bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep machine learning for detection of acoustic wave reflections
Authors: Haile Mulugeta A , Zhu Edward , Hsu Christopher , Bradley Natasha
Published: October 2019

Acoustic emission signals are information rich and can be used to estimate the size and location of damage in structures. However, many existing algorithms may be deceived by indirectly propagated acoustic emission waves which are modulated by reflection boundaries within the structures. We propose two deep learning models to identify such waves such that existing algorithms for damage detection and localization may be used. The first approach uses long short-term memory recurrent neural networks to learn distinct patterns directly from the time-series data. In the second approach, we transform the time-series data into spectrograms and utilize convolutional neural networks to perform binary classification by leveraging spectro-temporal features. We achieved 80% classification accuracy using long short-term memory and near-perfect accuracy using convolutional neural networks on a dataset of acoustic emission signals generated by the Hsu-Nielsen sources. Both long short-term memory and convolutional neural network models were able to learn general and context-specific features of the direct and reflected acoustic emission waves. Once accurately identified, the indirectly propagating waves are filtered out while the directly propagating waves are used for source location using existing methods.
Crack growth monitoring using fundamental shear horizontal guided waves
Authors: Chua Chien An , Cawley Peter
Published: October 2019

Monitoring cracks in critical sections of steel structures is a topic of growing interest. Existing high-frequency ultrasonic techniques have good detection sensitivities but poor inspection coverage, requiring an impractical number of transducers to monitor large areas. Low-frequency guided waves are used for corrosion detection in pipelines but are insufficiently sensitive for many crack detection applications. The sensitivity can be improved using higher frequencies and by placing the receiving transducers closer to the defect. This study evaluates the monitoring performance of an SH0 mode system at frequencies just below the high-order mode cut-off. Baseline subtraction with temperature compensation was applied to experimental data generated by a ring of transducers on a 6-in diameter pipe. It was found that the residual signals after baseline subtraction were normally distributed so the random fluctuations could be reduced by coherent averaging; it was thereby possible to reliably detect a 2 mm × 1 mm notch simulating a crack located one pipe diameter along the pipe from the transducer ring. The damage detection performance at different locations along the pipe was assessed by analysing receiver operating characteristic curves generated by adding simulated defects to multiple experimental measurements without damage. At a fixed standoff distance, the damage detection performance increases with the square root of the number of averaged signals and is also improved by averaging the signals received by transducers covering the main lobe of the reflection from the defect. When the defect is located more than about one pipe circumference from the transducer ring, the optimal performance is obtained by averaging across all the transducers in the ring, corresponding to monitoring the T(0,1) pipe mode. Therefore, an SH0 mode monitoring system has great potential for crack monitoring applications, particularly for welds in pipes.
Psychological Interventions for Individuals Bereaved by Homicide: A Systematic Review
Authors: Alves-Costa Filipa , Hamilton-Giachritsis Catherine , Christie Hope , van Denderen Mariëtte , Halligan Sarah
Published: October 2019

Research has demonstrated that approximately 45–50% of individuals show healthy levels of psychological and physical functioning in the first 12 months post-loss. Homicidal bereavement (loss due to murder or manslaughter) does not appear to follow this pattern. Homicide-related mental health difficulties are a serious problem worldwide, displaying high rates of lifetime incidence, high chronicity, and role impairment. Individuals are at increased risk to develop symptoms of post-traumatic stress disorder (PTSD), complicated grief (CG), and depression. Nevertheless, a systematic review specifically on the efficacy of psychological interventions following homicidal loss has not yet been conducted. The current systematic review (registered via PROSPERO) aimed to review the psychological interventions available and report their effectiveness. Of 77 records, 7 met predefined inclusion criteria. Studies presented different methodologies, tested different clinical models, and treatment conditions. Thus, a narrative systematic review was conducted. Studies included manualized interventions to deliver 1:1 and group sessions. Cognitive behavioral therapy, restorative retelling, and eye movement desensitization and reprocessing were the main models used together with psychoeducational elements about trauma and grief responses. Overall, symptoms of PTSD, CG, and depression decreased significantly postintervention. Sustained improvements were reported for PTSD and depressive symptoms at the follow-up measurements. Mixed results were found regarding how individual (age, gender) and external factors (time since loss, relationship with the deceased) impact on symptom progression. As a result of differences in methodologies, categorization of therapies, methodological differences, and small sample sizes, important questions remain unanswered. Further randomized controlled trials and expert consensus could be considered.
Commentary on Potential Crisis in Nurse Practitioner Preparation in the United States
Authors: Bellflower Bobby , Likes Wendy
Published: October 2019

Nurse practitioner preparation and education, while evolving, still remains at a crossroads. In a recent article by Mundinger and Carter, a timeline and analysis of the number of Doctor of Nursing Practice (DNP) programs in the United States clearly demonstrated that since inception of the DNP degree, 85% of DNP programs are nonclinical. Many of the nonclinical programs in leadership and administration do not require additional clinical preparation beyond the bachelor’s or master’s degree in nursing. Thus, registered nurses and advanced practice registered nurses (APRNs) may obtain a DNP degree without additional clinical skill preparation beyond a baccalaureate or master’s degree, respectively. Several aspects of the nonclinical DNP are concerning. Among the most challenging issues that nonclinical DNPs present is confusion on the part of other health care providers and the public. The relatively low number of clinically focused DNP programs is also problematic. If we do not prepare APRNs at the clinical doctoral level, then other providers such as physician assistants will meet the health care needs of the community. The future of APRNs could be threatened, especially in primary care.
Hispanic-Serving Institutions and Web Accessibility: Digital Equity for Hispanic Students With Disabilities in the 21st Century
Authors: Taylor Z. W. , Burnett Christopher A.
Published: October 2019

The Americans with Disabilities Act (ADA) mandates that all Title IV-participating institutions of higher education publish web accessible websites for students with disabilities. This study sought to evaluate the web accessibility of Hispanic-Serving Institutional (HSI) websites ( n = 217). Results suggest that the average HSI website landing page included 447 errors, violating ADA. Most errors were related to font size, color contrast, and hyperlinks and pictures. Implications for research, practice, and support for Hispanic students with disabilities are addressed.
Intervention to Modify Habits: A Scoping Review
Authors: Fritz Heather , Hu Yi-Ling , Gahman Kevin , Almacen Chen , Ottolini Jon
Published: October 2019

Intervening to change clients’ habits in the course of their everyday occupations could improve health. Habit formation interventions are an emerging area of science, however, and there is a need to better understand the current state of habit intervention research. The objective of this study is to examine the evidence related to habit formation interventions to modify health habits among adults. We performed a scoping review of peer-review articles published since January 1, 2008. The majority of the 18 studies included in the review were randomized control trials using one of two measures to assess habit change. Studies targeted a range of habits. Trial results were mixed but supportive of habit formation approaches. Through habit formation interventions, a range of everyday behaviors can become a habit. Occupational therapy professionals can use data and results generated from this review to inform the development of occupation-based habit formation treatments.
Non-surgical management of isolated proximal phalangeal fractures with immediate mobilization
Authors: Byrne Brent , Jacques Angela , Gurfinkel Reuven
Published: October 2019

We performed a prospective, observational study using a non-surgical, conservative protocol with immediate mobilization for the treatment of 101 isolated stable or initially unstable proximal phalangeal fractures. The patients were evaluated at the time of discharge from therapy treatment, mean 7 weeks (range 3–15) after conservative treatment. These patients achieved a median proximal interphalangeal joint extension of −4° (IQR 0, −8), a mean total active motion of 253° (SD 20) and minimal pain. We conclude that a non-surgical, conservative protocol can be used for patients with isolated proximal phalangeal fractures without uncorrectable finger rotation or fracture angulation exceeding 25° in the sagittal plane or 10° in the coronal plane following closed reduction. Our data supports that a conservative protocol can be the good option for isolated stable or initially unstable proximal phalangeal fractures.

Level of evidence: IV
Micro air vehicles energy transportation for a wireless power transfer system
Authors: Polo Jose , Hontecillas Lluís , Izquierdo Ignacio , Casas Oscar
Published: October 2019

The aim of this work is to demonstrate the feasibility use of an Micro air vehicles (MAV) in order to power wirelessly an electric system, for example, a sensor network, using low-cost and open-source elements. To achieve this objective, an inductive system has been modelled and validated to power wirelessly a sensor node using a Crazyflie 2.0 as MAV. The design of the inductive system must be small and light enough to fulfil the requirements of the Crazyflie. An inductive model based on two resonant coils is presented. Several coils are defined to be tested using the most suitable resonant configuration. Measurements are performed to validate the model and to select the most suitable coil. While attempting to minimize the weight at transmitter’s side, on the receiver side it is intended to efficiently acquire and manage the power obtained from the transmitter. In order to prove its feasibility, a temperature sensor node is used as demonstrator. The experiment results show successfully energy transportation by MAV, and wireless power transfer for the resonant configuration, being able to completely charge the node battery and to power the temperature sensor.
Assessment of Regular and NPH Insulin Concentration via Two Methods of Quantification: The Washington State Insulin Concentration Study (WICS)
Authors: Neumiller Joshua J. , Chen Gang , Newsome Cheyenne , Hughes Sally , Lazarus Philip , White John R.
Published: October 2019

Background:

Recent reports have suggested that insulin vials purchased in community pharmacies do not meet the minimum required intact insulin concentration (≥95 U/mL) as defined by the United States Pharmacopeia. We sought to independently obtain multidose human insulin vials from a variety of community pharmacies across the state of Washington and quantitatively measure intact insulin.

Methods:

Sixty 10-mL vials of insulin ( n = 30 regular human insulin and n = 30 neutral protamine Hagedorn insulin) were purchased and assayed. To ensure random selection of lots and supply chain sources, insulin samples were purchased on a variety of calendar dates from various pharmacy locations across Washington State, inclusive of both chain and independent pharmacies. All samples were assessed for intact insulin concentration via both Ultra Performance Liquid Chromatography coupled with UV detection (UPLC-UV) and Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS).

Results:

When considering all samples ( N = 60), the mean concentration was 101.8 ± 4.4and 91.5 ± 1.9 U/mL as determined by UPLC-UV and UPLC-MS, respectively. Measured concentrations ranged from 90.0 to 108.4 U/mL when assayed by UV UPLC and 86.1 to 95.4 U/mL for UPLC-MS.

Conclusion:

To our knowledge, this is the first study following the report by Carter et al that assessed human insulin concentrations by both UPLC-UV and UPLC-MS. These findings are important because they demonstrate that the results obtained from these two methods differ and that the method used must be considered when interpreting findings.
Tibiotalocalcaneal Arthrodesis Using a Novel Retrograde Intramedullary Nail
Authors: Steele John R. , Lazarides Alexander L. , DeOrio James K.
Published: October 2019

Background. Tibiotalocalcaneal (TTC) arthrodesis is a common treatment option for complex hindfoot pathology. Overall union rates range from 50% to 86% but can be even lower in certain populations. A novel retrograde intramedullary nail has recently been developed. The purpose of this study was to report fusion rates, time to weight-bearing, and complications with the use of the A3 Fusion Nail. Methods. All patients 18 years or older who underwent TTC arthrodesis with an A3 Fusion Nail at a single institution from 2010 to 2015 with a minimum 3-month follow-up were included in this study. Rates of successful fusion, time to union, time to weight-bearing, and complications were evaluated. A total of 20 patients with an average age of 58.1 years and an average follow-up of 12.5 months met inclusion criteria. Results. Successful TTC arthrodesis was achieved in 14 of 20 patients (70%) overall. Average time to union was 8.1 months, and average time to weight-bearing was 6.8 weeks. Of 20 patients, 17 (85%) required femoral head allograft for bulk bone defects, and the union rate in this subset of patients was 76.5%. The rates of revision surgery (10%) and complications were low. Conclusion. The A3 Fusion Nail demonstrated a favorable safety profile and achieved TTC arthrodesis at a rate consistent with historical data despite being used in a patient population at high risk for nonunion. In patients with bulk bone defects at high risk for nonunion, the A3 Fusion Nail demonstrated superior rates of fusion (76.5%) to those reported in the literature (50%).

Level of Evidence: Level III: Retrospective cohort study
Allergic Comorbidity of Asthma or Wheezing, Allergic Rhinitis, and Eczema: Result From 333 029 Allergic Children in Shanghai, China
Authors: Ji Heyu , Hu Yi , Zhang Ting , Wang Yizhong , Shen Li , Wang Shu , Chen Min , Wei Mingyue , Yu Guangjun
Published: October 2019

Background

Allergic diseases have become a worldwide public health concern. A defining feature of allergic diseases is they often coexist in children from birth to adolescence.

Objective

To investigate the prevalence of comorbid allergic diseases in allergic children in Shanghai, China.

Methods

A retrospective study of 333 029 children diagnosed with allergic diseases aged 0 to 12 years (mean age: 3.04 years, 59.3% boys) was conducted using the electronic medical records of Shanghai Children’s Hospital from January 2013 to July 2018. Comorbidity of allergic diseases is defined as the coexistence of 2 or 3 following diseases in the same child such as asthma (AS)/wheezing, allergic rhinitis (AR), or eczema (EC).

Results

The proportion of children with comorbid allergic diseases was 6.7% (22 351/333 029). Among them, EC + AS/wheezing was the most common (61.3%, 13 711/22 351). Children with a comorbidity had significantly earlier disease onset age than subjects with only 1 disease (2.72 vs 3.06, P < .05). The serum total immunoglobulin E (tIgE) levels of children with comorbid allergic diseases were higher than those with only 1 disease. In children with a disease onset age of 0 to 9 years, the levels of tIgE for children with AS/wheezing + EC were higher than children with AS/wheezing only or EC only; in children with disease onset age of 2 to 5 and 10 to 12 years, the levels of tIgE for children with AS/wheezing + AR were higher than children with AS/wheezing only or AR only; in children with a disease onset age of 2 to 5 years, the levels of tIgE for children with AR + EC were higher than children with AR only or EC only.

Conclusion

Comorbidity of allergic diseases is common in children in Shanghai, China. The onset age of comorbidity is earlier than that of only 1 disease, and the levels of serum tIgE are higher in patients with an allergic comorbidity.
The Experiences of School Counselors Who Collaborate With Clinical Mental Health Counselors
Authors: Appling Brandee M. , Tuttle Malti , May Viola Simone
Published: October 2019

The current research study explored the experiences of collaboration between K–12 school counselors and clinical mental health counselors (CMHCs). Through transcendental phenomenology, we examined the perspectives of 10 practicing school counselors who have collaborated with CMHCs. We identified seven main themes that highlighted the essence of these experiences: (a) key factors for effective collaboration, (b) “no ego on the table,” (c) benefits of collaboration, (d) roadblocks to collaboration, (e) eliminating roadblocks to collaboration, (f) preservice training, and (g) forging forward in practice. Implications and recommendations from this study inform practicing counselors and counselor education programs about these collaboration experiences and the need for collaboration to support the academic and social/emotional success of K–12 students.
Using Targeted Feedback to Address Common Student Misconceptions in Introductory Programming: A Data-Driven Approach
Authors: Qian Yizhou , Lehman James D.
Published: October 2019

With the expansion of computer science (CS) education, CS teachers in K-12 schools should be cognizant of student misconceptions and be prepared to help students establish accurate understanding of computer science and programming. Digital tools, such as automated assessment systems, can be useful and supportive in teaching CS courses. This two-stage design-based research (DBR) study investigated the effects of targeted feedback in an automated assessment system for addressing common misconceptions of high school students in a Java-based introductory programming course. Based on students’ common errors and underlying misconceptions, targeted feedback messages were designed and provided for students. The quantitative analysis found that with targeted feedback students were more likely to correct the errors in their code. The qualitative analysis of students’ solutions revealed that when improving the code, students receiving feedback made fewer intermediate incorrect solutions. In other words, the targeted feedback messages may help to promote conceptual change and facilitate learning. Although the findings of this exploratory study showed evidence of the power of digital tools, more research is needed to make technology benefit more CS teachers.
Regional Wait Times for Patients With Nonmelanoma Skin Cancer in Southwestern Ontario
Authors: Fan Stacy , Hackett Jesse , Lutz Kristina , Heaton Graham , Symonette Caitlin , Grant Aaron
Published: October 2019

Background:

Nonmelanoma skin cancer (NMSC) affects many Canadians. Although morbidity and mortality are rare, the burden to patients and the health-care system is significant. This study aims to evaluate current plastic surgery wait times and care pathways for patients with NMSC in Southwestern Ontario.

Methods:

A retrospective chart review of 225 patients treated in Ontario from 2015 to 2018 was conducted. Inclusion criteria included patients with an NMSC managed with surgical excision. Referral information was compared. Primary outcomes were wait times: from referral to consultation, referral to excision, and consultation to excision. Data were analyzed using Student t test with equal variance.

Results:

One-hundred forty-three patients were included from the academic cohort and 82 from the community cohort. Referrals to academic and community surgeons included lesion location (90% and 97.6%, respectively), but less frequently included size (18% and 29.2%, respectively). Most referrals to academic surgeons included biopsy results (78.6%), as opposed to community referrals (25.6%). Patients in the academic cohort waited 15.3 ± 12.7 weeks from referral to consultation, and 15.7 ± 13 weeks from referral to excision. Patients from the community cohort waited significantly shorter periods of 4.9 ± 3.1 ( P < .001) and 11.7 ± 9.9 weeks ( P = .016), respectively. However, patients of the academic cohort waited 2.4 ± 7.1 weeks from consultation to excision, while patients in the community cohort waited 6.7 ± 9.6 weeks ( P < .001). Rates of negative peripheral margins on pathology were similar between groups, at 89.5% of the academic cohort and 88.9% of the community cohort. Deep margins were positive 5.7% of the time at the academic sites and 6.2% of the time in the community.

Conclusions:

Patients referred to academic centres waited significantly longer periods of time in several parameters compared to those referred to a community surgeon. However, academic surgeons often had expedited consultation-to-excision time frame. This study provides important data for future quality improvement initiatives in NMSC care.
Corporate Governance and Non-financial Performance of Medium-sized Firms in Nigeria: A CB-SEM Approach
Authors: Adedeji Babatunji Samuel , Uzir Md Uzir Hossain , Rahman Mohammad Mizanur , Jerin Ishraq
Published: October 2019

This study investigates the perceptions of firm executives with respect to the extent of the influence of corporate governance (CG) practices on the non-financial performance (NFP) of medium-sized firms in Nigeria. The theoretical support for the research is from the stakeholder and agency theories. The cross-sectional survey and the cluster and stratified probability proportionate sampling methods are adopted, while the data collection is through a structured questionnaire that covers four CG indicators of board size, director’s qualification, ownership structure and board audit committee. The co-variance-based structural equation modelling (CB-SEM) technique ensures the analysis of the data collected. The result indicates that CG has significant positive effect on firms’ NFP. This outcome supports the urgent need for the development and execution of CG code of ethics for the non-listed firms alongside a regulatory agency for ensuring monitoring and compliance. The drawbacks are inclusive of the measure of variables on linear relationship basis and non-adoption of the longitudinal approach for the study. Future studies need to look at the usage of the intervening variables which, can further aid in evaluating the relationships of the research variables and their indirect and total effects.
Tracking penguins, sensing petroleum: “Data gaps” and the politics of marine ecology in the South Atlantic
Authors: Blair James J. A.
Published: October 2019

Drawing on ethnographic research in the Falkland Islands (Malvinas), this paper analyzes how disputed oil interests become embedded in data infrastructures for environmental governance. Nearly four decades after a war that cemented the South Atlantic archipelago’s British status, offshore oil discoveries have led Argentina's government to renew its sovereignty claim, arguing that the islands are within its waters. Nonetheless, the British Falkland Islands Government (FIG) has licensed unilateral drilling. Centering on a “data gap” project, financed by the FIG and its oil licensees, the article describes how marine ecologists tag penguins with tracking sensors, as part of a new geographic data infrastructure for the South Atlantic. Data representing penguin foraging are supposed to feed into environmental impact assessments for oil exploration. The article demonstrates how these data and confidence ratings in environmental impact statements reinforce access to and control over maritime territory and resources. Extending recent claims that data have become key actors within environmental governance networks, this research finds that particular data practices may actually enhance fossil fuel industry interests through measures of transparency, leaving ambiguous matters related to transboundary impacts and local pollution unresolved.
Alternate Measure of Disability Intensity: Modified Rankin Scale
Authors: Chakrabartty Satyendra Nath
Published: October 2019

Objective: This study was aimed to propose an alternate method of scoring the intensity of disability in a patient, which will facilitate ranking and classifying a group of patients in mutually exclusive classes along with the quantification of progress made by a patient or the effect of interventions and also tracking the path of improvement of a patient and estimating the survival curve for drawing useful conclusions.

Method: A nonparametric measure of disability intensity in terms of Cos θi for the ith patient is proposed to avoid limitations of the usual scoring of modified Rankin scale and satisfies many desired properties. Two measures of interrater agreement in terms of standard error of measurement and coefficient of variation are also proposed and their relationships with Cos θi are detailed. Illustration with hypothetical data involving 30 patients and 10 raters was undertaken.

Results: Distribution of Cos θ was close to normal. Principal component analysis of Cos θ resulted in one factor explaining 64% of variance. Inconsistent raters were identified. Coefficient of variation appears to perform better than the standard error of measurement. Split-half reliability of raters in terms of angular association was higher. Similarly, split-half reliability of disability intensity (Cos θ) was higher. Average disability intensity [Formula: see text] showed similar empirical results with rigorous method of most preferred direction of a finite number of angles.

Conclusions: The proposed simple measures will help the researchers and practitioners to make meaningful analysis and draw meaningful conclusions. Future studies may be undertaken to rescale Likert data to scales having properties of interval-level measurement and study the proposed measures in detail.
Evaluating the Trade, Revenue and Welfare Implication of Plantation Crops under ASEAN–India FTA
Authors: Jagdambe Subhash , Mouzam Shaikh Mohd
Published: October 2019

This article examines the impact of ASEAN–India Free Trade Agreement on India’s special products categories, namely, coffee, tea and pepper based on partial equilibrium model. The Software for Market Analysis and Restrictive Trade (SMART) model has been used to estimate the trade creation (TC) and trade diversion (TD) effect, revenue effect and welfare effect for the above-mentioned commodities. The results from the SMART simulation analysis indicate that the increase in trade for both the scenarios is mainly driven by TC rather than TD. Further, the study also assesses how the total trade effect is distributed across the major ASEAN countries for each commodity and found that Indonesia and Vietnam are the biggest gainers in terms of TC effect in both the scenarios.

JEL Classification: F13, F15, Q1
Facing Double Jeopardy: The Transition Experiences of Latina Family Caregivers of Young Adults With Disabilities Living in a Rural Community
Authors: Francis Grace L. , Gross Judith M. S. , Lavín Carlos E. , Casarez Velazquez Lu Ankely , Sheets Nicholas
Published: October 2019

The transition for young adults with disabilities from high school to gainful employment is often difficult. This transition is even harder for students from minority or marginalized backgrounds, including young adults who identify as Latino. As the Latino population increases in the United States, it is imperative that the transition from high school to employment becomes more effective for Latino young adults with disabilities. Using a portion of Bronfenbrenner’s Model of Human Development as a framework, we explore the experiences of Spanish-speaking Latina caregivers of young adults with disabilities to better understand the contextual and environmental factors that influence family systems as young adults with disabilities prepare to transition from high school to adulthood. Our findings highlight important factors in the micro-, meso-, exo-, and macrosystems, including the importance of family and community, distrust of authority, and the impact of discrimination. Implications for practice and future research are discussed.
Chemical intolerance: involvement of brain function and networks after exposure to extrinsic stimuli perceived as hazardous
Authors: Azuma Kenichi , Uchiyama Iwao , Tanigawa Mari , Bamba Ikuko , Azuma Michiyo , Takano Hirohisa , Yoshikawa Toshikazu , Sakabe Kou
Published: October 2019

Background

Chemical intolerance (CI) is a chronic condition characterized by recurring and severe symptoms triggered by exposure to low levels of odorous or pungent substances. The etiology of CI has been a controversial subject for a long time. The aim of this review is to summarize findings on the neurological processing of sensory information during and after exposure to low levels of odorous or pungent substances in individuals with CI, focusing on the brain function and networks.

Methods

Scientific studies on CI published between 2000 and 2019 in academic peer-reviewed journals were systematically searched using medical and scientific literature databases. Only peer-reviewed articles reporting original research from experimental human studies directly associated with CI, and involving related neurological responses or brain imaging after exposure to odorous or pungent substances (i.e., in chemical provocation tests), were considered.

Results

Forty-seven studies were found to be eligible for a full-text review. Twenty-three studies met the selection criteria and were included in this review. Evidence indicated that differences between subjects with CI and healthy controls were observed by brain imaging during and after exposure to odorous or pungent substances. Differences in brain imaging were also observed between initial exposure and after exposure to these substances. Neurological processing of sensory information after exposure to extrinsic stimuli in the limbic system and related cortices were altered in subjects with CI. A previous documentable exposure event was likely to be involved in this alteration.

Conclusions

This review documents consistent evidence for the altered neurological processing of sensory information in individuals with CI. Further neurophysiological research exploring the processing of extrinsic stimuli and cognition of sensation through the limbic system and related cortices in CI, and the appearance of symptoms in individuals with CI, are required.
Glycosylator: a Python framework for the rapid modeling of glycans
Authors: Lemmin Thomas , Soto Cinque
Published: October 2019

Background

Carbohydrates are a class of large and diverse biomolecules, ranging from a simple monosaccharide to large multi-branching glycan structures. The covalent linkage of a carbohydrate to the nitrogen atom of an asparagine, a process referred to as N-linked glycosylation, plays an important role in the physiology of many living organisms. Most software for glycan modeling on a personal desktop computer requires knowledge of molecular dynamics to interface with specialized programs such as CHARMM or AMBER. There are a number of popular web-based tools that are available for modeling glycans (e.g., GLYCAM-WEB (http://https://dev.glycam.org/gp/) or Glycosciences.db (http://www.glycosciences.de/)). However, these web-based tools are generally limited to a few canonical glycan conformations and do not allow the user to incorporate glycan modeling into their protein structure modeling workflow.

Results

Here, we present Glycosylator, a Python framework for the identification, modeling and modification of glycans in protein structure that can be used directly in a Python script through its application programming interface (API) or through its graphical user interface (GUI). The GUI provides a straightforward two-dimensional (2D) rendering of a glycoprotein that allows for a quick visual inspection of the glycosylation state of all the sequons on a protein structure. Modeled glycans can be further refined by a genetic algorithm for removing clashes and sampling alternative conformations. Glycosylator can also identify specific three-dimensional (3D) glycans on a protein structure using a library of predefined templates.

Conclusions

Glycosylator was used to generate models of glycosylated protein without steric clashes. Since the molecular topology is based on the CHARMM force field, new complex sugar moieties can be generated without modifying the internals of the code. Glycosylator provides more functionality for analyzing and modeling glycans than any other available software or webserver at present. Glycosylator will be a valuable tool for the glycoinformatics and biomolecular modeling communities.
Diploid hybrid fish derived from the cross between female Bleeker’s yellow tail and male topmouth culter, two cyprinid fishes belonging to different subfamilies
Authors: Li Shengnan , Xie Lihua , Xiao Jun , Yuan Liujiao , Zhou Tian , Luo Kaikun , Zhang Chun , Zhao Rurong , Tao Min , Liu Shaojun
Published: October 2019

Background

Bleeker’s yellow tail (Xenocypris davidi Bleeker, YT) and topmouth culter (Culter alburnus Basilewsky, TC) are both famous and important economic freshwater fish in China. YT, a kind of omnivorous fish, has strong resistance. TC, a kind of carnivorous fish, has high-quality meat but poor resistance. Distant hybridization can integrate the advantages of both parents. There has been no previous report regarding hybrid fish derived from female YT × male TC. It is expected that hybridization of these two kinds of fish will result in F1 hybrids with improved characteristics, such as faster growth rate, stronger resistance, and high-quality meat, which are of great significance in fish genetic breeding.

Results

In this study, we investigated the main biological characteristics of diploid hybrid fish derived from female YT × male TC. The hybrids had an intermediate number of upper lateral line scales between those for YT and TC. The hybrids were diploids with 48 chromosomes and had the same karyotype formula as their parents. The hybrids generated variations in 5S rDNA (designated class IV: 212 bp) and lost specific 5S rDNA derived from the maternal parent (designated class II: 221 bp), which might be related to hybridization. In terms of reproductive traits, all the tested female hybrids exhibited normal gonadal development, and the two-year-old F1 females produced mature eggs. However, all the tested testes of the male hybrids could not produce mature sperm. It is possible that the hybrid lineage will be established by back-crossing the fertile female hybrids and their parents.

Conclusions

Obtaining a fertile female hybrid fish made the creation of a new type of fish possible, which was significant in fish genetic breeding.
Comprehensive analysis of bZIP transcription factors uncovers their roles during dimorphic floret differentiation and stress response in Cleistogenes songorica
Authors: Yan Qi , Wu Fan , Ma Tiantian , Zong Xifang , Ma Qian , Li Jie , Zhao Yufeng , Wang Yanrong , Zhang Jiyu
Published: October 2019

Background

Transcription factors act as important regulators of transcription networks. Basic leucine zipper (bZIP) transcription factors have been shown to be involved in multiple biological processes in plants. However, no information is available for the bZIP family in Cleistogenes songorica, which is an important xerophytic and allotetraploid grass in desert grasslands.

Results

In this study, 86 CsbZIPs were identified in the allotetraploid C. songorica genome. For location analysis, CsbZIPs were distributed evenly across two subgenomes of C. songorica. Phylogenetic tree analysis among three species indicated that CsbZIPs were evolutionarily more closely related to OsbZIPs than AtbZIPs. Syntenic and phylogenetic analyses confirmed that the CsbZIPs were mainly expanded by whole-genome duplication events. Furthermore, it was determined that rice and C. songorica might have undergone purified selection during their long evolutionary history by calculating the Ks values and Ka/Ks ratios of orthologous gene pairs. By analysing the expression patterns of CsbZIPs in different tissues and under abiotic stresses, 21 CsbZIP genes were differentially expressed between chasmogamous (CH) and cleistogamous (CL) flowers, including two FLOWERING LOCUS D (FD) genes. In shoots and roots, 79.1 and 87.2% of the CsbZIP genes, respectively, displayed transcript changes under at least one stress treatment, such as heat, cold, drought and salt. Strikingly, 17 common CsbZIP genes showed differential expression under stress response and during CL flowering. Co-expression network, GO annotation and real-time quantitative reverse transcription PCR (qRT-PCR) analyses revealed a close relationship between CL flowering-associated genes and abiotic stress-related genes.

Conclusions

BZIP TFs were comprehensively analysed and identified in allotetraploid C. songorica. Our results provide insights into the evolutionary history of the bZIP family in C. songorica and provide abiotic stress-responsive and CL-associated candidate CsbZIP genes for potential applications in the genetic improvement of plants.
Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) post-larvae in response to M. rosenbergii nodavirus (MrNV) infection: de novo assembly and functional annotation
Authors: Pasookhush Phongthana , Hindmarch Charles , Sithigorngul Paisarn , Longyant Siwaporn , Bendena William G. , Chaivisuthangkura Parin
Published: October 2019

Background

Macrobrachium rosenbergii, is one of a major freshwater prawn species cultured in Southeast Asia. White tail disease (WTD), caused byMacrobrachium rosenbergiinodavirus (MrNV), is a serious problem in farm cultivation and is responsible for up to 100% mortality in the post larvae stage. Molecular data on howM. rosenbergiipost-larvae launches an immune response to an infection withMrNV is not currently available. We therefore compared the whole transcriptomic sequence ofM. rosenbergiipost-larvae before and afterMrNV infection.

Results

Transcriptome forM. rosenbergiipost-larvae demonstrated high completeness (BUSCO Complete: 83.4%, fragmentation: 13%, missing:3.3%, duplication:16.2%; highest ExN50 value: 94%). The assembled transcriptome consists of 96,362 unigenes with N50of 1308 bp. The assembled transcriptome was successfully annotated against the NCBI non-redundant arthropod database (33.75%), UniProt database (26.73%), Gene Ontology (GO) (18.98%), Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups (EggNOG) (20.88%), and Kyoto Encyclopedia of Genes and Genome pathway (KEGG) (20.46%). GO annotations included immune system process, signaling, response to stimulus, and antioxidant activity. Differential abundance analysis using EdgeR showed 2413 significantly up-regulated genes and 3125 significantly down-regulated genes during the infection ofMrNV.

Conclusions

This study reported a highly complete transcriptome from the post-larvae stage of giant river prawn,M. rosenbergii.Differential abundant transcripts duringMrNV infection were identified and validated by qPCR, many of these differentially abundant transcripts as key players in antiviral immunity. These include known members of the innate immune response with the largest expression change occurring in theM. rosenbergiipost-larvae afterMrNV infection such as antiviral protein, C-type lectin, prophenol oxidase, caspase, ADP ribosylation factors, and dicer.
2-DE-based proteomic analysis of protein changes associated with etiolated mesocotyl growth in Zea mays
Authors: Niu Liangjie , Wu Zhaokun , Liu Hui , Wu Xiaolin , Wang Wei
Published: October 2019

Background

The mesocotyl connects the coleoptilar node and the basal part of the seminal root of maize (Zea mays) seedling. The mesocotyl pushes the shoot of the seedling out of the soil during seed germination; thus, its growth is highly related to deep-sowing tolerance. Although many studies on the maize mesocotyl have been carried out at physiological and molecular levels, the proteomic changes associated with cellular and physiological activities during mesocotyl growth are still unknown.

Results

In the present study, the maize hybrid Zhengdan 958 was used to study mesocotyl growth and accompanying protein changes.The dark-grown etiolated mesocotyls exhibited a slow-fast-slow feature, with significant changes in the levels of indole-3-acetic acid (IAA) and cellulose and the activity of peroxidase (POD). In particular, POD activity increased with mesocotyl growth, showing higher activity at the mature (lower) end of the mesocotyl. For the proteomic analysis, soluble proteins were extracted from etiolated mesocotyls dark-grown for 48 h, 84 h, and 132 h, corresponding to the initial, rapid, and slow growth periods, respectively, and subjected to separation by two-dimensional gel electrophoresis (2-DE). As a result, 88 differentially abundant proteins (DAPs) were identified using MALDI-TOF-TOF analysis. At 48 h, most DAPs were stress proteins, heat shock proteins and storage proteins; at 84 h, oxidation/reduction proteins, carbohydrate biogenesis-related proteins and cytoskeleton-related proteins were highly accumulated; at 132 h, the most striking DAPs were those involved in the synthesis and modification of the cell wall and the biogenesis of carbohydrates. Gene ontology (GO) analysis showed that changes in the abundance and proportion of DAPs were consistent with cellular and physiological activities and biological processes during mesocotyl growth. The accumulation of nine DAPs of interest was verified by immunoblotting and RT-qPCR.

Conclusions

The present study revealed that the protein patterns in 2-D gels differed greatly with mesocotyl growth. At different growth periods, a specific set of DAPs participate in various biological processes and underlie the cellular and physiological activities of the mesocotyl. These results contributed to the understanding of mesocotyl growth and the cultivation of maize lines with deep-sowing tolerance.
Mitochondrial genome in Hypsizygus marmoreus and its evolution in Dikarya
Authors: Wang Gang , Lin Jingxian , Shi Yang , Chang Xiaoguang , Wang Yuanyuan , Guo Lin , Wang Wenhui , Dou Meijie , Deng Youjin , Ming Ray , Zhang Jisen
Published: October 2019

Background

Hypsizygus marmoreus, a high value commercialized edible mushroom is widely cultivated in East Asia, and has become one of the most popular edible mushrooms because of its rich nutritional and medicinal value. Mitochondria are vital organelles, and play various essential roles in eukaryotic cells.

Results

In this study, we provide the Hypsizygus marmoreus mitochondrial (mt) genome assembly: the circular sequence is 102,752 bp in size and contains 15 putative protein-coding genes, 2 ribosomal RNAs subunits and 28 tRNAs. We compared the mt genomes of the 27 fungal species in the Pezizomycotina and Basidiomycotina subphyla, with the results revealing that H. marmoreus is a sister to Tricholoma matsutake and the phylogenetic distribution of this fungus based on the mt genome. Phylogenetic analysis shows that Ascomycetes mitochondria started to diverge earlier than that of Basidiomycetes and supported the robustness of the hyper metric tree. The fungal sequences are highly polymorphic and gene order varies significantly in the dikarya data set, suggesting a correlation between the gene order and divergence time in the fungi mt genome. To detect the mt genome variations in H. marmoreus, we analyzed the mtDNA sequences of 48 strains. The phylogeny and variation sited type statistics of H. marmoreus provide clear-cut evidence for the existence of four well-defined cultivations isolated lineages, suggesting female ancestor origin of H. marmoreus. Furthermore, variations on two loci were further identified to be molecular markers for distinguishing the subgroup containing 32 strains of other strains. Fifteen conserved protein-coding genes of mtDNAs were analyzed, with fourteen revealed to be under purifying selection in the examined fungal species, suggesting the rapid evolution was caused by positive selection of this gene.

Conclusions

Our studies have provided new reference mt genomes and comparisons between species and intraspecies with other strains, and provided future perspectives for assessing diversity and origin of H. marmoreus.
A Eurasia-wide polyploid species complex involving 6x Trifolium ambiguum, 2x T. occidentale and 4x T. repens produces interspecific hybrids with significance for clover breeding
Authors: Williams Warren M. , Verry Isabelle M. , Ansari Helal A. , Hussain S. Wajid , Ullah Ihsan , Ellison Nicholas W.
Published: October 2019

Background

Trifolium ambiguumoccurs as a 2x, 4x, 6xpolyploid series in W Asia. The 6xform is the most agronomically desirable, having strong rhizomatous spread and drought tolerance. These traits would be potentially very valuable if they could be transferred to white clover (T. repens) which is the most important agronomic clover species. However, to-date, no fertile interspecific hybrids with 6x T. ambiguumare available. Previously, 2x T. occidentalefrom W Europe has produced synthetic fertile hybrids with both 2xand 4x T. ambiguumand these were inter-fertile with white clover. Here we ask whether 2x T. occidentalecan form fertile hybrids with 6x T. ambiguumand act as a genetic bridge to white clover and bring these species together as part of a common gene pool.

Results

Ten verified F1(6x T. ambiguumx 2x T. occidentale) hybrids were produced by embryo rescue and seven were studied further. All four investigated for chromosome number were 2n = 4x = 32 and FISH confirmed the expected 21 T. ambiguumand 8 T. occidentalechromosomes. Hybrid fertility was extremely low but 2nfemale gametes functioned with white clover pollen to produce seeds. Derived plants were confirmed using FISH and were successfully backcrossed to white clover to produce partially fertile breeding populations.

Conclusions

AlthoughT. occidentaleand 6x T. ambiguumare widely separated by geography and ecological adaptation they have maintained enough genomic affinity to produce partially fertile hybrids. Inter-fertility of the hybrids with allotetraploidT. repensshowed thatT. occidentalecan provide a genetic bridge between 6x T. ambiguumand white clover to produce plants with new phenotypes combining the traits of all three species. Use of this information should enable potentially valuable stress tolerance traits from 6x T. ambiguumto be used in white clover breeding for the first time.