ADHD
Authors: Gardner Denise M. , Gerdes Alyson C.
Published: September 2013

Objective: The purpose of this essay is to examine peer relationships in youth with ADHD and to review current peer functioning interventions. Method: The studies included in this review were identified using the following search terms: “attention-deficit/hyperactivity disorder,” “ADHD,” “peer relationships,” “friendships,” “social skills,” “intervention,” and “treatment.” Other than a few seminal studies published prior to 2000, studies included were published between 2000 and 2012. Results/Discussion: Background information regarding peer relationship difficulties and specific social skills deficits of youth with ADHD is reviewed and current social skills and friendship intervention programs are examined. Future directions also are provided.
Subjective well-being, social work, and the environment: The impact of the socio-political context of practice on social worker happiness
Authors: Shier Micheal L , Graham John R
Published: September 2013

The environmental context of direct social work practice has been found to impact social worker subjective well-being. Most research focus on the geographic and cultural characteristics of that practice environment. To expand this knowledge domain a qualitative inquiry has been undertaken to understand what aspects of the socio-political environment impacted social worker well-being.

Findings

This qualitative study, with a sample of social workers ( n = 19), found three themes related to the socio-political environment that can contribute to practitioner well-being. Respondents identified that their subjective well-being is impacted by: (1) perceptions of practitioners by community members, (2) conflict with social work program mandates, and (3) changes with the social welfare system.

Applications

Possible methods of addressing these issues to improve workplace functioning for social workers are discussed along with areas of future research.
Contrasting alternative explanations for the consequences of category spanning: A study of restaurant reviews and menus in San Francisco
Authors: Kovács Balázs , Johnson Rebeka
Published: September 2013

Recent literature on organizational category spanning demonstrates that organizations that span multiple categories on average suffer social and economic disadvantages in markets. While multiple mechanisms have been proposed to explain this finding, most studies do not test directly nor contrast these mechanisms. In this article, we contrast two of the main mechanisms proposed in the literature: the audience-side typicality-based explanation (category spanners are atypical of each categories spanned) and the producer-side quality-based explanation (category spanners produce lower quality output because they cannot develop expertise in any of the categories spanned). We find evidence for both mechanisms. Furthermore, we argue that quality and typicality interact such that high-quality organizations can benefit from being atypical. Finally, we contrast two kinds of spanning, “fusion” and “food court,” and argue that their effects are different depending on the overall quality of the organization. Our empirical setting is the restaurant domain, and we analyze menus and reviews of 474 restaurants located in San Francisco.
Cochrane corner: local corticosteroid injection for carpal tunnel syndrome
Authors: Stark H. , Amirfeyz R.
Published: September 2013

Background:

Carpal tunnel syndrome is a clinical syndrome manifested by signs and symptoms of irritation of the median nerve at the carpal tunnel in the wrist. Local corticosteroid injection for carpal tunnel syndrome has been studied but its effectiveness is unknown.

Objectives:

To evaluate the effectiveness of local corticosteroid injection for carpal tunnel syndrome versus placebo injection or other non-surgical interventions.

Search methods:

We searched the Cochrane Neuromuscular Disease Group Trials register (searched May 2006), MEDLINE (searched January 1966 to May 2006), EMBASE (searched January 1980 to May 2006) and CINAHL (searched January 1982 to May 2006).

Selection criteria:

Randomized or quasi-randomized studies.

Data collection and analysis:

Three authors independently selected the trials and rated their overall quality. Relative risks and 95% confidence intervals were calculated for each trial and summary relative risks and 95% confidence intervals were also calculated.
MicroRNAs responsive to Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis LPS modulate expression of genes regulating innate immunity in human macrophages
Authors: Naqvi Afsar R , Fordham Jezrom B , Khan Asma , Nares Salvador
Published: September 2013

MicroRNAs (miRNAs) are a class of small, noncoding RNAs that regulate post-transcriptional expression of their respective target genes and are responsive to various stimuli, including LPS. Here we examined the early (4 h) miRNA responses of THP1-differentiated macrophages challenged with LPS derived from the periodontal pathogens, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis or environmentally-modified LPS obtained from P. gingivalis grown in cigarette smoke extract. Predicted miRNA-gene target interactions for LPS-responsive miR-29b and let-7f were confirmed using dual-luciferase assays and by transfection experiments using miRNA mimics and inhibitors. Convergent and divergent miRNA profiles were observed in treated samples where differences in miRNA levels related to the type, concentration and incubation times of LPS challenge. Dual-luciferase experiments revealed miR-29b targeting of interleukin-6 receptorα (IL-6Rα) and IFN-γ inducible protein 30 and let-7f targeting of suppressor of cytokine signaling 4 and thrombospondin-1. Transfection experiments confirmed miR-29b and let-7f modulation of IL-6Rα and SOCS4 protein expression levels, respectively. Thus, we have demonstrated convergent/divergent miRNA responses to wild type LPS and its environmentally-modified LPS, and demonstrate miRNA targeting of key genes linked to inflammation and immunity. Our data indicate that these LPS-responsive miRNAs may play a key role in fine-tuning the host response to periodontal pathogens.
Modulation of virus-induced innate immunity and type 1 diabetes by IL-1 blockade
Authors: Hara Naoko , Alkanani Aimon K , Dinarello Charles A , Zipris Danny
Published: September 2013

We used the LEW1.WR1 model of Kilham rat virus (KRV)-induced type 1 diabetes (T1D) to test the hypothesis that blocking IL-1 pathways early in the course of the disease can modulate virus-induced innate immunity and prevent disease progression. Administering KRV plus IL-1 receptor antagonist (Anakinra) for 14 d prevented insulitis and T1D. Anakinra reversed the KRV-induced systemic inflammation evidenced by the accumulation of T cells in the spleen and pancreatic lymph nodes on d 5 post-infection. Blocking IL-1 modulated the level of IRF-7 and IL-6 gene expression in the spleen and the p40 subunit of IL-12 and IL-23 in the serum. Anakinra did not interfere with the ability of LEW1.WR1 rats to clear the virus from the spleen, pancreatic lymph nodes or serum. Consistent with these data, normal levels of KRV-specific adaptive immune responses were detected in in the spleen and peripheral blood of the treated animals. Finally, blocking IL-1 pathways reversed the KRV-induced modulation of gut bacterial communities. The data may imply that IL-1 pathways are directly linked with early mechanisms whereby KRV infection leads to islet destruction, raising the hypothesis that blocking IL-1 pathways early in the course of the disease could be a useful therapeutic approach for disease prevention.
Integrating Clinical Services for HIV, Tuberculosis, and Cryptococcal Disease in the Developing World
Authors: Vijayan Tara , Klausner Jeffrey D.
Published: September 2013

The success of antiretroviral therapy (ART) programs in the developing world is limited by the lack of adequate diagnostic tests to screen for life-threatening opportunistic infections such as tuberculosis (TB) and cryptococcal disease. Furthermore, there is an increasing need for implementation research in measuring the effectiveness of currently available rapid diagnostic tests. The recently developed lateral flow assays for both cryptococcal disease and TB have the potential to improve care and greatly reduce the time to initiation of ART among individuals who need it the most. However, we caution that the data on feasibility and effectiveness of these assays are limited and such research agendas must be prioritized.
Integrating in vitro sensitivity and dose-response slope is predictive of clinical response to ABL kinase inhibitors in chronic myeloid leukemia
Authors: Vainstein Vladimir , Eide Christopher A. , O’Hare Thomas , Shukron Ofir , Druker Brian J.
Published: September 2013

Key Points

Decreased in vitro dose-response slope tracks with resistance BCR-ABL mutants to ABL tyrosine kinase inhibitors. Integrating in vitro dose-response slope, the IC50 of various BCR-ABL mutants, and clinical PK data can predict CML patients’ response to TKIs.
Riemann-Liouville fractional Hermite-Hadamard inequalities. Part I: for once differentiable geometric-arithmetically s-convex functions
Authors: Liao YuMei , Deng JianHua , Wang JinRong
Published: September 2013

By using the definition of geometric-arithmetically s-convex functions in (Analysis 33:197-208, 2013) and first-order fractional integral identities in (Math. Comput. Model. 57:2403-2407, 2013; J. Appl. Math. Stat. Inform. 8:21-28, 2012; Comput. Math. Appl. 63:1147-1154, 2012), we present some interesting Riemann-Liouville fractional Hermite-Hadamard inequalities for differentiable geometric-arithmetically s-convex functions. Both beta function and incomplete beta function are used in the desired estimations.

MSC:26A33, 26A51, 26D15.
Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data
Authors: Kruczyk Marcin , Umer Husen M , Enroth Stefan , Komorowski Jan
Published: September 2013

Background

Finding peaks in ChIP-seq is an important process in biological inference. In some cases, such as positioning nucleosomes with specific histone modifications or finding transcription factor binding specificities, the precision of the detected peak plays a significant role. There are several applications for finding peaks (called peak finders) based on different algorithms (e.g. MACS, Erange and HPeak). Benchmark studies have shown that the existing peak finders identify different peaks for the same dataset and it is not known which one is the most accurate. We present the first meta-server called Peak Finder MetaServer (PFMS) that collects results from several peak finders and produces consensus peaks. Our application accepts three standard ChIP-seq data formats: BED, BAM, and SAM.

Results

Sensitivity and specificity of seven widely used peak finders were examined. For the experiments we used three previously studied Transcription Factors (TF) ChIP-seq datasets and identified three of the selected peak finders that returned results with high specificity and very good sensitivity compared to the remaining four. We also ran PFMS using the three selected peak finders on the same TF datasets and achieved higher specificity and sensitivity than the peak finders individually.

Conclusions

We show that combining outputs from up to seven peak finders yields better results than individual peak finders. In addition, three of the seven peak finders outperform the remaining four, and running PFMS with these three returns even more accurate results. Another added value of PFMS is a separate report of the peaks returned by each of the included peak finders.
Australian and Pacific contributions to the genetic diversity of Norfolk Island feral chickens
Authors: Langford S Shannan M , Kraitsek Spiridoula , Baskerville Bruce , Ho Simon YW , Gongora Jaime
Published: September 2013

Background

Norfolk Island has a population of feral chickens which could be the result of domestic stock introduced onto the island by British settlers in 1788. However, there is ongoing debate about their origins because multiple human arrivals to the island may have brought chickens with them. Here we investigate the genetic origins of these feral chickens by sequencing their mitochondrial control region. We infer their phylogenetic relationships using a large dataset of novel sequences from Australian mainland domestic chickens and published sequences from around the world.

Results

Eleven control region haplotypes were found among the Norfolk Island feral and Australian mainland domestic chickens. Six of the Norfolk Island haplotypes fall within haplogroup E, but given the worldwide distribution of this haplogroup, the putative European origin of these chickens requires further investigation. One haplotype common among Norfolk Island and Australian samples belonged to a subgroup of haplogroup D, which appears to be restricted to chickens from Indonesia, Vanuatu and Guam.

Conclusions

Our data show that at least two mitochondrial DNA haplogroups (D and E) have contributed to the genetic make-up of Norfolk Island feral chickens. In addition, we have provided insights into the discrete geographical distribution and diversity of the chicken haplogroup D. In view of the worldwide interest in the characterisation of poultry resources, further assessment of chicken populations of Island Southeast Asia and the Pacific region is warranted.
Comparative methylomics between domesticated and wild silkworms implies possible epigenetic influences on silkworm domestication
Authors: Xiang Hui , Li Xin , Dai Fangyin , Xu Xun , Tan Anjiang , Chen Lei , Zhang Guojie , Ding Yun , Li Qiye , Lian Jinmin , Willden Andrew , Guo Qiuhong , Xia Qingyou , Wang Jun , Wang Wen
Published: September 2013

Background

In contrast to wild species, which have typically evolved phenotypes over long periods of natural selection, domesticates rapidly gained human-preferred agronomic traits in a relatively short-time frame via artificial selection. Under domesticated conditions, many traits can be observed that cannot only be due to environmental alteration. In the case of silkworms, aside from genetic divergence, whether epigenetic divergence played a role in domestication is an unanswered question. The silkworm is still an enigma in that it has two DNA methyltransferases (DNMT1 and DNMT2) but their functionality is unknown. Even in particular the functionality of the widely distributed DNMT1 remains unknown in insects in general.

Results

By embryonic RNA interference, we reveal that knockdown of silkworm Dnmt1 caused decreased hatchability, providing the first direct experimental evidence of functional significance of insect Dnmt1. In the light of this fact and those that DNA methylation is correlated with gene expression in silkworms and some agronomic traits in domesticated organisms are not stable, we comprehensively compare silk gland methylomes of 3 domesticated (Bombyx mori) and 4 wild (Bombyx mandarina) silkworms to identify differentially methylated genes between the two. We observed 2-fold more differentiated methylated cytosinces (mCs) in domesticated silkworms as compared to their wild counterparts, suggesting a trend of increasing DNA methylation during domestication. Further study of more domesticated and wild silkworms narrowed down the domesticates’ epimutations, and we were able to identify a number of differential genes. One such gene showing demethyaltion in domesticates correspondently displays lower gene expression, and more interestingly, has experienced selective sweep. A methylation-increased gene seems to result in higher expression in domesticates and the function of its Drosophila homolog was previously found to be essential for cell volume regulation, indicating a possible correlation with the enlargement of silk glands in domesticated silkworms.

Conclusions

Our results imply epigenetic influences at work during domestication, which gives insight into long time historical controversies regarding acquired inheritance.
Comprehensive transcriptomic study on horse gram (Macrotyloma uniflorum): De novo assembly, functional characterization and comparative analysis in relation to drought stress
Authors: Bhardwaj Jyoti , Chauhan Rohit , Swarnkar Mohit Kumar , Chahota Rakesh Kumar , Singh Anil Kumar , Shankar Ravi , Yadav Sudesh Kumar
Published: September 2013

Background

Drought tolerance is an attribute maintained in plants by cross-talk between multiple and cascading metabolic pathways. Without a sequenced genome available for horse gram, it is difficult to comprehend such complex networks and intercalated genes associated with drought tolerance of horse gram (Macrotyloma uniflorum). Therefore, de novo transcriptome discovery and associated analyses was done for this highly drought tolerant yet under exploited legume to decipher its genetic makeup.

Results

Eight samples comprising of shoot and root tissues of two horse gram genotypes (drought-sensitive; M-191 and drought-tolerant; M-249) were used for comparison under control and polyethylene glycol-induced drought stress conditions. Using Illumina sequencing technology, a total of 229,297,896 paired end read pairs were generated and utilized for de novo assembly of horse gram. Significant BLAST hits were obtained for 26,045 transcripts while, 3,558 transcripts had no hits but contained important conserved domains. A total of 21,887 unigenes were identified. SSRs containing sequences covered 16.25% of the transcriptome with predominant tri- and mono-nucleotides (43%). The total GC content of the transcriptome was found to be 43.44%. Under Gene Ontology response to stimulus, DNA binding and catalytic activity was highly expressed during drought stress conditions. Serine/threonine protein kinase was found to dominate in Enzyme Classification while pathways belonging to ribosome metabolism followed by plant pathogen interaction and plant hormone signal transduction were predominant in Kyoto Encyclopedia of Genes and Genomes analysis. Independent search on plant metabolic network pathways suggested valine degradation, gluconeogenesis and purine nucleotide degradation to be highly influenced under drought stress in horse gram. Transcription factors belonging to NAC, MYB-related, and WRKY families were found highly represented under drought stress. qRT-PCR validated the expression profile for 9 out of 10 genes analyzed in response to drought stress.

Conclusions

De novo transcriptome discovery and analysis has generated enormous information over horse gram genomics. The genes and pathways identified suggest efficient regulation leading to active adaptation as a basal defense response against drought stress by horse gram. The knowledge generated can be further utilized for exploring other underexploited plants for stress responsive genes and improving plant tolerance.
Estradiol prevents olfactory dysfunction induced by A-β 25–35 injection in hippocampus
Authors: Bernal-Mondragón Carlos , Rivas-Arancibia Selva , Kendrick Keith M , Guevara-Guzmán Rosalinda
Published: September 2013

Background

Some neurodegenerative diseases, such as Alzheimer and Parkinson, present an olfactory impairment in early stages, and sometimes even before the clinical symptoms begin. In this study, we assess the role of CA1 hippocampus (structure highly affected in Alzheimer disease) subfield in the rats’ olfactory behavior, and the neuroprotective effect of 17 beta estradiol (E2) against the oxidative stress produced by the injection of amyloid beta 25–35.

Results

162 Wistar rats were ovariectomized and two weeks after injected with 2 μl of amyloid beta 25–35 (A-β25–35) in CA1 subfield. Olfactory behavior was evaluated with a social recognition test, odor discrimination, and search tests. Oxidative stress was evaluated with FOX assay and Western Blot against 4-HNE, Fluoro Jade staining was made to quantify degenerated neurons; all these evaluations were performed 24 h, 8 or 15 days after A-β25–35 injection. Three additional groups treated with 17 beta estradiol (E2) were also evaluated. The injection of A-β25–35 produced an olfactory impairment 24 h and 8 days after, whereas a partial recovery of the olfactory behavior was observed at 15 days. A complete prevention of the olfactory impairment was observed with the administration of E2 two weeks before the amyloid injection (A-β25–35 24 h + E2) and one or two weeks after (groups 8 A-β +E2 and 15 A-β +E2 days, respectively); a decrease of the oxidative stress and neurodegeneration were also observed.

Conclusions

Our finding shows that CA1 hippocampus subfield plays an important role in the olfactory behavior of the rat. The oxidative stress generated by the administration of A-β25–35 is enough to produce an olfactory impairment. This can be prevented with the administration of E2 before and after amyloid injection. This suggests a possible therapeutic use of estradiol in Alzheimer’s disease.
Development-associated microRNAs in grains of wheat (Triticum aestivumL.)
Authors: Meng Fanrong , Liu Hao , Wang Ketao , Liu Lulu , Wang Shaohui , Zhao Yanhong , Yin Jun , Li Yongchun
Published: September 2013

Background

MicroRNAs (miRNAs) are a class of regulatory small RNAs (sRNAs) that down-regulate target genes by mRNA degradation or translational repression. Numerous plant miRNAs have been identified. Evidence is increasing for their crucial roles during plant development. In the globally important crop of wheat (Triticum aestivum L.), the process by which grains are formed determines yield and end-use quality. However, little is known about miRNA-mediated developmental regulation of grain production. Here, we applied high-throughput sRNA sequencing and genome-wide mining to identify miRNAs potentially involved in the developmental regulation of wheat grains.

Results

Four sRNA libraries were generated and sequenced from developing grains sampled at 5, 15, 25, and 30 days after pollination (DAP). Through integrative analysis, we identified 605 miRNAs (representing 540 families) and found that 86 are possibly involved in the control of grain-filling. Additionally, 268 novel miRNAs (182 families) were identified, with 18 of them also potentially related to that maturation process. Our target predictions indicated that the 104 grain filling-associated miRNAs might target a set of wheat genes involved in various biological processes, including the metabolism of carbohydrates and proteins, transcription, cellular transport, cell organization and biogenesis, stress responses, signal transduction, and phytohormone signaling. Together, these results demonstrate that the developmental steps by which wheat grains are filled is correlated with miRNA-mediated gene regulatory networks.

Conclusions

We identified 605 conserved and 268 novel miRNAs from wheat grains. Of these, 104 are potentially involved in the regulation of grain-filling. Our dataset provides a useful resource for investigating miRNA-mediated regulatory mechanisms in cereal grains, and our results suggest that miRNAs contribute to this regulation during a crucial phase in determining grain yield and flour quality.
Cardiac metabolism in a new rat model of type 2 diabetes using high-fat diet with low dose streptozotocin
Authors: Mansor Latt S , Gonzalez Eileen R , Cole Mark A , Tyler Damian J , Beeson Jessica H , Clarke Kieran , Carr Carolyn A , Heather Lisa C
Published: September 2013

Background

To study the pathogenesis of diabetic cardiomyopathy, reliable animal models of type 2 diabetes are required. Physiologically relevant rodent models are needed, which not only replicate the human pathology but also mimic the disease process. Here we characterised cardiac metabolic abnormalities, and investigated the optimal experimental approach for inducing disease, in a new model of type 2 diabetes.

Methods and results

Male Wistar rats were fed a high-fat diet for three weeks, with a single intraperitoneal injection of low dose streptozotocin (STZ) after fourteen days at 15, 20, 25 or 30 mg/kg body weight. Compared with chow-fed or high-fat diet fed control rats, a high-fat diet in combination with doses of 15–25 mg/kg STZ did not change insulin concentrations and rats maintained body weight. In contrast, 30 mg/kg STZ induced hypoinsulinaemia, hyperketonaemia and weight loss. There was a dose-dependent increase in blood glucose and plasma lipids with increasing concentrations of STZ. Cardiac and hepatic triglycerides were increased by all doses of STZ, in contrast, cardiac glycogen concentrations increased in a dose-dependent manner with increasing STZ concentrations. Cardiac glucose transporter 4 protein levels were decreased, whereas fatty acid metabolism-regulated proteins, including uncoupling protein 3 and pyruvate dehydrogenase (PDH) kinase 4, were increased with increasing doses of STZ. Cardiac PDH activity displayed a dose-dependent relationship between enzyme activity and STZ concentration. Cardiac insulin-stimulated glycolytic rates were decreased by 17% in 15 mg/kg STZ high-fat fed diabetic rats compared with control rats, with no effect on cardiac contractile function.

Conclusions

High-fat feeding in combination with a low dose of STZ induced cardiac metabolic changes that mirror the decrease in glucose metabolism and increase in fat metabolism in diabetic patients. While low doses of 15–25 mg/kg STZ induced a type 2 diabetic phenotype, higher doses more closely recapitulated type 1 diabetes, demonstrating that the severity of diabetes can be modified according to the requirements of the study.