bluuebunny/crossref_metadata_2025 huggingface dataset:
Australia and pandemics v BLM: No, Love Lost (at the High Court) Part II
Authors: Wood Asmi
Published: June 2021

In this second part, the article recognises the time that the High Court has ‘bought’ the nation to allow it to address long-standing injustices. This part argues that common law protections are inadequate when faced with an Executive that is populist and panders to the worst elements of its support base, with more political mileage to be gained through talk about war with China over Taiwan, or vaccines and border lockdowns. For the nation and for Black lives, however, constitutional entrenchment of racial equality will provide the best protection available under the current system. Failure of ‘the people’ to force their leaders to entrench racial equality is a blight on the entire community, with irrational fears created by the Executive being the veil that blinds the majority to injustice or that Black lives do matter in White Australia.
Protest, policing and law during COVID-19: On the legality of mass gatherings in a health crisis
Authors: Martin Greg
Published: June 2021

This article considers the legal status of protest rights in Australia during the COVID-19 public health crisis. It discusses jurisprudence of the New South Wales Supreme Court regarding the legality of mass gatherings for the purpose of protest during the COVID pandemic. Balancing protest rights with risks to community safety posed by possible coronavirus transmission at public assemblies, the Court has sometimes allowed and sometimes prohibited protests. The article critically examines the policing of protest during the pandemic and explores some of the implications of comparing emergency measures introduced during the COVID crisis with similar measures introduced in the wake of the 9/11 terror attacks.
“Communitas in Crisis”: An Autoethnography of Psychosis Under Lockdown
Authors: Fixsen Alison
Published: June 2021

In this article, I use autoethnography to examine time spent on an acute psychiatric ward during the COVID-19 lockdown. I employ the device of “communitas in crisis” to emphasize the precarious nature of this experience and the extent to which, for myself at least, informal social interactions with fellow patients and “communitas” were significant features of my hospital experience and subsequent discharge. I suggest that a lack of emphasis on inpatient to inpatient relationships in the recovery literature is an omission and a reflection of psychiatry’s authority struggles with both service users and professionals, along with a general perception of psychosis as individual rather than as a socially constructed phenomenon. I also suggest that, especially in the wake of greater social distancing, mental health and social services should safeguard against psychological and social isolation by creating more spaces for struggling people to interact without fear or prejudice.
Peer Prompting and Reinforcement for Supporting Positive Behavioral Development in Students With EBD
Authors: Wang Jing , Maggin Daniel M. , Zarate Kary
Published: June 2021

Peer-mediated interventions (PMIs) are an effective support for students with emotional and behavioral disorders (EBD) for improving targeted behavioral skills. As one of the most important strategies in PMI, peer prompting and reinforcement (PR) provides an effective approach for developing and maintaining positive behavior. This article provides practitioners serving elementary school students with and/or at risk for EBD with a step-by-step process for implementing PMI using PR strategy, including steps for intervention intensification when data suggest that as a path forward.
Older Individuals Convicted of Sexual Offenses: A Literature Review
Authors: Crookes Rebecca L. , Tramontano Carlo , Brown Sarah J. , Walker Kate , Wright Hayley
Published: June 2021

The population of older individuals convicted of sexual offenses (OSOs) is rapidly increasing. However, we have little understanding of their characteristics (e.g., demographic, psychological, individual, offense, and risk) and needs. To identify any similarities or differences that are unique to older individuals convicted of sexual offending, it is important to compare such characteristics across the adult lifespan. Therefore, the aim of this systematic review was to specify and synthesize the current knowledge of characteristics across the adult lifespan of the population of individuals convicted of sexual offenses. Five databases were searched and 10,680 results were screened, resulting in 100 studies included in the final review. The findings were grouped into four emergent themes: age of onset and prevalence; offender and offense characteristics; age and the risk of reoffending; and treatment. Implications of the findings from this review are discussed in relation to future research and clinical practice.
Health Information on Waterpipe Lounge Menus to Educate Young Adults: Pilot Study Findings
Authors: Kidanu Azieb W. , Shi Rui , Cruz-Cano Raul , Feldman Robert H. , Butler James , Dyer Typhanye V. , Fryer Craig S. , Clark Pamela I.
Published: June 2021

Background

For years, tobacco risk communication has largely focused on cigarette smoking. New strategies must be developed to adapt to emerging tobacco products, such as waterpipe tobacco smoking (WTS).

Aims

The purpose of this pilot study was to determine the preliminary effects of health information on waterpipe lounge menus on the perceptions of harm and risk from WTS and inform future efficacy interventions for health communication (i.e., educating populations on the risks, harms, and health consequences of WTS).

Method

Participants aged 18 to 24 years ( n = 213) who smoked waterpipe at least monthly were randomized to one of four waterpipe lounge menu groups using a two-by-two experimental design with “warning message” and “nicotine content” as factors.

Results

Those who viewed waterpipe lounge menus that included a warning message had greater perceived relative harm to health and perceived risk of decreased lung function from WTS. Those who viewed waterpipe lounge menus that included nicotine content had greater perceived risk of heart attack from WTS.

Discussion

Participants who were exposed to health warnings of WTS and information on the nicotine content of waterpipe tobacco increased on measures of perceived relative harm and risk of health consequences.

Conclusion

The pilot test results indicate promise for providing health information on waterpipe lounge menus to educate young adults on the harms and risks of WTS.
Aquarium Visitor Engagement with an Ocean Plastics Exhibit: Effects on Self-Reported Intended Single-Use Plastic Reductions and Plastic-Related Environmental Stewardship Actions
Authors: Baechler Britta R. , Granek Elise F. , Carlin-Morgan Kerry A. , Smith Tina E. , Nielsen-Pincus Max
Published: June 2021

Plastic pollution requires, among a suite of other interventions, education to inspire behavioral change and reduce consumption of single-use items. We designed and installed an ocean plastics exhibit at the Oregon Coast Aquarium in Newport, Oregon, USA. We evaluated visitor engagement and the effects of the exhibit on their reported single-use plastic and plastic-related environmental stewardship intentions. Timed interaction observations ( n = 317) revealed children (0–17 years) engaged more with interactive elements than adults (18–80+ years). Ten single-use plastic reduction and plastic stewardship intentions were evaluated through structured questionnaires; the top three behaviors visitors intended to change were: using a reusable straw (37.4%), cleaning the beach (37.4%), and bring-your-own bag to the store or market (33.0%). 18 to 29 year olds had the highest change in desire to address the ocean plastics problem before and after seeing the exhibit, but the lowest likelihood of engaging in either single-use plastics reduction or plastic stewardship actions of all age groups.
Police Officer Use of Force Mindset and Street-Level Behavior
Authors: Paoline Eugene A. , Terrill William , Somers Logan J.
Published: June 2021

Police use of force has been the focus of a number of external assessments of the occupation for over 50 years. Recent concerns have, once again, prompted calls for additional research on the correlates of this behavior, especially as it relates to officer use of force mindset. Relying on a framework articulated as part of a use of force symposium of academics and practitioners, the current study utilizes survey and behavioral data from officers in six police agencies to examine dimensions of use of force mindset among officers, and the degree to which attitudinal mindset influences use of force behavior. The implications for police scholarship and practice are discussed.
Diagnostic- and sex-based differences in depression symptoms in autistic and neurotypical early adolescents
Authors: Schwartzman Jessica M , Williams Zachary J , Corbett Blythe A
Published: June 2021

Prevalence rates of depression are higher in autistic youth than neurotypical peers, yet the effects of autism spectrum disorder diagnosis and sex on depressive symptom severity remain incompletely understood, particularly in specific age groups. Using the Children’s Depression Inventory, Second Edition, this study explored diagnostic- and sex-based differences in depressive symptom severity in a sample of 212 autistic and neurotypical early adolescents (10:0–13:5 years). Significant group differences were found according to autism spectrum disorder diagnosis [ d = 0.587, 95% confidence interval (0.308, 0.867)] and sex [ d = 0.365, 95% confidence interval (0.089, 0.641)], with more depressive symptoms endorsed in the autism spectrum disorder and female groups. However, the interaction of diagnosis and sex was not significant, suggesting an additive risk of autism spectrum disorder status and female sex. Item-level analyses showed diagnostic differences on nearly half of the CDI-2 items with higher severity in the autism spectrum disorder group (Probability of Superiority range = 0.42–0.65), differences within the sexes, and differences by diagnosis, which persisted when limiting analyses to children with high levels of depressive symptoms. A more nuanced understanding of symptom endorsement and the roles of diagnosis and sex may uncover salient intervention targets for depression in the unique context of autism spectrum disorder.

Lay abstract

Depression is more common in autistic adolescents than their neurotypical peers, but the effects of diagnosis and sex on the severity and types of depressive symptoms remain unclear. The study explored diagnostic- and sex-based differences in depressive symptoms in 212 autistic and neurotypical early adolescents. Results show that autism spectrum disorder and female may pose elevated risks, and depressive symptoms related to interpersonal problems and negative self-esteem are more frequent in autism spectrum disorder. Autistic males and females endorsed similar severity and type of depressive symptoms, but unique differences emerged when compared to sex-matched neurotypical peers. Exploratory analyses in a clinical subsample of early adolescents with elevated depressive symptoms (Children’s Depression Inventory, Second Edition, Total T-score ⩾60) revealed more endorsement of beliefs of worthlessness in autistic early adolescents. Findings suggest initial intervention targets for treating depression in autistic early adolescents.
Mathematical modeling and experimental study on solid–liquid suspension separation in ultrasonic standing wave field
Authors: Wang Yajing , Wu Liqun , Wang Yaxing , Fan Yafei
Published: June 2021

A new method of removing waste chips is proposed by focusing on the key factors affecting the processing quality and efficiency of high energy beams. Firstly, a mathematical model has been established to provide the theoretical basis for the separation of solid–liquid suspension under ultrasonic standing wave. Secondly, the distribution of sound field with and without droplet has been simulated. Thirdly, the deformation and movement of droplets are simulated and tested. It is found that the sound pressure around the droplet is greater than the sound pressure in the droplet, which can promote the separation of droplets and provide theoretical support for the ultrasonic suspension separation of droplet; under the interaction of acoustic radiation force, surface tension, adhesion, and static pressure, the droplet is deformed so that the gas fluid around the droplet is concentrated in the center to achieve droplet separation, and the droplet just as a flat ball with a central sag is stably suspended in the acoustic wave node.
Optimizing the ultrasonication effect in stir-casting process of aluminum hybrid composite using desirability function approach and artificial neural network
Authors: Kamaraj Logesh , Hariharasakthisudhan P , Arul Marcel Moshi A
Published: June 2021

The ultrasonic-assisted stir-casting technique improves the uniform dispersion of nano-reinforcements in aluminum hybrid metal matrix composites. In the present study, the process parameters of the ultrasonic-assisted stir-casting method, such as ultrasonic vibration time, and depth of ultrasonic vibration along with the speed of mechanical stirrer, are optimized on A356 hybrid composite material optimally reinforced with aluminum nitride, multiwalled carbon nanotubes, graphite particles, and aluminum metal powder using the desirability function approach. The process parameters are optimized against the response factors such as porosity, ultimate tensile strength, and wear rate of the composites. The optimum combination of input factors is identified as stirring speed (600 r/min), ultrasonic vibration time (2 min), and depth of ultrasonic vibration (40 mm) among the selected range. The corresponding output response values are found to be porosity (1.4%), ultimate tensile strength (247 MPa), and wear rate (0.0013 mm3/min). The ANOVA results have revealed that depth of ultrasonic vibration showed significant contribution among the input factors. An artificial neural network model is developed and validated for the given set of experimental data.
Systematic Review of Studies on Visual Phonics
Authors: Kart Ayse N.
Published: June 2021

Visual Phonics is a multisensory teaching tool that has the potential to improve reading outcomes. The purpose of this systematic review is to examine studies on Visual Phonics to provide a comprehensive understanding of the effects on code-related skills. Thirteen studies met the inclusion criteria. The results demonstrate that Visual Phonics can be an effective strategy to teach code-related skills for at-risk hearing kindergarteners and d/Deaf and hard of hearing students, regardless of the degree of hearing loss, grade placement, communication method, home language, and prevalence of an additional disability. A number of these studies contain limitations such as a small sample size, difficulty with obtaining a randomized sample, lack of a control group, and difficulty with the generalization of findings. Therefore, there is a need for additional research on the effects of Visual Phonics and its progression to becoming an evidence-based practice.
KDM1A and KDM3A promote tumor growth by upregulating cell cycle-associated genes in pancreatic cancer
Authors: Hou Xuyang , Li Qiuguo , Yang Leping , Yang Zhulin , He Jun , Li Qinglong , Li Daming
Published: June 2021

Pancreatic cancer is a highly malignant cancer of the pancreas with a very poor prognosis. Methylation of histone lysine residues is essential for regulating cancer physiology and pathophysiology, mediated by a set of methyltransferases (KMTs) and demethylases (KDMs). This study surveyed the expression of methylation regulators functioning at lysine 9 of histone 3 (H3K9) in pancreatic lesions and explored the underlying mechanisms. We analyzed KDM1A and KDM3A expression in clinical samples by immunohistochemical staining and searching the TCGA PAAD program and GEO datasets. Next, we identified the variation in tumor growth in vitro and in vivo after knockdown of KDM1A or KDM3A and explored the downstream regulators of KDM1A and KDM3A via RNA-seq, and gain- and loss-of-function assays. Eleven H3K9 methylation regulators were highly expressed in pancreatic cancer, and only KDM1A and KDM3A expression positively correlated with the clinicopathological characteristics in pancreatic cancer. High expression of KDM1A or KDM3A positively correlated with pathological grade, lymphatic metastasis, invasion, and clinical stage. Kaplan–Meier analysis indicated that a higher level of KDM1A or KDM3A led to a shorter survival period. Knockdown of KDM1A or KDM3A led to markedly impaired tumor growth in vitro and in vivo. Mechanistically, CCNA2, a cell cycle-associated gene was partially responsible for KDM1A knockdown-mediated effect and CDK6, also a cell cycle-associated gene was partially responsible for KDM3A knockdown-mediated effect on pancreatic cancer cells. Our study demonstrates that KDM1A and KDM3A are highly expressed in pancreatic cancer and are intimately correlated with clinicopathological factors and prognosis. The mechanism of action of KDM1A or KDM3A was both linked to the regulation of cell cycle-associated genes, such as CCNA2 or CDK6, respectively, by an H3K9-dependent pathway.
Driving and steering collision avoidance system of autonomous vehicle with model predictive control based on non-convex optimization
Authors: Song Yuho , Huh Kunsoo
Published: June 2021

A planar motion control system is proposed for autonomous vehicles not only to follow the lanes, but also to avoid collisions by braking, accelerating, and steering. The supervisor is designed first to determine the desired speed and the risk of the maneuvering due to road boundaries and obstacles. In order to allow lane changes on multi-lane roads, the model predictive controller is formulated based on the probabilistic non-convex optimization. The micro-genetic algorithm is applied to calculate the target speed and target steering angle in real time. A software-in-the-loop unit is constructed with the Rapid Control Prototyping device in the vehicle communication environment. The performance of the proposed system is verified for various collision avoidance scenarios and the simulation results demonstrate the safe and effective driving performance of autonomous vehicles with no collision on multi-lane road.
Establishment of instantaneous milling force prediction model for multi-directional CFRP laminate
Authors: Ning Haifeng , Zheng Hualin , Yuan Xinman
Published: June 2021

Carbon fiber reinforced polymer (CFRP) is widely used in the aerospace field due to its light weight and high strength. The CFRP milling process is prone to damage such as burrs and tears. The cutting force is closely related to the damage of CFRP and tool wear. In this paper, a back propagation (BP) neural network model of cutting force and edge force coefficients was established. The model considers the effects of instantaneous uncut chip thickness, fiber cutting angle, spindle speed, and axial depth of cut. The unidirectional CFRP laminate instantaneous milling model considering the cutting edge force was further established. The instantaneous milling force prediction model was extended to multi-directional CFRP laminates. And the relationship between the damage mechanism of CFRP and the instantaneous milling force was analyzed. Experiments have proved that the instantaneous milling force prediction model built in this paper has high accuracy.
Does participatory ergonomics reduce musculoskeletal pain in sonographers? A mixed methods study
Authors: Sweeney Kristie , Ginn Karen , Spurway Jacqueline , Clarke Jillian , Mackey Martin
Published: June 2021

Introduction

Sonographers in the Western New South Wales Local Health District (WNSWLHD) reported a musculoskeletal pain prevalence rate of 95%. Participatory ergonomics, where workers are consulted about improving work conditions, was utilised to identify work-related musculoskeletal disorder (WMSD) risks and potential solutions. The aim of this study was to compare the prevalence of WMSD in a cohort of sonographers before and after implementation of ergonomic changes that were driven by recommendations from a participatory ergonomics approach.

Methods

This observational mixed methods study analysed the impact of participatory ergonomic-driven interventions on changes on musculoskeletal pain in a cohort of sonographers employed within the WNSWLHD. A retrospective analysis of 10 sonographer WMSD pain surveys over five sites was completed, along with semi-structured interviews regarding which interventions were perceived as useful, which interventions were not implemented and any barriers to implementation.

Results

Installation of patient monitors, use of ergonomic scanning techniques and job rotation were perceived as responsible for decreased musculoskeletal pain. Taking lunch breaks and microbreaks, use of antifatigue mats and having two sonographers perform mobile exams were not fully implemented. No interventions were perceived as responsible for increased pain.

Conclusion

This small study provides preliminary evidence that a participatory ergonomics approach facilitated identification of occupation and site-specific risks for WMSD in the WNSWLHD, allowing implementation of ergonomic changes to be tailored to the workplace, resulting in a safer work environment for sonographers.
Sport coaches’ positive emotions, task performance, and well-being: The mediating role of work satisfaction
Authors: Cho Heetae , Kim Sunghoon , Lee Ye Hoon
Published: June 2021

Although previous studies have uncovered various factors to understand sport coaches’ life, the role of positive emotions toward coaching experience and their impacts on behavioral and psychological outcomes remain unknown. As such, the purpose of this study was to examine the influence of sport coaches’ positive emotions on their work satisfaction and task performance and further measure the factors that would facilitate the understanding of sport coaches’ well-being. A total of 519 responses were collected from sport coaches in Singapore. Results showed that all the hypothesized relationships were significant, highlighting work satisfaction to play a mediating role in the relationship between positive emotions and task performance and between positive emotions and well-being. The findings of this study contribute to the advancement of the theoretical knowledge on the role of positive emotions in the context of sport management and provide valuable practical implications for sport organizations.
Appropriateness of transthoracic echocardiography in preoperative elective joint arthroplasty patients
Authors: Yuan Victor , Cowie Brian S
Published: June 2021

Elective joint arthroplasty is a commonly performed procedure with postoperative cardiovascular complications occurring in up to 3% of elderly patients. Preoperative cardiac evaluation, including transthoracic echocardiography, may improve risk stratification and optimise perioperative outcomes in patients having non-cardiac surgery.

This study aimed to investigate the frequency, indications, appropriateness and consequences of preoperative transthoracic echocardiography in elective joint arthroplasty patients. A one-year retrospective audit was conducted for patients who had elective joint arthroplasties performed at St Vincent's Hospital Melbourne. Patient demographics, transthoracic echocardiography indication, time between transthoracic echocardiography being ordered, performed and its impact on date of surgery were obtained via database and manual chart review. Appropriateness of transthoracic echocardiography was determined in accordance with international guidelines. This study analysed 609 elective joint arthroplasties. Of these, 116 (19%) already had a recent transthoracic echocardiography. Of the remaining 493 patients, 192 (39%) received a resting transthoracic echocardiography. Only 92 (48%) of the transthoracic echocardiography’s ordered were deemed appropriate. Transthoracic echocardiography resulted in a significant delay of 31 days in time to surgery.

This study indicates that almost 40% of elective joint arthroplasty patients with no recent echocardiogram are having a resting transthoracic echocardiography as part of their preoperative assessment. In 52% of cases, these are not clearly appropriate and result in delays to surgery.
Thirty-day morbidity and mortality following revision total shoulder arthroplasty in octogenarians
Authors: Gupta Puneet , Quan Theodore , Zimmer Zachary R
Published: June 2021

Background

Octogenarians are at an increased risk of morbidity and mortality following various surgeries, but this has not yet been well explored in octogenarians undergoing revision total shoulder arthroplasty (RTSA). Thus, the purpose of this study was to analyze whether octogenarians undergoing RTSA are at an increased risk of 30-day postoperative complications, readmissions, and mortality relative to the younger geriatric population.

Methods

Data of patients who underwent RTSA from 2013 to 2018 were obtained from a large de-identified database. Patients were divided into two cohorts: ages 65–79 and ages 80–89. Demographic data, comorbidities, and postoperative complications were collected and compared between the two cohorts. Bivariate and multivariate analyses were performed.

Results

On bivariate analyses, patients aged 80–89 were more likely to develop pulmonary embolism (p = 0.014) and extended length of stay more than 3 days (p = 0.006) compared to the cohort aged 65–79. Following adjustment on multivariate analyses, 80–89 years old patients no longer had an increased likelihood of pulmonary embolism or extended length of stay compared to the 65–79 age group. Octogenarians were not found to have higher rates of 30-day readmissions (p = 0.782), mortality (p = 0.507), reoperation (p = 0.785), pneumonia (p = 0.417), urinary tract infection (p = 0.739), or sepsis (p = 0.464) compared to the cohort aged 65–79 following RTSA.

Conclusion

Age greater than 80 should not be used independently as a factor for evaluating whether a geriatric patient is a proper candidate for RTSA.
How Productive Are the Microfinance Institutionsin Bangladesh? An Application of Malmquist Productivity Index
Authors: Rana Md. Sohel , Banna Hasanul , Mia Md Aslam , Ismail Izlin Binti , Ismail Mohd Nazari Bin
Published: June 2021

The poverty reduction and financial inclusion of Sustainable Development Goals (SDG) by 2030 can be significantly facilitated by the microfinance industry. However, it is pertinent to assess the sustainability of microfinance institutions (MFIs) in serving this purpose. The estimation of productivity of MFIs in Bangladesh gives a glimpse of their ability to fulfil the dual objectives of financial sustainability and social outreach. Hence, this study aims to measure the productivity of MFIs in Bangladesh using secondary data obtained from the Microfinance Information Exchange (MIX) market. The study employs Malmquist Productivity Index (MPI), which is an extension of the Data Envelopment Analysis (DEA) to estimate the overall, social and financial productivities of 26 MFIs in Bangladesh during the period from 2009 to 2018. In general, this study revealed that majority of the MFIs’ overall productivity score varies between 0.9 and 1.20. Moreover, we observed that the social and financial productivities of MFIs in Bangladesh progressed during the entire study period, except for the years 2011 and 2017. This development may be attributed to the average growth in catch-up and technological effect witnessed during the study period. The study has also applied sensitivity analysis by changing the output to evaluate the robustness of the overall productivity results; consequently, the new estimates followed a similar pattern (mostly) and further corroborate the outcomes of this study.

JEL Classifications: C14, O43, G21
Renal tubular acidosis and acute kidney injury secondary to cemiplimab
Authors: Rashidi Arash , Herlitz Leal , Tariq Hafsa
Published: June 2021

Immune therapies have transformed the landscape of oncology. Immune checkpoint inhibitors are group of medications, which activate T-Cells to fight against cancer cells. Acute tubulointrestitial nephritis is the most common form of kidney immune-related adverse event. With more use of ICPIs, renal immune related side effects are being recognized more. Here we present a case of renal tubular acidosis with acute kidney injury in a patient with squamous cell carcinoma of the skull who was on Cemiplimab.
Early postoperative pain as a risk factor of shoulder stiffness after arthroscopic rotator cuff repair
Authors: Guity Mohammad Reza , Sobhani Eraghi Amir , Hosseini-Baharanchi Fatemeh Sadat
Published: June 2021

Background

The role of postoperative pain in incidence of shoulder stiffness (SS) after shoulder arthroscopy has not been thoroughly investigated. The present study was conducted to assess the effects of early postoperative pain (EPOP) on onset of SS after arthroscopic rotator cuff (RC) repair.

Materials and methods

In a retrospective analysis of a prospectively collected database, 335 patients who underwent arthroscopic RC repair were evaluated. RC tendons were sutured to the bone using the double-row technique. EPOP was evaluated 1 week after surgery using the visual analog scale (VAS). SS was assessed 3 months after surgery and was categorized into moderate or severe based on shoulder range of motion (ROM). Each type of complication including SS was identified and recorded.

Results

Postoperative shoulder stiffness (POSS) was identified in 121 patients (36.2%) that was moderate in 86 patients (70.1%) and severe in 35 patients (28.9%). After 1 week, VAS pain score was equal to 7.7 ± 3.1 and 4.5 ± 2.1 in the patients with and without stiffness, respectively (p < 0.001). Diabetes and traumatic tear were found to be associated with postoperative stiffness (p = 0.046 and p < 0.001, respectively). Similar associations were found on multivariate analysis of data. VAS pain score was higher in the patients with severe stiffness compared with those with moderate stiffness (p < 0.001).

Conclusions

Our findings revealed that EPOP is associated with shoulder stiffness after arthroscopic RC repair. Therefore, strategies to ameliorate EPOP could be opted to decrease rate of POSS.

Level of evidence

Level IV
Devising Hyperthermia Dose of NIR-Irradiated Cs0.33WO3 Nanoparticles for HepG2 Hepatic Cancer Cells
Authors: Hu Po-Sheng , Chou Hsiu-Jen , Chen Chi-An , Wu Po-Yi , Hsiao Kai-Hsien , Kuo Yu-Min
Published: June 2021

Hyperthermia is one of the most patient-friendly methods to cure cancer diseases owing to its noninvasiveness, minimally induced side-effects and toxicity, and easy implementation, prompting the development of novel therapeutic methods like photothermally triggering dose system. This research herein interrogates the variables of photothermal effects of Cs0.33WO3 nanoparticles (NPs), the duration of irradiation, optical power density and NP concentration, upon HepG2 liver cancer cell line in vitro, leading to the formulation of a near-infrared (NIR)-irradiated thermal dose. Expressly, the NPs with particulate feature sizes of 120 nm were synthesized through a series of oxidation–reduction (REDOX) reaction, thermal annealing and wet-grinding processes, and the subsequent characterization of physical, compositional, optical, photothermal properties were examined using dynamic light scattering (DLS), energy-dispersive X-ray spectroscopy (EDS), scanning and tunneling electron microscopies (SEM and TEM), X-ray diffraction (XRD) and visible-near-infrared (VIS–NIR) photospectroscopy. Cytotoxicity of the NPs and its irradiation parameters were obtained for the HepG2 cells. By incubating the cells with the NPs, the state of endocytosis was verified, and the dependence of cellular survival rate on the variable parameters of photothermal dose was determined while maintaining the medium temperature of the cell-containing culture dish at human body temperature around 36.5 °C.
Proteomic and Transcriptomic Analyses Provide Novel Insights into the Crucial Roles of Host-Induced Carbohydrate Metabolism Enzymes in Xanthomonas oryzae pv. oryzae Virulence and Rice-Xoo Interaction
Authors: Wu Guichun , Zhang Yuqiang , Wang Bo , Li Kaihuai , Lou Yuanlai , Zhao Yancun , Liu Fengquan
Published: June 2021

Background

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial leaf blight, a devastating rice disease. The Xoo-rice interaction, wherein wide ranging host- and pathogen-derived proteins and genes wage molecular arms race, is a research hotspot. Hence, the identification of novel rice-induced Xoo virulence factors and characterization of their roles affecting rice global gene expression profiles will provide an integrated and better understanding of Xoo-rice interactions from the molecular perspective.

Results

Using comparative proteomics and an in vitro interaction system, we revealed that 5 protein spots from Xoo exhibited significantly different expression patterns (|fold change| > 1.5) at 3, 6, 12 h after susceptible rice leaf extract (RLX) treatment. MALDI-TOF MS analysis and pathogenicity tests showed that 4 host-induced proteins, including phosphohexose mutase, inositol monophosphatase, arginase and septum site-determining protein, affected Xoo virulence. Among them, mutants of two host-induced carbohydrate metabolism enzyme-encoding genes, ΔxanA and Δimp, elicited enhanced defense responses and nearly abolished Xoo virulence in rice. To decipher rice differentially expressed genes (DEGs) associated with xanA and imp, transcriptomic responses of ΔxanA-treated and Δimp-treated susceptible rice were compared to those in rice treated with PXO99A at 1 and 3 dpi. A total of 1521 and 227 DEGs were identified for PXO99A vs Δimp at 1 and 3 dpi, while for PXO99A vs ΔxanA, there were 131 and 106 DEGs, respectively. GO, KEGG and MapMan analyses revealed that the DEGs for PXO99A vs Δimp were mainly involved in photosynthesis, signal transduction, transcription, oxidation-reduction, hydrogen peroxide catabolism, ion transport, phenylpropanoid biosynthesis and metabolism of carbohydrates, lipids, amino acids, secondary metabolites, hormones, and nucleotides, while the DEGs from PXO99A vs ΔxanA were predominantly associated with photosynthesis, signal transduction, oxidation-reduction, phenylpropanoid biosynthesis, cytochrome P450 and metabolism of carbohydrates, lipids, amino acids, secondary metabolites and hormones. Although most pathways were associated with both the Δimp and ΔxanA treatments, the underlying genes were not the same.

Conclusion

Our study identified two novel host-induced virulence factors XanA and Imp in Xoo, and revealed their roles in global gene expression in susceptible rice. These results provide valuable insights into the molecular mechanisms of pathogen infection strategies and plant immunity.
Computational comparison of common event-based differential splicing tools: practical considerations for laboratory researchers
Authors: Muller Ittai B. , Meijers Stijn , Kampstra Peter , van Dijk Steven , van Elswijk Michel , Lin Marry , Wojtuszkiewicz Anna M. , Jansen Gerrit , de Jonge Robert , Cloos Jacqueline
Published: June 2021

Background

Computational tools analyzing RNA-sequencing data have boosted alternative splicing research by identifying and assessing differentially spliced genes. However, common alternative splicing analysis tools differ substantially in their statistical analyses and general performance. This report compares the computational performance (CPU utilization and RAM usage) of three event-level splicing tools; rMATS, MISO, and SUPPA2. Additionally, concordance between tool outputs was investigated.

Results

Log-linear relations were found between job times and dataset size in all splicing tools and all virtual machine (VM) configurations. MISO had the highest job times for all analyses, irrespective of VM size, while MISO analyses also exceeded maximum CPU utilization on all VM sizes. rMATS and SUPPA2 load averages were relatively low in both size and replicate comparisons, not nearing maximum CPU utilization in the VM simulating the lowest computational power (D2 VM). RAM usage in rMATS and SUPPA2 did not exceed 20% of maximum RAM in both size and replicate comparisons while MISO reached maximum RAM usage in D2 VM analyses for input size. Correlation coefficients of differential splicing analyses showed high correlation (β > 80%) between different tool outputs with the exception of comparisons of retained intron (RI) events between rMATS/MISO and rMATS/SUPPA2 (β < 60%).

Conclusions

Prior to RNA-seq analyses, users should consider job time, amount of replicates and splice event type of interest to determine the optimal alternative splicing tool. In general, rMATS is superior to both MISO and SUPPA2 in computational performance. Analysis outputs show high concordance between tools, with the exception of RI events.
PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets
Authors: Pradier Léa , Tissot Tazzio , Fiston-Lavier Anna-Sophie , Bedhomme Stéphanie
Published: June 2021

Background

Plasmids are mobile genetic elements that often carry accessory genes, and are vectors for horizontal transfer between bacterial genomes. Plasmid detection in large genomic datasets is crucial to analyze their spread and quantify their role in bacteria adaptation and particularly in antibiotic resistance propagation. Bioinformatics methods have been developed to detect plasmids. However, they suffer from low sensitivity (i.e., most plasmids remain undetected) or low precision (i.e., these methods identify chromosomes as plasmids), and are overall not adapted to identify plasmids in whole genomes that are not fully assembled (contigs and scaffolds).

Results

We developed PlasForest, a homology-based random forest classifier identifying bacterial plasmid sequences in partially assembled genomes. Without knowing the taxonomical origin of the samples, PlasForest identifies contigs as plasmids or chromosomes with a F1 score of 0.950. Notably, it can detect 77.4% of plasmid contigs below 1 kb with 2.8% of false positives and 99.9% of plasmid contigs over 50 kb with 2.2% of false positives.

Conclusions

PlasForest outperforms other currently available tools on genomic datasets by being both sensitive and precise. The performance of PlasForest on metagenomic assemblies are currently well below those of other k-mer-based methods, and we discuss how homology-based approaches could improve plasmid detection in such datasets.
UniBind: maps of high-confidence direct TF-DNA interactions across nine species
Authors: Puig Rafael Riudavets , Boddie Paul , Khan Aziz , Castro-Mondragon Jaime Abraham , Mathelier Anthony
Published: June 2021

Background

Transcription factors (TFs) bind specifically to TF binding sites (TFBSs) at cis-regulatory regions to control transcription. It is critical to locate these TF-DNA interactions to understand transcriptional regulation. Efforts to predict bona fide TFBSs benefit from the availability of experimental data mapping DNA binding regions of TFs (chromatin immunoprecipitation followed by sequencing - ChIP-seq).

Results

In this study, we processed ~ 10,000 public ChIP-seq datasets from nine species to provide high-quality TFBS predictions. After quality control, it culminated with the prediction of ~ 56 million TFBSs with experimental and computational support for direct TF-DNA interactions for 644 TFs in > 1000 cell lines and tissues. These TFBSs were used to predict > 197,000 cis-regulatory modules representing clusters of binding events in the corresponding genomes. The high-quality of the TFBSs was reinforced by their evolutionary conservation, enrichment at active cis-regulatory regions, and capacity to predict combinatorial binding of TFs. Further, we confirmed that the cell type and tissue specificity of enhancer activity was correlated with the number of TFs with binding sites predicted in these regions. All the data is provided to the community through the UniBind database that can be accessed through its web-interface (https://unibind.uio.no/), a dedicated RESTful API, and as genomic tracks. Finally, we provide an enrichment tool, available as a web-service and an R package, for users to find TFs with enriched TFBSs in a set of provided genomic regions.

Conclusions

UniBind is the first resource of its kind, providing the largest collection of high-confidence direct TF-DNA interactions in nine species.
Construction of a high-density linkage map and graphical representation of the arrangement of transcriptome-based unigene markers on the chromosomes of onion, Allium cepa L.
Authors: Fujito Satoshi , Akyol Turgut Yigit , Mukae Takuya , Wako Tadayuki , Yamashita Ken-ichiro , Tsukazaki Hikaru , Hirakawa Hideki , Tanaka Keisuke , Mine Yoko , Sato Shusei , Shigyo Masayoshi
Published: June 2021

Background

Genomic information for Allium cepa L. is limited as it is heterozygous and its genome is very large. To elucidate potential SNP markers obtained by NGS, we used a complete set of A. fistulosum L.-A. cepa monosomic addition lines (MALs) and doubled haploids (DHs). These were the parental lines of an A. cepa mapping population for transcriptome-based SNP genotyping.

Results

We mapped the transcriptome sequence reads from a series of A. fistulosum-A. cepa MALs onto the unigene sequence of the doubled haploid shallot A. cepa Aggregatum group (DHA) and compared the MAL genotype call for parental bunching onion and shallot transcriptome mapping data. We identified SNP sites with at least four reads on 25,462 unigenes. They were anchored on eight A. cepa chromosomes. A single SNP site was identified on 3,278 unigenes and multiple SNPs were identified on 22,184 unigenes. The chromosome marker information was made public via the web database Allium TDB (http://alliumtdb.kazusa.or.jp/). To apply transcriptome based genotyping approach for genetic mapping, we gathered RNA sequence data from 96 lines of a DHA × doubled haploid bulb onion A. cepa common onion group (DHC) mapping population. After selecting co-dominant SNP sites, 16,872 SNPs were identified in 5,339 unigenes. Of these, at least two SNPs with identical genotypes were found in 1,435 unigenes. We developed a linkage map using genotype information from these unigenes. All unigene markers mapped onto the eight chromosomes and graphical genotyping was conducted based on the unigene order information. Another 2,963 unigenes were allocated onto the eight chromosomes. To confirm the accuracy of this transcriptome-based genetic linkage map, conventional PCR-based markers were used for linkage analysis. All SNP - and PCR-based markers were mapped onto the expected linkage groups and no inconsistency was found among these chromosomal locations.

Conclusions

Effective transcriptome analysis with unique Allium resources successfully associated numerous chromosome markers with unigene information and a high-density A. cepa linkage map. The information on these unigene markers is valuable in genome sequencing and useful trait detection in Allium.
Immunization with Pneumocystis carinii A121–85 antigen activates immune function against P. carinii
Authors: Tong Tong , Wang Zhongxin , Xu Yuanhong , Shen Jilu
Published: June 2021

Background

Pneumocystis pneumonia (PcP), which is caused by Pneumocystis carinii, is a life-threatening infection that affects immunocompromised individuals. Unfortunately, chemoprophylaxis and dapsone are only effective for half of the patients with PcP, indicating that additional preventive methods are needed. We predicated the pneumocystis surface protein A12 sequence 1–85 by DNAStar software and BepiPred, and identified it as a potential vaccine candidate by bioresearch.

Methods

We used recombinant A121–85 as antigen to immunized mice and detected serum titer of IgG, expression of inflammatory factors by EILSA, qRT-PCR and flow cytometry.

Results

Our results showed that immunization with recombinant A121–85 increased the serum titer of IgG, promoted the secretion of T lymphocytes, increased the expression of inflammatory factors, and elevated lung inflammatory injury in mice.

Conclusions

Our findings suggest that A121–85 is a potential vaccine target for preventing Pneumocystis carinii. The evaluation of A121–85-elicited antibodies in the prevention of PcP in humans deserves further investigation.
Application of machine learning in bacteriophage research
Authors: Nami Yousef , Imeni Nazila , Panahi Bahman
Published: June 2021

Phages are one of the key components in the structure, dynamics, and interactions of microbial communities in different bins. It has a clear impact on human health and the food industry. Bacteriophage characterization using in vitro approaches are time/cost consuming and laborious tasks. On the other hand, with the advent of new high-throughput sequencing technology, the development of a powerful computational framework to characterize the newly identified bacteriophages is inevitable for future research. Machine learning includes powerful techniques that enable the analysis of complex datasets for knowledge discovery and pattern recognition. In this study, we have conducted a comprehensive review of machine learning methods application using different types of features were applied in various aspects of bacteriophage research including, automated curation, identification, classification, host species recognition, virion protein identification, and life cycle prediction. Moreover, potential limitations and advantages of the developed frameworks were discussed.
The characterization of key physiological traits of medicinal cannabis (Cannabis sativa L.) as a tool for precision breeding
Authors: Naim-Feil Erez , Pembleton Luke W. , Spooner Laura E. , Malthouse Alix L. , Miner Amy , Quinn Melinda , Polotnianka Renata M. , Baillie Rebecca C. , Spangenberg German C. , Cogan Noel O. I.
Published: June 2021

Background

For millennia, drug-type cannabis strains were extensively used for various medicinal, ritual, and inebriant applications. However, cannabis prohibition during the last century led to cultivation and breeding activities being conducted under clandestine conditions, while scientific development of the crop ceased. Recently, the potential of medicinal cannabis has been reacknowledged and the now expanding industry requires optimal and scientifically characterized varieties. However, scientific knowledge that can propel this advancement is sorely lacking. To address this issue, the current study aims to provide a better understanding of key physiological and phenological traits that can facilitate the breeding of advanced cultivars.

Results

A diverse population of 121 genotypes of high-THC or balanced THC-CBD ratio was cultivated under a controlled environment facility and 13 plant parameters were measured. No physiological association across genotypes attributed to the same vernacular classification was observed. Floral bud dry weight was found to be positively associated with plant height and stem diameter but not with days to maturation. Furthermore, the heritability of both plant height and days to maturation was relatively high, but for plant height it decreased during the vegetative growth phase. To advance breeding efficacy, a prediction equation for forecasting floral bud dry weight was generated, driven by parameters that can be detected during the vegetative growth phase solely.

Conclusions

Our findings suggest that selection for taller and fast-growing genotypes is likely to lead to an increase in floral bud productivity. It was also found that the final plant height and stem diameter are determined by 5 independent factors that can be used to maximize productivity through cultivation adjustments. The proposed prediction equation can facilitate the selection of prolific genotypes without the completion of a full cultivation cycle. Future studies that will associate genome-wide variation with plants morphological traits and cannabinoid profile will enable precise and accelerated breeding through genomic selection approaches.