bluuebunny/crossref_metadata_2025 huggingface dataset:
Missing in Action: Gifted Black Girls in Science, Technology, Engineering, and Mathematics
Authors: Collins Kristina Henry , Joseph Nicole M. , Ford Donna Y.
Published: December 2019

Many commonplace stories, including the authors and those they have heard, substantiate a critical and undeniable truth: marginalized and underrepresented students’ development through the science, technology, engineering, and mathematics (STEM) pipeline is centered on race and gender and is impacted by (un)intentional and (in)formal interactions with other variables. A noticeable issue in STEM and gifted education is the poor presence of Black girls. We contend that for females, the disconnect between grades, class performance, and interest is all too familiar. This is true even if they are gifted, and especially for Black girls. This article is written with the resolve to address the underpinning complexity of contemporary challenges of underrepresentation of gifted Black girls in STEM, which are rooted in intersectional issues of race and sex discrimination. We address barriers and offer recommendations for change, mostly grounded in relevant theories.
Wear analysis of waste marble dust-filled polymer composites with an integrated approach based on design of experiments and neural computation
Authors: Nayak Sandip Kumar , Satapathy Alok
Published: December 2019

Waste marble dust is a solid waste generated during the cutting and polishing of marble pieces in construction sites and also in marble processing industries. This paper reports on the utilization of this waste as a filler material in particulate-filled polymer composite. Polyester-based composites are prepared with different weight proportions of waste marble dust and the dry sliding wear behavior of these composites is studied. Wear trials are conducted using a pin-on-disc test apparatus based on the Taguchi’s L25 orthogonal array as per ASTM G 99-05. The effects of different parameters on the specific wear rate of the composites are studied and an optimum combination of parameters is obtained for the least wear rate. Based on the experimental data, a prediction model using the artificial neural network is used to predict the specific wear rate of the composites at a wider range of operating parameters, within and beyond the test region. The morphologies of the worn surfaces are studied by a scanning electron microscope to ascertain the wear mechanism of the composites at different conditions. This work thus opens up a new avenue for the value added utilization of a waste like marble dust in tribological applications.
The anatomy of police legitimacy: Dialogue, power and procedural justice
Authors: Martin Richard , Bradford Ben
Published: December 2019

In a series of recent influential papers, Anthony Bottoms and Justice Tankebe make the case for a ‘dialogic model’ of police legitimacy, wherein legitimacy is envisaged as emergent in a process through which the police, as power-holders, make claims to authority which are, in turn, responded to by audiences. Our aim in this article is to analyse this model. We argue that while it has the potential to direct legitimacy research along paths hitherto poorly explored, there is a need for conceptual refinement and development in three key respects. First, through recognition of micro- and meso-levels of legitimation. Second, acknowledgement that police claims-making is contingent on the authorization and endorsement of other actors. Third, a fuller consideration of the qualified role of dialogue—i.e. communication between police and policed—in public audiences’ legitimacy assessments. In the spirit of critical engagement and conceptual exploration, this article develops these three insights to propose a modified version of the dialogic model.
A new test method for evaluating the long-term performance of fiber-reinforced concrete pipes
Authors: Al Rikabi Fouad T , Sargand Shad M , Khoury Issam , Kurdziel John
Published: December 2019

Synthetic fibers have been used recently to minimize the need for steel reinforcement in the concrete pipe to enhance their ductility. However, synthetic fiber has properties that may change over time due to its viscoelastic behavior. The objective of this study is to investigate the long-term performance of fiber-reinforced concrete pipes using a new test frame. A three-dimensional finite element model was created for the long-term testing frame to ensure its compliance with the American Society for Testing and Materials requirement. The finite element results showed that the testing frame successfully transferred the load to the concrete as the pipe cracked at the location where high flexural stresses are expected. Concrete pipe reinforced with synthetic fiber dosage of 9 kg/m3 along the steel reinforcement area of 5.7 cm2/m was tested to evaluate the concrete pipe system performance. The pipe was tested under two load stages for 120 days each. Load stages 1 and 2 included applying 40% and 70% of the ultimate load obtained by the authors in a previous study, respectively. The strain and deflection increased linearly within 5 days of applying the load and then leveled off. The pipe showed a slight increase in the crack width and deflection, indicating that fiber creep did not have a significant impact on the long-term performance of the concrete pipe. Also, it was observed that strain values surpassed those for plain concrete material, suggesting that including synthetic fiber in the concrete pipe mix enhanced the pipe ductility.
Propensity weighting: how to minimise comparative bias in non-randomised studies?
Authors: Moons Philip
Published: December 2019

Non-randomised study designs are frequently used by researchers in cardiovascular nursing and allied professions. Baseline differences between the groups to be compared may introduce bias in the results. Methods for causal inference address this issue. One such method is propensity weighting, in which two or more treatments/exposure groups are weighted to make the groups as comparable as possible. As such, it mimics a randomised controlled trial design. In this article, the Twang package is presented for propensity weighting, and its use is exemplified in a study on smoking and cannabis consumption in adults with congenital heart disease.
Ground tire rubber (GTR) surface modification using thiol-ene click reaction: Polystyrene grafting to modify a GTR/polystyrene (PS) blend
Authors: Liang Huan , Gagné Jacob Dion , Faye Adrien , Rodrigue Denis , Brisson Josée
Published: December 2019

In this work, a thiol-ene click reaction was used to graft polystyrene (PS) chains onto the surface of ethylene propylene diene monomer-based ground tire rubber (GTR). A thiol-terminated PS (11 kg mol−1) was selected, due to its commercial availability, to modify a postconsumer GTR. The resulting PS-grafted GTR (GTR- g-PS) particles were analyzed via Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and X-ray photoelectron spectroscopy (XPS) to detect surface changes on treated samples. An increase in aliphatic and aromatic carbon atoms was observed by FTIR and XPS, while grafted material was observed by SEM on the GTR surface, confirming that grafting took place. Then, composites were prepared from these GTR- g-PS particles and from PS by solution evaporation, at 50 wt%. A significant increase in tensile (20%) and storage moduli (from 80% at 65°C to 510% at 95°C) was observed by dynamic mechanical thermal analysis when compared to composites prepared with untreated GTR. In addition, GTR samples showed improved thermal resistance, as attested by the shift in degradation temperature for 10% mass loss (from 400°C for GTR to 450°C for GTR- g-PS). This increases the possible range of processing temperature and service temperature (applications) for introduction of GTR in other polymer matrices.
Women pay their way on income contingent student debt
Authors: West Tracey
Published: December 2019

Does the gender pay gap affect women’s ability to repay their student debt? This study investigates the extent to which an income contingent scheme benefits women because of their individual earnings. Using the Australian Household, Income, and Labour Dynamics in Australia Survey, gender differences in debt repayment behaviour over the past two decades was examined. The regression model comprised interaction terms including risk-averse, low socio-economic status, low wealth and low income. The industries where the majority of women are employed – education and health – were also examined. It was found that over 2002–2014, women generally had less student debt than men, but those who were low income carried more debt. This is the first study to include an analysis of student debt by industry through a gender lens. Given the increasing amount of student debt Australians are carrying, it is important for policymakers to pay attention to its effects to ensure fairness and equity.
Home-Based Exercise Prehabilitation During Preoperative Treatment for Pancreatic Cancer Is Associated With Improvement in Physical Function and Quality of Life
Authors: Ngo-Huang An , Parker Nathan H. , Bruera Eduardo , Lee Rebecca E. , Simpson Richard , O’Connor Daniel P. , Petzel Maria Q. B. , Fontillas Rhodora C. , Schadler Keri , Xiao Lianchun , Wang Xuemei , Fogelman David , Sahai Sunil K. , Lee Jeffrey E. , Basen-Engquist Karen , Katz Matthew H. G.
Published: December 2019

Purpose: To investigate relationships among physical activity, changes in physical function, and health-related quality of life (HRQOL) among patients with pancreatic adenocarcinoma enrolled in a home-based exercise prehabilitation program. Methods: Patients with resectable pancreatic adenocarcinoma receiving preoperative chemotherapy and/or chemoradiation were enrolled on this prospective, single-arm trial and were advised to perform ≥60 minutes each of moderate-intensity aerobic exercise and strengthening exercise weekly. Activity was measured via self-report and accelerometers, including moderate-to-vigorous physical activity (MVPA), light physical activity (LPA), and sedentary activity (SA). Physical function measures at baseline and restaging follow-up included 6-minute walk test (6MWT), 5 times sit-to-stand (5×STS), handgrip strength (HGS), 3-m walk for gait speed (GS), and the PROMIS Physical Function Short Form. HRQOL was measured via the FACT-Hep questionnaire. Results: Fifty participants with mean age 66 years (standard deviation = 8 years) were enrolled. The 6MWT, 5×STS, and GS significantly improved from baseline to restaging follow-up (P=.001, P=.049, and P=.009, respectively). Increases in self-reported aerobic exercise, weekly MVPA, and LPA were associated with improvement in 6MWT (β=.19, P=.048; β=.18, P=.03; and β=.08, P=.03, respectively) and self-reported physical functioning (β=.02, P=.03; β=.03, P=.005; and β=.01, P=.02, respectively). Increased weekly LPA was associated with increased HRQOL (β=.03, P=.02). Increased SA was associated with decreased HRQOL (β=-.02,P=.01). Conclusions: Patients with potentially resectable pancreatic cancer exhibit meaningful improvement in physical function with prehabilitation; physical activity was associated with improved physical function and HRQOL. These data highlight the importance of physical activity during treatment for pancreatic cancer.
Training Inhibitory Control Induced Robust Neural Changes When Behavior Is Affected: A Follow-up Study Using Cognitive Event-Related Potentials
Authors: Schroder Elisa , Dubuson Macha , Dousset Clémence , Mortier Elena , Kornreich Charles , Campanella Salvatore
Published: December 2019

Cognitive training results in significant, albeit modest, improvements in specific cognitive functions across a range of mental illnesses. Inhibitory control, defined as the ability to stop the execution of an automatic reaction or a planned motor behavior, is known to be particularly important for the regulation of health behaviors, including addictive behaviors. For example, several studies have indicated that inhibitory training can lead to reduced alcohol consumption or a loss of weight/reduced energy intake. However, the exact neurocognitive mechanisms that underlie such behavioral changes induced by training are still matter of debate. In the present study, we investigated the long-term impact (ie, at 1 week posttraining) of an inhibitory training program (composed of 4 consecutive daily training sessions of 20 minutes each) on the performance of a Go/No-go task. Healthy participants were randomly assigned to 1 of 3 designated groups: (1) an Inhibition Training (IT) group that received training based on a hybrid flanker Go/No-go task; (2) a group that received a noninhibition-based (ie, episodic memory; EM) training; and (3) a No-Training (NT) group to control for test-retest effects. Each group underwent 3 sessions of a Go/No-go task concomitant with the recording of event-related potentials. Our results revealed a specific impact of the Inhibitory Training on the Go/No-go task, indexed by a faster process compared with the other 2 groups. This effect was neurophysiologically indexed by a faster N2 component on the difference NoGo-Go waveform. Importantly, effects at both the behavioral and at the neural level were still readily discernible 1 week posttraining. Thus, our data clearly corroborate the notion that cognitive training is effective, while also indicating that it may persist over time.
Reservation-based traffic management for autonomous intersection crossing
Authors: Choi Myungwhan , Rubenecia Areeya , Choi Hyo Hyun
Published: December 2019

A scheduling scheme for autonomous intersection crossing is proposed and evaluated. The scheduling scheme determines the flow of autonomous vehicles into an intersection without traffic signals. The objective of the scheduling scheme is to schedule the vehicles’ entrances into the intersection such that there will be no collision among vehicles and the intersection is efficiently utilized. Our scheduling scheme uses reservation-based scheduling approach, and the scheduling is formulated as an optimization problem to find the best sequence of vehicles’ entrances into the intersection. Our scheme is made more practical by allowing the vehicles to move at any speed within a speed range, and it is shown that it is fast enough to be used in real time. Through simulation, it is also shown that our scheduling scheme significantly outperforms the first-come, first-served approach, which is the approach used by other reservation-based scheduling schemes.
Pre-operative direct puncture embolization of head and neck hypervascular tumors using SQUID 12
Authors: Pedicelli Alessandro , Lozupone Emilio , Valente Iacopo , Snider Francesco , Rigante Mario , D’Argento Francesco , Alexandre Andrea , Garignano Giuseppe , Chiumarulo Luigi , Paludetti Gaetano , Colosimo Cesare
Published: December 2019

Objective

The authors have evaluated their experience in pre-operative direct puncture embolization of hypervascular tumors of the head and neck using SQUID 12, an embolic liquid agent.

Methods

Between July 2016 and March 2019, the authors retrospectively reviewed clinical, embolization and surgical data of 11 consecutive patients with 12 hypervascular head and neck tumors who had undergone pre-operative embolization using SQUID 12. Percutaneous embolizations were performed by inserting a 19-22 Gauge needle directly into the tumor under ultrasound, fluoroscopic and/or endoscopic guidance. The hub of the needle was connected to a 15-cm DMSO-compatible extension tube, and the SQUID 12 was injected.

Results

Total or near-total devascularization was achieved in 11 over 12 cases. Complete en-bloc tumor removal by surgery was achieved in all cases. Only one patient required blood transfusion. No major periprocedural adverse events were recorded.

Conclusions

Direct puncture embolization of hypervascular tumors of the head and neck using SQUID 12 seems to be safe and effective. It may offer almost complete devascularization due to homogenous, deep penetration in the tumor, with optimal visibility of the agent throughout the percutaneous procedure. It may reduce intraoperative blood loss and the need for transfusion, thus facilitating complete surgical resection.
Analytical calculation and analysis of air gap magnetic field for electromechanical integrated toroidal drive
Authors: Liu Xin , Wang Hongda
Published: December 2019

This article introduces the operating principle and structural characteristics of the electromechanical integrated toroidal drive system. For its inner and outer toroidal double-stator structure, the equivalent current method is applied to calculate its spatial magnetic field, which is produced by the sector cylindrical magnetic teeth and the helical variable cross-section magnetic beam. For the application of the equivalent current method in the modeling of the magnetic field, an effective correction method is proposed. The flux density calculation models for the main magnetic field in the inner and outer air gaps are established under the unified coordinate system, and the analytical expression of magnetic field distribution in spatial air gap is deduced. Finally, the feasibility of the mathematical analytical model is verified by comparing the analytical calculation results with the finite element simulation results. The influences of the main structural parameters on the distribution of the air gap magnetic field and the torque are analyzed, which lay a theoretical foundation for the optimal design of the electromechanical integrated toroidal drive system.
Adaptive dose-finding based on safety and feasibility in early-phase clinical trials of adoptive cell immunotherapy
Authors: Wages Nolan A , Fadul Camilo E
Published: December 2019

Background/aims:

Dose feasibility is a challenge that may arise in the development of adoptive T cell therapies for cancer. In early-phase clinical trials, dose is quantified either by a fixed or per unit body weight number of cells infused. It may not be feasible, however, to administer a patient’s assigned dose due to an insufficient number of cells harvested or functional heterogeneity of the product. The study objective becomes to identify the maximum tolerated dose with high feasibility of being administered. This article describes a new dose-finding method that adaptively accounts for safety and feasibility endpoints in guiding dose allocation.

Methods:

We propose an adaptive dose-finding method that integrates accumulating feasibility and safety data to select doses for participant cohorts in early-phase trials examining adoptive cell immunotherapy. We sequentially model the probability of dose-limiting toxicity and the probability of feasibility using independent beta-binomial models. The probability model for toxicity borrows information across all dose levels using isotonic regression, allowing participants infused at a lower dose than his or her planned dose to contribute safety data to the dose-finding algorithm. We applied the proposed methodology in a single simulated trial and evaluated its operating characteristics through extensive simulation studies.

Results:

In simulations conducted for a phase I study of adoptive immunotherapy for newly diagnosed glioblastoma, the proposed method demonstrates the ability to identify accurately the feasible maximum tolerated doses and to treat participants at and around these doses. Over 10 hypothesized scenarios studied, the percentage of correctly selecting the true feasible and maximum tolerated dose ranged from 50% to 90% with sample sizes averaging between 21 and 24 participants. A comparison to the only known existing method accounting for safety and feasibility yields competitive performance.

Conclusion:

We have developed a new practical adaptive dose-finding method to assess feasibility in early-phase adoptive cell therapy trials. A design that incorporates feasibility, as a function of the quantity and quality of the product manufactured, in addition to safety will have an impact on the recommended phase II doses in studies that evaluate patient outcomes.
The Growth of Multi-Academy Trusts in England: Emergent Structures and the Sponsorship of Underperforming Schools
Authors: Simon Catherine A , James Chris , Simon Alan
Published: December 2019

In England, schools are able to take on academy status, which is intended by the central government to give them greater autonomy (DfE, 2018). Groups of academies can form multi-academy trusts (MATs), which typically grow in size with additional schools becoming academies and joining. One mechanism for MAT growth is sponsorship, which occurs when an underperforming school is required to become an academy and to join a MAT to facilitate its improvement. It was to explore the emerging patterns of MATs and their operation, especially in relation to sponsorship, that the research we report here was carried out. The research was conducted in two phases. In the first phase, we sought to establish the emerging patterns of MATs that sponsor underperforming schools. In the second phase, we interviewed MAT chief executive officers (CEOs) to further explore emerging patterns of MATs, the factors affecting the growth of MATs and the nature of sponsorship. Our analysis shows the development of a complex and potentially unsustainable state schooling system in England, managed by Regional School Commissioners (RSCs) and dependent on the altruistic values and motivations of CEOs of MATs to improve schools that are underperforming.
Ultrasound measurement of brain tissue movement in humans: A systematic review
Authors: Ince Jonathan , Alharbi Meshal , Minhas Jatinder S , Chung Emma ML
Published: December 2019

Introduction

It has long been suggested that ultrasound could be used to measure brain tissue pulsations in humans, but potential clinical applications are relatively unexplored. The aim of this systematic review was to explore and synthesise available literature on ultrasound measurement of brain tissue motion in humans.

Methods

Our systematic review was designed to include predefined study selection criteria, quality evaluation, and a data extraction pro-forma, registered prospectively on PROSPERO (CRD42018114117). The systematic review was conducted by two independent reviewers.

Results

Ten studies were eligible for the evidence synthesis and qualitative evaluation. All eligible studies confirmed that brain tissue motion over the cardiac cycle could be measured using ultrasound; however, data acquisition, analysis, and outcomes varied. The majority of studies used tissue pulsatility imaging, with the right temporal window as the acquisition point. Currently available literature is largely exploratory, with measurements of brain tissue displacement over a narrow range of health conditions and ages. Explored health conditions include orthostatic hypotension and depression.

Conclusion

Further studies are needed to assess variability in brain tissue motion estimates across larger cohorts of healthy subjects and in patients with various medical conditions. This would be important for informing sample size estimates to ensure future studies are appropriately powered. Future research would also benefit from a consistent framework for data analysis and reporting, to facilitate comparative research and meta-analysis. Following standardisation and further healthy participant studies, future work should focus on assessing the clinical utility of brain tissue pulsation measurements in cerebrovascular disease states.
Long-Term Results of Hip Arthroplasty Using Extensive Porous-Coated Stem—A Minimum Follow-Up of 15 Years
Authors: Park Myung Hoon , Youn Yung Hun , Kang Joon Soon , Moon Kyoung Ho
Published: December 2019

Introduction:

We report the clinical and radiographic results of hip arthroplasty using extensive porous-coated stems over 15 years in Korea.

Methods:

This retrospective study included 210 patients (268 hips) who underwent total hip arthroplasties (232 hips) and bipolar hemiarthroplasties (36 hips) between June 1996 and December 2002 for avascular necrosis of the femoral head, hip fracture, or osteoarthritis, after excluding those who died or were lost to follow-up. One senior author (K.H.M.) evaluated Harris Hip Score (HHS); limping gait; and leg length discrepancy, and 3 independent reviewers assessed the radiographic findings, including the level of stress shielding, Dorr classification, subsidence and loosening of femoral stem, heterotopic ossification (Brooker classification), osteolysis of acetabulum, wear rate of the polyethylene liner, component loosening, and revision rate.

Results:

The mean follow-up duration was 16.9 years and average age at operation was 50.9 years. The HHS improved at the last follow-up. Stress shielding was grade 1 in 185 hips, grade 2 in 35 hips, grade 3 in 37 hips, and grade 4 in 11 hips. Femoral stem subsidence was <3 mm in 4 hips and >3 mm in 6 hips. Femoral stems with stable bony ingrowth were observed in 258 hips, fibrous stable femoral stems in 4 hips, and unstable femoral stems in 6 hips. Heterotopic ossification was class 1 in12 and class 2 in 4 hips. Revision surgery was performed for periprosthetic osteolysis of cup (45 hips), recurrent dislocation (1), unstable femoral stem (1), and infection (1). The Kaplan-Meier survivorship at the 15-year follow-up was 86.2%. The survivorship of femoral stem at 15 years was 99.3%, and if including impending revision due to unstable femoral stem was 97.1%.

Disscussion:

This study has all the limitations inherent with a retrospective design. However, a large number of patients in this cohort operated on by a single surgeon and a long-term follow-up are some of the potential advantages of the current study.

Conclusions:

At the 15-year follow-up, extensive porous-coated stem showed relatively good survivorship even in geriatric patients (Dorr type C).
Early Progressive Maxillary Changes with Nasoalveolar Molding: Randomized Controlled Clinical Trial
Authors: Saad M.S. , Fata M. , Farouk A. , Habib A.M.A. , Gad M. , Tayel M.B. , Marei M.K.
Published: December 2019

Objectives:

Quantitative assessment of 3-dimensional progressive changes of the maxillary geometry in unilateral cleft lip palate (UCLP) with and without nasoalveolar molding (NAM).

Methods:

The study was designed as a prospective 2-arm randomized controlled clinical trial conducted in parallel. Forty infants with nonsyndromic UCLP were randomly assigned into a NAM-treated group (n = 20) and non–NAM treated group (n = 20). A total of 120 laser-scanned maxillary casts were collected and blindly analyzed via a modified algorithm at T0 (initial visit; baseline), T1 (after 3 wk; first interval), and T2 (after 6 wk; second interval). The main outcome measures were the amount and rate of cleft gap changes, the midline position, and the transverse, sagittal, and vertical growth through intervals.

Results:

More than 50% of the cleft gap (56.42%; P < 0.001) was reduced in the first 3 wk of alveolar molding (AM). The end point of the AM was obtained in 6 wk (86.25%; P < 0.001); then, the kinks of the greater segment were noticed. The AM effect decreased as far as posterior; the anterior arch width reduced slightly (1.23%; P < 0.001), while the middle and posterior arches increased slightly (P > 0.999 and P = 0.288, respectively). The posterior arch width was the least changing and was considered a baseline, while the anterior was the pivot of the segment rotation. Both groups showed different patterns of segment rotation and sagittal growth. The non–NAM treated group showed a slight increase in cleft gap length, arch width, and midline position.

Conclusion:

Based on this study, it was concluded that the NAM treatment is effective in minimizing cleft severity and realigning maxillary segments without the deterioration of the transverse and vertical arch growth. Near follow-up visits are recommended to monitor the rapid gap reduction within the first 3 wk. Further trials are recommended to compare the outcomes regarding the sagittal growth to reference values ( ClinicalTrials.gov NCT03029195).

Knowledge Transfer Statement:

The results of this study will help clinicians understand nasoalveolar molding biomechanics that may improve the treatment outcomes for patients with unilateral cleft lip and palate. The trial data can be a valuable guide to the qualitative and quantitative predictive virtual molding in computer aided design–simulated nasoalveolar molding therapy. The modified algorithm can be used by researchers to quantify the rate, the sequence, and the direction of the maxillary segments movement in unilateral cleft lip and palate.
MIRIA: a webserver for statistical, visual and meta-analysis of RNA editing data in mammals
Authors: Feng Xikang , Wang Zishuai , Li Hechen , Li Shuai Cheng
Published: December 2019

Background

Adenosine-to-inosine RNA editing can markedly diversify the transcriptome, leading to a variety of critical molecular and biological processes in mammals. Over the past several years, researchers have developed several new pipelines and software packages to identify RNA editing sites with a focus on downstream statistical analysis and functional interpretation.

Results

Here, we developed a user-friendly public webserver named MIRIA that integrates statistics and visualization techniques to facilitate the comprehensive analysis of RNA editing sites data identified by the pipelines and software packages. MIRIA is unique in that provides several analytical functions, including RNA editing type statistics, genomic feature annotations, editing level statistics, genome-wide distribution of RNA editing sites, tissue-specific analysis and conservation analysis. We collected high-throughput RNA sequencing (RNA-seq) data from eight tissues across seven species as the experimental data for MIRIA and constructed an example result page.

Conclusion

MIRIA provides both visualization and analysis of mammal RNA editing data for experimental biologists who are interested in revealing the functions of RNA editing sites. MIRIA is freely available at https://mammal.deepomics.org.
A unified STR profiling system across multiple species with whole genome sequencing data
Authors: Liu Yilin , Xu Jiao , Chen Miaoxia , Wang Changfa , Li Shuaicheng
Published: December 2019

Background

Short tandem repeats (STRs) serve as genetic markers in forensic scenes due to their high polymorphism in eukaryotic genomes. A variety of STRs profiling systems have been developed for species including human, dog, cat, cattle, etc. Maintaining these systems simultaneously can be costly. These mammals share many high similar regions along their genomes. With the availability of the massive amount of the whole genomics data of these species, it is possible to develop a unified STR profiling system. In this study, our objective is to propose and develop a unified set of STR loci that could be simultaneously applied to multiple species.

Result

To find a unified STR set, we collected the whole genome sequence data of the concerned species and mapped them to the human genome reference. Then we extracted the STR loci across the species. From these loci, we proposed an algorithm which selected a subset of loci by incorporating the optimized combined power of discrimination. Our results show that the unified set of loci have high combined power of discrimination, >1−10−9, for both individual species and the mixed population, as well as the random-match probability, <10−7 for all the involved species, indicating that the identified set of STR loci could be applied to multiple species.

Conclusions

We identified a set of STR loci which shared by multiple species. It implies that a unified STR profiling system is possible for these species under the forensic scenes. The system can be applied to the individual identification or paternal test of each of the ten common species which are Sus scrofa (pig), Bos taurus (cattle), Capra hircus (goat), Equus caballus (horse), Canis lupus familiaris (dog), Felis catus (cat), Ovis aries (sheep), Oryctolagus cuniculus (rabbit), and Bos grunniens (yak), and Homo sapiens (human). Our loci selection algorithm employed a greedy approach. The algorithm can generate the loci under different forensic parameters and for a specific combination of species.
A protocol to evaluate RNA sequencing normalization methods
Authors: Abrams Zachary B. , Johnson Travis S. , Huang Kun , Payne Philip R. O. , Coombes Kevin
Published: December 2019

Background

RNA sequencing technologies have allowed researchers to gain a better understanding of how the transcriptome affects disease. However, sequencing technologies often unintentionally introduce experimental error into RNA sequencing data. To counteract this, normalization methods are standardly applied with the intent of reducing the non-biologically derived variability inherent in transcriptomic measurements. However, the comparative efficacy of the various normalization techniques has not been tested in a standardized manner. Here we propose tests that evaluate numerous normalization techniques and applied them to a large-scale standard data set. These tests comprise a protocol that allows researchers to measure the amount of non-biological variability which is present in any data set after normalization has been performed, a crucial step to assessing the biological validity of data following normalization.

Results

In this study we present two tests to assess the validity of normalization methods applied to a large-scale data set collected for systematic evaluation purposes. We tested various RNASeq normalization procedures and concluded that transcripts per million (TPM) was the best performing normalization method based on its preservation of biological signal as compared to the other methods tested.

Conclusion

Normalization is of vital importance to accurately interpret the results of genomic and transcriptomic experiments. More work, however, needs to be performed to optimize normalization methods for RNASeq data. The present effort helps pave the way for more systematic evaluations of normalization methods across different platforms. With our proposed schema researchers can evaluate their own or future normalization methods to further improve the field of RNASeq normalization.
G6PD genetic variations in neonatal Hyperbilirubinemia in Indonesian Deutromalay population
Authors: Wisnumurti Dewi A. , Sribudiani Yunia , Porsch Robert M. , Maskoen Ani M. , Rahayuningsih Sri E. , Asni Eni K. , Sleutels Frank , van Ijcken Wilfred F. J. , Sukadi Abdurachman , Achmad Tri H.
Published: December 2019

Background

Neonatal jaundice is a common finding in newborns in Asia, including Indonesia. In some cases, the serum total bilirubin levels exceeds the 95th percentile for hours of life (neonatal hyperbilirubinemia). Severe neonatal hyperbilirubinemia (NH) could lead to kernicterus and neonatal death.Glucose-6-Phosphage Dehydrogenase(G6PD)genetic variations and deficiency have been reported in several studies to be associated with NH. This study aimed to analyze theG6PDgenetic variations and its activity in neonates with and without hyperbilirubinemia in the Deutromalay Indonesian population.

Methods

Deoxyribose Nucleic Acid (DNA) was isolated from peripheral blood of 116 and 115 healthy term neonates with and without hyperbilirubinemia. All infants underwent the following laboratory examinations: routine hematologic evaluation, Coombs test, G6PD activity measurement using the Randox kit method, and serum total bilirubin level. All exons of theG6PDgene were targeted for deep sequencing using MiSeq (Illumina). An association study ofG6PDpolymorphisms with NH was performed using PLINK.

Results

The prevalence of G6PD deficiency in neonates with and without hyperbilirubinemia in Indonesian Deutromalay population were 1.72% (95% Confidence Interval (CI): 0.6–4.1%) and 1.74% (95% CI: 0.7–4.1%), respectively. The most commonG6PDpolymorphisms, i.e. rs1050757/c.* + 357A > G, rs2230037/c.1311C > T, and rs2071429/c.1365-13 T/IVS11, were identified. However, none of those polymorphisms and their haplotype were associated with NH (p > 0.05, Odds Ratio (OR) ~1.00). The prevalence ofG6PDmutations in neonates with and without hyperbilirubinemia were 6.8% (95% CI: 2.3–11.5%) and 6.9% (95% CI: 2.3–11.6%), respectively. The most frequently identifiedG6PDmutation was the Viangchan variant (p.V291 M), which was followed by the Canton (p.R459L) and Vanua Lava (p.L128P) variants. Two novel mutations were identified both in case (p.V369A, p.I167F) and control (p.L474=, p.I36T) groups.

Conclusion

The prevalence of G6PD deficiency is low in neonates with or without hyperbilirubinemia in Deutromalay Indonesian population. The majority ofG6PDmutations identified among Indonesian Deutromalay population in this study are Viangchan, Canton and Vanua Lava variants.
Traumatic posterior Atlanto-axial dislocation: case report of an atypical C1-C2 dislocation with an anterior arch fracture of C1
Authors: Ghailane Soufiane , Alsofyani Mohammad A. , Pointillart Vincent , Bouloussa Houssam , Gille Olivier
Published: December 2019

Background

An atypical case of a traumatic posterior C1-C2 dislocation with an anterior arch fracture of C1 is reported. A novel conservative treatment for this rare lesion is described.

Case presentation

An eighty-nine-year-old male fell off a ladder at home and presented with an acute traumatic cervical spine trauma, which we believe involved a distraction mechanism. The patient was neurologically intact; he denied any weakness, numbness or paresthesia. A preoperative CT-scan demonstrated a posterior dislocation with an anterior arch of C1 fracture. Conservative management was elected. Reduction was achieved by closed manual reduction under general anesthesia. A postoperative CT demonstrated a complete reduction of the atlanto-axial dislocation.

Conclusion

Based on this case report and relevant literature, we present an unusual lesion of the upper cervical spine treated nonoperatively with closed manual reduction under general anesthesia. To date, there is no available consensus for the management of these lesions.
Antibody blockade of Dectin-2 suppresses house dust mite-induced Th2 cytokine production in dendritic cell- and monocyte-depleted peripheral blood mononuclear cell co-cultures from asthma patients
Authors: Chen Ming-Han , Huang Ming-Ting , Yu Wen-Kuang , Lee Shinn-Shing , Wang Jia-Horng , Cheng Ting-Jen R. , Bowman Michael R. , Hsieh Shie-Liang
Published: December 2019

Background

Dectin-2, which is a C-type lectin, interacts with the house dust mite (HDM)Dermatophagoides pteronyssinusallergen. This study aimed to investigate whether Dectin-2 blockade by antagonistic monoclonal antibodies (MoAbs) attenuates HDM-induced allergic responses.

Methods

Two anti-Dectin-2 MoAbs were generated and validated for specific binding to Dectin-2 Fc fusion protein (Dectin-2.Fc) and inhibition of Dectin-2.Fc/HDM interaction. Patients with asthma exhibiting high titers of anti-D. pteronyssinusIgE were enrolled. Peripheral blood mononuclear cells with depleted CD14+monocytes were obtained from these patients and co-cultured with autologous monocyte-derived conventional dendritic cells in the presence ofD. pteronyssinusor its group 2 allergens (Der p 2). Interleukin (IL)-5 and IL-13 levels in the culture supernatants were determined using ELISA in the presence or absence of anti-Dectin-2 MoAbs.

Results

Two MoAbs, 6A4G7 and 17A1D10, showed specific binding to recombinant Dectin-2.Fc and inhibited HDM binding to Dectin-2.Fc. Both anti-Dectin-2 MoAbs inhibited IL-5 and IL-13 production in co-cultures with Der p 2 stimulation in a dose-dependent manner. 6A4G7 and 17A1D10 (3 μg/mL) significantly inhibited Der p 2-induced (3 μg/mL) IL-5 production by 69.7 and 86.4% and IL-13 production by 84.0 and 81.4%, respectively. Moreover, this inhibitory effect of the two MoAbs remained significant in the presence ofD. pteronyssinus.

Conclusions

Anti-Dectin-2 MoAbs significantly inhibited HDM-induced allergic responses in vitro and therefore have the potential to become therapeutic agents in mite-induced allergic diseases.
Electronic cigarette vapour increases virulence and inflammatory potential of respiratory pathogens
Authors: Gilpin Deirdre F. , McGown Katie-Ann , Gallagher Kevin , Bengoechea Jose , Dumigan Amy , Einarsson Gisli , Elborn J. Stuart , Tunney Michael M.
Published: December 2019

Introduction

Bacteria have been extensively implicated in the development of smoking related diseases, such as COPD, by either direct infection or bacteria-mediated inflammation. In response to the health risks associated with tobacco exposure, the use of electronic cigarettes (e-cigs) has increased. This study compared the effect of e-cig vapour (ECV) and cigarette smoke (CSE) on the virulence and inflammatory potential of key lung pathogens (Haemophilus influenzae, Streptococcus pneumoniae, Staphylococcus aureusandPseudomonas aeruginosa).

Methods

Biofilm formation, virulence in theGalleria mellonellainfection model, antibiotic susceptibility and IL-8/TNF-α production in A549 cells, were compared between bacteria exposed to ECV, CSE and non-exposed bacteria.

Results

Statistically significant increases in biofilm and cytokine secretion were observed following bacterial exposure to either ECV or CSE, compared to non-exposed bacteria; the effect of exposure to ECV on bacterial phenotype and virulence was comparable, and in some cases greater, than that observed following CSE exposure. Treatment of A549 cells with cell signaling pathway inhibitors prior to infection, did not suggest that alternative signaling pathways were being activated following exposure of bacteria to either ECV or CSE.

Conclusions

These findings therefore suggest that ECV and CSE can induce changes in phenotype and virulence of key lung pathogens, which may increase bacterial persistence and inflammatory potential.
Risk factor assessment for clinical malaria among forest-goers in a pre-elimination setting in Phu Yen Province, Vietnam
Authors: Canavati Sara E. , Kelly Gerard C. , Quintero Cesia E. , Vo Thuan Huu , Tran Long Khanh , Ohrt Colin , Ngo Thang Duc , Tran Duong Thanh , Martin Nicholas J.
Published: December 2019

Background

The transition from malaria control to elimination requires understanding and targeting interventions among high-risk populations. In Vietnam, forest-goers are often difficult to test, treat and follow-up for malaria because they are highly mobile. If undiagnosed, forest-goers can maintain parasite reservoirs and contribute to ongoing malaria transmission.

Methods

A case–control study was conducted to identify malaria risk factors associated with forest-goers in three communes in Phu Yen Province, Vietnam. Cases (n = 81) were residents from the study area diagnosed with malaria and known to frequent forest areas. Controls (n = 94) were randomly selected forest-going residents from within the study area with no identified malaria infection. Participants were interviewed face-to-face using a standard questionnaire to identify malaria risk factors. Logistic regression was used to calculate odds ratios (ORs) and 95% CI for risk factors after adjusting for socio-demographic characteristics.

Results

Among the cases, malaria infection varied by species: 66.7% were positive for Plasmodium falciparum, 29.6% for Plasmodium vivax, and 3.7% were diagnosed as mixed infection. Cases were less likely than controls to use treated nets (aOR = 0.31; 95% CI 0.12–0.80), work after dark (aOR = 2.93; 95% CI 1.35, 6.34), bath in a stream after dark (aOR = 2.44; 95% CI 1.02–5.88), and collect water after dark (aOR = 1.99; 95% CI 1.02–3.90).

Conclusions

As Vietnam moves toward malaria elimination, these findings can inform behaviour change communication and malaria prevention strategies, incorporating the risk of after-dark and water-related activities, in this priority and difficult-to-access population group.
RETRACTED ARTICLE: m6A modification-mediated CBX8 induction regulates stemness and chemosensitivity of colon cancer via upregulation of LGR5
Authors: Zhang Yi , Kang Min , Zhang Bin , Meng Fanchao , Song Jun , Kaneko Hiroshi , Shimamoto Fumio , Tang Bo
Published: December 2019

Background

Colon cancer (CC) cells can exhibit stemness and expansion capabilities, which contribute to resistance to conventional chemotherapies. Aberrant expression of CBX8 has been identified in many types of cancer, but the cause of this aberrant CBX8 expression and whether CBX8 is associated with stemness properties in CC remain unknown.

Methods

qRT-PCR and IHC were applied to examine CBX8 levels in normal and chemoresistant CC tissues. Cancer cell stemness and chemosensitivity were evaluated by spheroid formation, colony formation, Western blot and flow cytometry assays. RNA-seq combined with ChIP-seq was used to identify target genes, and ChIP, IP and dual luciferase reporter assays were applied to explore the underlying mechanisms.

Results

CBX8 was significantly overexpressed in chemoresistant CC tissues. In addition, CBX8 could promote stemness and suppress chemosensitivity through LGR5. Mechanistic studies revealed that CBX8 activate the transcription of LGR5 in a noncanonical manner with assistance of Pol II. CBX8 recruited KMT2b to the LGR5 promoter, which maintained H3K4me3 status to promote LGR5 expression. Moreover, m6A methylation participated in the upregulation of CBX8 by maintaining CBX8 mRNA stability.

Conclusions

Upon m6A methylation-induced upregulation, CBX8 interacts with KMT2b and Pol II to promote LGR5 expression in a noncanonical manner, which contributes to increased cancer stemness and decreased chemosensitivity in CC. This study provides potential new therapeutic targets and valuable prognostic markers for CC.
Chronic kidney disease: a review of proteomic and metabolomic approaches to membranous glomerulonephritis, focal segmental glomerulosclerosis, and IgA nephropathy biomarkers
Authors: Taherkhani Amir , Farrokhi Yekta Reyhaneh , Mohseni Maede , Saidijam Massoud , Arefi Oskouie Afsaneh
Published: December 2019

Chronic Kidney Disease (CKD) is a global health problem annually affecting millions of people around the world. It is a comprehensive syndrome, and various factors may contribute to its occurrence. In this study, it was attempted to provide an accurate definition of chronic kidney disease; followed by focusing and discussing on molecular pathogenesis, novel diagnosis approaches based on biomarkers, recent effective antigens and new therapeutic procedures related to high-risk chronic kidney disease such as membranous glomerulonephritis, focal segmental glomerulosclerosis, and IgA nephropathy, which may lead to end-stage renal diseases. Additionally, a considerable number of metabolites and proteins that have previously been discovered and recommended as potential biomarkers of various CKDsusing ‘-omics-’ technologies, proteomics, and metabolomics were reviewed.