bluuebunny/crossref_metadata_2025 huggingface dataset:
Nimotuzumab as Additional Therapy for GLIOMA in Pediatric and Adolescent: A Systematic Review
Authors: Parenrengi Muhammad A , Suryaningtyas Wihasto , Al Fauzi Asra , Hafid Bajamal Abdul , Kusumastuti Kurnia , Utomo Budi , Muslim Hidayat Thamrin Ahmad , Sulistiono Bagus
Published: February 2022

Introduction

Pediatric gliomas represent the most common brain tumor in children and its higher grades are associated with higher recurrence and low survival rate. All therapeutic modalities are reported to be insufficient to achieve satisfactory result, with follow-up treatment such as adjuvant radiotherapy and chemotherapy recommended to increase survival and hinder tumor progression. Nimotuzumab is a monoclonal antibody that acts as an inhibitor of epidermal growth factor receptor found on the surface of glioma cells and had been studied for its usage in pediatric gliomas in recent years.

Methods

A systematic review is performed according to Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. A through literature search was conducted on PubMed, Scopus, Cochrane, and clinicaltrials.gov database. Articles were selected systematically based on the PRISMA protocol and reviewed completely. The relevant data were summarized and discussed. We measured overall survival, progression-free survival, and adverse Events (AE) for nimotuzumab usage as an adjunct therapy in pediatric glioma population.

Result

From 5 studies included for qualitative analysis, 151 patients are included with overall survival (OS) that vary from 3.2–22.8 mo, progression-free survival (PFS) from 1.7–21.6 mo, and relatively low serious adverse events (0–21) are recorded. Follow-up ranged from 2.4–66 mo with four studies reporting diffuse intrinsic pontine glioma (DIPG) patients and only one study reporting nimotuzumab usage in pediatric high-grade glioma (HGG) patients with better outcome in HGG patients than DIPG.

Conclusion

There are no significant differences in the PFS and OS of nimotuzumab as adjunct therapy for pediatric compared to result of standard therapy in majority of previous studies. There were also no differences in the AE of nimotuzumab for pediatric glioma between studies, and low event of serious adverse events indicating its safety. But still there is an evidence of possible benefit of nimotuzumab as adjuvant therapy in pediatric glioma. We recommend further studies with larger number of patients that may lead to possibly different results. There should also be more studies with better level of evidence to further validate the effect of nimozutumab on pediatric glioma.
A CBPR-Enhanced Delphi Method: The Measurement Approaches to Partnership Success Case Study
Authors: Brush Barbara L. , Lee Shoou-Yih D. , Gabrysiak Adena , Jensen Megan , Wilson-Powers Eliza , Coombe Chris M. , Chandanabhumma P. Paul , Valerio Melissa , Israel Barbara A. , Lachance Laurie
Published: February 2022

As part of a 5-year study to develop and validate an instrument for measuring success in long-standing community-based participatory research (CBPR) partnerships, we utilized the Delphi method with a panel of 16 community and academic CBPR experts to assess face and content validity of the instrument’s broad concepts of success and measurement items. In addition to incorporating quantitative and qualitative feedback from two online surveys, we included a 2-day face-to-face meeting with the Expert Panel to invite open discussion and diversity of opinion in line with the CBPR principles framing and guiding the study. The face-to-face meeting allowed experts to review the survey data (with maintained anonymity), convey their perspectives, and offer interpretations that were untapped in the online surveys. Using a CBPR approach facilitated a synergistic process that moved above and beyond the consensus achieved in the initial Delphi rounds, to enhance the Delphi technique and the development of items in the instrument.
Conceptualizing Services and Service Innovation: A Practice Theory Study of the Swedish Music Market
Authors: Skålén Per , Gummerus Johanna
Published: February 2022

In today’s complex and interconnected marketplace, the study of services and service innovation among multiple actors is an underdeveloped, but a theoretically and managerially relevant research area for enabling value cocreation. Building on general practice theory, the scarce prior service research that has drawn on practice theory, and an empirical study of the Swedish music market, this paper outlines a framework that conceptualizes services and service innovation among multiple actors by focusing on value cocreation practices (VCPs). The framework contributes to service research by conceptualizing services as bundles of VCPs, providing a theoretical foundation for the research that studies services as activities. It also contributes to service research by conceptualizing service innovation as the creation of VCPs. The paper shows how actors’ concrete activities, in combination with the valancing of VCPs existing in the market, induce service innovation. A future agenda for research on services and service innovation is also proposed. In addition to these theoretical contributions, the paper offers practical insights into how managers, with the help of the framework, may broaden their focus to include the shared VCPs of the markets to secure a competitive advantage.
Immune Checkpoint Inhibitors in Triple Negative Breast Cancer: The Search for the Optimal Biomarker
Authors: Qureshi Sadaf , Chan Nancy , George Mridula , Ganesan Shridar , Toppmeyer Deborah , Omene Coral
Published: February 2022

Triple negative breast cancer (TNBC) is a high-risk and aggressive malignancy characterized by the absence of estrogen receptors (ER) and progesterone receptors (PR) on the surface of malignant cells, and by the lack of overexpression of human epidermal growth factor 2 (HER2). It has limited therapeutic options compared to other subtypes of breast cancer. There is now a growing body of evidence on the role of immunotherapy in TNBC, however much of the data from clinical trials is conflicting and thus, challenging for clinicians to integrate the data into clinical practice. Landmark phase III trials using immunotherapy in the early-stage neoadjuvant setting concluded that the addition of immunotherapy to chemotherapy improved the pathologic complete response (pCR) rate compared to chemotherapy with placebo while others found no significant improvement in pCR. Phase III trials have investigated the utility of immunotherapy in previously untreated metastatic TNBC, and these studies have similarly arrived at inconsistent conclusions. Some studies showed no benefit while others demonstrated a clinically significant improvement in overall survival in the PD-L1 positive population. It is not yet clear which biomarkers are most useful, and assays for these biomarkers have not been standardized. Given the often serious and severe side effects of immunotherapy, it is important and necessary to identify predictive biomarkers of response and resistance in order to enhance patient selection. In this review, we will discuss both the challenges of traditional biomarkers and the opportunities of emerging biomarkers for patient selection.
Exercising power in autoethnographic vignettes to constitute critical knowledge
Authors: Huber Guy
Published: February 2022

This article shows how autoethnographic vignettes can be used as a reflexive tool to problematize the power relations in which organizational ethnographers participate when doing and representing their fieldwork. Foucault’s analysis of the ethical self-formation process provides the impetus to explore the embodied experiences of my autoethnographic study of a cooperative retail outlet in New York. In questioning how power and knowledge reflexively generated my actions and interpretations, I frame this autoethnography as a means of critically reflecting on my own practice as a researcher. By writing about our own embodied interactions with others through discourses that constitute our experiences, we begin to understand how power is exercised in practice. I conclude by discussing the practical benefits for researchers of writing autoethnographic vignettes and, in particular, for doctoral students seeking to become qualitative researchers in the field.
Commentary: Development of Therapeutics for Congenital Cytomegalovirus Infection
Authors: Whitley Richard J
Published: February 2022

In the mid 1980’s, I flew from Birmingham, Alabama to San Francisco, rented a car, and drove to Palo Alto so that I could meet with John Martin at Syntex. John, along with Julian Verheyden, synthesized ganciclovir, which had significant in vitro activity against cytomegalovirus (CMV) in vitro. This drug provided my colleagues and me an opportunity to evaluate it as a therapeutic agent for congenital CMV infection, knowing full well that it was mutagenic, teratogenic, and carcinogenic. John in his wisdom convinced the management of Syntex to provide ganciclovir for this disease, allowing me to study this drug in symptomatic congenitally infected children through the NIAID Collaborative Antiviral Study Group (CASG). Certainly, no other person or company would advocate for the use of such a medication in children, regardless of disease severity, because of its toxicity profile. Since these early days, ganciclovir, and subsequently its prodrug valganciclovir, have become the standard of care for the treatment of congenital cytomegalovirus infection. The following commentary defines the need and progress in the development of therapy
Game of Thrones tourism and the (re)imagination of the new Northern Ireland
Authors: Mannheimer Emily , Reijnders Stijn , Brandellero Amanda
Published: February 2022

For decades, Northern Ireland was best known for the violent conflict referred to as the Troubles. However, the filming of HBO's Game of Thrones in Northern Ireland has had a profound effect on boosting tourism numbers as well as the country's image in the global awareness. This article examines the role of Game of Thrones tour guides as cultural mediators who are uniquely positioned to redefine the image of Northern Ireland. Through an analysis of the guides’ tour narratives, this article demonstrates how tour guides redefine the past and construct an image for the future of Northern Ireland via the fantasy world of Game of Thrones. It concludes that tourism provides a platform for communicating new social imaginaries.
Aortic stenosis: An important cause of collapse to be considered in a polytrauma patient
Authors: Rajinder Singh  , Bhajneek Grewal  , Wajid Raza  , Siddeshwar Patil
Published: February 2022

Undiagnosed and underlying medical co-morbidities are known to have a role in the causation of or contribution to injuries sustained in cases of polytrauma. Syncope provoked by valvular heart disease is one such example. Thorough clinical assessment is needed to ensure such diagnoses are detected and treated, whilst ensuring a patient’s ongoing rehabilitation needs are met. Here, the authors report a case of polytrauma, most likely secondary to severe aortic stenosis, causing syncope which was diagnosed at a later stage due to ongoing symptomatology. Delay in picking up such diagnoses can contribute to mortality in these patients or affect morbidity by having a detrimental impact on a patient’s functional recovery.
Urban Youth and Terrorism: A Quantitative Analysis (Are Youth Bulges Relevant Anymore?)
Authors: Korotayev Andrey , Romanov Daniil , Zinkina Julia , Slav Maxim
Published: February 2022

Both urbanization and a high share of youth (“youth bulge”) have been shown to correlate with higher levels of political violence, in general, and terrorism, in particular. In this article, we test the hypothesis that urbanization and general youth bulge (share of aged 15–29 in the adult population) should produce a particularly significant impact on the level of terrorist activity when acting together due to the interaction effect. Performed negative binomial regressions (both with and without interaction term) support this hypothesis. We also test the impact of “urban youth bulge” (share of urban youth in the total adult population), and it turns out to be a much more significant predictor of terrorism than either general youth bulge or urbanization taken separately. This finding is shown to have substantial practical implications, indicating that urban youth bulges are likely to retain their relevance in the forthcoming decades, in contrast to general youth bulges.
Nonoperative Management of Humerus Fractures in Patients With Ispilateral Hemiparesis or Hemiplegia
Authors: Patel Raahil S. , Bartoletta John J. , Munaretto Nicholas F. , Tagliero Adam J. , Rhee Peter C.
Published: February 2022

Background:

Patients with upper limb dysfunction from a brain injury often have different goals of treatment and expectations following a fracture of the upper extremity. This study retrospectively reviewed outcomes of nonoperative management of acute humerus fractures in patients with severe ipsilateral hemiparesis or hemiplegia.

Methods:

Patients who had sustained an acute humerus fracture managed nonoperatively, greater than 1 year following an upper motor neuron (UMN) injury resulting in ipsilateral severe hemiparesis or hemiplegia at a single tertiary care center from 1988 to 2019, were reviewed. Fractures were classified using the AO-Müller/Orthopaedic Trauma Association and/or Neer classifications. Primary outcome measures included House classification level of function, pain, achievement of and time to radiographic union, and the need for subsequent surgical procedures.

Results:

Ten distinct nonoperatively managed humerus fractures—3 proximal (11A23), 5 mid-shaft (12A2b = 1, 12A2c = 2, 12A3a = 1, 12A2b = 1), and 2 distal (13A2 = 1, 13 C1 = 1)—were identified in 8 patients (6 women and 2 men) with ipsilateral hemiparesis or hemiplegia. The median radiographic follow-up was 20 months (range: 78 days to 12 years). The median clinical follow-up was 33.5 months (range: 100 days to 12 years). All patients presented with severe pain that was absent at final follow-up. Radiographic union was achieved in all patients with a mean time to union of 90.9 ± 39.3 days (range: 35-185 days). No patients required operative management.

Conclusions:

Nonoperative management of humerus fractures in patients with an ipsilateral UMN injury might result in reliable pain relief and union without the need for further surgical intervention. Management of humerus fractures in this patient population should be individualized toward their goals of care.
Predicting the availability of continuous mining systems using LSTM neural network
Authors: Gomilanovic Miljan , Stanic Nikola , Milijanovic Dejan , Stepanovic Sasa , Milijanovic Aleksandar
Published: February 2022

This work deals with a model development to predict the availability of continuous systems at the open pits using the artificial neural networks. The main idea of this work is to improve the analytical approach with initial assumption that the time length distributions of a faulty system have an exponential distribution. Data related to the I ECC(excavator, conveyors, crushing plant) system of the Open Pit Drmno Kostolac are used for this work. The aim of this work is to improve a model for predicting the availability of continuous systems at the open pits. On the basis of [Formula: see text], [Formula: see text], and [Formula: see text] values, presented in this work, it is concluded that the model, obtained by the use of neural network, has a higher predictive power compared to the analytical approach. A corresponding simulation is created on the basis of obtained model that should a scope of the system availability for each type of failure. Also, a more precise image of the availability of continuous systems at the open pits is given on the basis of simulation.
Association between coronavirus disease morbidity and mortality rates and BCG vaccination policies in OECD countries. Authors’ reply
Authors: Senoo Yuki , Suzuki Yousuke , Tsuda Kenji , Tanimoto Tetsuya , Takahashi Kenzo
Published: February 2022

We appreciate the reviewer’s comment to our article on the correlation between the national BCG vaccination policy and coronavirus disease 2019 among Organisation for Economic Co-operation and Development countries as of April 20, 2020. In this letter, we further updated the data up to November 1, 2020, and found that the updated results also arrive at the similar conclusion as the accepted article.
A COVID-19 outbreak in a long-term care facility in Massachusetts: Rapidity and extent of spread, resident symptoms, and mortality
Authors: Whitcomb Nicholas , Monteleone Maureen , Johansen Paul , Matthews Mark , Aucoin Paula , Burt Donald , Whitcomb Winthrop
Published: February 2022

In the spring of 2020, COVID-19 spread rapidly through a long-term care facility in Massachusetts. 74 (of 134 total) residents tested positive, with 72 testing positive in the first three weeks of the outbreak. Fatigue, anorexia, myalgia, and confusion were the most common symptoms. 21 residents (28%) testing positive subsequently died.
Effect of the COVID-19 Pandemic on Sports-Related Injuries Evaluated in US Emergency Departments
Authors: Sabbagh Ramsey S. , Shah Nihar S. , Kanhere Arun P. , Hoge Connor G. , Thomson Cameron G. , Grawe Brian M.
Published: February 2022

Background:

Organized athletics are undergoing a gradual resumption after a prolonged hiatus in 2020 because of the coronavirus disease 2019 (COVID-19) pandemic.

Purpose/Hypothesis:

The purpose of this study was to evaluate the effect of the 2020 COVID-19 period on emergency department (ED) visits for sports-related injuries in the United States. It was hypothesized that such visits decreased in response to the pandemic conditions.

Study Design:

Descriptive epidemiology study.

Methods:

A selection of sports (baseball, basketball, softball, soccer, American football, weightlifting, track and field, martial arts, boxing, golf, personal fitness, cycling, tennis, and ice hockey) were classified as being an organized team, organized individual, or nonorganized sport. The National Electronic Injury Surveillance System database was then queried for ED visits for sports-related injuries between January 1, 2018, and December 31, 2020, and we compared weighted national injury estimates and injury characteristics from athletes presenting to EDs in 2018 and 2019 versus those from the 2020 COVID-19 pandemic period and between March 1 and May 31, 2020 (government-imposed lockdown period). Bivariate comparisons between variables were conducted using chi-square analysis, with strength of association assessed using odds ratios.

Results:

The 164,151 unweighted cases obtained from the query resulted in a weighted national estimate of 5,664,795 sports-related injuries during the study period. Overall, there was a 34.6% decrease in sports-related ED visits in 2020 compared with the yearly average between 2018 and 2019 (baseline). The number of ED visits in 2020 decreased by 53.9% versus baseline for injuries incurred by participation in an organized team sport and by 34.9% for injuries incurred by participation in an organized individual sport. The number of ED visits during the 2020 lockdown period decreased by 76.9% versus baseline for injuries incurred by participation in an organized team sport and by 65.8% for injuries incurred by participation in an organized individual sport. Injuries sustained while participating in a nonorganized sport remained relatively unaffected and decreased by only 8.1% in 2020.

Conclusion:

ED visits in the United States for injuries sustained while participating in an organized team or individual sport underwent a decrease after the beginning of the COVID-19 pandemic in 2020, especially during the lockdown period.
A Typology of COVID-19 Data Gaps and Noise From Long-Term Care Facilities: Approximating the True Numbers
Authors: Hill Terry E. , Farrell David J.
Published: February 2022

Although there is agreement that COVID-19 has had devastating impacts in long-term care facilities (LTCFs), estimates of cases and deaths have varied widely with little attention to the causes of this variation. We developed a typology of data vulnerabilities and a strategy for approximating the true total of COVID-19 cases and deaths in LTCFs. Based on iterative qualitative consensus, we categorized LTCF reporting vulnerabilities and their potential impacts on accuracy. Concurrently, we compiled one dataset based on LTCF self-reports and one based on confirmatory matching with California’s COVID-19 databases, including death certificates. Through March 2021, Alameda County LTCFs reported 6663 COVID-19 cases and 481 deaths. In contrast, our confirmatory matching file includes 5010 cases and 594 deaths, corresponding to 25% fewer cases but 23% more deaths. We argue that the higher (self-report) case total approximates the lower bound of true COVID-19 cases, and the higher (confirmed match) death total approximates the lower bound of true COVID-19 deaths, both of which are higher than state and federal counts. LTCFs other than nursing facilities accounted for 35% of cases and 29% of deaths. Improving the accuracy of COVID-19 figures, particularly across types of LTCFs, would better inform interventions for these vulnerable populations.
Impact of DHCWs’ Safety Perception on Vaccine Acceptance and Adoption of Risk Mitigation Strategies
Authors: Coker M.O. , Subramanian G. , Davidow A. , Fredericks-Younger J. , Gennaro M.L. , Fine D.H. , Feldman C.A.
Published: February 2022

Objectives:

To estimate the association between safety perception on vaccine acceptance and adoptions of risk mitigation strategies among dental health care workers (DHCWs).

Methods:

A survey was emailed to DHCWs in the New Jersey area from December 2020 to January 2021. Perceived safety from regular SARS-CoV-2 testing of self, coworkers, and patients and its association with vaccine hesitancy and risk mitigation were ascertained. Risk Mitigation Strategy (RiMS) scores were computed from groupings of office measures: 1) physical distancing (reduced occupancy, traffic flow, donning of masks, minimal room crowding), 2) personal protective equipment (fitted for N95; donning N95 masks; use of face shields; coverings for head, body, and feet), and 3) environmental disinfection (suction, air filtration, ultraviolet, surface wiping).

Results:

SARS-CoV-2 testing of dental professionals, coworkers, and patients were perceived to provide safety at 49%, 55%, and 68%, respectively. While dentists were least likely to feel safe with regular self-testing for SARS-CoV-2 (P < 0.001) as compared with hygienists and assistants, they were more willing than hygienists (P = 0.004; odds ratio, 1.79 [95% CI, 1.21 to 2.66]) and assistants (P < 0.001; odds ratio, 3.32 [95% CI, 1.93 to 5.71]) to receive the vaccine. RiMS scores ranged from 0 to 19 for 467 participants (mean [SD], 10.9 [2.9]). RiMS scores did not significantly differ among groups of DHCWs; however, mean RiMS scores were higher among those who received or planned to receive the COVID-19 vaccine than those with who did not (P = 0.004). DHCWs who felt safer with regular testing had greater RiMS scores than those who did not (11.0 vs. 10.3, P = 0.01).

Conclusions:

Understanding DHCWs’ perception of risk and safety is crucial, as it likely influences attitudes toward testing and implementation of office risk mitigation policies. Clinical studies that correlate risk perception and RiMS with SARS-CoV-2 testing are needed to demonstrate the effectiveness of RiMS in dental care settings.

Knowledge Transfer Statement:

Educators, clinicians, and policy makers can use the results of this study when improving attitudes toward testing and implementation of risk mitigation policies within dental offices, for current and future pandemics.
Patterns of comorbidity and multimorbidity among middle-aged and elderly women in peri-urban Tanzania
Authors: Stieglitz Laura-Marie , Bärnighausen Till , Leyna Germana H. , Kazonda Patrick , Killewo Japhet , Rohr Julia K. , Kohler Stefan
Published: February 2022

Background

Multimorbidity poses an increasing challenge to health care systems in Sub-Saharan Africa. We studied the extent of multimorbidity and patterns of comorbidity among women aged 40 years or older in a peri-urban area of Dar es Salaam, Tanzania.

Methods

We assessed 15 chronic conditions in 1528 women who participated in a cross-sectional survey that was conducted within the Dar es Salaam Urban Cohort Study (DUCS) from June 2017 to July 2018. Diagnoses of chronic conditions were based on body measurements, weight, blood testing, screening instruments, and self-report.

Results

The five most prevalent chronic conditions and most common comorbidities were hypertension (49.8%, 95% CI 47.2 to 52.3), obesity (39.9%, 95% CI 37.3 to 42.4), anemia (36.9%, 95% CI 33.3 to 40.5), signs of depression (32.5%, 95% CI 30.2 to 34.9), and diabetes (30.9%, 95% CI 27.6 to 34.2). The estimated prevalence of multimorbidity (2+ chronic conditions) was 73.8% (95% CI 71.2 to 76.3). Women aged 70 years or older were 4.1 (95% CI 1.5 to 10.9) times mores likely to be affected by multimorbidity and had 0.7 (95% CI 0.3 to 1.2) more chronic conditions than women aged 40 to 44 years. Worse childhood health, being widowed, not working, and higher food insecurity in the household were also associated with a higher multimorbidity risk and level.

Conclusion

A high prevalence of multimorbidity in the general population of middle-aged and elderly women suggests substantial need for multimorbidity care in Tanzania. Comorbidity patterns can guide multimorbidity screening and help identify health care and prevention needs.
Lasting shift in the gut microbiota in patients with acute myeloid leukemia
Authors: Rashidi Armin , Ebadi Maryam , Rehman Tauseef Ur , Elhusseini Heba , Halaweish Hossam Fathi , Kaiser Thomas , Holtan Shernan G. , Khoruts Alexander , Weisdorf Daniel J. , Staley Christopher
Published: February 2022

Previous studies have shown that the gut microbiota of patients with acute myeloid leukemia (AML) is disrupted during induction chemotherapy; however, the durability of microbiota changes is unknown. This is an important knowledge gap, because reduced microbiota diversity at the time of stem cell transplantation weeks to months after the initial chemotherapy has been associated with higher mortality after transplantation. By sequencing the gut microbiota in 410 longitudinal stool samples from 52 patients with AML, we found that, during inpatient chemotherapy, the gut microbiota is stressed beyond its ability to recover its original state. Despite major reductions in antibiotic pressure and other disturbances to the microbiota after hospital discharge, the trajectory of microbiota recovery yields new communities that are highly dissimilar to baseline. This lasting shift in the gut microbiota is relevant for subsequent phases of curative therapy and is a potential target for novel microbiota protective/restorative interventions. This trial was registered at www.clinicaltrials.gov as #NCT03316456.
Distance correlation application to gene co-expression network analysis
Authors: Hou Jie , Ye Xiufen , Feng Weixing , Zhang Qiaosheng , Han Yatong , Liu Yusong , Li Yu , Wei Yufen
Published: February 2022

Background

To construct gene co-expression networks, it is necessary to evaluate the correlation between different gene expression profiles. However, commonly used correlation metrics, including both linear (such as Pearson’s correlation) and monotonic (such as Spearman’s correlation) dependence metrics, are not enough to observe the nature of real biological systems. Hence, introducing a more informative correlation metric when constructing gene co-expression networks is still an interesting topic.

Results

In this paper, we test distance correlation, a correlation metric integrating both linear and non-linear dependence, with other three typical metrics (Pearson’s correlation, Spearman’s correlation, and maximal information coefficient) on four different arrays (macrophage and liver) and RNA-seq (cervical cancer and pancreatic cancer) datasets. Among all the metrics, distance correlation is distribution free and can provide better performance on complex relationships and anti-outlier. Furthermore, distance correlation is applied to Weighted Gene Co-expression Network Analysis (WGCNA) for constructing a gene co-expression network analysis method which we named Distance Correlation-based Weighted Gene Co-expression Network Analysis (DC-WGCNA). Compared with traditional WGCNA, DC-WGCNA can enhance the result of enrichment analysis and improve the module stability.

Conclusions

Distance correlation is better at revealing complex biological relationships between gene profiles compared with other correlation metrics, which contribute to more meaningful modules when analyzing gene co-expression networks. However, due to the high time complexity of distance correlation, the implementation requires more computer memory.
Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat
Authors: Crescente Juan M. , Zavallo Diego , del Vas Mariana , Asurmendi Sebastián , Helguera Marcelo , Fernandez Elmer , Vanzetti Leonardo S.
Published: February 2022

Background

Plant miRNAs are a class of small non-coding RNAs that can repress gene expression at the post-transcriptional level by targeting RNA degradation or promoting translational repression. There is increasing evidence that some miRNAs can derive from a group of non-autonomous class II transposable elements called Miniature Inverted-repeat Transposable Elements (MITEs).

Results

We used public small RNA and degradome libraries fromTriticum aestivumto screen for microRNAs production and predict their cleavage target sites. In parallel, we also created a comprehensive wheat MITE database by identifying novel elements and compiling known ones. When comparing both data sets, we found high homology between MITEs and 14% of all the miRNAs production sites detected. Furthermore, we show that MITE-derived miRNAs have preference for targeting degradation sites with MITE insertions in the 3’ UTR regions of the transcripts.

Conclusions

Our results revealed that MITE-derived miRNAs can underlay the origin of some miRNAs and potentially shape a regulatory gene network. Since MITEs are found in millions of insertions in the wheat genome and are closely linked to genic regions, this kind of regulatory network could have a significant impact on the post-transcriptional control of gene expression.
Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery
Authors: Barbitoff Yury A. , Abasov Ruslan , Tvorogova Varvara E. , Glotov Andrey S. , Predeus Alexander V.
Published: February 2022

Background

Accurate variant detection in the coding regions of the human genome is a key requirement for molecular diagnostics of Mendelian disorders. Efficiency of variant discovery from next-generation sequencing (NGS) data depends on multiple factors, including reproducible coverage biases of NGS methods and the performance of read alignment and variant calling software. Although variant caller benchmarks are published constantly, no previous publications have leveraged the full extent of available gold standard whole-genome (WGS) and whole-exome (WES) sequencing datasets.

Results

In this work, we systematically evaluated the performance of 4 popular short read aligners (Bowtie2, BWA, Isaac, and Novoalign) and 9 novel and well-established variant calling and filtering methods (Clair3, DeepVariant, Octopus, GATK, FreeBayes, and Strelka2) using a set of 14 “gold standard” WES and WGS datasets available from Genome In A Bottle (GIAB) consortium. Additionally, we have indirectly evaluated each pipeline’s performance using a set of 6 non-GIAB samples of African and Russian ethnicity. In our benchmark, Bowtie2 performed significantly worse than other aligners, suggesting it should not be used for medical variant calling. When other aligners were considered, the accuracy of variant discovery mostly depended on the variant caller and not the read aligner. Among the tested variant callers, DeepVariant consistently showed the best performance and the highest robustness. Other actively developed tools, such as Clair3, Octopus, and Strelka2, also performed well, although their efficiency had greater dependence on the quality and type of the input data. We have also compared the consistency of variant calls in GIAB and non-GIAB samples. With few important caveats, best-performing tools have shown little evidence of overfitting.

Conclusions

The results show surprisingly large differences in the performance of cutting-edge tools even in high confidence regions of the coding genome. This highlights the importance of regular benchmarking of quickly evolving tools and pipelines. We also discuss the need for a more diverse set of gold standard genomes that would include samples of African, Hispanic, or mixed ancestry. Additionally, there is also a need for better variant caller assessment in the repetitive regions of the coding genome.
The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization
Authors: Dudová Zdenka , Conte Nathalie , Mason Jeremy , Stuchlík Dalibor , Peša Radim , Halmagyi Csaba , Perova Zinaida , Mosaku Abayomi , Thorne Ross , Follette Alex , Pivarč Ľuboslav , Šašinka Radim , Usman Muhammad , Neuhauser Steven , Begley Dale A. , Krupke Debra M. , Frassà Massimiliano , Fiori Alessandro , Corsi Riccardo , Vezzadini Luca , Isella Claudio , Bertotti Andrea , Bult Carol , Parkinson Helen , Medico Enzo , Meehan Terrence , Křenek Aleš
Published: February 2022

Background

Patient-derived xenografts (PDX) mice models play an important role in preclinical trials and personalized medicine. Sharing data on the models is highly valuable for numerous reasons – ethical, economical, research cross validation etc. The EurOPDX Consortium was established 8 years ago to share such information and avoid duplicating efforts in developing new PDX mice models and unify approaches to support preclinical research. EurOPDX Data Portal is the unified data sharing platform adopted by the Consortium.

Main body

In this paper we describe the main features of the EurOPDX Data Portal (https://dataportal.europdx.eu/), its architecture and possible utilization by researchers who look for PDX mice models for their research. The Portal offers a catalogue of European models accessible on a cooperative basis. The models are searchable by metadata, and a detailed view provides molecular profiles (gene expression, mutation, copy number alteration) and treatment studies. The Portal displays the data in multiple tools (PDX Finder, cBioPortal, and GenomeCruzer in future), which are populated from a common database displaying strictly mutually consistent views.

(Short) Conclusion

EurOPDX Data Portal is an entry point to the EurOPDX Research Infrastructure offering PDX mice models for collaborative research, (meta)data describing their features and deep molecular data analysis according to users’ interests.
De novo genome assembly and functional annotation for Fusarium langsethiae
Authors: Zuo Ya , Verheecke-Vaessen Carol , Molitor Corentin , Medina Angel , Magan Naresh , Mohareb Fady
Published: February 2022

Background

Fusarium langsethiae is a T-2 and HT-2 mycotoxins producing species firstly characterised in 2004. It is commonly isolated from oats in Northern Europe. T-2 and HT-2 mycotoxins exhibit immunological and haemotological effects in animal health mainly through inhibition of protein, RNA and DNA synthesis. The development of a high-quality and comprehensively annotated assembly for this species is therefore essential in providing the molecular understanding and the mechanism of T-2 and HT-2 biosynthesis in F. langsethiae to help develop effective control strategies.

Results

The F. langsethiae assembly was produced using PacBio long reads, which were then assembled independently using Canu, SMARTdenovo and Flye. A total of 19,336 coding genes were identified using RNA-Seq informed ab-initio gene prediction. Finally, predicting genes were annotated using the basic local alignment search tool (BLAST) against the NCBI non-redundant (NR) genome database and protein hits were annotated using InterProScan. Genes with blast hits were functionally annotated with Gene Ontology.

Conclusions

We developed a high-quality genome assembly of a total length of 59 Mb and N50 of 3.51 Mb. Raw sequence reads and assembled genome is publicly available and can be downloaded from: GenBank under the accession JAFFKB000000000.

All commands used to generate this assembly are accessible via GitHub: https://github.com/FadyMohareb/fusarium_langsethiae.
HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly
Authors: Sim Sheina B. , Corpuz Renee L. , Simmonds Tyler J. , Geib Scott M.
Published: February 2022

Background

Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de novo assemblies in non-model organisms. Though adapter contamination filtering is routine in traditional short-read analysis pipelines, it has not been widely adopted for HiFi workflows.

Results

Analysis of 55 publicly available HiFi datasets revealed that a read-sanitation step to remove sequence artifacts derived from PacBio library preparation from read pools is necessary as adapter sequences can be erroneously integrated into assemblies.

Conclusions

Here we describe the nature of adapter contaminated reads, their consequences in assembly, and present HiFiAdapterFilt, a simple and memory efficient solution for removing adapter contaminated reads prior to assembly.
HPV prevalence among young adult women living with and without HIV in Botswana for future HPV vaccine impact monitoring
Authors: McClung Nancy , Mathoma Anikie , Gargano Julia W. , Nyepetsi Naledi Gape , Querec Troy D. , Onyekwuluje Juanita , Mine Madisa , Morroni Chelsea , Luckett Rebecca , Markowitz Lauri E. , Ramogola-Masire Doreen
Published: February 2022

Introduction

In 2015, Botswana introduced quadrivalent human papillomavirus (HPV) vaccine for girls aged 9–13 years. To establish a baseline HPV prevalence for future HPV vaccine impact monitoring, we evaluated HPV prevalences among the youngest unvaccinated women in Botswana and compared HPV prevalences among women living with HIV (WLHIV) and without HIV.

Methods

Women aged 18–22 years were recruited from the University of Botswana and HIV clinics in Gaborone from October 2019–January 2021. Demographic and behavioral characteristics were self-reported during structured interviews; HIV clinical characteristics were abstracted from medical charts. Self-collected vaginal swabs were tested for 28 HPV types using Seegene Anyplex II HPV28. We compared prevalence of any HPV, high risk (HR)-HPV, and quadrivalent HPV vaccine types (HPV6/11/16/18) among WLHIV and women without HIV and evaluated risk factors for prevalence of HR-HPV.

Results

A total of 306 WLHIV and 500 women without HIV were recruited. Compared to women without HIV, WLHIV were more likely to be sexually experienced (86.6% versus 74.4%) and have ≥ 3 lifetime sex partners (55.3% versus 27.8%). All HPV type prevalences were significantly higher among WLHIV compared to women without HIV, including prevalence of any HPV (82.7% versus 63.0%), HR-HPV (72.9% versus 53.8%), and quadrivalent vaccine HPV types (34.3% versus 21.0%). Among WLHIV, there were no differences between those perinatally and non-perinatally infected for HPV prevalences, number of HPV types detected, CD4 count, or viral load.

Conclusions

Over one-third of WLHIV and nearly a quarter of those without HIV had vaccine-type HPV detected. This study supports need for the national HPV vaccination program in Botswana and provides important baseline data for future evaluation of impact of the program.
Socio-demographic characteristics associated with the dietary diversity of Thai community-dwelling older people: results from the national health examination survey
Authors: Chalermsri Chalobol , Rahman Syed Moshfiqur , Ekström Eva-Charlotte , Muangpaisan Weerasak , Aekplakorn Wichai , Satheannopakao Warapone , Ziaei Shirin
Published: February 2022

Background

Dietary diversity (DD) is an indicator of nutrient intake and is related to health outcomes in older people. Currently, limited research exists regarding factors associated with DD in older people in developing countries, such as Thailand, despite rapid growth in this population. Therefore, this study aims to examine the association between socio-demographic characteristics and DD in Thai older people.

Methods

A cross-sectional study based on the fifth Thai National Health Examination Survey (NHES-V) conducted between 2013 and 2015 was performed. A total of 7,300 nationally representative older participants aged ≥ 60 years were included. The individual-level dietary diversity score (DDS) was assessed as the frequency of consumption of eight food groups using food frequency questionnaires. Each food group was scored from 0 to 4 according to the frequency of consumption. The DDS was calculated as the sum of the scores, ranging from 0 to 32. Socio-demographic characteristics, including age, sex, highest education level, wealth index, living conditions, and residential area, were assessed. Data were analyzed using multiple linear regression and adjusted for complex survey design.

Results

The participants had a mean age of 69.7 (SD 7.6) years. The mean DDS of participants was 18.4 (SD 3.9). In the adjusted model, a higher educational level, a higher wealth index, and living in an urban area were positively associated with DDS, with adjusted β (95% CI) values of 1.37 (1.04, 1.70) for secondary education or higher, 0.81 (0.55, 1.06) for the richest group, and 0.24 (0.10, 0.44) for living in an urban area. Nevertheless, living alone had negative associations with DDS, with a β (95% CI) of - 0.27 (- 0.53, - 0.00).

Conclusions

This study showed that a higher educational level, a higher wealth index, and living in an urban area had a positive association, whereas living alone had a negative association with DD among Thai older participants. Interventions aiming to improve dietary diversity among older people might benefit from targeting more vulnerable groups, particularly those with less education and wealth, those living alone, or those in rural areas.
Associations between adipokines gene polymorphisms and knee osteoarthritis: a meta-analysis
Authors: Wang Yuqing , Meng Fanqiang , Wu Jing , Long Huizhong , Li Jiatian , Wu Ziying , He Hongyi , Wang Haochen , Wang Ning , Xie Dongxing
Published: February 2022

Background

Adipokines gene polymorphisms are speculated to be associated with the risk of knee osteoarthritis (OA), but evidence remains conflicting. This study therefore aimed to examine whether associations exist between adipokines gene polymorphisms and knee OA by considering the evidence collected from eligible studies through a meta-analysis.

Methods

A systematic search was performed on PubMed, Embase, Web of Science, China National Knowledge Infrastructure (CNKI), and Wanfang up to March 31, 2020. Meta-analysis was carried out by focusing on the associations between adipokines gene polymorphisms and knee OA with the allele model, dominant model, and recessive model.

Results

The present meta-analysis included 5 eligible studies for ADIPOQ rs1501299 with 1,021 cases and 1,097 controls, 3 eligible studies for ADIPOQ rs2241766 with 549 cases and 544 controls, 3 eligible studies for LEPR rs1137101 with 808 cases and 856 controls, 2 eligible studies for VISFATIN rs4730153 with 339 cases and 680 controls and 2 eligible studies for VISFATIN rs16872158 with 339 cases and 680 controls. Significant association was observed between LEPR rs1137101 and knee OA in the overall population (recessive: OR = 0.40, 95% CI 0.21–0.79). Limited data revealed that associations may exist between ADIPOQ rs2241766 and knee OA in Asians (dominant: OR = 1.35, 95% CI 1.03–1.78), between VISFATIN rs4730153 and knee OA in Asians (allele: OR = 0.58, 95% CI 0.41–0.83; dominant: OR = 0.57, 95% CI 0.39–0.83), and between VISFATIN rs16872158 and knee OA in Asians (allele: OR = 1.84, 95% CI 1.26–2.68; dominant: OR = 1.94, 95% CI 1.31–2.89).

Conclusions

Adipokines gene polymorphisms may be associated with knee OA. The association was observed in LEPR rs1137101 in the present study. In addition, limited data revealed that associations may also exist in ADIPOQ rs2241766, VISFATIN rs4730153 and VISFATIN rs16872158.

Prospero registration

CRD42020187664.
Resection and reconstruction for radial polydactyly Type IV-D in 206 cases: a retrospective clinical analysis
Authors: Liu Yuzhou , Xu Xiuyue , Wang Le , Lao Jie , Zhuang Yongqing , Fang Yousheng
Published: February 2022

Background

Radial Polydactyly Type IV-D deformity is difficult to treat because of the most complex bone and soft tissue anomalies. Resection and reconstruction for one of the two thumbs was an option for treatment.

Objective

The study was to present our method of resection and reconstruction with a new incision for radial polydactyly Type IV-D and evaluate the clinical efficacy comprehensively using Rotterdam assessment system in a large sample.

Methods

206 cases of type IV-D thumb duplication underwent resection and reconstruction surgical treatment between 2010 and 2019. Two equal triangle flap incisions were designed around the radial thumb. The radial thumb was resected and the ulnar thumb was reconstructed in aspects of bone, tendons, ligaments and abductor pollicis brevis.

The clinical results were evaluated using Rotterdam assessment system.

Results

The mean follow–up period was 2.2 years (SD 1.5). The mean age of the patients was 9 months (SD 1.8) at the time of operation. The mean ranges of active IP and MP joint flexion and extension were 110° and 26°. The mean angulations for IP and MP joint instabilities were 3° and 11°, relatively. Angulation for palmar abduction was 58°. The mean appearance domain score was 8.9. The average parental satisfaction score was 2.5 and the average patient-reported pain score was 2.1. The mean functional domain score for all patients was 6.6. The average appearance domain score was 8.9. The mean patient-reported domain score was 4.5. The mean Rotterdam outcome score was 20.0, equivalent to 67% of the full score. The postoperative score of patients over two years old was significantly lower than that of patients under two years old.

Conclusion

Resection and reconstruction method with two equal triangle flap incisions was a recommended treatment for radial polydactyly Type IV-D.

Level of evidence

IV