bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service
Authors: Tangaro Marco Antonio , Mandreoli Pietro , Chiara Matteo , Donvito Giacinto , Antonacci Marica , Parisi Antonio , Bianco Angelica , Romano Angelo , Bianchi Daniela Manila , Cangelosi Davide , Uva Paolo , Molineris Ivan , Nosi Vladimir , Calogero Raffaele A. , Alessandri Luca , Pedrini Elena , Mordenti Marina , Bonetti Emanuele , Sangiorgi Luca , Pesole Graziano , Zambelli Federico 
Published: November 2021

AbstractBackgroundImproving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research. For instance, one of the many ramifications of the COVID-19 global pandemic has been to make even more evident the importance of having bioinformatics tools and data readily actionable by researchers through convenient access points and supported by adequate IT infrastructures. One of the most successful efforts in improving the availability and usability of bioinformatics tools and data is represented by the Galaxy workflow manager and its thriving community. In 2020 we introduced Laniakea, a software platform conceived to streamline the configuration and deployment of “on-demand” Galaxy instances over the cloud. By facilitating the set-up and configuration of Galaxy web servers, Laniakea provides researchers with a powerful and highly customisable platform for executing complex bioinformatics analyses. The system can be accessed through a dedicated and user-friendly web interface that allows the Galaxy web server’s initial configuration and deployment.Results“Laniakea@ReCaS”, the first instance of a Laniakea-based service, is managed by ELIXIR-IT and was officially launched in February 2020, after about one year of development and testing that involved several users. Researchers can request access to Laniakea@ReCaS through an open-ended call for use-cases. Ten project proposals have been accepted since then, totalling 18 Galaxy on-demand virtual servers that employ ~ 100 CPUs, ~ 250 GB of RAM and ~ 5 TB of storage and serve several different communities and purposes. Herein, we present eight use cases demonstrating the versatility of the platform.ConclusionsDuring this first year of activity, the Laniakea-based service emerged as a flexible platform that facilitated the rapid development of bioinformatics tools, the efficient delivery of training activities, and the provision of public bioinformatics services in different settings, including food safety and clinical research. Laniakea@ReCaS provides a proof of concept of how enabling access to appropriate, reliable IT resources and ready-to-use bioinformatics tools can considerably streamline researchers’ work.
Binding affinity prediction for protein–ligand complex using deep attention mechanism based on intermolecular interactions
Authors: Seo Sangmin , Choi Jonghwan , Park Sanghyun , Ahn Jaegyoon 
Published: November 2021

AbstractBackgroundAccurate prediction of protein–ligand binding affinity is important for lowering the overall cost of drug discovery in structure-based drug design. For accurate predictions, many classical scoring functions and machine learning-based methods have been developed. However, these techniques tend to have limitations, mainly resulting from a lack of sufficient energy terms to describe the complex interactions between proteins and ligands. Recent deep-learning techniques can potentially solve this problem. However, the search for more efficient and appropriate deep-learning architectures and methods to represent protein–ligand complex is ongoing.ResultsIn this study, we proposed a deep-neural network model to improve the prediction accuracy of protein–ligand complex binding affinity. The proposed model has two important features, descriptor embeddings with information on the local structures of a protein–ligand complex and an attention mechanism to highlight important descriptors for binding affinity prediction. The proposed model performed better than existing binding affinity prediction models on most benchmark datasets.ConclusionsWe confirmed that an attention mechanism can capture the binding sites in a protein–ligand complex to improve prediction performance. Our code is available athttps://github.com/Blue1993/BAPA.
Characterization of phytohormone and transcriptome profiles during protocorm-like bodies development of Paphiopedilum
Authors: Guo Beiyi , Zeng Songjun , Yin Yuying , Li Lin , Ma Guohua , Wu Kunlin , Fang Lin 
Published: November 2021

Abstract
Background
Paphiopedilum, commonly known as slipper orchid, is an important genus of orchid family with prominent horticultural value. Compared with conventional methods such as tillers and in vitro shoots multiplication, induction and regeneration of protocorm-like bodies (PLBs) is an effective micropropagation method in Paphiopedilum. The PLB initiation efficiency varies among species, hybrids and varieties, which leads to only a few Paphiopedilum species can be large-scale propagated through PLBs. So far, little is known about the mechanisms behind the initiation and maintenance of PLB in Paphiopedilum.

Results
A protocol to induce PLB development from seed-derived protocorms of Paphiopedilum SCBG Huihuang90 (P. SCBG Prince × P. SCBG Miracle) was established. The morphological characterization of four key PLB developmental stages showed that significant polarity and cell size gradients were observed within each PLB. The endogenous hormone level was evaluated. The increase in the levels of indoleacetic acid (IAA) and jasmonic acid (JA) accompanying the PLBs differentiation, suggesting auxin and JA levels were correlated with PLB development. Gibberellic acid (GA) decreased to a very low level, indicated that GA inactivation may be necessary for shoot apical meristem (SAM) development.
Comparative transcriptomic profiles of four different developmental stages of P. SCBG Huihuang90 PLBs explore key genes involved in PLB development. The numbers of differentially expressed genes (DEGs) in three pairwise comparisons (A vs B, B vs C, C vs D) were 1455, 349, and 3529, respectively. KEGG enrichment analysis revealed that DEGs were implicated in secondary metabolite metabolism and photosynthesis. DEGs related to hormone metabolism and signaling, somatic embryogenesis, shoot development and photosynthesis were discussed in detail.

Conclusion
This study is the first report on PLB development in Paphiopedilum using transcriptome sequencing, which provides useful information to understand the mechanisms of PLB development.
Unraveling the role of male reproductive tract and haemolymph in cantharidin-exuding Lydus trimaculatus and Mylabris variabilis (Coleoptera: Meloidae): a comparative transcriptomics approach
Authors: Fratini Emiliano , Salvemini Marco , Lombardo Fabrizio , Muzzi Maurizio , Molfini Marco , Gisondi Silvia , Roma Elia , D’Ezio Veronica , Persichini Tiziana , Gasperi Tecla , Mariottini Paolo , Di Giulio Andrea , Bologna Marco Alberto , Cervelli Manuela , Mancini Emiliano 
Published: November 2021

Abstract
Background
Meloidae (blister beetles) are known to synthetize cantharidin (CA), a toxic and defensive terpene mainly stored in male accessory glands (MAG) and emitted outward through reflex-bleeding. Recent progresses in understanding CA biosynthesis and production organ(s) in Meloidae have been made, but the way in which self-protection is achieved from the hazardous accumulation and release of CA in blister beetles has been experimentally neglected. To provide hints on this pending question, a comparative de novo assembly transcriptomic approach was performed by targeting two tissues where CA is largely accumulated and regularly circulates in Meloidae: the male reproductive tract (MRT) and the haemolymph. Differential gene expression profiles in these tissues were examined in two blister beetle species, Lydus trimaculatus (Fabricius, 1775) (tribe Lyttini) and Mylabris variabilis (Pallas, 1781) (tribe Mylabrini). Upregulated transcripts were compared between the two species to identify conserved genes possibly involved in CA detoxification and transport.

Results
Based on our results, we hypothesize that, to avoid auto-intoxication, ABC, MFS or other solute transporters might sequester purported glycosylated CA precursors into MAG, and lipocalins could bind CA and mitigate its reactivity when released into the haemolymph during the autohaemorrhaging response. We also found an over-representation in haemolymph of protein-domains related to coagulation and integument repairing mechanisms that likely reflects the need to limit fluid loss during reflex-bleeding.

Conclusions
The de novo assembled transcriptomes of L. trimaculatus and M. variabilis here provided represent valuable genetic resources to further explore the mechanisms employed to cope with toxicity of CA in blister beetle tissues. These, if revealed, might help conceiving safe and effective drug-delivery approaches to enhance the use of CA in medicine.
Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress
Authors: Salgado Fernanda Ferreira , Vieira Letícia Rios , Silva Vivianny Nayse Belo , Leão André Pereira , Grynberg Priscila , do Carmo Costa Marcos Mota , Togawa Roberto Coiti , de Sousa Carlos Antônio Ferreira , Júnior Manoel Teixeira Souza 
Published: November 2021

Abstract
Background
Several mechanisms regulating gene expression contribute to restore and reestablish cellular homeostasis so that plants can adapt and survive in adverse situations. MicroRNAs (miRNAs) play roles important in the transcriptional and post-transcriptional regulation of gene expression, emerging as a regulatory molecule key in the responses to plant stress, such as cold, heat, drought, and salt. This work is a comprehensive and large-scale miRNA analysis performed to characterize the miRNA population present in oil palm (Elaeis guineensis Jacq.) exposed to a high level of salt stress, to identify miRNA-putative target genes in the oil palm genome, and to perform an in silico comparison of the expression profile of the miRNAs and their putative target genes.

Results
A group of 79 miRNAs was found in oil palm, been 52 known miRNAs and 27 new ones. The known miRNAs found belonged to 28 families. Those miRNAs led to 229 distinct miRNA-putative target genes identified in the genome of oil palm. miRNAs and putative target genes differentially expressed under salinity stress were then selected for functional annotation analysis. The regulation of transcription, DNA-templated, and the oxidation-reduction process were the biological processes with the highest number of hits to the putative target genes, while protein binding and DNA binding were the molecular functions with the highest number of hits. Finally, the nucleus was the cellular component with the highest number of hits. The functional annotation of the putative target genes differentially expressed under salinity stress showed several ones coding for transcription factors which have already proven able to result in tolerance to salinity stress by overexpression or knockout in other plant species.

Conclusions
Our findings provide new insights into the early response of young oil palm plants to salinity stress and confirm an expected preponderant role of transcription factors - such as NF-YA3, HOX32, and GRF1 - in this response. Besides, it points out potential salt-responsive miRNAs and miRNA-putative target genes that one can utilize to develop oil palm plants tolerant to salinity stress.
The need for area under the curve measurements in the field of ganciclovir therapeutic drug monitoring in children: a case report
Authors: Duval Xavier , Lemaitre Florian , Pertuisel Sophie , Probert Jamie , Gandemer Virginie , Verdier Marie-Clémence , Tron Camille 
Published: November 2021

Abstract
Background
Ganciclovir pharmacokinetics is characterized by a high variability in drug exposure. Usually, monitoring of ganciclovir exposure is performed by measuring trough concentration. However, due to the specificity of pediatric pharmacokinetics, trough concentration measurements may not be a relevant surrogate of ganciclovir exposure. Area under the curve of concentration (AUC) may be a more appropriate biomarker.

Case presentation
We report the case of 3.6-year-old boy with Emberger syndrome with a cytomegalovirus reactivation occurring after allogenic hematopoietic stem cell transplantation. After a few days of treatment with intravenous ganciclovir, sub-therapeutic trough ganciclovir concentrations were measured (< 0.5 µg/mL) and viral load still increased. Ganciclovir dosage was increased by two-fold to deal with this treatment failure. Trough concentrations remained sub-therapeutic. The patient had hematologic disorder therefore it was decided to estimate ganciclovir AUC to assess more accurately drug exposure before any further dosage modification. AUC0–12 h was measured at 51 μg h/mL, which was within the therapeutic range (40–60 μg h/mL). Afterward, viral load decreased and became undetectable.

Conclusions
This case report highlights that monitoring ganciclovir exposure based on AUC should be performed to tailor drug dosage in order to improve treatment efficacy and safety in pediatric patients.
Antibiotic prophylaxis for prevention against Lyme disease following tick bite: an updated systematic review and meta-analysis
Authors: Zhou Guozhong , Xu Xin , Zhang Yu , Yue Peng , Luo Shiqi , Fan Yuxin , Chen Jingjing , Liu Meixiao , Dong Yan , Li Bingxue , Kong Jing , Wen Shiyuan , Liu Aihua , Bao Fukai 
Published: November 2021

Abstract
Background
In areas where Lyme disease is endemic, bites from ticks are common, but no vaccine is currently available against Lyme disease for humans. Therefore, the feasibility of using antibiotic prophylaxis to prevent Lyme disease after a tick bite is worth further exploration. Previous meta-analyses lack sufficient power to demonstrate the efficacy of about antibiotic prophylaxis for the prevention of Lyme disease following a tick bite. In this study, we explored more precise evidence and attempted to identify and update optimum treatment strategies.

Methods
We searched PubMed, Embase, and the Cochrane Library for studies until March 23, 2021. We included studies if the enrolled patients were randomly allocated to a treatment or control group within 72 h following a tick bite and had no clinical evidence of Lyme disease at enrolment. The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guidelines were followed for data abstraction. Two authors (GZZ and XX) independently reviewed the abstracts and identified articles for detailed assessment. We used a random-effects model to calculate the pooled results and reported the 95% confidence interval (CI). Study quality was assessed using a modified Jadad scale, and publication bias was assessed using Egger’s test. We calculated the risk ratio (RR) for the rates of unfavorable events in patients who received intervention versus the control group. This study is registered with PROSPERO, number CRD42021245002.

Results
Six studies (3,766 individuals) were included. The pooled rate of unfavorable events in persons receiving treatment and the control group were 0.4% (95%CI: 0.1–1.1%) and 2.2% (95%CI: 1.6–3.0%), respectively. The pooled RR was 0.38 (95%CI: 0.22–0.66). Subgroup analysis revealed that the pooled RR was 0.29 (95%CI: 0.14–0.60) in the single-use 200-mg doxycycline group; 0.28 (95%CI: 0.05–1.67) in a 10-day course group (Amoxicillin, Penicillin or tetracycline); and 0.73 (95%CI: 0.25–2.08) in a topical antibiotic treatment group (Azithromycin).

Conclusions
The available evidence supports the use of antibiotics for the prevention of Lyme disease, and reveals advantages of using single-dose; however, further confirmation is needed.
Association between antenatal ultrasound findings and neonatal outcomes in rural Uganda: a secondary analysis
Authors: Horn Delia , Edwards Erika , Ssembatya Renny , DeStigter Kristen , Dougherty Anne , Ehret Danielle 
Published: November 2021

Abstract
Background
Although the use of prenatal ultrasound services has increased in low- income and lower middle-income countries, there has not been a concurrent improvement in perinatal mortality. It remains unknown whether individual ultrasound findings in this setting are associated with neonatal death or the need for resuscitation at delivery. If associations are identified by ultrasound, they could be used to inform the birth attendant and counsel the family regarding risk, potentially altering delivery preparedness in order to reduce neonatal mortality.

Methods
This was a secondary analysis of data collected from a prospective cohort. Data was gathered at Nawanyago Health Centre III in Kamuli District, Uganda. Participants included pregnant women who received second and third trimester prenatal ultrasound scans and delivered at that center between July 2010 and August 2018. All ultrasounds were performed at Nawanyago and deliveries were attended solely by midwives or nurses. Predictor variables included the following ultrasound findings: fetal number, fetal presentation, and amniotic fluid volume. The primary outcome was bag-mask ventilation (BMV) of the neonate at delivery. The secondary outcome was stillbirth or neonatal death in the delivery room.

Results
Primary outcome data was available for 1105 infants and secondary outcome data was available for 1098 infants. A total of 33 infants received BMV at delivery. The odds of receiving BMV at delivery was significantly increased if amniotic fluid volume was abnormal (OR 4.2, CI 1.2-14.9) and there were increased odds for multiple gestation (OR 1.9, CI 0.7-5.4) and for non-vertex fetal presentation (OR 1.4, CI 0.6-3.2) that were not statistically significant. Stillbirth or neonatal death in the delivery room was diagnosed for 20 infants. Multiple gestation (OR 4.7, CI 1.6-14.2) and abnormal amniotic fluid volume (OR 4.8, CI 1.0-22.1) increased the odds of stillbirth or neonatal death in the delivery room, though only multiple gestation was statistically significant.

Conclusion
Common findings that are easily identifiable on ultrasound in low- and lower middle-income countries are associated with adverse perinatal outcomes. Education could lead to improved delivery preparedness, with the potential to reduce perinatal mortality. This was a preliminary study; larger prospective studies are needed to confirm these findings.
Exploring factors associated with pregnant women’s experiences of material hardship during COVID-19: a cross-sectional Qualtrics survey in the United States
Authors: Johnson Laura 
Published: November 2021

AbstractBackgroundThe COVID-19 pandemic has exacerbated the financial insecurity of women and their families globally. Some studies have explored the impact of financial strain among pregnant women, in particular, during the pandemic. However, less is known about the factors associated with pregnant women’s experiences of material hardship.MethodsThis cross-sectional study used a non-probability sample to examine the factors associated with pregnant women’s experiences of material hardship during the COVID-19 pandemic. In January 2021, 183 pregnant women living in the United States participated in an online Qualtrics panel survey. In addition to socio-demographic characteristics, individuals were asked about their finances and predictors of financial well-being, mental health symptoms, and intimate partner violence (IPV) experiences. Chi-square analysis and one-way ANOVA were used to examine whether women’s experiences with material hardship and associated factors differed by income level (i.e., less than $20,000; $20,000 to $60,000; more than $60,000). Ordinary least squares regression was used to calculate unadjusted and adjusted estimates.ResultsStudy findings showed that the majority of women in the sample experienced at least one form of material hardship in the past year. Individuals with an annual household income less than $20,000 reported the highest average number of material hardships experienced (M = 3.7,SD = 2.8). Compared to women with household incomes less than $20,000, women with incomes of more than $60,000 reported significantly fewer material hardships, less financial strain, and higher levels of financial support, economic self-efficacy, and economic-self-sufficiency. Women with incomes of $60,000 or more also reported significantly lower levels of psychological abuse, and a smaller percentage met the cut-off for anxiety. Economic self-sufficiency, financial strain, posttraumatic stress disorder, and economic abuse were all significantly associated with material hardship.ConclusionsA contribution of this study is that it highlights the significant, positive association between economic abuse, a unique form of IPV, and material hardship among pregnant women during the pandemic. These findings suggest the need for policy and practice interventions that help to ameliorate the financial insecurity experienced by some pregnant women, as well as respond to associated bidirectional vulnerabilities (e.g., mental health symptoms, experiences of IPV).
Wheel of Wellbeing (WoW) health promotion program: Australian participants report on their experiences and impacts
Authors: Spain Daniel , Stewart Victoria , Betts Helen , Wheeler Amanda J. 
Published: November 2021

AbstractBackgroundCommunity-based mental health promotion programs focus on improving individual and community wellbeing by strengthening resilience and building capacity to support positive health outcomes. The Wheel of Wellbeing (WoW) is an example of such a program, promoting activities that support social engagement and positive emotions within a holistic framework underpinned by positive psychology. WoW is intended to be flexibly implemented in each community, training community members who implement behaviour change activities in their local community, workplace and educational settings.MethodThis study aimed to understand the opinions and experiences of a sample of individuals who had participated in a range of WoW training programs; documenting the impact on participant behaviours and professional practices, and how the WoW framework was subsequently employed within their communities. Using Ripple Effects Mapping evaluation processes to guide a focus group, nine WoW training participants collectively reflected on the program impacts, generating consensus themes and a mind map. Mind map qualitative data were entered into XMIND mapping software and reviewed with the focus group transcription and field notes.ResultsThematic analysis identified three themes: increased community involvement and engagement (strengthening community connections); improved health, emotions and behaviour (motivating change to health behaviours); and flexible resources which could be utilised in a range of settings (easily incorporated in the existing organisational cultures).ConclusionsThe results of this study support the premise that the WoW framework can be an effective framework for guiding wellbeing promotion activities, with participants championing a ‘ripple effect’ across individual, family, friendship, professional and community networks.