bluuebunny/crossref_metadata_2025 huggingface dataset:
Prospects for the use of Arctic routes in the context of climate change and the implementation of the concept of sustainable development of the Arctic zone
Authors: Gogoleva Valentina , Kirsanova Natalia , Zyabkina Tatyana , Dolgopolova Tatyana
Published: April 2023

The urgent need to solve environmental problems and meet the needs of people requires finding alternative ways to deliver goods in the most environmentally friendly and safe way. In addition, the climatic changes occurring on our planet open up additional prospects for the use of the Arctic for economic purposes, in particular, the use of the Northern Sea Route for cargo transportation. In the modern world economy, sea cargo transportation accounts for about 80% of all cargo transportation. The main cargo flow is carried out through the Southern Sea Route (SSR), along which goods are transported from Europe to Asia. For quite a long period of time, shipowners and logistics companies did not perceive the Arctic region as an alternative to traffic from Asia to Europe or North America, while navigation in the Arctic was much more than just transport shipping. At the same time, the situation has changed significantly in the 21stcentury. The interest in this region among the states of the Arctic zone, as well as other countries, is connected not only with the presence there of large reserves of mineral resources, solving geopolitical problems, but also the search for alternative sea routes for cargo transportation between Europe, North America and Asia. In connection with the blockade of the Suez Canal in March 2021, the question of the need to redirect cargo transportation to alternative routes – the Northern Sea Route (NSR), as part of the Northeast Passage, and the Northwest Passage became acute. The Suez Canal is the busiest and longest sea artery. In addition, this area is unsafe due to frequent attacks by pirates. Due to the geographical features of the SSR the presence of sufficiently narrow places along the route - under the condition of increasing traffic, does not contribute to the free passage of ships. Meanwhile, the active melting of the Arctic ice in the foreseeable future will allow navigation along Arctic routes at higher latitudes and without the escort of icebreaker transport. All of the above allows us to consider navigation in the Arctic latitudes as an actual alternative to the Southern Route, which will serve as the beginning of sustainable development of the Arctic region.
Financial potential as a basis for ensuring environmental and economic security of the Arctic regions
Authors: Ulchenko Mikhail , Ponomarev Nikita
Published: April 2023

Large-scale industrial development of the Arctic territories is a steady course of development that the world economy has been following for several decades. This development is facilitated by global warming, which creates prerequisites for the freeing more and more territories from ice, depletion of resources, especially hydrocarbons, as well as the emergence of new technologies that allow extraction of minerals in difficult conditions for economic activity in the Arctic. Given the vulnerability of the Arctic natural systems, the issues of environmental and economic security, as a result of such development, come to the fore. The study, analyzes the financial capabilities of the Arctic regions and concludes that they have significant financial potential, which, if used rationally, should contribute to ensuring economic and environmental security. The paper proposes the authors’ interpretation of the concept of financial potential of the region. The review of domestic and foreign scientific literature showed that many works are devoted to topical issues of ensuring environmental and economic security of the Arctic regions, but the impact of financial potential on these categories is currently undefined. The paper also analyzes the financial potential of economic entities operating in the Arctic zone of the Russian Federation. It has been revealed that of the nine regions of the Russian Federation classified as Arctic, only one - the Krasnoyarsk Territory - has the value of the indicator characterizing the share of break-even enterprises, which exceeds the average Russian values. At the same time, when assessing the coefficient of provision with tax payments, in seven out of nine regions the value of this coefficient exceeds the average Russian values.
Development of tourism in the Arctic regions of the Russian Federation: the environmental aspect
Authors: Kuchumov Artur , Karpova Galina , Pecheritsa Elena , Voloshinova Marina
Published: April 2023

The article considers the opportunities for the development of tourism in the regions of the Arctic Zone of the Russian Federation in the environmental aspect. The authors examine the existing problems of the development of Arctic tourism in the Russian Federation, which include: low attractiveness of Arctic tourism for most Russian tourists, large investments with a long payback period, unacceptability of anthropogenic impact on the Arctic ecosystem, lack of modern passenger terminals, difficult transport accessibility of locations with specially protected natural areas. Analyzing the foreign experience of tourism development in the Arctic territories, the authors offer recommendations for the development of tourism in the Arctic zone of the Russian Federation. It also includes: support for indigenous peoples of the Arctic in order to increase employment of indigenous peoples while preserving their lifestyle, habits, and culture; assistance in cooperation and interaction with PR and marketing agencies, as well as design studios for creation of new souvenir lines; assistance in organizing excursions acquainting with the life of local residents, their traditional cuisine and local rituals, conducting educational seminars, organizing events for temporary residence in families of indigenous minorities; creation of information and tourist centers; development of events, ethnographic, and environmental types of tourism, intra-city tourism, addressing the lack of modern accommodation facilities and transport accessibility; assessment of environmental potential of specially protected natural areas in the Arctic Zone of the Russian Federation, so that the latter do not suffer from an influx of visitors; building of electric and hybrid polar expedition ships.
Northern labyrinths: potential for interdisciplinary research and a resource for international tourism
Authors: Paranina Alina , Paranin Roman , Grigoryev Alexey , Larchenko Lyubov , Kiseleva Margarita
Published: April 2023

The article presents the scientific rationale for the project of creating a geographic database on northern labyrinths ancient stone structures and petroglyphs located on the coasts and islands of Northern Europe. The aim of the project is to conduct interdisciplinary research of labyrinths-gnomons (tools for orientation in space and time according to the Sun) as a source of information about ancient marine communications, development of navigation technologies, as well as coastal changes in the Arctic region and climatic rhythms of our planet. The research algorithm includes standard methods of complex geographical descriptions; solution of the equation based on the main trigonometric function; analysis of stable relationships in the system “object - landscape - geographic space - Earth - Universe”. The relationship of the structure of labyrinths performing instrumental functions with the geographical latitude, as well as with the long-period rhythms of the planet, which are most clearly manifested in the Arctic region, is considered. The influence of navigation technologies on the physical development of geographic space and its modeling at the local (toponyms), regional (territorial systems and communications) and global levels (modern scientific picture of the world and ancient information models preserved in mythopoetic form) is shown. It is concluded that the creation of a regional geographic database on labyrinths will contribute to the preservation of cultural heritage sites, replenishment of the resources of international tourism in the Arctic region, the development of scientific communications uniting scientists from the northern countries.
Efficience économique et financement des solutions fondées sur la nature : le cas du bassin versant de la Brague
Authors: Arfaoui Nabila , Gnonlonfin Amandine , Piton Guillaume , Douai Ali
Published: April 2023

Cet article évalue l’efficience économique de stratégies de prévention du risque d’inondation en vue d’éclairer la décision de financement des acteurs publics. Le cas de la protection contre les crues « éclair » (courtes et violentes) de la Brague et des inondations associées de la basse vallée à Biot et Antibes (Alpes-Maritimes) est pris comme exemple. Dans cette perspective, nous proposons une double analyse coût-bénéfice (ACB) dans le contexte particulier de la loi Gemapi (gestion des milieux aquatiques et protection contre les inondations) et des stratégies dites « SFN » (solutions fondées sur la nature). L’ACB top-down éclaire les décisions des acteurs nationaux et régionaux tandis que l’ACB bottom-up répond aux préoccupations des acteurs locaux en évaluant l’acceptabilité sociale des stratégies étudiées.
The Association of Abnormal Doppler and Abnormal Amniotic Fluid Volume in the Third Trimester of Pregnancy with Preterm Birth in Pregnant Women in Agra, India
Authors: Gupta Anjali , Choorakuttil Rijo Mathew , Nirmalan Praveen K.
Published: April 2023

Aim This article determines the association and diagnostic effectiveness of abnormal Doppler and abnormal amniotic fluid volume (AFV) in the third trimester of pregnancy with preterm births.

Methods The third trimester screening protocol of the Samrakshan program of the Indian Radiological and Imaging Association utilizes trimester-specific fetal Doppler studies and ultrasound assessments, estimation of the risk for preterm preeclampsia (PE), assessment of the fetal environment, growth, and structure, and staging of fetal growth restriction. A multivariate logistic regression model was used to explore associations of abnormal Doppler and AFV with preterm birth. The diagnostic effectiveness of Doppler and amniotic fluid measurements for preterm births was assessed.

Results One hundred and sixty-one (25.6%) of the 630 women had a preterm birth before 37 gestational weeks. Eighty (21.1%) of the 379 women with normal AFV and normal fetal Doppler studies in the third trimester had a preterm birth. The proportion of preterm birth declined from 35.14% in 2019 to 19.53% in 2022 (chi-square test p = 0.009). Preterm birth was associated with preterm PE (adjusted odds ratio: 3.66, 95% confidence interval: 1.42, 9.44) in a multivariate logistic regression model. Both abnormal fetal Doppler and AFV did not have a good discriminatory ability for preterm births.

Conclusion Integration of fetal Doppler studies helped reduce the preterm birth rate by providing an objective measure of fetal well-being, contrary to a common belief that the use of color Doppler in the third trimester may result in iatrogenic increased preterm birth. Preterm births are associated with preterm PE and early identification of high-risk women and early initiation of low-dose aspirin may have an added benefit on preterm birth rates.
Practice of L-Asparaginase Usage: A Survey among Healthcare Providers Treating Children with Cancer in India
Authors: MV Archana , VS Kalasekhar , Munikoty Vinay , Bhat Ramitha R. , Achyutrao Atul , Lakshmi R Vani , Bhat K Vasudeva
Published: April 2023

Introduction L-asparaginase is an essential chemotherapeutic agent in the therapy of acute lymphoblastic leukemia (ALL), which has led to improvement in survival. In low- and middle-income countries like India, the outcomes in ALL are inferior compared with the published literature, one of the causes of which is believed to be due to the inferior quality of bioequivalent asparaginase.

Objective The following survey attempts to understand the practice of using this agent among oncologists treating children with cancer in our country.

Methods The researchers designed a structured online questionnaire comprising 25 aspects of L-asparaginase usage in the study. The questionnaire was directed to the healthcare providers involved in treating children with cancer in India.

Results Of the total 80 responses recorded, 51 (64%) respondents had more than 5 years of experience in pediatric oncology and were treating at least 5 to 10 newly diagnosed ALL patients per month. Forty-one (51%) respondents utilized native asparaginase, and 21 (26.3%) oncologists used PEGylated-asparaginase exclusively. The most common route of administration was the intramuscular route (66.3%). Seventy percent of respondents utilized native form at a dose of 10,000 IU/m2 and 20% at 6,000 IU/m2. The amounts used for PEGylated L-asparaginase were 1,000,IU/m2, 2,500,IU/m2, and variable doses in 48, 40, and 10% of responses, respectively. Though serum asparaginase assay (SAA) was not measured routinely in most of the centers, 39 (48.8%) healthcare providers perceived performing SAA helps to make the clinical decision.

Conclusion This survey shows a wide variation in L-asparaginase usage among healthcare providers caring for children with cancer in our country. As L-asparaginase is the pivotal component of ALL therapy, uniformity in its usage and dosing with the possibility of monitoring SAA due to the quality of bioequivalent may be one of the critical steps toward improving outcomes in ALL in our country.
Characteristics and Outcomes of Intrahospital Transfers from Neonatal Intensive Care to Pediatric Intensive Care Units
Authors: Mazur Lauren , Veten Ahmed , Ceneviva Gary , Pradhan Sandeep , Zhu Junjia , Thomas Neal J. , Krawiec Conrad
Published: April 2023

Objective Critically ill children may be transferred from the neonatal intensive care unit (NICU) to the pediatric intensive care unit (PICU) for further critical care, but the frequency and outcomes of this patient population are unknown. The aims of this study are to describe the characteristics and outcomes in patients transferred from NICU to PICUs. We hypothesized that a higher-than-expected mortality would be present for patients with respiratory or cardiovascular diagnoses that underwent a NICU to PICU transition and that specific factors (timing of transfer, illness severity, and critical care interventions) are associated with a higher risk of mortality in the cardiovascular group.

Study Design Retrospective analysis of Virtual Pediatric Systems, LLC (2011–2019) deidentified cardiovascular and respiratory NICU to PICU subject data. We evaluated demographics, PICU length of stay, procedures, disposition, and mortality scores. Pediatric Index of Mortality 2 (PIM2) score was utilized to determine the standardized mortality ratio (SMR).

Results SMR of 4,547 included subjects (3,607 [79.3%] cardiovascular and 940 [20.7%] respiratory) was 1.795 (95% confidence interval: 1.62–1.97, p < 0.0001). Multivariable logistic regression analysis demonstrated transfer age (cardiovascular: odds ratio, 1.246 [1.10–1.41], p = 0.0005; respiratory: 1.254 [1.07–1.47], p = 0.0046) and PIM2 scores (cardiovascular: 1.404 [1.25–1.58], p < 0.0001; respiratory: 1.353 [1.08–1.70], p = 0.0095) were significantly associated with increased odds of mortality.

Conclusion In this present study, we found that NICU to PICU observed deaths were high and various factors, particularly transfer age, were associated with increased odds of mortality. While the type of patients evaluated in this study likely influenced mortality, further investigation is warranted to determine if transfer timing is also a factor.

Key Points
Peer-to-peer: The Social Transmission of Symptoms Online
Authors: Tan Winston , Pickup Brydee , Faasse Kate , Colagiuri Ben , Barnes Kirsten
Published: April 2023

Background

Social learning can be highly adaptive—for example, avoiding a hotplate your friend just burnt themselves on—but it has also been implicated in symptom transmission. Social learning is particularly pertinent given the rapid increase in the use of online mediums for social interaction. Yet, little is known about the social transmission of symptoms online or social chains extending further than a single model–observer interaction.

Purpose

To explore whether socially induced symptoms could be propagated through a three-generation social transmission chain in an online setting.

Methods

We explored the social transmission of cybersickness following a virtual reality (VR) experience through online webcam interactions. One hundred and seventy-seven adults viewed a VR video in one of four links along a social transmission chain, after: viewing an actor model cybersickness to the VR video (First-Generation); viewing the First-Generation participant undergo VR (Second-Generation); viewing the Second-Generation participant undergo VR (Third-Generation); or naïve (Control).

Results

Cybersickness was strongest in First-Generation participants, indicating social transmission from the model. This was mediated by expectancy and anxiety. Whether or not subsequent generations experienced cybersickness depended on what the observed participant verbally reported, which is consistent with social transmission.

Conclusions

Results demonstrate that symptoms can be readily transmitted online, and that expectancy and anxiety are involved. Although it is inconclusive as to whether symptoms can propagate along a social transmission chain, there is some evidence of protection from symptoms when a model who does not report any symptoms is observed. As such, this research highlights the role of social transmission in the modulation of symptoms through virtual mediums.
A Migrant’s Chronotopic Identities in Playful Talk in a Classroom
Authors: Tode Tomoko
Published: April 2023

This case study investigates a migrant adult’s identity work in playful talk occurring spontaneously in a classroom for Literacy Education and Second Language Learning for Adults (LESLLA). Based on 12 hours of video-recorded interactions among four learners and their teacher, I identified five playful episodes. This paper focuses on two episodes instigated by a woman who told stories of her outside lives. Discourse analysis was performed through the lens of chronotope (timespace) to examine how she navigated multiple chronotopes, including the front-region classroom chronotope, to negotiate identities and how playful language was related to her chronotopic identity work. Playfulness began in the periphery of the classroom chronotope; then the playful language in it led to the playful formulation of outside-life chronotopes where her agentive identity was constructed. Her full semiotic behaviours blurred the boundaries between the classroom chronotope and the outside chronotope so that the other participants could witness her agency. The study concludes that the classroom chronotope itself showed signs of change in a forward-looking direction.
Machine learning for synergistic network pharmacology: a comprehensive overview
Authors: Noor Fatima , Asif Muhammad , Ashfaq Usman Ali , Qasim Muhammad , Tahir ul Qamar Muhammad
Published: April 2023

Network pharmacology is an emerging area of systematic drug research that attempts to understand drug actions and interactions with multiple targets. Network pharmacology has changed the paradigm from ‘one-target one-drug’ to highly potent ‘multi-target drug’. Despite that, this synergistic approach is currently facing many challenges particularly mining effective information such as drug targets, mechanism of action, and drug and organism interaction from massive, heterogeneous data. To overcome bottlenecks in multi-target drug discovery, computational algorithms are highly welcomed by scientific community. Machine learning (ML) and especially its subfield deep learning (DL) have seen impressive advances. Techniques developed within these fields are now able to analyze and learn from huge amounts of data in disparate formats. In terms of network pharmacology, ML can improve discovery and decision making from big data. Opportunities to apply ML occur in all stages of network pharmacology research. Examples include screening of biologically active small molecules, target identification, metabolic pathways identification, protein–protein interaction network analysis, hub gene analysis and finding binding affinity between compounds and target proteins. This review summarizes the premier algorithmic concepts of ML in network pharmacology and forecasts future opportunities, potential applications as well as several remaining challenges of implementing ML in network pharmacology. To our knowledge, this study provides the first comprehensive assessment of ML approaches in network pharmacology, and we hope that it encourages additional efforts toward the development and acceptance of network pharmacology in the pharmaceutical industry.
Development of Different Separation Techniques for Impurity Profiling of Neostigmine Methylsulfate: A Comparative Study
Authors: El Mously Dina A , Mostafa Nadia M , Hassan Nagiba Y , El-Sayed Ghada M
Published: April 2023

Different separation techniques have been employed to resolve mixtures of multicomponent preparations over the last few decades. They could be efficiently applied for impurity profiling of active drug substances. Impurity profiling has become a critical procedure in pharmaceutical companies to comply with numerous regulatory standards. Isolation and characterization of impurities are crucial for obtaining data that proves biological safety and efficacy. In this contribution, different HPLC, capillary electrophoresis (CE) and TLC-densitometric methods were developed for the determination of neostigmine methylsulfate (NEO) along with 3-hydroxyphenyltrimethyl ammonium methylsulfate (3-HPA) and 3-dimethylaminophenol (DAP) as its impurities in the presence of citric acid. The linearity for NEO was attained in the range of 5–120 μg/mL and 10–60 μg/mL for the HPLC and CE methods, respectively. Regarding the impurities, linearity was obtained over the range of 10–30 μg/mL for 3-HPA and 5–30 μg/mL for DAP in the two proposed methods. For the TLC method, NEO and DAP were determined within the range of 1–11 μg/band, whereas 3-HPA was assayed over the range of 2–12 μg/band. The suggested methods can be securely utilized for routine analysis of the cited components in quality control laboratories.
FOXK1 regulates Wnt signalling to promote cardiogenesis
Authors: Sierra-Pagan Javier E , Dsouza Nikita , Das Satyabrata , Larson Thijs A , Sorensen Jacob R , Ma Xiao , Stan Patricia , Wanberg Erik J , Shi Xiaozhong , Garry Mary G , Gong Wuming , Garry Daniel J
Published: April 2023

Aims

Congenital heart disease (CHD) is the most common genetic birth defect, which has considerable morbidity and mortality. We focused on deciphering key regulators that govern cardiac progenitors and cardiogenesis. FOXK1 is a forkhead/winged helix transcription factor known to regulate cell cycle kinetics and is restricted to mesodermal progenitors, somites, and heart. In the present study, we define an essential role for FOXK1 during cardiovascular development.

Methods and results

We used the mouse embryoid body system to differentiate control and Foxk1 KO embryonic stem cells into mesodermal, cardiac progenitor cells and mature cardiac cells. Using flow cytometry, immunohistochemistry, cardiac beating, transcriptional and chromatin immunoprecipitation quantitative polymerase chain reaction assays, bulk RNA sequencing (RNAseq) and assay for transposase-accessible chromatin using sequencing (ATACseq) analyses, FOXK1 was observed to be an important regulator of cardiogenesis. Flow cytometry analyses revealed perturbed cardiogenesis in Foxk1 KO embryoid bodies (EBs). Bulk RNAseq analysis at two developmental stages showed a significant reduction of the cardiac molecular program in Foxk1 KO EBs compared to the control EBs. ATACseq analysis during EB differentiation demonstrated that the chromatin landscape nearby known important regulators of cardiogenesis was significantly relaxed in control EBs compared to Foxk1 KO EBs. Furthermore, we demonstrated that in the absence of FOXK1, cardiac differentiation was markedly impaired by assaying for cardiac Troponin T expression and cardiac contractility. We demonstrate that FOXK1 is an important regulator of cardiogenesis by repressing the Wnt/β-catenin signalling pathway and thereby promoting differentiation.

Conclusion

These results identify FOXK1 as an essential transcriptional and epigenetic regulator of cardiovascular development. Mechanistically, FOXK1 represses Wnt signalling to promote the development of cardiac progenitor cells.
Visceral adiposity index and the risk of heart failure, late-life cardiac structure, and function in ARIC study
Authors: Xu Chaoguang , Guo Yue , Zhang Shaozhao , Lai Yuhui , Huang Mengting , Zhan Rongjian , Liu Menghui , Xiong Zhenyu , Huang Yiquan , Huang Rihua , Liao Xinxue , Zhuang Xiaodong , Cai Zhixiong
Published: April 2023

Background

It is well established that obesity is associated with the risk of heart failure (HF). However, the data about relationship between visceral fat and the risk of HF are limited.

Aims

We aim to evaluate the association between visceral obesity assessed by visceral adiposity index (VAI) and incident HF and left ventricular (LV) structure and function in Atherosclerosis Risk in Communities (ARIC) study.

Methods

We included 12 161 participants (aged 54.1 ± 5.8 years) free of history of HF and coronary heart disease at baseline (1987–89) in ARIC study. We used multivariable Cox hazard regression models to assess the association between the VAI and incident HF. We further explored the effects of the VAI on LV geometry and function among 4817 participants with echocardiographic data using multivariable linear regression analysis and multinomial logistic regression.

Results

During a median follow-up of 22.5 years, a total of 1904 (15.7%) participants developed HF. After adjustment for traditional HF risk factors, 1 unit increase in the baseline VAI was associated with an 8% higher risk of incident HF [hazard ratio (HR): 1.08, 95% confidence interval (CI): 1.06–1.11]. Results were similar when participants were categorized by VAI tertiles. Compared with participants in the lowest tertile of VAI, those in the second tertile and third tertile had a greater risk of incident HF [HR (95% CI): 1.19 (1.05–1.34) and 1.42 (1.26–1.61), respectively]. For the analyses of the HF subtypes, the higher VAI was only associated with the risk of HF with preserved ejection fraction, not with HF with reduced ejection fraction. In addition, the greater VAI was associated with worse LV diastolic function and abnormal LV geometry including concentric remodelling, concentric hypertrophy, and eccentric hypertrophy.

Conclusion

This study shows that higher VAI was independently associated with the increased risk of incident HF and abnormal LV geometry and LV diastolic dysfunction.
Intensive blood pressure lowering and the risk of new-onset diabetes in patients with hypertension: a post-hoc analysis of the STEP randomized trial
Authors: Yang Ruixue , Zhu Yanqi , Xu Mengdan , Tao Yanhua , Cong Wenwen , Cai Jun
Published: April 2023

Aims

The strategy of blood pressure intervention in the elderly hypertensive patients (STEP) trial reported the cardiovascular benefit of intensive systolic blood pressure (SBP) control in patients with hypertension. The association between intensive SBP lowering and the risk of new-onset diabetes is unclear. This study aimed to evaluate the effect of intensive SBP lowering on the incidence of new-onset diabetes.

Methods and results

Participants in STEP who had baseline fasting serum glucose (FSG) concentrations <7.0 mmol/L and no history of diabetes or hypoglycaemic medication use were included. The primary outcome was new-onset diabetes defined as the time to first occurrence of FSG concentrations ≥7.0 mmol/L. The secondary outcome was new-onset impaired fasting glucose (FSG: 5.6–6.9 mmol/L) in participants with normoglycemia. A competing risk proportional hazards regression model was used for analysis. The cohort comprised 5601 participants (mean age: 66.1 years) with a mean baseline SBP of 145.9 mmHg. Over a median follow-up of 3.42 years, 273 (9.6%) patients in the intensive SBP group (target, 110 to <130 mmHg) and 262 (9.5%) in the standard SBP group (target, 130 to <150 mmHg) developed diabetes (adjusted hazard ratio, 1.01; 95% confidence interval (CI), 0.86–1.20). The adjusted hazard ratio for the secondary outcome was 1.04 (95% CI, 0.91–1.18). The mean highest FSG concentration during the follow-up was 5.82 and 5.84 mmol/L in the intensive and standard groups, respectively.

Conclusion

Intensive SBP lowering is not associated with an altered risk of new-onset diabetes or impaired fasting glucose in hypertensive patients.

Registration

STEP ClinicalTrials.gov, number: NCT03015311.
The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics
Authors: Cornet Luc , Durieu Benoit , Baert Frederik , D'hooge Elizabet , Colignon David , Meunier Loic , Lupo Valérian , Cleenwerck Ilse , Daniel Heide-Marie , Rigouts Leen , Sirjacobs Damien , Declerck Stéphane , Vandamme Peter , Wilmotte Annick , Baurain Denis , Becker Pierre
Published: April 2023

Background

Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing well-characterized biological material to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts).

Findings

This public toolbox allows researchers without a specific training in bioinformatics to perform robust phylogenomic analyses. Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling.

Technical details

Nextflow workflows are launched by a single command and are available on the GEN-ERA GitHub repository (https://github.com/Lcornet/GENERA). All the workflows are based on Singularity containers to increase reproducibility.

Testing

The toolbox was developed for a diversity of microorganisms, including bacteria and fungi. It was further tested on an empirical dataset of 18 (meta)genomes of early branching Cyanobacteria, providing the most up-to-date phylogenomic analysis of the Gloeobacterales order, the first group to diverge in the evolutionary tree of Cyanobacteria.

Conclusion

The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be used by all researchers interested in microbial taxonomy, as exemplified by our case study on Gloeobacterales.
Chromosome-scale genome assembly of Prunus pusilliflora provides novel insights into genome evolution, disease resistance, and dormancy release in Cerasus L.
Authors: Jiu Songtao , Chen Baozheng , Dong Xiao , Lv Zhengxin , Wang Yuxuan , Yin Chunjin , Xu Yan , Zhang Sen , Zhu Jijun , Wang Jiyuan , Liu Xunju , Sun Wanxia , Yang Guoqian , Li Meng , Li Shufeng , Zhang Zhuo , Liu Ruie , Wang Lei , Manzoor Muhammad Aamir , José Quero-García , Wang Shiping , Lei Yahui , Yang Ling , Dirlewanger Elisabeth , Dong Yang , Zhang Caixi
Published: April 2023

Prunus pusilliflora is a wild cherry germplasm resource distributed mainly in Southwest China. Despite its ornamental and economic value, a high-quality assembled P. pusilliflora genome is unavailable, hindering our understanding of its genetic background, population diversity, and evolutionary processes. Here, we de novo assembled a chromosome-scale P. pusilliflora genome using Oxford Nanopore, Illumina, and chromosome conformation capture sequencing. The assembled genome size was 309.62 Mb, with 76 scaffolds anchored to eight pseudochromosomes. We predicted 33 035 protein-coding genes, functionally annotated 98.27% of them, and identified repetitive sequences covering 49.08% of the genome. We found that P. pusilliflora is closely related to Prunus serrulata and Prunus yedoensis, having diverged from them ~41.8 million years ago. A comparative genomic analysis revealed that P. pusilliflora has 643 expanded and 1128 contracted gene families. Furthermore, we found that P. pusilliflora is more resistant to Colletotrichum viniferum, Phytophthora capsici, and Pseudomonas syringae pv. tomato (Pst) DC3000 infections than cultivated Prunus avium. P. pusilliflora also has considerably more nucleotide-binding site-type resistance gene analogs than P. avium, which explains its stronger disease resistance. The cytochrome P450 and WRKY families of 263 and 61 proteins were divided into 42 and 8 subfamilies respectively in P. pusilliflora. Furthermore, 81 MADS-box genes were identified in P. pusilliflora, accompanying expansions of the SVP and AGL15 subfamilies and loss of the TM3 subfamily. Our assembly of a high-quality P. pusilliflora genome will be valuable for further research on cherries and molecular breeding.
The SmNPR4-SmTGA5 module regulates SA-mediated phenolic acid biosynthesis in Salvia miltiorrhiza hairy roots
Authors: Ding Meiling , Zhang Bin , Zhang Shuo , Hao RongRong , Xia Yu , Ma Pengda , Dong Juane
Published: April 2023

Phenolic acids are the main bioactive compounds in Salvia miltiorrhiza, which can be increased by salicylic acid (SA) elicitation. However, the specific molecular mechanism remains unclear. The nonexpresser of PR genes 1 (NPR1) and its family members are essential components of the SA signaling pathway. Here, we report an NPR protein, SmNPR4, that showed strong expression in hairy root after SA treatment, acting as a negative moderator of SA-induced phenolic acid biosynthesis in S. miltiorrhiza (S. miltiorrhiza). Moreover, a basic leucine zipper family transcription factor SmTGA5 was identified and was found to interact with SmNPR4. SmTGA5 activates the expression of phenolic acid biosynthesis gene SmTAT1 through binding to the as-1 element. Finally, a series of biochemical assays and dual gene overexpression analysis demonstrated that the SmNPR4 significantly inhibited the function of SmTGA5, and SA can alleviate the inhibitory effect of SmNPR4 on SmTGA5. Overall, our results reveal the molecular mechanism of salicylic acid regulating phenolic acid biosynthesis in S. miltiorrhiza and provide new insights for SA signaling to regulate secondary metabolic biosynthesis.
An exploration of hospital pharmacists’ attitudes and opinions towards undertaking research
Authors: Shenton Julie , Fitzpatrick Ray , Gifford Alison
Published: April 2023

Objectives

This research aimed to explore the attitudes and opinions of hospital pharmacists to undertaking research to understand the drivers, drawbacks, barriers and enablers to engagement and explore the characteristics of research-active pharmacy departments.

Methods

A qualitative approach was employed using case study methodology where interviews were undertaken with the chief pharmacist and a cohort of research-active pharmacists at four secondary care NHS Trusts. Each of the four case study sites had high levels of research activity among pharmacists and a model of support for them to undertake research.

Key findings

Research experience was identified as a significant driver, as was a pharmacy department having a research culture. Drawbacks identified related to the impact of research on service delivery, and the difficulty associated with backfilling posts with funding from grants. Lack of time, difficulty obtaining funding, lack of personal competence and research not being prioritised were identified as barriers to engagement, as were a lack of understanding and awareness of research and a lack of appreciation of its value. Key enablers included having time to conduct research and having access to individuals with research expertise. Research-active pharmacy departments all had a supportive chief pharmacist, a culture for research and mechanisms of support in place.

Conclusions

To increase research engagement among pharmacists in the hospital sector, there needs to be cultural change at a professional level to drive engagement and give individuals the time and skills to be undertake research.
Characterization of western corn rootworm (Coleoptera: Chrysomelidae) susceptibility to foliar insecticides in northeast Nebraska
Authors: Dang Timothy B , Vélez Ana M , Valencia-Jiménez Arnubio , Reinders Jordan D , Stricklin Emily E , Carroll Matthew W , Pilcher Clinton D , Krumm Jeffrey T , Head Graham P , Meinke Lance J
Published: April 2023

Foliar-applied insecticides are commonly used for adult western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), control in Nebraska but little efficacy data is available. Anecdotal reports of reduced efficacy in areas of northeast Nebraska led to the conduct of this study. Objectives were to (i) evaluate the efficacy of commercial applications of commonly used formulated insecticides (bifenthrin, lambda-cyhalothrin, chlorpyrifos, or tank mixes) for WCR control in 7 northeast Nebraska counties during 2019 and 2020 and (ii) conduct adult WCR concentration-response vial bioassays with bifenthrin, chlorpyrifos, and dimethoate active ingredients on a subset of field populations. Whole plant counts (WPC) were used to measure WCR densities in insecticide-treated and untreated maize fields before and after insecticide application. Field control was excellent with organophosphate/pyrethroid tank mixes as proportional change in mean WPC of treated fields was significantly reduced (>0.90) versus untreated fields where little change in WPC occurred. The exception was one treated Boone County field where proportional reduction in WPC was ≤0.78. Bioassays revealed LC50s and resistance ratios of most populations exposed to bifenthrin and dimethoate were not significantly different than the susceptible control. Most populations exhibited a low level of chlorpyrifos resistance when compared to the susceptible control. Field and lab data suggest the local onset of practical WCR field-evolved resistance to bifenthrin in Boone County and chlorpyrifos in Boone and Colfax counties. Results of this study will increase our understanding of WCR resistance evolution, serve as a comprehensive baseline for future research, and inform WCR management programs.
Clinical results of carbon-ion radiotherapy for stage I non-small cell lung cancer with concomitant interstitial lung disease: a Japanese national registry study (J-CROS-LUNG)
Authors: Okano Naoko , Suefuji Hiroaki , Nakajima Mio , Tokumaru Sunao , Kubo Nobuteru , Yoshida Daisaku , Suzuki Osamu , Ishikawa Hitoshi , Satouchi Miyako , Nakayama Haruhiko , Shioyama Yoshiyuki
Published: April 2023

Anti-cancer treatments for lung cancer patients with interstitial lung disease (ILD) are challenging. The treatment options for ILD are often limited because of concerns that treatments can cause acute exacerbation (AE) of ILD. This study aimed to analyze the outcomes of carbon-ion radiotherapy (CIRT) for stage I non-small cell lung cancer (NSCLC) with ILD, using a multi-institutional registry. Patients with ILD who received CIRT for stage I NSCLC in CIRT institutions in Japan were enrolled. The indication for CIRT was determined by an institutional multidisciplinary tumor board, and CIRT was performed in accordance with institutional protocols. Thirty patients were eligible. The median follow-up duration was 30.3 months (range, 2.5–58 months), and the total dose ranged from 50 Gy (relative biological effectiveness [RBE]) to 69.6 Gy (RBE), and five different patterns of fractionation were used. The beam delivery method was passive beam in 19 patients and scanning beam in 11 patients. The 3-year overall survival (OS), cause-specific survival, disease-free survival (DFS) and local control (LC) rates were 48.2%, 62.2%, 41.2% and 88.1%, respectively. Grade > 2 radiation pneumonitis occurred in one patient (3.3%). In conclusion, CIRT is a safe treatment modality for stage I NSCLC with concomitant ILD. CIRT is a safe and feasible treatment option for early lung cancer in ILD patients.
A scoping review: the psychosocial barriers that exist for people with vulvodynia
Authors: Niedenfuehr Jenny , Edwards Mary , King Lindsey M
Published: April 2023

Background

Vulvodynia, including generalized vulvodynia and vestibulodynia, affects at least 8% to 16% of people with a vulva and may have a negative impact on one’s quality of life, psychological health, interpersonal relationships, and individual behaviors.

Aim

The aim of this scoping review is to synthesize and analyze the emerging literature of vulvodynia research while determining what psychosocial barriers exist for people with vulvodynia.

Methods

A rigorous literature search was completed in 6 databases: PubMed, CINAHL, Embase, Web of Science, APA PsycInfo, and Academic Search Premier. Key terms and subject headings, including Medical Subject Headings, were used to systematically search these databases. Two reviewers were utilized to assess the reference list and reduce bias.

Outcomes

A total of 671 articles were discovered during the search, which was narrowed down to 73 that included at least 1 psychosocial barrier that patients experience in the United States and Canada.

Results

The findings of the literature search revealed the various psychosocial barriers that patients commonly face: pain, anxiety, depression, catastrophization, fear, lack of self-efficacy, low desire and arousal, negative body image, stigma, distress, posttraumatic stress disorder, child maltreatment and abuse, mistrust, invalidation and isolation, low levels of self-compassion, negative partner support, low relationship satisfaction, lack of physical affection, emotional regulation, and avoidance and lack of approach goals. In addition to psychosocial barriers, structural determinants and environmental barriers—such as delayed diagnosis, low health literacy, cost, transportation, and racial disparities—adversely affected individuals with vulvodynia.

Clinical Implications

This review should serve as a guide for researchers, medical providers, and program developers to understand all the barriers that patients may face.

Strengths and Limitations

This review comprehensively highlights existing psychological barriers while promoting structural and environmental barriers that people with vulvodynia face. More research and greater emphasis on the underlying physical conditions that contribute to vulvodynia are needed to effectively educate providers and patients on vulvar pain conditions.

Conclusions

This scoping review highlights the numerous barriers faced by patients with vulvodynia and serves to improve education for patients and providers to achieve earlier diagnoses and better patient outcomes.
Urban wildlife and arborists: environmental governance and the protection of wildlife during tree care operations
Authors: Martin Alexander J F , Almas Andrew D
Published: April 2023

When working with urban trees, arborists can negatively impact urban wildlife. There have been recent efforts to strengthen wildlife protection and conservation during arboricultural practices, both legislatively and voluntarily through arboriculture organizations. To examine arborists’ perceptions of these environmental policies and understand their experiences with urban wildlife, we conducted an international online survey of 805 arborists. Many respondents (n = 481, 59.8%) reported being involved in tree work that resulted in wildlife injury or death, despite most respondents reportedly modifying work plans or objectives after encountering wildlife (n = 598, 74.3%). Decisions to modify or cease work were most heavily influenced by the legal protection of species, wildlife having young, and the overall management objectives. Support for new wildlife best management practices (BMPs) was high (n = 718, 90.3%), as was awareness of wildlife and arboriculture-related legislation (n = 611, 77.2%). The findings demonstrate support amongst arborists for the implementation of wildlife policies to protect wildlife in urban forestry; however, implementation of such policies would require a non-prescriptive approach that is relevant to a diversity of wildlife concerns globally, causing concern amongst arborists about the applicability of such a document. Concerns also included the economic impacts of voluntary wildlife protection policies in arboriculture, where competitors may not adhere to industry standards or best practices. Given the support of arborists for increased wildlife protection policies, we recommend the development of international wildlife-focused BMPs for arboriculture, especially as an intermediary until legislation can be implemented or more rigorously enforced.
Associations Between Psycho-Social-Spiritual Interventions, Fewer Aggressive End-of-Life Measures, and Increased Time After Final Oncologic Treatment
Authors: Schultz Michael , Baziliansky Svetlana , Mitnik Inbal , Ulitzur Nirit , Illouz Shay , Katra Duaa , Givoli Simon , Campisi-Pinto Salvatore , Bar-Sela Gil , Zalman Daniela
Published: April 2023

Background

Little is known about the impact of spiritual caregivers, psychologists, and social workers on desired end-of-life (EoL) medical outcomes, such as reduced use of aggressive care in the final 2 weeks of life, having more time between the last active oncological treatment and death, and increased hospice use.

Patients and Methods

We conducted a prospective study of 180 patients with cancer and their families, their interactions with social work, psychology, and spiritual care, and the above three treatment outcomes.

Results

We found that having one or more spiritual care visits (adjusted odds ratio (AOR) = 2.02; P = .04), having more quality visits with the psychologist (P = .01), and speaking with someone about one’s inner resources (AOR = 2.25; P = .03) all correlated with reduced EoL aggressive care. The key interventions correlating with increased time after final treatment were more visits with the spiritual caregiver or the social worker (AOR = 1.30; P < .001), and speaking about the medical treatment (AOR = 1.54; P < .001) and about interpersonal relationships (AOR = 2.28; P < .001). A subjectively good-quality connection with the spiritual caregiver correlated with increased hospice use (AOR = 10.00; P = .01).

Conclusions

Patients with cancer who availed themselves of the spiritual care, psychology, and social work services, each profession in distinct ways, had significantly different outcomes in their EoL medical treatment, including undergoing fewer futile aggressive measures, having more time after their last active treatment, and using hospice services more. These outcomes directly bear on improved quality of life and reduced costs.