bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expediting knowledge acquisition by a web framework for Knowledge Graph Exploration and Visualization (KGEV): case studies on COVID-19 and Human Phenotype Ontology
Authors: Peng Jacqueline , Xu David , Lee Ryan , Xu Siwei , Zhou Yunyun , Wang Kai 
Published: June 2022

Abstract
Background
Knowledges graphs (KGs) serve as a convenient framework for structuring knowledge. A number of computational methods have been developed to generate KGs from biomedical literature and use them for downstream tasks such as link prediction and question answering. However, there is a lack of computational tools or web frameworks to support the exploration and visualization of the KG themselves, which would facilitate interactive knowledge discovery and formulation of novel biological hypotheses.

Method
We developed a web framework for Knowledge Graph Exploration and Visualization (KGEV), to construct and visualize KGs in five stages: triple extraction, triple filtration, metadata preparation, knowledge integration, and graph database preparation. The application has convenient user interface tools, such as node and edge search and filtering, data source filtering, neighborhood retrieval, and shortest path calculation, that work by querying a backend graph database. Unlike other KGs, our framework allows fast retrieval of relevant texts supporting the relationships in the KG, thus allowing human reviewers to judge the reliability of the knowledge extracted.

Results
We demonstrated a case study of using the KGEV framework to perform research on COVID-19. The COVID-19 pandemic resulted in an explosion of relevant literature, making it challenging to make full use of the vast and heterogenous sources of information. We generated a COVID-19 KG with heterogenous information, including literature information from the CORD-19 dataset, as well as other existing knowledge from eight data sources. We showed the utility of KGEV in three intuitive case studies to explore and query knowledge on COVID-19. A demo of this web application can be accessed at http://covid19nlp.wglab.org. Finally, we also demonstrated a turn-key adaption of the KGEV framework to study clinical phenotypic presentation of human diseases by Human Phenotype Ontology (HPO), illustrating the versatility of the framework.

Conclusion
In an era of literature explosion, the KGEV framework can be applied to many emerging diseases to support structured navigation of the vast amount of newly published biomedical literature and other existing biological knowledge in various databases. It can be also used as a general-purpose tool to explore and query gene-phenotype-disease-drug relationships interactively.
Enablers and barriers to post-discharge follow-up among women who have undergone a caesarean section: experiences from a prospective cohort in rural Rwanda
Authors: Nkurunziza Theoneste , Riviello Robert , Kateera Frederick , Nihiwacu Edison , Nkurunziza Jonathan , Gruendl Magdalena , Klug Stefanie J. , Hedt-Gauthier Bethany 
Published: June 2022

Abstract
Background
Caesarean sections account for roughly one third of all surgical procedures performed in low-income countries. Due to lack of standardised post-discharge follow-up protocols and practices, most of available data are extracted from clinical charts during hospitalization and are thus sub-optimal for answering post-discharge outcomes questions. This study aims to determine enablers and barriers to returning to the hospital after discharge among women who have undergone a c-section at a rural district hospital in Rwanda.

Methods
Women aged ≥ 18 years who underwent c-section at Kirehe District Hospital in rural Rwanda in the period March to October 2017 were prospectively followed. A structured questionnaire was administered to participants and clinical data were extracted from medical files between March and October 2017. At discharge, consenting women were given an appointment to return for follow-up on postoperative day 10 (POD 10) (± 3 days) and provided a voucher to cover transport and compensation for participation to be redeemed on their return. Study participants received a reminder call on the eve of their scheduled appointment. We used a backward stepwise logistic regression, at an α = 0.05 significance level, to identify enablers and barriers associated with post-discharge follow-up return.

Results
Of 586 study participants, the majority (62.6%) were between 21–30 years old and 86.4% had a phone contact number. Of those eligible, 90.4% returned for follow-up. The predictors of return were counselling by a female data collector (OR = 9.85, 95%CI:1.43–37.59) and receiving a reminder call (OR = 16.47, 95%CI:7.07–38.38). Having no insurance reduced the odds of returning to follow-up (OR = 0.03, 95%CI:0.03–0.23), and those who spent more than 10.6 Euro for transport to and from the hospital were less likely to return to follow-up (OR = 0.14, 95%CI:0.04- 0.50).

Conclusion
mHealh interventions using calls or notifications can increase the post-discharge follow-up uptake. The reminder calls to patients and discharge counselling by a gender-matching provider had a positive effect on return to care. Further interventions are needed targeting the uninsured and patients facing transportation hardship. Additionally, association between counselling of women patients by a female data collector and greater return to follow-up needs further exploration to optimize counselling procedures.
Carriage of mutations R462Q (rs 486907) and D541E (rs 627928) of the RNASEL gene and risk factors in patients with prostate cancer in Burkina Faso
Authors: Kadanga Essonan , Zouré Abdou Azaque , Zohoncon Théodora M. , Traoré Lassina , Ky Bienvenu Désiré , Yonli Albert Théophane , Traoré Djé Djénèba Aïda , Bazié Bapio Valery Jean Télesphore Elvira , Sombié Herman Karim , Sorgho Pegdwendé Abel , Tovo Sessi Frida Appoline , Traoré Kalifou , Ouedraogo Teega-Wendé Clarisse , Djigma Florencia W. , Simpore Jacques 
Published: June 2022

Abstract
Background
Prostate cancer (Pca) is a public health problem that affects men, usually of middle age or older. It is the second most common cancer diagnosed in men and the fifth leading cause of death. The RNASEL gene located in 1q25 and identified as a susceptibility gene to hereditary prostate cancer, has never been studied in relation to prostate cancer in Burkina Faso. The aim of this study was to analyze the carriage of RNASEL R462Q and D541E mutations and risks factors in patients with prostate cancer in the Burkina Faso.

Methods
This case–control study included of 38 histologically diagnosed prostate cancer cases and 53 controls (cases without prostate abnormalities). Real-time PCR genotyping of R462Q and D541E variants using the TaqMan® allelic discrimination technique was used. Correlations between different genotypes and combined genotypes were investigated.

Results
The R462Q variant was present in 5.3% of cases and 7.5% of controls. The D541E variant was present in 50.0% of cases and 35% of controls. There is no association between R462Q variants (OR = 0.60; 95%IC, 0.10–3.51; p = 0.686) and D541E variants (OR = 2.46; 95%IC, 0.78–7.80; p = 0.121) and genotypes combined with prostate cancer. However, there is a statistically significant difference in the distribution of cases according to the PSA rate at diagnosis (p ˂ 0.001). For the Gleason score distribution, only 13.2% of cases have a Gleason score greater than 7. There is a statistically significant difference in the Gleason score distribution of cases (p ˂ 0.001).

Conclusions
These variants, considered in isolation or in combination, are not associated with the risk of prostate cancer.
Adsorption behavior of Cr(VI) by biomass-based adsorbent functionalized with deep eutectic solvents (DESs)
Authors: Li Qian , Huang Qing , Pan Xin Ya , Yu Hang , Zhao Zi Tong 
Published: June 2022

AbstractThis study was aimed to evaluate the performance of DESs functionalized peanut shell (PSD) as biosorbent for removing Cr(VI) from water. The effects of pretreatment, initial concentration, adsorption temperature, kinetics, adsorption isotherm, and thermodynamics were investigated. Scanning electron microscopy (SEM) and Point of Zero charge (pHpzc) techniques were used for characterization of the adsorbents. The results showed that the rigid structure of peanut shell was broken down after DESs modification and the point of zero charge was 6.02 for peanut shell and 6.84 for PSD, which exhibited a slightly acid character. Based on the comparisons of linear and nonlinear analysis of four kinetic models and four isotherms, the pseudo-second-order kinetic model was found to be suitable for describing the adsorption process. The presence of a boundary effect was observed within the range of research, indicating that internal diffusion was not the only rate-controlling step. The equilibrium data were well represented by the Langmuir model rather than the Freundlich, Temkin, and Dubinin–Radushkevich models. The maximum capacity derived was 5.36 mg g−1. Changes in Gibb’s free energy, enthalpy, and entropy revealed that Cr(VI) adsorption onto modified peanut-shell powders was a spontaneous and endothermic process. However, the highest desorption efficiency was only 8.77% by using NaOH as a desorbing agent.
Graphical abstract
Establish an allele-specific real-time PCR for Leishmania species identification
Authors: Wu Yun , Jiang Mengyuan , Li Shaogang , Waterfield Nicholas R. , Yang Guowei 
Published: June 2022

Abstract
Background
Leishmaniasis is a serious neglected tropical disease that may lead to life-threatening outcome, which species are closely related to clinical diagnosis and patient management. The current Leishmania species determination method is not appropriate for clinical application. New Leishmania species identification tool is needed using clinical samples directly without isolation and cultivation of parasites.

Methods
A probe-based allele-specific real-time PCR assay was established for Leishmania species identification between Leishmania donovani and L. infantum for visceral leishmaniasis (VL) and among L. major, L. tropica and L. donovani/L. infantum for cutaneous leishmaniasis (CL), targeting hypoxanthine-guanine phosphoribosyl transferase (HGPRT) and spermidine synthase (SPDSYN) gene with their species-specific single nucleotide polymorphisms (SNPs). The limit of detection of this assay was evaluated based on 8 repeated tests with intra-assay standard deviation < 0.5 and inter-assay coefficients of variability < 5%. The specificity of this assay was tested with DNA samples obtained from Plasmodium falciparum, Toxoplasma gondii, Brucella melitensis and Orientia tsutsugamushi. Total 42 clinical specimens were used to evaluate the ability of this assay for Leishmania species identification. The phylogenetic tree was constructed using HGPRT and SPDSYN gene fragments to validate the performance of this assay.

Results
This new method was able to detect 3 and 12 parasites/reaction for VL and CL respectively, and exhibited no cross-reaction with P. falciparum, T. gondii, B. melitensis, O. tsutsugamushi and non-target species of Leishmania. Twenty-two samples from VL patients were identified as L. donovani (n = 3) and L. infantum (n = 19), and 20 specimens from CL patients were identified as L. major (n = 20), providing an agreement of 100% compared with sequencing results. For further validation, 29 sequences of HGPRT fragment from nine Leishmania species and 22 sequences from VL patients were used for phylogenetic analysis, which agreed with the results of this new method. Similar results were obtained with 43 sequences of SPDSYN fragment from 18 Leishmania species and 20 sequences from CL patients.

Conclusions
Our assay provides a rapid and accurate tool for Leishmania species identification which is applicable for species-adapted therapeutic schedule and patient management.

Graphical Abstract
Dispersal and seasonal movements of Pacific halibut (Hippoglossus stenolepis) in the eastern Bering Sea and Aleutian Islands, as inferred from satellite-transmitting archival tags
Authors: Loher Timothy 
Published: June 2022

Abstract
Background
Understanding connectivity is critical to the management of exploited fish stocks, but migratory dynamics of Pacific halibut (Hippoglossus stenolepis) in the Bering Sea and Aleutian Islands region are not well-understood. In the current study, 145 Pacific halibut ≥ 82 cm fork length were tagged with Pop-up Archival Transmitting (PAT) tags to evaluate interannual dispersal, seasonal migration, and depth-specific habitat use.

Results
Endpoint locations obtained after 1 year at liberty (n = 79), fishery recoveries after 2–3 years at liberty (n = 5), and at-liberty geopositions based on light data (n = 5313 estimates from 109 fish) indicated geographically distinct movement patterns: Pacific halibut tagged in the Western and Central Aleutian Islands remained within the island groups in which the fish had been tagged; fish in the eastern Bering Sea remained in that ocean basin, moving among International Pacific Halibut Commission (IPHC) regulatory areas and into Russian waters; those tagged south of Unimak Pass in IPHC Regulatory Area 4A displayed the greatest amount of emigration, dispersing eastward both seasonally and interannually to as far south as Washington State. Analysis of daily maximum depth and temperature data from 113 individuals demonstrated group-level variation in summer temperatures experienced by the fish and in the timing, duration, and synchrony of movement to deep-water wintering grounds.

Conclusions
Depth-specific habitat use was suggestive of regionally explicit migratory contingents, while interannual dispersal patterns were consistent with the existence of multiple functional spawning units. The results may guide future research to examine cross-basin connectivity in the Northern Bering Sea and provide inputs for numerical modelling of individual movements, larval advection, and recruitment analyses.
A systematic quality rating of available mobile health apps for borderline personality disorder
Authors: Steubl Lena Sophia , Reimann Josephin , Simon Laura , Terhorst Yannik , Stach Michael , Baumeister Harald , Sander Lasse Bosse , Messner Eva-Maria 
Published: June 2022

Abstract
Background
Mobile health apps (MHAs) may offer a mean to overcome treatment barriers in Borderline Personality Disorder (BPD) mental health care. However, MHAs for BPD on the market lack transparency and quality assessment.

Methods
European app stores were systematically searched, and two independent trained reviewers extracted relevant MHAs. Employed methods and privacy and security details documentation of included MHAs were extracted. MHAs were then assessed and rated using the German version of the standardized Mobile Application Rating Scale (MARS-G). Mean values and standard deviations of all subscales (engagement, functionality, aesthetics, information, and therapeutic gain) and correlations with user ratings were calculated.

Results
Of 2977 identified MHAs, 16 were included, showing average quality across the four main subscales (M = 3.25, SD = 0.68). Shortcomings were observed with regard to engagement (M = 2.87, SD = 0.99), potential therapeutic gain (M = 2.67, SD = 0.83), existing evidence base (25.0% of included MHAs were tested empirically), and documented privacy and security details. No significant correlations were found between user ratings and the overall total score of the MARS-G or MARS-G main subscales.

Conclusions
Available MHAs for BPD vary in quality and evidence on their efficacy, effectiveness, and possible adverse events is scarce. More substantial efforts to ensure the quality of MHAs available for patients and a focus on transparency, particularly regarding privacy and security documentation, are necessary.
Laboratory research of solvent-assisted menthol sols as temporary consolidants in archaeological excavation applications
Authors: Zhang Wenjin , Wang Xuemei , Han Xiangna , Meng Chenglei , Huang Xiao , Luo Hongjie 
Published: June 2022

Abstract
Temporary consolidation is a quite common practice during archeological excavations nowadays. Melts of cyclododecane or menthol are among the most used consolidants. When using melting protocol to consolidate fragile heritages in archaeological excavation sites, one of the most frequently encountered challenges is the poor penetration of the melt into the heritages, especially in cases of low environmental temperatures, high water content or compact substrates. In this work, we explore the possibility of using solvent-assisted menthol sols as temporary consolidant. Six common organic liquids are individually introduced into menthol at a concentration of 9.1 wt% to formulate room temperature menthol sols. Their potentials as temporary consolidants are systematically investigated. Experimental data indicate that solvent polarity is the most important feature for temporary consolidation purpose and ethanol with medium polarity is among the most appropriate solvents. Laboratory research results show that much better penetration behavior and good consolidation performances can be achieved in menthol-ethanol sol. The as-prepared menthol-ethanol sol is applied in Liangzhu archeological excavation site with satisfactory outcomes. This work shows that menthol-ethanol sol is an excellent temporary consolidation material for archaeological excavation purpose especially in extremely wet condition.
Spatiotemporal evolution of the coupling coordination between inheritance of local culture and new-style urbanization in China
Authors: Yan Lu , Shen Xia , Pengling Liu 
Published: June 2022

Abstract
The rapid new-style urbanization process in China has had a significant impact on the inheritance and protection of local culture. This paper quantitatively analyzes the spatiotemporal difference regarding the coupling coordination between the inheritance of local culture and the new-style urbanization process in China. It is found that during the period between 1991 and 2017, the coexistence of inheritance of local culture and new-style urbanization in China has successively undergone three stages, and at present, the coupling coordination between these two processes is still at a relatively low level, featuring significant differences across various regions and a progressive decrease in the degree of coupling coordination from east to west in China. However, the economically underdeveloped regions, especially ethnic minority regions, are under far greater pressure in terms of coordinated coexistence of both the inheritance of local culture and new-style urbanization.
Effective food hygiene principles and dietary intakes to reinforce the immune system for prevention of COVID-19: a systematic review
Authors: Mirzay-Razaz Jalaledin , Hassanghomi Majid , Ajami Marjan , Koochakpoor Glareh , Hosseini-Esfahani Firoozeh , Mirmiran Parvin 
Published: June 2022

Abstract
Background
This study aimed at reviewing effective food hygiene principles and dietary intakes to reinforce the immune system for prevention of corona virus disease 2019 (COVID-19).

Methods
The systematic literature search was performed in three databases from Jan. 2020 up to 10th July 2020. English articles that focused on nutrition, food, immunity and corona virus were searched. Systematic and narrative reviews were included.

Results
After evaluation of search papers, 27 relevant articles were used in this review. The importance of nutrients, phytochemicals, probiotics and some spices were highlighted for enhancing immunity during the COVID-19 pandemic. A healthy dietary pattern with proper energy intake provides sufficient nutrients. The unhealthy dietary pattern is linked with inflammation and risk factors related to high mortality in patients with severe COVID-19 infection. Different thermal procedures have been used for the inactivation of viruses. It is recommended not to consume raw or undercooked animal products.

Conclusions
It is critical to ensure that the nutritional needs of the population are met and sustained based on standards during a COVID-19 pandemic. Clear advice on adequate calorie intake and an optimal healthy diet to support the immune function should be provided. Good hygiene practices must be performed by everyone and done in the food industry.
The human impact of commercial delivery cycling injuries: a pilot retrospective cohort study
Authors: Sarkies Mitchell N. , Hemmert Cameron , Pang Yu-Chen , Shiner Christine T. , McDonell Karon , Mitchell Rebecca , Lystad Reidar P. , Novy Michael , Christie Lauren J. 
Published: June 2022

Abstract
Background
Commercial delivery cyclists represent a uniquely vulnerable and poorly understood road user. The primary aim of this study was to pilot whether cycling injuries could be categorised as either commercial or non-commercial using documentation entered into routine hospital medical records, in order to determine the feasibility of conducting a large cohort study of commercial cycling injuries in the future. A secondary aim was to determine which key demographic, incident and injury characteristics were associated with commercial versus non-commercial cycling injuries in emergency.

Methods
Pilot retrospective cohort study of adults presenting to an acute public hospital emergency department between May 2019 and April 2020 after sustaining a cycling-related injury. Multinomial logistic regression was used to examine the demographic, incident and injury characteristics associated with commercial compared to non-commercial cycling.

Results
Of the 368 people presenting to the emergency department with a cycling-related injury, we were able to categorise 43 (11.7%) as commercial delivery cyclists, 153 (41.6%) as non-commercial cyclists and the working status of 172 (46.7%) was unable to be confirmed. Both commercial and unconfirmed cyclists were more likely to be younger than non-commercial cyclists. Compared to non-commercial cyclists, commercial cyclists were 11 times more likely to speak a language other than English (AOR 11.3; 95% CI 4.07–31.30; p<0.001), less likely to be injured from non-collision incidents than vehicle collisions (AOR 0.36; 95% CI 0.15–0.91; p=0.030) and were over 13 times more likely to present to the emergency department between 8.00pm and 12.00am compared to the early morning hours (12.00 to 8.00am) (AOR 13.43; 95% CI 2.20–82.10; p=0.005).

Conclusions
The growth of commercial cycling, particularly through online food delivery services, has raised concern regarding commercial cyclist safety. Improvements in the recording of cycling injury commercial status is required to enable ongoing surveillance of commercial cyclist injuries and establish the extent and risk factors associated with commercial cycling.