bluuebunny/crossref_metadata_2025 huggingface dataset:
An active learning Kriging-based method combining the weight information entropy function and the adaptive candidate sample pool
Authors: Li Jingkui , Liu Wenqi , Zhou Yan , Li Zhandong
Published: July 2022

The reliability analysis methods based on the Kriging model have been explored to update the design of experiments (DoE), but the number of calls to the performance function is high. In this paper, a new active learning method combining the weight information entropy function (WH) and the adaptive candidate sample pool is proposed to improve the reliability analysis efficiency. Based on the information entropy function (H), the learning function WH is constructed to consider Kriging variance and the joint probability density function (PDF). In this proposed method, the sample points can be assigned different weight by the learning function WH according to the important degrees of sample points. The point which not only nears the limit state function (LSF), but also has a high probability density function value and large Kriging variance is assigned more weight than others. To select the sample points with lower confidence level, the adaptive candidate sample pool is generated by Markov Chain Monte Carlo (MCMC) simulation. The Kriging model can be updated efficiently by the proposed method. Four numerical examples and an engineering example with implicit performance function are used to verify the efficiency and accuracy of the proposed method. The results show that the proposed method can significantly improve the computational efficiency of the reliability analysis without losing accuracy.
Body-worn cameras: An effective or cosmetic policing response to domestic and family violence?
Authors: Pfitzner Naomi , Walklate Sandra , McCulloch Jude
Published: July 2022

Drawing together the literature on police body-worn cameras and video-recorded evidence in domestic and family violence matters, this article explores whether technology can ‘fix’ criminal justice responses to domestic and family violence. We argue that the use of police body-worn cameras and digitally recorded audio-visual evidence in domestic and family violence matters is not a cure-all for deficiencies in criminal justice responses to domestic and family violence. While the use of such technologies may alleviate some of the deficiencies highlighted in the Australian state of Victoria’s 2016 Royal Commission into Family Violence, it raises serious concerns about victim’s agency and privacy. We argue that the introduction of such technologies requires significant investment in training and education – for police to adapt to their changed role and for judicial officers, legal practitioners and potential jurors in understanding and interpreting victim survivor behaviour on film.
Sheilas and the Beeb: How the BBC provided liberating pathways for ABC women in the early years of television
Authors: Andrews Kylie
Published: July 2022

This article discusses the important role the BBC played in advancing the careers of ABC women in the post-war era. Adopting an integrated, transnational approach, it revisualises the British broadcasting empire from a dominion perspective, a gendered perspective. This research follows ABC television producers as they undertook transformative, transnational excursions and recognises the necessary mobility, flexibility and ingenuity women activated in order to succeed. It identifies how they exploited the imbalanced dominion dynamic and strategically used their BBC experiences to counteract the compromising gender constraints of their local production environments.
Comparison of GPS derived variables based on home versus away matches in the Asian professional soccer team
Authors: Nobari Hadi , Fani Maryam , Mainer-Pardos Elena , Oliveira Rafael
Published: July 2022

Professional soccer with high training loads is defined with weekly competition. The purpose of this study was to compare external training load data of GPS derived variables that preceded a home versus away match. Twenty-two weeks of a national league meet schedule were analyzed, which included 11 home and 11 away matches. Twelve professional soccer players (age, 28.6 ± 2.7 years; height, 182.1 ± 8.6 cm; BMI, 22.6 ± 0.7 kg/m2) participated in this study. All matches were monitored using GPSPORTS systems Pty Ltd. The following variables were selected: total duration of the matches and training sessions, high-speed running distance (18–23 km h−1), sprint distance (>23 km h−1), maximal speed, body load, metabolic power, accelerations Zone1 (<2 m s−2) (AccZ1), accelerations Zone2 (2 –4 m s−2) (AccZ2), accelerations Zone3 (>4 m s−2) (AccZ3), decelerations Zone1 (<−2 m s−2) (DecZ1), decelerations Zone2 (−2 to −4 m s−2) (DecZ2) and decelerations Zone3 (>−4 m s−2) (DecZ3). The results indicated that metabolic power showed higher values at home than away matches [ p = 0.047, ES = 0.53, (−0.28, 1.34)]. Furthermore, there was a higher value in accumulated external training load that preceded away matches for high-speed running and lower value [ p < 0.001, ES = −0.95 (−1.79, −0.10)] for DecZ1 than home matches. In conclusion, external load variables had a higher value in home matches. However, the results showed that high-speed running was higher in away matches, which could be the discretion of the coaches to prepare players for different conditions on the opponent’s field.
Cultivating reflective teachers: Challenging power and promoting pedagogy of self-assessment in Australian, Bhutanese, and Canadian teacher education programs
Authors: DeLuca Christopher , Willis Jill , Dorji Khandu , Sherman Ann
Published: July 2022

In this article, we look at three teacher education programs across three countries—Australia, Bhutan, and Canada—to examine how reflection is cultivated in pre-service teachers (also referred to as teacher candidates) through a pedagogy of self-assessment. We begin from the premise that a cornerstone of effective teaching is the capacity of an educator to reflect on their practice and to use their reflections for professional growth and development. Qualitative data were collected from teacher candidates from one teacher education program in each country to obtain the views and reflections of teacher candidates about the power and pedagogy of self-assessment to inform their learning and development. Analysis of results led to three overarching themes: (a) consistent learning priorities of pre-service teachers as they engage with reflection; (b) pedagogical features that leverage self-assessment strategies to enhance reflective practice; and (c) the possibilities for reflection to facilitate a professional stance towards learning. Each theme is discussed with consideration for teacher education practices and theory.
Comparative Analysis of Secondary Outcomes in Treatment of Charcot Neuropathy: A Systematic Review
Authors: Nsekpong Tyler B. , Amin Atish S. , Ali Shahrukh R. , Beasley Brian J. , Panchbhavi Vinod , Jupiter Daniel C.
Published: July 2022

Background:

Charcot neuroarthropathy (CN) is commonly associated with diabetic neuropathy and can predispose patients to amputations. Management remains a challenge, with no definitive treatment. This study examines major postoperative complications associated with open reduction with internal (intramedullary) nails, fixation, external fixation, or combined internal and external fixation for correction of the deformity.

Methods:

We reviewed available literature using PubMed, OvidSP, Scopus, and Cochrane and searched bibliographies of the included studies to identify additional pertinent references. After review and agreement among 4 raters, a total of 15 studies were included in this analysis.

Results:

Hardware removal rates were 0.133 for intramedullary nails, 0.007 for external fixators, and 0.050 for combined fixation. Rates of hardware complication were 0.182 for intramedullary nails and 0.007 for external fixators. Wound dehiscence occurred at rates of 0.059 for intramedullary nails and 0.216 for combined fixation. The rate of deep infections was 0.031 for intramedullary nails, 0.032 for external fixators, and 0.113 for combined fixation. The rate of irrigation and debridement was 0.007 for external fixators.

Conclusion:

Rates of hardware removal (13.3%) and complications (18.2%) were high with intramedullary nails. Dehiscence (21.6%) and deep infection (11.3%) were high in combined fixation. Other complications occurred relatively rarely.

Level of Evidence:

Level III
A Method for Entubulating Exposed Nerve Ends Following Neurectomy Using a Porcine Extracellular Matrix Nerve Cap
Authors: Thomajan Craig H.
Published: July 2022

Compression and irritation at the plantar aspect of the transverse intermetatarsal ligament may lead to a compressive neuropathy called Morton’s neuroma. There are many treatment options for Morton’s neuroma, with the most common surgical option being traction neurectomy. While there has been success in many surgical procedures, up to 35% of patients treated with traction neurectomy have recurrent pain and up to one-third of these patients have a recurrent stump neuroma. These neuromas are caused by abnormal axonal growth during regeneration, leading to an unorganized mass of fibrotic collagenous tissues, Schwann cells, and axons. More recent surgical treatments of neuromas have included nerve capping, which has been proposed to prevent painful neuroma formation by isolating the nerve end from external chemosignaling and reducing disorganized axonal outgrowth. An off-the-shelf, biocompatible porcine small intestine submucosa (pSIS) derived nerve cap with internal chambering has been investigated in a rodent study, which showed less pain sensitivity and less axonal swirling indicative of reduced likelihood of neuroma formation. Furthermore, a recent clinical study indicated that patients experienced a significant reduction in pain 3 months after Morton’s neuroma excision followed by repair using a nerve cap. This article describes the surgical technique of the aforementioned clinical study to mitigate neuroma formation, where a Morton’s neuroma is excised, and the remaining proximal nerve stump is inserted within a nerve cap and buried in the surrounding muscle.

Level of Evidence: Level V: Expert opinion
T2 Hypointense Schwannoma Masquerading As A Vascular Lesion: A Case Report
Authors: Kons Zachary A. , Regenhardt Robert W. , Dmytriw Adam A. , Vranic Justin E. , Huynh Anh. , Frosch Matthew P. , Borges Lawrence F. , Patel Aman B. , Romero Javier M. , Stapleton Christopher J.
Published: July 2022

Spinal schwannomas are rare nerve root tumors that typically produce subtle symptoms from nerve root compression. These tumors are known to be heterogeneously hyperintense on T2-weighted MRI and avidly enhance with contrast. However, here we describe an L5 spinal schwannoma in a 66-year-old woman that was hypointense on T2-weighted imaging with other radiographic findings more closely aligning with a vascular lesion. The neuroradiologic characteristics on MRI, time resolved MR angiography, and catheter digital subtraction angiography are presented. The patient underwent a full workup for possible dural arteriovenous fistula and thrombosed venous varix before the nerve sheath tumor was discovered intraoperatively and confirmed as a schwannoma on histopathology.
Inner Peace in a Global Crisis: A Case Study of Supported Spiritual Individuation in Acute Onset Phase of COVID-19
Authors: Mistur Elisabeth J. , Scalora Suza C. , Crete Abigail A. , Anderson Micheline R. , Athan Aurélie M. , Chapman Amy L. , Miller Lisa J.
Published: July 2022

Emerging-adult undergraduates (ages 18–25) are at increased risk for mental illness, exacerbated by the COVID-19 pandemic. Simultaneously, emerging adults face developmental tasks including identity development, finding meaning and purpose, and spiritual individuation. A case study approach is used to elucidate processes of undergraduates coping with collective trauma as a potential pathway to trauma-related spiritual growth via Awakened Awareness for Adolescents (AA-A) and emerging adults, a spiritual-mind-body wellness intervention. Awakened Awareness for Adolescents fosters enhanced spiritual perception to support spiritual individuation for improved mental health and well-being. Processes of spiritual individuation supported by AA-A during the COVID-19 pandemic from February to May 2020 are presented using students’ qualitative data and self-report measures of psychopathology, spiritual well-being, emotional regulation, and cognition. Shared cohort ( N = 15) themes and one in-depth case (1) reveal ideographic processes of personal transformation and spiritual growth, (2) generate hypotheses around pathways of trauma-related spiritual growth and spiritual individuation for future research.
Enhancing language task engagement in the instructed language classroom: Voices from Chinse English as a foreign language students and teachers
Authors: Zhang Xue , Huang Yue , Liu Ying
Published: July 2022

Drawing upon self-determination theory, flow theory, and the engagement literature, this study explored language tasks that English as a foreign language (EFL) college students and teachers preferred within their language classrooms and identified common conditions underlying these tasks that could facilitate learners’ engagement. With qualitative survey data collected from 392 Chinese college students and 54 English language teachers, this study confirmed the six principle task engagement conditions, namely, authenticity, social interaction, challenge, autonomy, learning support, and interest, and further extended the conceptualization with Chinese EFL population. In particular, both students and teachers perceived social interaction and interest as the most important task conditions in support of engagement; however, they perceived challenge and autonomy as less important. Divergences emerge, with regard to the perceptions towards authenticity and learning support. These findings provide EFL teachers with insights on how to interpret and incorporate these conditions into task designs so as to enhance engagement.
Hypertrophic Cardiomyopathy in the Elderly: A Case Identified With Genetic Screening
Authors: Del Rio-Pertuz Gaspar , Sethi Pooja , Swaminath Deephak , Argueta-Sosa Erwin
Published: July 2022

Hypertrophic cardiomyopathy (HCM) is a hereditary disease with an autosomal dominant pattern of inheritance, that is caused by a mutation in one of several sarcomere genes that encodes components of the contractile system of the heart. Hypertrophic cardiomyopathy has been described as a disease that is more heavily diagnosed in the second decade of life, that may present with abnormal syncopal episodes or sudden cardiac death. However, with a better understanding of the genetic changes that occur in HCM and with improved imaging techniques, there has now been an increased recognition of a late-onset disease that can occur in the elderly population. We report a case of a 73-year-old woman who was found to have HCM after various clinical events took place.
Quality of acute stroke care in Romania: Achievements and gaps between 2017 and 2022
Authors: Tiu Cristina , Terecoasă Elena Oana , Tuță Sorin , Bălașa Rodica , Simu Mihaela , Sabău Monica , Stan Adina , Radu Răzvan Alexandru , Tiu Vlad , Cășaru Bogdan , Negrilă Anca , Panea Cristina
Published: July 2022

Romania has one of the highest incidences of stroke and one of the highest mortality rates in Europe. The mortality rate due to treatable causes is also very high and is associated with the lowest public spending on healthcare in the European Union. Nonetheless, significant achievements in acute stroke care have been made in Romania in the last 5 years, most notably the increase of the national thrombolysis rate from 0.8% to 5.4%. Numerous educational workshops and constant communication with the stroke centers led to a solid and active stroke network. Due to the joint efforts of this stroke network and the ESO-EAST project, the quality of stroke care has significantly improved. However, Romania still faces many problems: a major lack of specialists in interventional neuroradiology and consequently a low number of stroke patients treated by thrombectomy and carotid revascularization procedures, a low number of neuro-rehabilitation centers and a country-wide lack of neurologists.
Hospitalization rates, stroke unit care, and recurrence rates in Austria’s stroke cohort Epidemiologic analysis of 102,107 patients in a nation-wide acute stroke cohort between 2015 and 2019
Authors: Heidinger Martin , Boehme Christian , Knoflach Michael , Lang Wilfried , Kiechl Stefan , Willeit Peter , Kleyhons Rainer , Tuerk Silvia
Published: July 2022

Introduction:

Continuous analysis of key epidemiologic data is irremissible to adapt health-care systems to trends in stroke epidemiology. We present data from 2015 to 2019 on quality indicators of stroke care, including rates on hospitalization, stroke unit care and recurrence rates using medical record-linkage of in-patient routine documentation.

Patients and methods:

We included stroke/TIA patients admitted to Austrian hospitals between 2015 and 2019 aged ⩾20 years using medical record-linkage.

Results:

In our cohort of 102,107 patients with 107,055 treatment episodes, we could show a significant decrease in 1-year cumulative age-adjusted hospitalization rates per 100,000 in TIA (86.3 [95% CI 84.1–88.5] vs 75.4 [95% CI 73.4–77.4], RR 0.87 [95% CI 0.85–0.90]), ischemic stroke (187.3 [95% CI 184.0–190.5] vs 173.4 [95% CI 170.4–176.5], RR 0.93 [95% CI 0.91–0.94]), and intracerebral hemorrhage (28.5 [95% CI 27.3–29.8] vs 22.8 [95% CI 21.7–23.9], RR 0.80 [95% CI 0.76–0.84]). In ischemic stroke the rate of stroke unit care increased significantly (55.7% vs 69.3%; RR 1.14 [95% CI 1.12–1.17]), and acute 1-year recurrences decreased significantly.

Discussion:

We found a decline of the annual age-adjusted cumulative hospitalization rates in stroke/TIA, a higher age of disease manifestation and less severe strokes, which is probably attributable to improved primary and secondary prevention in Austria. The proportion of patients treated at stroke units increased significantly, however a geographical and age-dependency is still evident.

Conclusion:

Age-adjusted hospitalization rates of stroke/TIA patients decreased, and stroke unit care is increasing but the goal of the Stroke Action Plan for Europe is yet to be reached.
Understanding National Level Logistics Costs: Methodological Approach
Authors: Chakrabartty Satyendra Nath
Published: July 2022

Logistics cost (LC) estimated by different methods are not comparable since cost components differ across countries and are not properly standardised, non-availability of comprehensive reliable data on LC and presence of number of qualitative components. No method of measuring LC has considered probability distributions of the components/dimensions. After review of methods to estimate LC, the article proposes to transfer the j-th component score emerging from questionnaire-based approach to a proposed score ([Formula: see text]) so that [Formula: see text] and follows normal distribution. Logistics cost index (LCI) of i-th country is taken as multiplicative aggregation of ratios of [Formula: see text] at the current period and base period of all components. The index avoids perfect substitutability of arithmetic aggregation, and it satisfies the desired properties of an index including time-reversal test and formation of chain-indices, and enables meaningful comparisons across time and space, better ranking and classifying the countries, identification of critical dimensions/components requiring policy changes, drawing path of decline or increase of LCI over time for a country, computing mean LCI for a group of countries and LCI at Global level, and undertaking statistical analysis under parametric set up. Future investigations suggested reflecting properties of the proposed LCI along with empirical relationships of sector-wise LCI and economic development.

JEL Codes: D57, E23, P44
Using the UDL Framework in Inquiry-Based Science Teaching to Support Students With Extensive Support Needs in Inclusive Classrooms
Authors: Ruhter Lindsay
Published: July 2022

The introduction of new next-generation, multidimensional science standards in the last few years has led to increased expectations in science achievement for all students, including students with extensive support needs (ESN). Inquiry-based teaching is an effective strategy to teach science to support attainment of these new expectations. However, few resources exist for teachers of students with ESN engaging in inquiry-based science instruction. The purpose of this article is to describe the Science Inquiry Lesson Supports Plan, a tool for teachers to organize inquiry-based science teaching within the Universal Design for Learning (UDL) framework for students with ESN in inclusive settings. General and special education teachers can plan science lessons using the 5E model of instruction to teach next-generation science in an inclusive setting, using UDL principles to remove barriers to learning.
P2X7R/NLRP3 signaling pathway-mediated pyroptosis and neuroinflammation contributed to cognitive impairment in a mouse model of migraine
Authors: Wang Yajuan , Shan Zhengming , Zhang Lily , Fan Shanghua , Zhou Yanjie , Hu Luyu , Wang Yue , Li Weidong , Xiao Zheman
Published: July 2022

Migraine is the second most common form of headache disorder and the second leading cause of disability worldwide. Cognitive symptoms ranked second resulting in migraine-related disability, after pain. P2X7 receptor (P2X7R) was recently shown to be involved in hyperalgesia in migraine. However, the role of P2X7R in migraine-related cognitive impairment is still ill-defined. The aim of this study was to explore the molecular mechanisms underlying migraine-related cognitive impairment and the role of P2X7R in it. Here we used a well-established mouse model of migraine that triggered migraine attacks by application of inflammatory soup (IS) to the dura. Our results showed that repeated dural IS stimulation triggered upregulation of P2X7R, activation of NLRP3 inflammasome, release of proinflammatory cytokines (IL-1β and IL-18) and activation of pyroptotic cell death pathway. Gliosis (microgliosis and astrogliosis), neuronal loss and cognitive impairment also occurred in the IS-induced migraine model. No significant apoptosis or whiter matter damage was observed following IS-induced migraine attacks. These pathological changes occurred mainly in the cerebral cortex and to a less extent in the hippocampus, all of which can be prevented by pretreatment with a specific P2X7R antagonist Brilliant Blue G (BBG). Moreover, BBG can alleviate cognitive impairment following dural IS stimulation. These results identified P2X7R as a key contributor to migraine-related cognitive impairment and may represent a potential therapeutic target for mitigating cognitive impairment in migraine.
“… Exercise opportunities became very important”: Scottish older adults’ changes in physical activity during Covid19’
Authors: Tomaz Simone A. , Ryde Gemma C. , Swales Bridgitte , Neely Kacey C. , Andreis Federico , Coffee Pete , Connelly Jenni , Kirkland Andrew , McCabe Louise , Watchman Karen , Martin Jack G. , Pina Ilaria , Whittaker Anna C.
Published: July 2022

Background

The purpose of this study was to explore perceived changes in physical activity (PA) due to Covid19 stay-at-home and social distancing guidance among older adults.

Methods

Participants (n = 1429, 77% female, 84% ≥60 years) living in Scotland completed an online survey in Summer 2020 measuring PA and wellbeing (indexed through loneliness, and health-related quality of life). The survey included open- and closed-ended questions about how these variables changed in response to Covid19 social distancing and ‘shielding’ guidelines.

Results

From the International Physical Activity Questionnaire (IPAQ), the majority reported high volumes of PA, indicative of being ‘moderately’ or ‘highly’ active. When asked specifically about strength training, 12% reported engagement on ≥2d/wk. Most participants reported that PA had changed during this time, citing reduced use of exercise facilities, increased active travel, and online PA classes; although only 16% reported engaging in PA online.

Conclusions

Higher levels of PA were found to be associated with better health-related quality of life. Additional efforts should be made to support PA engagement in older adults, including strength training and other tailored approaches to support individual needs.
The role of ZNF143 overexpression in rat liver cell proliferation
Authors: Ye Bingyu , Shen Wenlong , Zhang Chunyan , Yu Mengli , Ding Xinru , Yin Man , Wang Yahao , Guo Xinjie , Bai Ge , Lin Kailin , Shi Shu , Li Ping , Zhang Yan , Yu Guoying , Zhao Zhihu
Published: July 2022

Background

Zinc finger protein 143(ZNF143), a member of the Krüppel C2H2-type zinc finger protein family, is strongly associated with cell cycle regulation and cancer development. A recent study suggested that ZNF143 plays as a transcriptional activator that promotes hepatocellular cancer (HCC) cell proliferation and cell cycle transition. However, the exact biological role of ZNF143 in liver regeneration and normal liver cell proliferation has not yet been investigated.

Methods

In our study, we constructed a stable rat liver cell line (BRL-3A) overexpressing ZNF143 and then integrated RNA-seq and Cleavage Under Targets and Tagmentation (CUT&Tag) data to identify the mechanism underlying differential gene expression.

Results

Our results show that ZNF143 expression is upregulated during the proliferation phase of liver regeneration after 2/3 partial hepatectomy (PH). The cell counting kit-8 (CCK-8) assay, EdU staining and RNA-seq data analyses revealed that ZNF143 overexpression (OE) significantly inhibited BRL-3A cell proliferation and cell cycle progression. We then performed CUT&Tag assays and found that approximately 10% of ZNF143-binding sites (BSs) were significantly changed genome-wide by ZNF143 OE. However, CCCTC-binding factor (CTCF) binding to chromatin was not affected. Interestingly, the integration analysis of RNA-seq and CUT&Tag data showed that some of genes affected by ZNF143 differential BSs are in the center of each gene regulation module. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that these genes are critical in the maintenance of cell identity.

Conclusion

These results indicated that the expression level of ZNF143 in the liver is important for the maintenance of cell identity. ZNF143 plays different roles in HCC and normal liver cells and may be considered as a potential therapeutic target in liver disease.
Transcriptome changes associated with apple (Malus domestica) root defense response after Fusarium proliferatum f. sp. malus domestica infection
Authors: Duan Yanan , Ma Shurui , Chen Xuesen , Shen Xiang , Yin Chengmiao , Mao Zhiquan
Published: July 2022

Background

Apple replant disease is a soilborne disease caused by Fusarium proliferatum f. sp. malus domestica strain MR5 (abbreviated hereafter as Fpmd MR5) in China. This pathogen causes root tissue rot and wilting leaves in apple seedlings, leading to plant death. A comparative transcriptome analysis was conducted using the Illumina Novaseq platform to identify the molecular defense mechanisms of the susceptible M.26 and the resistant M9T337 apple rootstocks to Fpmd MR5 infection.

Results

Approximately 518.1 million high-quality reads were generated using RNA sequencing (RNA-seq). Comparative analysis between the mock-inoculated and Fpmd MR5 infected apple rootstocks revealed 28,196 significantly differentially expressed genes (DEGs), including 14,572 up-regulated and 13,624 down-regulated genes. Among them, the transcriptomes in the roots of the susceptible genotype M.26 were reflected by overrepresented DEGs. MapMan analysis indicated that a large number of DEGs were involved in the response of apple plants to Fpmd MR5 stress. The important functional groups identified via gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were responsible for fundamental biological regulation, secondary metabolism, plant-pathogen recognition, and plant hormone signal transduction (ethylene and jasmonate). Furthermore, the expression of 33 up-regulated candidate genes (12 related to WRKY DNA-binding proteins, one encoding endochitinase, two encoding beta-glucosidases, ten related to pathogenesis-related proteins, and eight encoding ethylene-responsive transcription factors) were validated by quantitative real-time PCR.

Conclusion

RNA-seq profiling was performed for the first time to analyze response of apple root to Fpmd MR5 infection. We found that the production of antimicrobial compounds and antioxidants enhanced plant resistance to pathogens, and pathogenesis-related protein (PR10 homologs, chitinase, and beta-glucosidase) may play unique roles in the defense response. These results provide new insights into the mechanisms of the apple root response to Fpmd MR5 infection.
Bioactivities evaluation of an endophytic bacterial strain Bacillus velezensis JRX-YG39 inhabiting wild grape
Authors: Feng Baozhen , Chen Dandan , Jin Ruixue , Li Erqin , Li Peiqian
Published: July 2022

Background

Botrytis cinerea can cause serious disease on lots of plant hosts during growth and postharvest storage. Biocontrol is known to be eco-friendly methods to control pathogens. Plant endophytic bacteria are generally considered as beneficial organisms, since they can promote plant growth and enhance plant immune system. Thus, screening biological control agents is very important for sustainable plant protection.

Results

Fifty-six endophytic bacteria were obtained from wild grape. Sixteen isolates and their extracts exhibited significant antifungal activity against B. cinerea. Particularly, strain JRX-YG39 with the strongest inhibition ability had a broad-spectrum antifungal activity. Combining 16S rDNA analysis and the phylogenetic results based on gyrA and gyrB genes, JRX-YG39 was assigned as Bacillus velezensis. JRX-YG39 could produce bioactive VOCs and obviously depressed mycelia growth of B. cinerea. It was confirmed that VOCs released by JRX-YG39 could significantly promote growth and induce defense of Arabidopsis thaliana. Thirty-one bioactive secondary metabolites were further identified from JRX-YG39 culture by gas chromatography–mass spectrometry analysis. Dibutyl phthalate, a potential antifungal substance, was the major compound accounting for 78.65%.

Conclusions

B. velezensis JRX-YG39 has wide broad-spectrum antagonistic activity and significant plant promotion activity. Hence, B. velezensis JRX-YG39 will provide a valuable constituent of modern agricultural practice as biofertilizers and biocontrol agents.
COMPILE: a GWAS computational pipeline for gene discovery in complex genomes
Authors: Hill Matthew J. , Penning Bryan W. , McCann Maureen C. , Carpita Nicholas C.
Published: July 2022

Background

Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity.

Results

COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer (Ostrinia nubilalis). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity.

Conclusions

The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.
Empirical assessment of alternative methods for identifying seasonality in observational healthcare data
Authors: Molinaro Anthony , DeFalco Frank
Published: July 2022

Background

Seasonality classification is a well-known and important part of time series analysis. Understanding the seasonality of a biological event can contribute to an improved understanding of its causes and help guide appropriate responses. Observational data, however, are not comprised of biological events, but timestamped diagnosis codes the combination of which (along with additional requirements) are used as proxies for biological events. As there exist different methods for determining the seasonality of a time series, it is necessary to know if these methods exhibit concordance. In this study we seek to determine the concordance of these methods by applying them to time series derived from diagnosis codes in observational data residing in databases that vary in size, type, and provenance.

Methods

We compared 8 methods for determining the seasonality of a time series at three levels of significance (0.01, 0.05, and 0.1), against 10 observational health databases. We evaluated 61,467 time series at each level of significance, totaling 184,401 evaluations.

Results

Across all databases and levels of significance, concordance ranged from 20.2 to 40.2%. Across all databases and levels of significance, the proportion of time series classified seasonal ranged from 4.9 to 88.3%. For each database and level of significance, we computed the difference between the maximum and minimum proportion of time series classified seasonal by all methods. The median within-database difference was 54.8, 34.7, and 39.8%, for p < 0.01, 0.05, and 0.1, respectively.

Conclusion

Methods of binary seasonality classification when applied to time series derived from diagnosis codes in observational health data produce inconsistent results. The methods exhibit considerable discord within all databases, implying that the discord is a result of the difference between the methods themselves and not due to the choice of database. The results indicate that researchers relying on automated methods to assess the seasonality of time series derived from diagnosis codes in observational data should be aware that the methods are not interchangeable and thus the choice of method can affect the generalizability of their work. Seasonality determination is highly dependent on the method chosen.
A comparative study on deep learning models for text classification of unstructured medical notes with various levels of class imbalance
Authors: Lu Hongxia , Ehwerhemuepha Louis , Rakovski Cyril
Published: July 2022

Background

Discharge medical notes written by physicians contain important information about the health condition of patients. Many deep learning algorithms have been successfully applied to extract important information from unstructured medical notes data that can entail subsequent actionable results in the medical domain. This study aims to explore the model performance of various deep learning algorithms in text classification tasks on medical notes with respect to different disease class imbalance scenarios.

Methods

In this study, we employed seven artificial intelligence models, a CNN (Convolutional Neural Network), a Transformer encoder, a pretrained BERT (Bidirectional Encoder Representations from Transformers), and four typical sequence neural networks models, namely, RNN (Recurrent Neural Network), GRU (Gated Recurrent Unit), LSTM (Long Short-Term Memory), and Bi-LSTM (Bi-directional Long Short-Term Memory) to classify the presence or absence of 16 disease conditions from patients’ discharge summary notes. We analyzed this question as a composition of 16 binary separate classification problems. The model performance of the seven models on each of the 16 datasets with various levels of imbalance between classes were compared in terms of AUC-ROC (Area Under the Curve of the Receiver Operating Characteristic), AUC-PR (Area Under the Curve of Precision and Recall), F1 Score, and Balanced Accuracy as well as the training time. The model performances were also compared in combination with different word embedding approaches (GloVe, BioWordVec, and no pre-trained word embeddings).

Results

The analyses of these 16 binary classification problems showed that the Transformer encoder model performs the best in nearly all scenarios. In addition, when the disease prevalence is close to or greater than 50%, the Convolutional Neural Network model achieved a comparable performance to the Transformer encoder, and its training time was 17.6% shorter than the second fastest model, 91.3% shorter than the Transformer encoder, and 94.7% shorter than the pre-trained BERT-Base model. The BioWordVec embeddings slightly improved the performance of the Bi-LSTM model in most disease prevalence scenarios, while the CNN model performed better without pre-trained word embeddings. In addition, the training time was significantly reduced with the GloVe embeddings for all models.

Conclusions

For classification tasks on medical notes, Transformer encoders are the best choice if the computation resource is not an issue. Otherwise, when the classes are relatively balanced, CNNs are a leading candidate because of their competitive performance and computational efficiency.
Incidence and risk factors of nasogastric feeding intolerance in moderately-severe to severe acute pancreatitis
Authors: Lin Jiajia , Lv Cheng , Wu Cuili , Zhang He , Liu Zirui , Ke Lu , Li Gang , Tong Zhihui , Tu Jianfeng , Li Weiqin
Published: July 2022

Background

The importance of enteral nutrition (EN) in acute pancreatitis (AP) has been emphasised. Nasogastric (NG) feeding has been the preferred route for EN delivery in most AP patients intolerant to oral intake. However, gastric feeding intolerance (GFI) was frequently reported, especially in patients with more severe diseases. This study aimed to investigate the incidence and risk factors for GFI in moderately-severe to severe AP.

Methods

This is a single-centre, retrospective study. All the data were extracted from an electronic database from April 2020 to May 2021. Data were prospectively collected during hospitalisation. Patients diagnosed with moderately-severe to severe AP and admitted within seven days from the onset of abdominal pain were assessed for eligibility. Patients who showed signs of intolerance to gastric feeding and required switching to nasojejunal (NJ) feeding were deemed GFI. Multivariable logistic regression was performed to assess potential risk factors of GFI.

Results

A total of 93 patients were analysed, of whom 24 were deemed GFI (25.8%), and the rest tolerated NG feeding well (n = 69). In patients with GFI, the median time of switching to NJ feeding was five days (interquartile range: 4–7 days) after admission. The multivariable analysis showed that respiratory failure (odds ratio = 3.135, 95% CI: 1.111–8.848,P = 0.031) was an independent risk factor for GFI.The mean daily energy delivery in the following three days after switching to NJ feeding was significantly higher than the first three days after initiation of NG feeding in patients with GFI [920.83 (493.33–1326) vs. 465 (252.25–556.67) kcal,P < 0.001].

Conclusion

GFI is common in moderately-severe to severe AP patients with an incidence of 25.8%, and the presence of respiratory failure may increase the risk of GFI.
The impact of treatment with bile acid sequestrants on quality of life in patients with bile acid diarrhoea
Authors: Kumar Aditi , Galbraith Niall , Al-Hassi Hafid O. , Jain Manushri , Phipps Oliver , Butterworth Jeffrey , Steed Helen , McLaughlin John , Brookes Matthew J.
Published: July 2022

Background

Bile acid diarrhoea (BAD) can be severely debilitating and negatively affect patients’ quality of life (QoL). We carried out a multi-centre prospective study exploring QoL outcomes in patients with BAD after treatment with colesevelam.

Methods

Patients with or without a positive 23-seleno-25-homotaurocholic acid (SeHCAT) scan were recruited and categorised into four groups: SeHCAT negative control group (CG), idiopathic BAD, post-cholecystectomy (PC) and post-terminal ileal resection for Crohn’s disease (CD). Patients with a positive SeHCAT were treated with colesevelam and dosing was titrated to symptomatic response. Patients were reviewed at 4- and 8-weekly intervals and QoL was evaluated by EQ-5D-3L, SF-36, IBDQ-32 at each visit (where relevant). Patients with a negative SeHCAT (CG cohort) completed one set of questionnaires before being discharged from the study.

Results

47 patients (BAD = 24, PC = 12, CD = 11) completed paired QoL questionnaires before and after treatment and 30 CG patients completed a baseline questionnaire. There was a significant improvement in IBDQ-32 mean scores before and after treatment in CD patients [134.6 (95%CI 112.5–156.6) and 158.4 (136.1–180.6), respectively (p = 0.007). Following treatment, BAD patients had significantly improved mean SF-36 scores in the “Role limitation due to physical health” dimension (p = 0.02) and in the overall mental component summary (p = 0.03). Prior to starting treatment, BAD patients had the lowest scores in the ‘activity’ dimension of the EQ-5D-3L (p = 0.04), which improved significantly after treatment (p = 0.002). Overall, the BAD and CD cohort showed improved mean scores with treatment in all components of the SF-36 and EQ-5D-3L, while the PC cohort showed a general decline in mean scores after treatment. 55% of patients clinically responded to treatment of which 41.7%, 58.3% and 81.8% responded from the BAD, PC and CD groups respectively. Correlations between those deemed as responders with improvements on the SF-36 and EQ-5D dimensions were not statistically significant.

Conclusion

Our results demonstrate improved QoL in the BAD and CD cohort with treatment. Further larger studies are recommended specifically investigating the PC cohort and whether patients may improve with newer treatments such as FXR agonists.

Trial registration Ethical approval REC Ref: 16/LO/1325.
Alternative splicing of Apoptosis Stimulating Protein of TP53-2 (ASPP2) results in an oncogenic isoform promoting migration and therapy resistance in soft tissue sarcoma (STS)
Authors: Tsintari Vasileia , Walter Bianca , Fend Falko , Overkamp Mathis , Rothermundt Christian , Lopez Charles D. , Schittenhelm Marcus M. , Kampa-Schittenhelm Kerstin M.
Published: July 2022

Background

Metastatic soft tissue sarcoma (STS) are a heterogeneous group of malignancies which are not curable with chemotherapy alone. Therefore, understanding the molecular mechanisms of sarcomagenesis and therapy resistance remains a critical clinical need. ASPP2 is a tumor suppressor, that functions through both p53-dependent and p53-independent mechanisms. We recently described a dominant-negative ASPP2 isoform (ASPP2κ), that is overexpressed in human leukemias to promote therapy resistance. However, ASPP2κ  has never been studied in STS. 

Materials and methods

Expression of ASPP2κ was quantified in human rhabdomyosarcoma tumors using immunohistochemistry and qRT-PCR from formalin-fixed paraffin-embedded (FFPE) and snap-frozen tissue. To study the functional role of ASPP2κ in rhabdomyosarcoma, isogenic cell lines were generated by lentiviral transduction with short RNA hairpins to silence ASPP2κ expression. These engineered cell lines were used to assess the consequences of ASPP2κ silencing on cellular proliferation, migration and sensitivity to damage-induced apoptosis. Statistical analyses were performed using Student’s t-test and 2-way ANOVA.

Results

We found elevated ASPP2κ mRNA in different soft tissue sarcoma cell lines, representing five different sarcoma sub-entities. We found that ASSP2κ mRNA expression levels were induced in these cell lines by cell-stress. Importantly, we found that the median ASPP2κ expression level was higher in human rhabdomyosarcoma in comparison to a pool of tumor-free tissue. Moreover, ASPP2κ levels were elevated in patient tumor samples versus adjacent tumor-free tissue within individual patients. Using isogenic cell line models with silenced ASPP2κ expression, we found that suppression of ASPP2κ enhanced chemotherapy-induced apoptosis and attenuated cellular proliferation.

Conclusion

Detection of oncogenic ASPP2κ in human sarcoma provides new insights into sarcoma tumor biology. Our data supports the notion that ASPP2κ promotes sarcomagenesis and resistance to therapy. These observations provide the rationale for further evaluation of ASPP2κ as an oncogenic driver as well as a prognostic tool and potential therapeutic target in STS.
Electronic patient-reported monitoring of symptoms during follow-up of ovarian cancer patients: a feasibility study
Authors: Kennedy Fiona , Shearsmith Leanne , Holmes Marie , Rogers Zoe , Carter Rob , Hofmann Uschi , Velikova Galina
Published: July 2022

Background

Ovarian cancer patients require monitoring for relapse. Innovative follow-up methods are increasingly being explored. An electronic patient-reported outcome (ePRO) follow-up pathway was developed for women treated for ovarian cancer. This feasibility study explored patient acceptability and compliance.

Methods

A single-arm non-blinded prospective feasibility study was undertaken at two hospitals. Participants were women who had completed treatment for ovarian cancer whose clinician was happy for them to be monitored remotely. Automated 3-monthly reminders were sent to participants to complete an ePRO questionnaire and obtain blood tests. Participants were reviewed over the phone by their clinical nurse specialist instead of attending clinic-based follow-up. The primary outcome was compliance (expected ePRO completions/blood tests) across the 12-month study period. Secondary outcomes were recruitment, attrition, resource use, symptom severity/alerts and patient acceptability.

Results

Twenty-four women consented (50% consent rate), and 13 remained on study at 12 months. Seven women relapsed, 3 chose to withdraw, and 1 withdrew for other clinical reasons. ePRO compliance was high and consistent at 75-82%, although the two hospitals differed. Adherence to the clinical protocol was evident for blood tests and contacts with staff (fewer visits, more phonecalls compared to an earlier audit). End-of-study feedback indicated high patient satisfaction.

Conclusions

Remote ePRO follow-up for ovarian cancer is feasible and acceptable to patients who are able and willing to participate. However, the low recruitment rate (ineligible + declined) indicate it is not suitable/acceptable to all patients immediately post-treatment. Further large-scale research and implementation work is required, especially in a post-COVID era.

Trial registration

ClinicalTrials.gov ID: NCT02847715 (first registered 19/05/2016).