bluuebunny/crossref_metadata_2025 huggingface dataset:
Entrepreneurial Opportunities as Responsibility
Authors: Bosse Douglas A. , Harrison Jeffrey S. , Pollack Jeffrey M. , Schrempf-Stirling Judith
Published: March 2022

Entrepreneurship involves cooperative efforts in which multiple stakeholders and resources are brought together to develop a valuable product or service. Accordingly, one key process through which entrepreneurs make progress exploiting their opportunities is by identifying, selecting, enrolling, and coordinating a network of stakeholders. However, although there is a widespread realization that bringing new ventures to life requires multiple stakeholders, precious little academic research has taken a holistic approach to stakeholder engagement. In this special issue we: (a) suggest that stakeholder theory provides a novel lens for viewing the critical entrepreneurial behavior of engaging stakeholders—and taking shared responsibility for an unmet opportunity, (b) describe the intriguing articles that encompass this special issue, and (c) offer our thoughts on directions for future research at the intersection of stakeholder theory and entrepreneurship.
Development of NCL equivalent serial and parallel python routines for meteorological data analysis
Authors: Gharat Jatin , Kumar Bipin , Ragha Leena , Barve Amit , Jeelani Shaik Mohammad , Clyne John
Published: March 2022

The NCAR Command Language (NCL) is a popular scripting language used in the geoscience community for weather data analysis and visualization. Hundreds of years of data are analyzed daily using NCL to make accurate weather predictions. However, due to its sequential nature of execution, it cannot properly utilize the parallel processing power provided by High-Performance Computing systems (HPCs). Until now very few techniques have been developed to make use of the multi-core functionality of modern HPC systems on these functions. In the recent trend, open-source languages are becoming highly popular because they support major functionalities required for data analysis and parallel computing. Hence, developers of NCL have decided to adopt Python as the future scripting language for analysis and visualization and to enable the geosciences community to play an active role in its development and support. This study focuses on developing some of the widely used NCL routines in Python. To deal with the analysis of large datasets, parallel versions of these routines are developed to work within a single node and make use of multi-core CPUs to achieve parallelism. Results show high accuracy between NCL and Python outputs and the parallel versions provided good scaling compared to their sequential counterparts.
Inquiry-based learning in music: Indicators and relationships between key pedagogical practices and the quality of critical thinking
Authors: Costes-Onishi Pamela , Kwek Dennis
Published: March 2022

Many scholars have advocated the addition of more intellectual activities in music classrooms, the most prominent being critical thinking through inquiry. Inquiry-based learning (IBL) has been recognized as necessary for teaching and learning that increases critical thinking skills and dispositions. This study describes an extensive list of indicators that could ascertain the pedagogical practices and intellectual quality of knowledge work indicating the strength of inquiry in music classrooms. It shows the relationships between these indicators that help us understand the enablers and hindrances to critical thinking as an aspect of IBL in music. The article focuses on the Descriptive Statistics results of 114 classroom observations for music at the Primary and Secondary levels, using coding schemes developed in the Singapore Core3-PP project from 2018 to 2020. The results confirm the gap identified in the literature that music classes lack significant inquiry work that would nurture critical thinking skills and dispositions. The findings provide pedagogical insights that can (a) inform educators on how to examine and grow their IBL practice in music lessons; (b) move music education’s objective toward a balanced development of music skills and knowledge construction; (c) develop critical musicality and independent musicianship among students; and (d) provide concrete measures for researchers to design interventions in the areas of teacher learning in IBL.
Controlled empowerment of women: intersections of feminism, HCI and political communication in India
Authors: Mangurkar Isha , Rangaswamy Nimmi
Published: March 2022

Twitter played a dominant role during the 2014 general elections in India, ushering a right-wing party into power. Political leaders employed Twitter to augment their public image and push right-wing campaign agendas to millions of followers. A prominent and strategic use of Twitter was credited to Prime Ministerial candidate Narendra Modi, portrayed as a visionary leader supporting economic development, social empowerment and good governance. Within this narrative, women's empowerment debates underwent multiple transformations. Through this article, we aim to establish the nature of discussions lying at the intersections of feminist thinking and internet technology. We study the discursive trajectory of women's empowerment against the backdrop of a right-wing political (Hindutva) ideology playing out on Twitter. Utilising the qualitative methods of Thematic Analysis and Feminist Relational Discourse Analysis, we study two cases highlighting feminist campaigns beginning in 2014: instant triple talaq, and the Sabarimala verdict. We analyse tweets in relation to these incidents and highlight the rhetorical inconsistency of right-wing leaders and supporters. We further discuss the implications of this inconsistency for the simultaneous suppression of voices demanding empowerment and amplification of those justifying religious tradition. Finally, we conclude by introducing the idea of the ‘controlled empowerment’ of women in support of our analysis.
The interpretation of relationships: Fieldwork as boundary-negotiation
Authors: Lombard Louisa
Published: March 2022

Following critiques of anthropologists’ involvement in colonialism and insufficient attention to power, friendship, solidarity, and closeness have become implicit ideals for fieldwork relationships. But distance is also inherent to respectful fieldwork relationships. I therefore argue for greater attention to boundaries—the ways we are able to mutually understand in the midst of, rather than by dissolving, difference and distance—and the labor and finesse that go into negotiating them. Foregrounding boundary work allows for a greater honesty about fieldwork relationships and facilitates the broadness of spirit that is the discipline’s hallmark. It also helps people who are most engaged in boundary work to grapple with it and not see that work as failure, weakness, or their taking “risks.” And it further helps one avoid imposing one’s own social ideals for egalitarianism or intimacy on one’s interlocutors. Boundaries are not the enemy of mutual understanding and integrity; in fact, boundaries facilitate them.
Fuzzy logic model expansion and optimization for predicting polyester cut-pile carpet thickness-loss
Authors: Javidpanah Masoud , Najar Saeed S , Dayiary Mansour , Tavana Reza , Varsei Mehdi
Published: March 2022

Thickness-loss is the most common problem in carpet after static and dynamic loading. Pile yarn properties as well as carpet structural parameters are mainly responsible for carpet thickness-loss. In the present research, an advanced version of recently developed fuzzy logic model is introduced. The model is able to predict thickness-loss of polyester carpets based on carpet pile density, pile height, and pile yarn count. Experimental work was performed to provide data for model knowledge base. Genetic algorithm was employed to optimize the fuzzy logic model parameters. Finally, lowest possible thickness-loss value together with corresponding values of carpet and pile yarn parameters bring this result was defined, using developed model. Modeling results showed that the model attained correlation coefficients as 0.9932, 0.9911, 0.9950, and 0.9957 between predicted and experimental values of carpet thickness-loss after low and high dynamic loading and static loading with short and long relaxation times, respectively. On the other hand, model predictions in four new unsighted conditions have brought correlation coefficients as 0.82, 0.89, 0.88, and 0.90 for low and high dynamic loading and static loading after short and long relaxation times, respectively. These results denote acceptable reliability of new developed model. Eventually, it is defined that levels of 850, 7.5, and 957.5 for carpet pile density, pile height, and pile yarn linear density, respectively, bring minimum carpet thickness-loss.
A Retrospective Study on Therapeutic Efficacy of Transarterial Chemoembolization Combined With Immune Checkpoint Inhibitors Plus Lenvatinib in Patients With Unresectable Hepatocellular Carcinoma
Authors: Teng Ying , Ding Xiaoyan , Li Wendong , Sun Wei , Chen Jinglong
Published: March 2022

Objective: We assessed the efficacy and safety of transarterial chemoembolization (TACE) in combination with lenvatinib plus programmed death receptor-1 (PD-1) signaling inhibitors (camrelizumab or sintilimab) in unresectable hepatocellular carcinoma (uHCC). Methods: In this retrospective study, patients with uHCC were pretreated with lenvatinib for 1 to 2 weeks before TACE. Camrelizumab or sintilimab were initially administered intravenously in 1 week after TACE of a 21-day cycle. Primary objectives were objective response rate (ORR) and disease control rate (DCR) by modified Response Evaluation Criteria in Solid Tumors (mRECIST). The secondary endpoints included the progression-free survival (PFS), overall survival (OS), and toxicity. Results: Between March 5, 2019 and February 30, 2021, 53 patients were screened for eligibility. At data cutoff, 35.8% of patients remained on treatment. Median follow-up was 15.4 months. Confirmed ORR in the 51 evaluable patients was 54.9% (95% CI 41.4%-67.7%). DCR was 84.3% (95% CI 72.0%-91.8%). Median PFS was 8.5 months (95% CI 6.4 to 10.6 months). The median OS was not estimable. Grade ≥3 treatment-related adverse events occurred in 32.1% of patients. No new safety signals were identified. Conclusion: TACE in combination with lenvatinib plus anti-PD-1 inhibitors may have promising antitumor activity in uHCC. Toxicities were manageable, with no unexpected safety signals.
Prediction of cardiac autonomic neuropathy using a machine learning model in patients with diabetes
Authors: Abdalrada Ahmad Shaker , Abawajy Jemal , Al-Quraishi Tahsien , Islam Sheikh Mohammed Shariful
Published: March 2022

Background:

Cardiac autonomic neuropathy (CAN) is a diabetes-related complication with increasing prevalence and remains challenging to detect in clinical settings. Machine learning (ML) approaches have the potential to predict CAN using clinical data. In this study, we aimed to develop and evaluate the performance of an ML model to predict early CAN occurrence in patients with diabetes.

Methods:

We used the diabetes complications screening research initiative data set containing 200 CAN-related tests on more than 2000 participants with type 2 diabetes in Australia. Data were collected on peripheral nerve functions, Ewing’s tests, blood biochemistry, demographics, and medical history. The ML model was validated using 10-fold cross-validation, of which 90% were used in training the model and the remaining 10% was used in evaluating the performance of the model. Predictive accuracy was assessed by area under the receiver operating curve, and sensitivity, specificity, positive predictive value, and negative predictive value.

Results:

Of the 237 patients included, 105 were diagnosed with an early stage of CAN while the remaining 132 were healthy. The ML model showed outstanding performance for CAN prediction with receiver operating characteristic curve of 0.962 [95% confidence interval (CI) = 0.939–0.984], 87.34% accuracy, and 87.12% sensitivity. There was a significant and positive association between the ML model and CAN occurrence ( p < 0.001).

Conclusion:

Our ML model has the potential to detect CAN at an early stage using Ewing’s tests. This model might be useful for healthcare providers for predicting the occurrence of CAN in patients with diabetes, monitoring the progression, and providing timely intervention.
Factors influencing utilization of early postnatal care services among postpartum women in Yirgalem town, Sidama Regional State, Ethiopia
Authors: Dona Aregahegn , Tulicha Tsedeke , Arsicha Admasu , Dabaro Desalegn
Published: March 2022

Objective:

Providing postnatal care services at right time could help to reduce maternal and newborn deaths. Thus, this study aimed to assess the factors influencing the utilization of early postnatal care services among postpartum women in Yirgalem town, Sidama Regional State, Ethiopia.

Methods:

A community-based cross-sectional study was done using structured and interviewer-administered questionnaires among randomly selected 306 postpartum women. Data were cleaned, coded, and entered into EpiData-3.1, and exported to Statistical Package for Social Science-21 for analysis. Descriptive statistics, bivariable, and multivariable logistic regression analysis were done. A p-value ⩽ 0.05 was used to consider statistically significant variables.

Results:

Generally, 202 (66.7%) visited a health facility for postpartum care. The prevalence of early postnatal care service utilization was 45.5% (95% confidence interval = 39.9–50.5). Mainly practiced services were physical examination (37%) and family planning (31%) services. Having formal education (adjusted odds ratio = 3.6; 95% confidence interval = 1.7–7.4), having antenatal care (adjusted odds ratio = 3.5; 95% confidence interval = 1.6–7.6), institutional delivery (adjusted odds ratio = 2.3; 95% confidence interval = 1.2–4.7), and getting advice from healthcare provider (adjusted odds ratio = 18.69; 95% confidence interval = 9.19–37.99) were factors significantly associated with early postnatal care service utilization.

Conclusion:

The practice of early postnatal care needs more attention in the study area. Improving the educational status of the women, strengthening healthcare providers’ counseling on the benefits of postnatal care, and inspiring pregnant women to use antenatal care and institutional delivery services will improve the use of postnatal care services on time.
Islamic Work Ethics, Affective Commitment, and Employee’s Performance in Family Business: Testing Their Relationships
Authors: Udin Udin , Dananjoyo Radyan , Shaikh Mohsin , Vio Linarta Densy
Published: March 2022

A family business is usually managed and run by family members to form and pursue a business vision that will ensure continuity across generations. Subsequently, this study aims to scrutinize and inspect the effect of Islamic work ethics on affective commitment and employee performance. Out of 273 questionnaires that were disseminated to employees of family businesses in Pati, Batang, and Demak districts of Central Java, Indonesia, 147 were filled out and completed questionnaires, reflecting a response rate of 53.8%. Based on the results from the structural equation modeling from AMOS 21, Islamic work ethics were confirmed to be positively and significantly associated with affective commitment and employee performance. The affective commitment was also positively and significantly related to employee performance. Consequently, this study will contribute to expanding the literature on the association between Islamic work ethics, affective commitment, and employee performance in Indonesian family businesses.
Development and Preliminary Validation of the Moral Reasoning Questionnaire for Secondary School Students
Authors: Lim Lyndon , Chapman Elaine
Published: March 2022

Moral reasoning is a key element of the Singapore Ministry of Education’s Character and Citizenship Education curriculum, and educators in Singapore are currently encouraged to facilitate growth in students’ moral reasoning based on the Stages of Moral Development established by Lawrence Kohlberg. To monitor students’ progress in this area, however, a validated test of moral reasoning is needed. A review of existing moral reasoning assessments indicated that none provide a practical means by which large numbers of students in Singapore classrooms can be assessed in this area. In this study, the Moral Reasoning Questionnaire (MRQ) was developed and validated to assess moral reasoning development in Singapore secondary classrooms. The MRQ presents moral dilemmas that integrate prosocial, anti-social, and social pressure elements within situations that would be familiar to Singapore secondary (grades 7–12, aged between 12 and 18) students. Evidence supported the reliability and validity of the MRQ. The MRQ could be applicable as a practical means to assess moral reasoning on a broad-scale basis.
Due Process Case Issues for Students With Emotional Disturbance
Authors: Gomez Mertie M. , Morgan Valerie R. , Schanding G. Thomas , Cheramie Gail M.
Published: March 2022

Due process hearings provide a formal resolution for disagreements that may arise within special education. The purpose of this study was to examine the types of issues that arise in due process cases for students with emotional disturbance (ED). The current study examined select due process hearings during 2014 to 2019 from four states for students with ED as the primary condition. The most frequently occurring issue for students with ED was programing related to the individualized educational program (68.3%). Collectively, both evaluations and disability identification were present in 65.8% of cases. Districts prevailed in approximately 43% of cases, with parents prevailing in approximately 36% of cases; 21% of hearing decisions were split. Limitations, future research directions, and implications are discussed.
COVID-19 mRNA Vaccine–Associated Uveitis Leading to Diagnosis of Sarcoidosis: Case Report and Review of Literature
Authors: Matsuo Toshihiko , Honda Hiroyuki , Tanaka Takehiro , Uraguchi Kensuke , Kawahara Masaaki , Hagiya Hideharu
Published: March 2022

A 34-year-old Japanese person with male gender identity who had been taking intramuscular injection of methyltestosterone depot for 11 years after bilateral mastectomy noticed blurred vision 5 days after the second vaccination for COVID-19 (Tozinameran; Pfizer-BioNTech) in the interval of 3 weeks following the first vaccination. The patient was diagnosed as granulomatous iritis with mutton-fat keratic precipitates and small iris nodules at the pupillary margin in the right eye and began to have 0.1% betamethasone eye drops with good response. The patient, however, continued to have fever and malaise and showed a high level of serum soluble interleukin-2 receptor (sIL-2R) even 4 weeks after the second vaccination. Computed tomographic scan disclosed mediastinal and bilateral hilar small lymphadenopathy together with limited granular lesion in the right lung. Gallium-67 scintigraphy demonstrated high uptake not only in mediastinal and hilar lymph nodes but also in bilateral parotid glands. Right parotid gland biopsy revealed noncaseating granulomas and proved pathological diagnosis of sarcoidosis. The systemic symptoms were relieved by oral prednisolone 20 mg daily. Even though the causal relationship remains undetermined, this case is unique at the point that vaccine-associated uveitis led to the detection of pulmonary lesions and lymphadenopathy, resulting in clinical and pathological diagnosis of sarcoidosis. In literature review, 3 patients showed sarcoidosis-like diseases after COVID-19 vaccination: 2 patients were diagnosed clinically as Lofgren syndrome with acute onset of erythema nodosum and ankle swelling, with or without mediastinal and hilar lymphadenopathy, whereas 1 patient with mediastinal lymphadenopathy but no uveitis was diagnosed pathologically by biopsy as sarcoidosis.
Modelling falls in Parkinson’s disease and normal ageing in mice using a complex motor task
Authors: Jackson Megan G. , Brennan Laura J. , Henderson Emily J. , Robinson Emma S. J.
Published: March 2022

Falls resulting from multifactorial deficits are common in both normal ageing and Parkinson’s disease. Resultant injuries can lead to increased hospitalisation and excess mortality. As the disease progresses, gait and balance deficits are relatively refractory to dopaminergic treatments suggesting another system is involved. Attentional impairment is a significant risk factor for falls, and disruption to both the cortical cholinergic system and striatal dopaminergic system increases falls in rats undergoing a complex motor task with high attentional load. However, it is unclear whether this translates to mice and whether normal ageing induces similar deficits. In this study, we use a complex motor task to test the effects of acute dopaminergic and cholinergic antagonism using alpha-flupentixol and scopolamine, respectively, in mice. We also test the effects of normal ageing on complex motor performance and whether these changes are sensitive to a clinical dose of the non-steroidal anti-inflammatory Rimadyl. Consistent with previous work, we show that cholinergic but not dopaminergic antagonism impaired task performance. However, a combined approach did not potentiate the deficit beyond observed with cholinergic antagonism alone. We also show that task performance is impaired in aged mice relative to younger controls, and that Rimadyl reduces number of foot slips in an age-specific manner. Overall, these data support prior work showing the importance of the cholinergic system in falls. The studies in aged mice found age-related impairments and a role for inflammation but did not find evidence of an interaction with attentional load, although only one manipulation was tested.
Tension Control UCL Reconstruction With Internal Brace Augmentation
Authors: Yalcin Sercan , Maier Jacob , Schickendantz Mark , Frangiamore Salvatore
Published: March 2022

Background:

Ulnar collateral ligament (UCL) rupture is a common injury, particularly in throwing athletes. It occurs either in the acute setting or due to repetitive microtrauma. UCL reconstruction has been a successful treatment with proper patient selection. A number of different surgical techniques have been described in the literature. We developed a novel surgical technique using internal brace augmentation to address the 2 most common causes of failure: suture failure and bone tunnel fracture.

Indications:

To provide information about this novel UCL reconstruction technique.

Technique Description:

The palmaris longus graft is harvested and prepared to be used as the autograft. A 5-cm curved incision is made over the medial epicondyle of the humerus. The UCL reconstruction is then performed using the double suspensory reconstruction technique followed by an internal brace augmentation.

Results:

Excellent clinical outcomes and high return to sports rates have been reported after UCL reconstruction. In this novel technique, the addition of the internal brace provides secondary interference fixation of the graft on the humeral side along with the additional support the brace itself provides.

Discussion/Conclusion:

Using internal brace augmentation increases the stability of the UCL reconstruction while preventing suture failure and bone tunnel fracture.
Prevalence of heavy chain MGUS by race and family history risk groups using a high-sensitivity screening method
Authors: Vachon Celine M. , Murray Josiah , Allmer Cristine , Larson Dirk , Norman Aaron D. , Sinnwell Jason P. , Dispenzieri Angela , Kleinstern Geffen , Visram Alissa , Kyle Robert A. , Rajkumar S. Vincent , Slager Susan L. , Kumar Shaji K. , Murray David L.
Published: March 2022

Mass-spectrometry (MS) assays detect lower levels of monoclonal proteins and result in earlier detection of monoclonal gammopathy of undetermined significance (MGUS). We examined heavy chain MGUS prevalence using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS among 3 risk groups, ages 50 or older: 327 African Americans (AA) and 1223 European Americans (EA) from a clinical biobank and 1093 unaffected first-degree relatives (FDR) of patients with hematologic disorders. Age- and sex-adjusted prevalence rates were directly standardized to 2010 United States population. Prevalence ratios were estimated for comparisons of AA and FDR to the EA group using the Poisson distribution. Results were also compared with population-based prevalence using conventional gel-based methods. Risk groups had similar sex and age distributions. MALDI-TOF MGUS prevalence was higher in the AA (16.5% [95% confidence interval (CI), 12.2%, 20.8%]) and FDR (18.3% [95% CI, 16.6%, 21.6%]) than in EA (10.8% [95% CI, 8.8%, 12.7%]), translating to prevalence ratios of 1.73 (95% CI, 1.31, 2.29) and 1.90 (95% CI, 1.55, 2.34), respectively. MALDI-TOF EA prevalence was over threefold higher than conventional estimates but showed similar age trends. Thus, the MALDI-TOF assay found greater numbers with MGUS but similar relative differences by race, family history, and age as prior studies.
Cystitis glandularis- rare cause of urinary bladder mass: case report and literature review
Authors: Ahmad Ahsan , Imbisat Md Zaid , Ranjan Nikhil , Tiwari Rajesh Kumar , Kumar Bipin , Khatoon Qurana
Published: March 2022

Background

Cystitis glandularis a rare benign proliferative disease of the urinary bladder mucosa is usually a microscopic finding and manifests rarely as a large visible macroscopic lesion of urinary bladder. Only few cases of cystitis glandularis presenting as urinary bladder mass in female patients have been reported in the literature. We are reporting a case of cystitis glandularis presenting as a urinary bladder mass in a very young female patient.

Case presentation.

Our patient, a young female 25 years of age presented in the Urology OPD with complaints of irritative lower urinary tract symptoms for two years and intermittent hematuria for one year. On evaluation, she was found to have a urinary bladder mass. Transurethral resection of her urinary bladder mass was done and on histopathological examination, it came out to be cystitis glandularis.

Conclusion

Clinical presentation of cystitis glandularis is variable. It may remain asymptomatic or could present as irritative lower urinary tract symptoms, hematuria, or mucus in the urine. It is normally a microscopic finding but could also present as an overt urinary bladder mass however this has been reported rarely in the literature.
A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes
Authors: Clark Lindsay V. , Mays Wittney , Lipka Alexander E. , Sacks Erik J.
Published: March 2022

Background

Given the economic and environmental importance of allopolyploids and other species with highly duplicated genomes, there is a need for methods to distinguish paralogs, i.e. duplicate sequences within a genome, from Mendelian loci, i.e. single copy sequences that pair at meiosis. The ratio of observed to expected heterozygosity is an effective tool for filtering loci but requires genotyping to be performed first at a high computational cost, whereas counting the number of sequence tags detected per genotype is computationally quick but very ineffective in inbred or polyploid populations. Therefore, new methods are needed for filtering paralogs.

Results

We introduce a novel statistic, Hind/HE, that uses the probability that two reads sampled from a genotype will belong to different alleles, instead of observed heterozygosity. The expected value of Hind/HE is the same across all loci in a dataset, regardless of read depth or allele frequency. In contrast to methods based on observed heterozygosity, it can be estimated and used for filtering loci prior to genotype calling. In addition to filtering paralogs, it can be used to filter loci with null alleles or high overdispersion, and identify individuals with unexpected ploidy and hybrid status. We demonstrate that the statistic is useful at read depths as low as five to 10, well below the depth needed for accurate genotype calling in polyploid and outcrossing species.

Conclusions

Our methodology for estimating Hind/HE across loci and individuals, as well as determining reasonable thresholds for filtering loci, is implemented in polyRAD v1.6, available at https://github.com/lvclark/polyRAD. In large sequencing datasets, we anticipate that the ability to filter markers and identify problematic individuals prior to genotype calling will save researchers considerable computational time.
The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development
Authors: Fisher Malcolm E. , Segerdell Erik , Matentzoglu Nicolas , Nenni Mardi J. , Fortriede Joshua D. , Chu Stanley , Pells Troy J. , Osumi-Sutherland David , Chaturvedi Praneet , James-Zorn Christina , Sundararaj Nivitha , Lotay Vaneet S. , Ponferrada Virgilio , Wang Dong Zhuo , Kim Eugene , Agalakov Sergei , Arshinoff Bradley I. , Karimi Kamran , Vize Peter D. , Zorn Aaron M.
Published: March 2022

Background

Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are interoperable across the biomedical research continuum. There is also an increasing need for methods to interrelate phenotypic data easily and accurately from experiments in animal models with human development and disease.

Results

Here we present theXenopusphenotype ontology (XPO) to annotate phenotypic data from experiments inXenopus, one of the major vertebrate model organisms used to study gene function in development and disease. The XPO implements design patterns from the Unified Phenotype Ontology (uPheno), and the principles outlined by the Open Biological and Biomedical Ontologies (OBO Foundry) to maximize interoperability with other species and facilitate ongoing ontology management. Constructed in Web Ontology Language (OWL) the XPO combines the existing uPheno library of ontology design patterns with additional terms from theXenopusAnatomy Ontology (XAO), the Phenotype and Trait Ontology (PATO) and the Gene Ontology (GO). The integration of these different ontologies into the XPO enables rich phenotypic curation, whilst the uPheno bridging axioms allows phenotypic data fromXenopusexperiments to be related to phenotype data from other model organisms and human disease. Moreover, the simple post-composed uPheno design patterns facilitate ongoing XPO development as the generation of new terms and classes of terms can be substantially automated.

Conclusions

The XPO serves as an example of current best practices to help overcome many of the inherent challenges in harmonizing phenotype data between different species. The XPO currently consists of approximately 22,000 terms and is being used to curate phenotypes by Xenbase, theXenopusModel Organism Knowledgebase, forming a standardized corpus of genotype–phenotype data that can be directly related to other uPheno compliant resources.
Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens
Authors: Asadollahpour Nanaei Hojjat , Kharrati-Koopaee Hamed , Esmailizadeh Ali
Published: March 2022

Background

Understanding how evolutionary forces relating to climate have shaped the patterns of genetic variation within and between species is a fundamental pursuit in biology. Iranian indigenous chickens have evolved genetic adaptations to their local environmental conditions, such as hot and arid regions. In the present study, we provide a population genome landscape of genetic variations in 72 chickens representing nine Iranian indigenous ecotypes (Creeper, Isfahan, Lari, Marand, Mashhad, Naked neck, Sari, Shiraz and Yazd) and two commercial lines (White Leghorn and Arian). We further performed comparative population genomics to evaluate the genetic basis underlying variation in the adaptation to hot climate and immune response in indigenous chicken ecotypes. To detect genomic signatures of adaptation, we applied nucleotide diversity (θπ) and FST statistical measurements, and further analyzed the results to find genomic regions under selection for hot adaptation and immune response-related traits.

Results

We assessed the relationship between the genetic diversity of indigenous chicken ecotypes and their genetic distances to two different commercial lines. The results of genetic structure analysis revealed clustering of indigenous chickens in agreement with their geographic origin. Among all studied chicken groups, the highest level of linkage disequilibrium (LD) (~ 0.70) was observed in White Leghorn group at marker pairs distance of 1 Kb. The results from admixture analysis demonstrated evidence of shared ancestry between Arian individuals and indigenous chickens, especially those from the north of the country. Our search for potential genomic regions under selection in indigenous chicken ecotypes revealed several immune response and heat shock protein-related genes, such as HSP70, HSPA9, HSPH1, HSP90AB1 and PLCB4 that have been previously unknown to be involved in environmental-adaptive traits. In addition, we found some other candidate loci on different chromosomes probably related with hot adaptation and immune response-related traits.

Conclusions

The work provides crucial insights into the structural variation in the genome of Iranian indigenous chicken ecotypes, which up to now has not been genetically investigated. Several genes were identified as candidates for drought, heat tolerance, immune response and other phenotypic traits. These candidate genes may be helpful targets for understanding of the molecular basis of adaptation to hot environmental climate and as such they should be used in chicken breeding programs to select more efficient breeds for desert climate.
Genome-wide characterization and expression analysis of Erf gene family in cotton
Authors: Zafar Muhammad Mubashar , Rehman Abdul , Razzaq Abdul , Parvaiz Aqsa , Mustafa Ghulam , Sharif Faiza , Mo Huijuan , Youlu Yuan , Shakeel Amir , Ren Maozhi
Published: March 2022

Background

AP2/ERF transcription factors are important in a variety of biological activities, including plant growth, development, and responses to biotic and abiotic stressors. However, little study has been done on cotton’s AP2/ERF genes, although cotton is an essential fibre crop. We were able to examine the tissue and expression patterns of AP2/ERF genes in cotton on a genome-wide basis because of the recently published whole genome sequence of cotton. Genome-wide analysis of ERF gene family within two diploid species (G. arboreum & G. raimondii) and two tetraploid species (G. barbadense, G. hirsutum) was performed.

Results

A total of 118, 120, 213, 220 genes containing the sequence of single AP2 domain were identified in G. arboreum, G. raimondii, G. barbadense and G. hirsutum respectively. The identified genes were unevenly distributed across 13/26 chromosomes of A and D genomes of cotton. Synteny and collinearity analysis revealed that segmental duplications may have played crucial roles in the expansion of the cotton ERF gene family, as well as tandem duplications played a minor role. Cis-acting elements of the promoter sites of Ghi-ERFs genes predict the involvement in multiple hormone responses and abiotic stresses. Transcriptome and qRT-PCR analysis revealed that Ghi-ERF-2D.6, Ghi-ERF-12D.13, Ghi-ERF-6D.1, Ghi-ERF-7A.6 and Ghi-ERF-11D.5 are candidate genes against salinity tolerance in upland cotton.

Conclusion

Overwhelmingly, the present study paves the way to better understand the evolution of cotton ERF genes and lays a foundation for future investigation of ERF genes in improving salinity stress tolerance in cotton.
Correlation between microRNA-320 and postoperative delirium in patients undergoing tibial fracture internal fixation surgery
Authors: Wang Bin , Yin Zeng , Lin Yanan , Deng Xiyuan , Liu Fanghao , Tao He , Dong Rui , Lin Xu , Bi Yanlin
Published: March 2022

Background

Although the incidence of postoperative delirium (POD) in the elderly after surgery are rising as individuals are living longer, the pathogenesis of POD remains poorly understood. It has been suggested that miRNA-320 may play a role in POD based on animal study and human study.

Methods

We first carried out an animal study, and designed and conducted a human study based on the result of animal study. The aged rats were randomly assigned to five groups: the control (C), anesthesia and surgery (AS), saline (NS), agomir-320 (AG), and antagomir-320 (AT) groups. Postoperative spatial learning and memory in rats were analyzed by the Morris water maze and the open field tests. The plasma levels of insulin-like growth factor-1 (IGF-1), amyloid precursor protein (APP) proteins, miRNA320 and IGF-1mRNA were measured by ELISA and qRT-PCR, respectively. A total of 240 Chinese Han patients over 65 years who underwent tibial fracture internal fixation were included in the PNDABLE study. POD cases and non-POD controls (1:1 matched) were selected by an anesthesiologist using Confusion Assessment Method.

Results

For Group AS, the escape latency was significantly longer and the ratio of time spent in the target quadrant was significantly reduced, APP and miR-320 were upregulated and IGF-1mRNA was downregulated compared with Group C. For Group AG, the escape latency was significantly longer and the ratio of time spent in the target quadrant was significantly reduced, APP and miR-320 were upregulated and IGF-1mRNA was downregulated compared with Group AS. For Group AT, the escape latency was significantly reduced and the ratio of time spent in the target quadrant was significantly longer, APP and miR-320 were downregulated and IGF-1mRNAwas upregulated compared with Group AS. Compared with NPOD patients, the expressions of plasma miR-320 and APP protein were increased and the expression of plasma IGF-1 mRNA was decreased in POD patients after surgery.

Conclusions

MiRNA-320 might play a role in up-regulating the levels of IGF-1mRNA and APP protein, which offered a new target for POD treatment.

Trial registration

Correlation of perioperative neurocognitive disorders with lifestyle and biomarkers.ChiCTR2000033439. Registered 1 June 2020.
Direct-to-consumer strategies to promote deprescribing in primary care: a pilot study
Authors: Linsky Amy M. , Kressin Nancy R. , Stolzmann Kelly , Pendergast Jacquelyn , Rosen Amy K. , Bokhour Barbara G. , Simon Steven R.
Published: March 2022

Background

Deprescribing, or the intentional discontinuation or dose-reduction of medications, is an approach to reduce harms associated with inappropriate medication use. We sought to determine how direct-to-patient educational materials impacted patient-provider discussion about and deprescribing of potentially inappropriate medications.

Methods

We conducted a pre-post pilot trial, using an historical control group, at an urban VA medical center. We included patients in one of two cohorts: 1) chronic proton pump inhibitor users (PPI), defined as use of any dose for 90 consecutive days, or 2) patients at hypoglycemia risk, defined by diabetes diagnosis; prescription for insulin or sulfonylurea; hemoglobin A1c < 7%; and age ≥ 65 years, renal insufficiency, or cognitive impairment. The intervention consisted of mailing medication-specific patient-centered EMPOWER (Eliminating Medications Through Patient Ownership of End Results) brochures, adapted to a Veteran patient population, two weeks prior to scheduled primary care appointments. Our primary outcome – deprescribing – was defined as clinical documentation of target medication discontinuation or dose-reduction. Our secondary outcome was documentation of a discussion about the target medication (yes/possible vs. no/absent). Covariates included age, sex, race, specified comorbidities, medications, and utilization. We used chi-square tests to examine the association of receiving brochures with each outcome.

Results

The 348 subjects (253 intervention, 95 historical control) were primarily age ≥ 65 years, white, and male. Compared to control subjects, intervention subjects were more likely to have deprescribing (36 [14.2%] vs. 4 [4.2%], p = 0.009) and discussions about the target medication (31 [12.3%] vs. 1 [1.1%], p = 0.001).

Conclusions

Targeted mailings of EMPOWER brochures temporally linked to a scheduled visit in primary care clinics are a low-cost, low-technology method associated with increases in both deprescribing and documentation of patient-provider medication discussions in a Veteran population. Leveraging the potential for patients to initiate deprescribing discussions within clinical encounters is a promising strategy to reduce drug burden and decrease adverse drug effects and harms.
Esophageal tuberculosis induced dysphagia: a case report
Authors: Olson Dylan , Liu Kevin C. , Merza Anthony P. , Tilahun Ermias , Aziz Aadam A.
Published: March 2022

Background

Patients can present for a wide variety of etiologies for dysphagia, and it is important to consider less common causes once common etiologies have been ruled out. Extrapulmonary Mycobacterium tuberculosis (TB) presentations are rare to see in the western populations due to relative lack of TB exposure and overall less immunocompromised populations, but should be considered for at-risk patients. Gastrointestinal (GI) TB is rare, and the GI tract is considered only the sixth most frequent site of extrapulmonary TB (EPTB).

Case presentation

This is a case report of a 35-year-old Ethiopian male presenting with dysphagia and retrosternal odynophagia who was found to have infiltration of mediastinal lymphadenopathy into the esophageal wall secondary to TB. This patient underwent an upper endoscopy, which revealed a linear 2 cm full thickness mucosal defect in the middle esophagus concerning for an infiltrative process with full thickness tear. Computed tomography (CT) of the chest demonstrated a subcarinal soft tissue mass that was inseparable from the esophagus. He was referred to thoracic surgery and underwent an exploratory mediastinal dissection. A mediastinoscopy scope was inserted and the mediastinal dissection was made until the subcarinal nodes were identified and removed. Biopsy results showed necrotizing and non-necrotizing granulomas, and acid-fast bacilli (AFB) culture from the surgically removed lymph node showed Mycobacterium TB complex growth. He had no known TB exposures and did not have any TB risk factors. He then followed up in infectious disease clinic and was managed with anti-tuberculosis treatment (ATT) with complete resolution of symptoms.

Conclusions

Our patient was ultimately found to have esophageal TB secondary to mediastinal invasion into the esophageal wall from lymphadenopathy associated with TB. This is an extremely rare presentation in western populations due to diminished exposure rates and overall less immunocompromised populations compared to impoverished countries with increased TB exposure and human immunodeficiency virus (HIV) infection rates. Although TB is not as commonly seen in western populations, it should be considered on the differential for any atypical presentations of GI diseases for patients with clinical or geographic risk factors.
Disease transmission and mass gatherings: a case study on meningococcal infection during Hajj
Authors: Coudeville Laurent , Amiche Amine , Rahman Ashrafur , Arino Julien , Tang Biao , Jollivet Ombeline , Dogu Alp , Thommes Edward , Wu Jianhong
Published: March 2022

Background

Mass gatherings can not only trigger major outbreaks on-site but also facilitate global spread of infectious pathogens. Hajj is one of the largest mass gathering events worldwide where over two million pilgrims from all over the world gather annually creating intense congestion.

Methods

We developed a meta-population model to represent the transmission dynamics of Neisseria meningitidis and the impact of Hajj pilgrimage on the risk of invasive meningococcal disease (IMD) for pilgrims population, local population at the Hajj site and country of origin of Hajj pilgrims. This model was calibrated using data on IMD over 17 years (1995–2011) and further used to simulate potential changes in vaccine policy and endemic conditions.

Results

The effect of increased density of contacts during Hajj was estimated to generate a 78-fold increase in disease transmission that impacts not only pilgrims but also the local population. Quadrivalent ACWY vaccination was found to be very effective in reducing the risk of outbreak during Hajj. Hajj has more limited impact on IMD transmission and exportation in the pilgrim countries of origin, although not negligible given the size of the population considered.

Conclusion

The analysis performed highlighted the amplifying effect of mass gathering on N. meningitidis transmission and confirm vaccination as a very effective preventive measure to mitigate outbreak risks.
Awareness of fetal movements and care package to reduce fetal mortality (AFFIRM): a trial-based and model-based cost-effectiveness analysis from a stepped wedge, cluster-randomised trial
Authors: Camacho Elizabeth M. , Whyte Sonia , Stock Sarah J. , Weir Christopher J. , Norman Jane E. , Heazell Alexander E. P.
Published: March 2022

Background

The AFFIRM intervention aimed to reduce stillbirth and neonatal deaths by increasing awareness of reduced fetal movements (RFM) and implementing a care pathway when women present with RFM. Although there is uncertainty regarding the clinical effectiveness of the intervention, the aim of this analysis was to evaluate the cost-effectiveness.

Methods

A stepped-wedge, cluster-randomised trial was conducted in thirty-three hospitals in the United Kingdom (UK) and Ireland. All women giving birth at the study sites during the analysis period were included in the study. The costs associated with implementing the intervention were estimated from audits of RFM attendances and electronic healthcare records. Trial data were used to estimate a cost per stillbirth prevented was for AFFIRM versus standard care. A decision analytic model was used to estimate the costs and number of perinatal deaths (stillbirths + early neonatal deaths) prevented if AFFIRM were rolled out across Great Britain for one year. Key assumptions were explored in sensitivity analyses.

Results

Direct costs to implement AFFIRM were an estimated £95,126 per 1,000 births. Compared to standard care, the cost per stillbirth prevented was estimated to be between £86,478 and being dominated (higher costs, no benefit). The estimated healthcare budget impact of implementing AFFIRM across Great Britain was a cost increase of £61,851,400/year.

Conclusions

Perinatal deaths are relatively rare events in the UK which can increase uncertainty in economic evaluations. This evaluation estimated a plausible range of costs to prevent baby deaths which can inform policy decisions in maternity services.

Trial registration

The trial was registered with www.ClinicalTrials.gov, number NCT01777022.