bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leveraging Artificial Intelligence and Data Science Techniques in Harmonizing, Sharing, Accessing and Analyzing SARS-COV-2/COVID-19 Data in Rwanda (LAISDAR Project): Study design and rationale
Authors: Nishimwe Aurore , Ruranga Charles , Musanabaganwa Clarisse , Mugeni Regine , Semakula Muhammed , Nzabanita Joseph , Kabano Ignace , Uwimana Annie , Utumatwishima Jean N , Kabakambira Jean Damascene , Uwineza Annette , Halvorsen Lars , Descamps Freija , Houghtaling Jared , Burke Benjamin , Bahati Odile , Bizimana Clement , Jansen Stefan , Twizere Celestin , Nkurikiyeyezu Kizito , Birungi Francine , Nsanzimana Sabin , Twagirumukiza Marc 
Published: March 2022

Abstract
Background: Since the outbreak of COVID-19 pandemic in Rwanda, a vast amount of SARS-COV-2/COVID-19-related data have been collected including COVID-19 testing and hospital routine care data. Unfortunately, those data are fragmented in silos with different data structures or formats and cannot be used to improve understanding of the disease, monitor its progress, and generate evidence to guide prevention measures. The objective of this project is to leverage the artificial intelligence (AI) and data science techniques in harmonizing datasets to support Rwandan government needs in monitoring and predicting the COVID-19 burden, including the hospital admissions and overall infection rates.Methods: The project will gather the existing data including hospital electronic health records (EHRs), the COVID-19 testing data and will link with longitudinal data from community surveys. The open-source tools from Observational Health Data Sciences and Informatics (OHDSI) will be used to harmonize hospital EHRs through the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). The project will also leverage other OHDSI tools for data analytics and network integration, as well as R Studio and Python. The network will include up to 15 health facilities in Rwanda, whose EHR data will be harmonized to OMOP CDM.Expected results: This study will yield a technical infrastructure where the 15 participating hospitals and health centres will have EHR data in OMOP CDM format on a local Mac Mini (“data node”), together with a set of OHDSI open-source tools. A central server, or portal, will contain a data catalogue of participating sites, as well as the OHDSI tools that are used to define and manage distributed studies. The central server will also integrate the information from the national Covid-19 registry, as well as the results of the community surveys. The ultimate project outcome is the dynamic prediction modelling for COVID-19 pandemic in Rwanda.Discussion: The project is the first on the African continent leveraging AI and implementation of an OMOP CDM based federated data network for data harmonization. Such infrastructure is scalable for other pandemics monitoring, outcomes predictions, and tailored response planning.
Association between the SIRT1 and SIRT3 levels and gene polymorphisms with infertility in war zones of Kermanshah province, Iran
Authors: Nasiri Abolfazl , Hosseini Sayed Mostafa , Rashidi Mohsen , Vaisi-Raygani Asad , Mozafari Hadi 
Published: March 2022

Abstract
The authors have requested that this preprint be removed from Research Square.
Assessing and improving the quality of Fortran code in scientific software: FortranAnalyser
Authors: García-Rodríguez Michael , Añel Juan A. , Rodeiro-Iglesias Javier 
Published: March 2022

Abstract
Scientific software often presents shortcomings when performing a static evaluation of the code. Moreover, a significant amount of this software is written in Fortran. However, only a few software tools analyse Fortran code, and they are not free software. Here we introduce FortranAnalyser, a multi-platform static analysis tool that generates a report helping to improve Fortran code quality. We explain its development cycle and main features and compare it to other existing tools. Also, we provide examples of application to codes from different scientific fields, with a particular case study of the process followed to improve one of the most used global climate models.
The BE(2)-M17 cell line has a better dopaminergic phenotype than the traditionally used for Parkinson´s research SH-SY5Y, which is mostly serotonergic
Authors: Carvajal-Oliveros Angel , Uriostegui-Arcos Maritere , Zurita Mario , Melchy-Perez Erika I. , Narváez-Padilla Verónica , Reynaud Enrique 
Published: March 2022

Abstract
SH-SY5Y is a cell line derived from human neuroblastoma. It is one of the most widely used in vitro models to study Parkinson’s disease. Surprisingly, it has been found that it does not develop a dopaminergic phenotype after differentiation, questioning its usefulness as a Parkinson’s model. There are other in vitro models with better dopaminergic characteristics. BE (2)-M17 is a human neuroblastoma cell line that differentiates when treated with retinoic acid. We compared the dopaminergic and serotonergic properties of both cell lines. BE (2)-M17 has higher basal levels of dopaminergic markers and acquires a serotonergic phenotype during differentiation while maintaining the dopaminergic phenotype. SH-SY5Y has higher basal levels of serotonergic markers but does not acquire a dopaminergic phenotype upon differentiation.
Application of different approaches to generate virtual patient populations for the Quantitative Systems Pharmacology model of erythropoiesis
Authors: Kolesova Galina , Stepanov Alexander , Lebedeva Galina , Demin Oleg 
Published: March 2022

Abstract
In a standard situation, a quantitative systems pharmacology model describes a “reference patient,” and the model parameters are fixed values allowing only the mean values to be described. However, the results of clinical trials include a description of variability in patients’ responses to a drug, which is typically expressed in terms of conventional statistical parameters, such as standard deviations (SDs) from mean values. Therefore, in this study, we propose and compare 4 different approaches: (1) Monte Carlo Markov Chain (MCMC); (2) model fitting to Monte Carlo sample; (3) population of clones; (4) stochastically bounded selection to generate virtual patient populations based on experimentally measured mean data and SDs. We applied these approaches to generate virtual patient populations in the QSP model of erythropoiesis. According to the results of our research, stochastically bounded selection showed slightly better results than the other 3 methods as it allowed the description of any number of patients from clinical trials and could be applied in the case of complex models with a large number of variable parameters.
Robotic natural orifice specimen extraction surgery for colorectal cancer: an open-label, single-arm study
Authors: Zhong Yun , Zhang Hao-bo , Luo Rui , Li Tai-yuan , Liu Dong-ning 
Published: March 2022

Abstract
Background: Robotic natural orifice specimen extraction surgery (NOSES) is a minimally invasive surgery for colorectal cancer patients. As an emerging procedure, its safety and feasibility require thorough investigation. This study aimed to evaluate preliminary data and provide evidence for the therapeutic benefits and clinical applicability of robotic NOSES in colorectal cancer patients.Methods: This was an open-label single-arm study that recruited patients with colorectal cancer and treated them with robotic NOSES, which was performed by three methods of specimen extraction: a: transanal specimen eversion and extra-abdominal resection technique (EVER); b: translumenal specimen extraction and extra-abdominal resection technique (EXER); c: intra-abdominal specimen resection and translumenal extraction technique (IREX). The primary outcome was the complication rate. Between September 1, 2019, and May 31, 2020, 118 individuals were screened, and 101 were included in the intention-to-treat population. Lastly, after further evaluation, 91 individuals were included in the per-protocol population. Safety analyses were performed using SPSS 22.0 (SPSS, Chicago, USA). P-value < 0.05 was considered statistically significant.Results: A total of 118 patients were screened, and 101 were enrolled for the robotic NOSES. Ten patients switched to traditional robotic-assisted surgery. Hypertension [13 (14.29%)] was the most common comorbidity. The overall complication rate was 18.68%, and the most common complication was anastomotic fistula (B and C level) [8 (8.79%)]. There was no significant difference in complication rate among the three methods of specimen extraction in the subgroup analysis (P = 0.638).Conclusion: Robotic NOSES can provide feasibility for colorectal cancer patients to a certain extent. The most prevalent surgical complication of robotic NOSES for colorectal cancer patients was anastomotic fistula (B and C level) [8 (8.79%)].
1,3-Diphenylurea derivatives inhibit cellular entry of influenza A virus and SARS-CoV-2
Authors: Kumar Nirmal , Taily Irshad , Singh Charandeep , Kumar Sahil , Sharma Anshul , Singh Priyanka , Thakur Krishan , Ringe Rajesh , Banerjee Prabal , Banerjee Indranil 
Published: March 2022

Abstract
Influenza A virus (IAV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are highly contagious pathogens that cause severe respiratory illnesses, often leading to hospitalization and death. Rapid emergence of mutant viral strains and waning immunity in the vaccinated individuals represent major challenges in the global fight against both the viruses. Complementing vaccine protection, a search for new therapeutic agents, effective against the existing and emerging viral strains, is an urgent priority. In this study, we identified 1,3-diphenylurea derivatives (DPUDs) as a new class of potential antiviral agents that robustly inhibited infections by different strains of IAV and SARS-CoV-2. Our study revealed, DPUDs primarily target the host cell entry of the viruses. That DPUDs affect the host processes exploited by IAV and SARS-CoV-2 for cellular entry, they are expected to be broadly effective against other related viruses that co-opt the same entry pathways.
Identifying genes associated with abiotic stress tolerance suitable for CRISPR/Cas9 editing in upland rice cultivars adapted to acid soils (version 2)
Authors: Barrero Luz Stella , Willmann Matthew , Craft Eric , Manna-Akther Kazi , Harrington Sandra , Garzon-Martinez Gina A. , Glahn Raymond , Piñeros Miguel A. , McCouch Susan 
Published: March 2022

Abstract
Five genes of large phenotypic effect known to confer abiotic stress tolerance in rice were selected to characterize allelic variation in commercial Colombian tropical japonica upland rice cultivars adapted to drought-prone acid soil environments (cv. Llanura11 and Porvenir12). Allelic variants of the genes ART1, DRO1, SUB1A, PSTOL1, and SPDT were characterized by PCR and/or Sanger sequencing in the two upland cultivars and compared with the Nipponbare and other reference genomes. Two genes were identified as possible targets for gene editing: SUB1A, Submergence 1A, to improve tolerance to flooding, and SPDT (SULTR3;4), SULTR-like Phosphorus Distribution Transporter, to improve phosphorus utilization efficiency and grain quality. Based on technical and regulatory considerations, SPDT was targeted for editing. The two upland cultivars were shown to carry the SPDT wild-type (non-desirable) allele based on sequencing, RNA expression, and phenotypic evaluations under hydroponic and greenhouse conditions. A gene deletion was designed using the CRISPR/Cas9system and specialized reagents were developed for SPDT editing, including vectors targeting the gene and a protoplast transfection transient assay. The desired edits were confirmed in protoplasts and serve as the basis for ongoing plant transformation experiments aiming to improve the P-use efficiency of upland rice grown in acidic soils.
Diseño participativo a través de la herramienta CoAnnotation en las Prácticas Externas universitarias
Authors: Domene Martos Soledad , Rodríguez-Gallego Margarita R. , Salas Ruíz Sandra , Corujo-Vélez María del Carmen 
Published: March 2022

Con el objetivo de mejorar la experiencia de la asignatura Prácticas Externas I, del Grado de Pedagogía de la Facultad de Ciencias de la Educación de la Universidad de Sevilla y para cubrir las necesidades sentidas por el profesorado y alumnado, se han llevado a cabo, durante el curso 2020-21, dos propuestas: blog colaborativo y simulaciones-videoconferencia para llevar a cabo un aprendizaje flexible en el aprendizaje de esta asignatura. Tras la creación y publicación de un vídeo en CoAnnotation, los miembros de la RedTicPraxis a través de un diseño participativo realizaron valoraciones de acuerdo con el objetivo planteado. El procedimiento seguido para el análisis de datos recogidos en CoAnnotation ha consistido en un sistema categorial, creado a través de las etiquetas y el software utilizado Atlas.ti versión 8.4. Los resultados demuestran que las categorías más destacadas son Buenas Prácticas, Colaboración y Función. Las dos modalidades, Blog y Simulación-Videoconferencia, han sido consideradas como buenas prácticas con TIC por el profesorado, estudiantes e instituciones. Estas herramientas les han permitido la recuperación de experiencias debido a la retroalimentación que ofrecen y el fomento de la reflexión sobre sus prácticas y las de sus compañeros/as.
Potential Application of Cephalosporins Carried in Organic or Inorganic Nanosystems against Gram-Negative Pathogens
Authors: Bezerra Brenda Maria Silva , Dantas de Mendonça y Araujo Sara Efigênia , Cordeiro de Macêdo Analara , Costa Kammila Martins Nicolau , Sato Mariana Rillo , Oshiro-Junior João Augusto 
Published: March 2022

Abstract:
Cephalosporins are β-lactam antibiotics, classified into five generations and extensively
used in clinical practice against infections caused by Gram-negative pathogens,
including Enterobacteriaceae and P. aeruginosa. Commercially, conventional pharmaceutical
forms require high doses to ensure clinical efficacy. Additionally, β-lactam resistance
mechanisms, such as the production of enzymes (called extended-spectrum β-lactamases)
and the low plasma half-life of these antibiotics, have been challenging in clinical
therapy based on the use of cephalosporins. In this context, its incorporation into nanoparticles,
whether organic or inorganic, is an alternative to temporally and spatially control
the drug release and improve its pharmacokinetic and pharmacodynamic limitations. Considering
this, the present review unites the cephalosporins encapsulated into organic and
inorganic nanoparticles against resistant and nonresistant enterobacteria. We divide
cephalosporin generation into subtopics in which we discuss all molecules approved by
regulatory agencies. In addition, changes in the side chains at positions R1 and R2 of the
central structure of cephalosporins for all semisynthetic derivatives developed were discussed
and presented, as the changes in these groups are related to modifications in pharmacological
and pharmacokinetic properties, respectively. Ultimately, we exhibit the advances
and differences in the release profile and in vitro activity of cephalosporins incorporated
in different nanoparticles.
Biological Activities and Therapeutic Potential of Irigenin on Gastric,
Lung, Prostate, Breast, and Endometrial Cancer: Pharmacological and
Analytical Aspects
Authors: Patel Dinesh Kumar 
Published: March 2022

Background:
Herbal medicine has been in used in the medicine for thousands of years due to its multiple pharmacological activities against different types of human disorders. Biological effectiveness and pharmacological activities of herbal medicines is mainly due to the presence of different kinds of phytoconstituents commonly called secondary metabolites. Isoflavones are naturally present in different types of plants and food materials and most of these phytocompounds have a wide range of biological activities including anti-tumor, anti-proliferative, anti-inflammatory, anti-microbial, anti-viral, anti-oxidant, and estrogen-like activities.

Methods:
Irigenin isolated from the rhizome of Belamcanda chinensis and the genus Iris showed a wide range of biological activities. Due to huge biological potential and the therapeutic benefit of irigenin in the medicine, here in the present investigation, scientific research data of irigenin has been collected from different literature sources (Science Direct, Google Scholar, PubMed, Google) and analyzed in order to know the therapeutic potential of irigenin in the medicine. Pharmacological activities scientific data of irigenin have been collected from Science Direct, Google Scholar, PubMed, Google databases and analyzed in the present work. Importance of different analytical techniques for isolation and separation of irigenin has been also discussed and presented in the present work.

Results:
Scientific data analysis of different research work revealed the biological importance of irigenin in the medicine. Irigenin is an O-methylated isoflavone found to be present in the Belamcanda chinensis and genus Iris. Scientific data analysis revealed the biological importance of irigenin against gastric cancer, lung carcinoma, prostate cancer, breast cancer, endometrial cancer, diabetic complications, inflammation and cardiac injury. Analytical data of irigenin revealed the importance of analytical techniques for the separation, isolation and identification of irigenin from various biological samples.

Conclusion:
Scientific data analysis of different research works revealed the biological importance and therapeutic potential of irigenin in the medicine.
Therapeutic Effects of Modified Tempeh on Glycemic Control and Gut
Microbiota Diversity in Diabetic Rats
Authors: Kusuma Rio Jati , Widada Jaka , Huriyati Emy , Julia Madarina 
Published: March 2022

Background:
The role of the gut microbiota in improving glycemic control in diabetic
patients is gaining attention. Tempeh is a fermented soy food from Indonesia that has antidiabetic
and antidysbiotic effects. Interestingly, modification of tempeh processing by adding lactic acid
bacteria has been reported to enhance the antidiabetic effect of tempeh.

Aim:
This study aimed to evaluate the effects of modified tempeh on serum glucose, insulin,
and gut microbiota diversity of diabetic rats.

Methods:
Modified tempeh was developed by adding lactic acid bacteria from fermented cassava
during tempeh processing. Diabetes was induced by injection of streptozotocin nicotinamide.
Normal tempeh or modified tempeh was added to the diet and replaced 15% or 30% of casein.
Serum glucose and insulin were analyzed before and after 30 days of intervention. At the end of
the experiment, the appendix was sampled for gut microbiota analysis.

Result:
Modified tempeh has a significantly higher number of lactic acid bacteria (9.99 ± 0.09
versus 7.74 ± 0.07 log CFU, p < 0.001) compared to normal tempeh. There was a significant difference
(p < 0.01) in serum glucose and insulin after treatment. Both tempeh supplements increased
the diversity of the gut microbiota. Gut microbiota diversity has a strong negative correlation
with delta glucose (r = -0.63, p < 0.001) and delta insulin resistance index (r = -0.54, p =
0.003).

Conclusion:
Modified tempeh has potential therapeutic antidiabetic activity, possibly through
increased diversity of the gut microbiota.
Efficacy, Benefits, and Harms of a Self-management App in a Swedish Trauma-Exposed Community Sample (PTSD Coach): Randomized Controlled Trial
Authors: Hensler Ida , Sveen Josefin , Cernvall Martin , Arnberg Filip K 
Published: March 2022

Background
Self-guided interventions may complement and overcome obstacles to in-person treatment options. The efficacy of app interventions targeting posttraumatic stress disorder (PTSD) is unclear, and results from previous studies on PTSD Coach—an app for managing trauma-related distress—are inconsistent.

Objective
This study investigates whether access to the Swedish version of the PTSD Coach affects posttraumatic stress, depressive, and somatic symptoms. In addition, we aim to assess the perceived helpfulness, satisfaction, negative effects, response, and remission related to PTSD Coach.

Methods
Adults who had experienced potentially traumatic events in the past 2 years were randomized (1:1) to have access to PTSD Coach (n=89) or be on the waitlist (n=90). We assessed clinical characteristics at baseline (semistructured interviews and self-rating scales) and after 3 months (self-rating scales). We analyzed the data in R software using linear mixed effects models, chi-square tests, and Fisher exact test.

Results
Intention-to-treat analyses indicated that access to PTSD Coach decreased posttraumatic stress and depressive symptoms but not somatic symptoms. More participants who had access to PTSD Coach responded with clinically significant improvement and fewer instances of probable PTSD after 3 months compared with waitlist controls. Overall, participants found that PTSD Coach was slightly to moderately helpful and moderately satisfactory. Half of the intervention group (36/71, 51%) reported at least one negative reaction related to using PTSD Coach (eg, disappointment with the app or its results, arousal of stress, or distressing memories).

Conclusions
Using PTSD Coach may trigger symptoms among a few users; however, most of them perceived PTSD Coach as helpful and satisfactory. This study showed that having access to PTSD Coach helped improve psychological trauma-related symptoms. In addition, we have discussed implications for future research and clinical practice.

Trial Registration
ClinicalTrials.gov NCT04094922; https://clinicaltrials.gov/ct2/show/NCT04094922
On the Question of the Ideology of the Eurasian Economic Union
Authors: Glazyev S. Yu. , Kefeli I. F. 
Published: March 2022

Aim. To update attention on the need to form the ideology of Eurasian integration, expressing not only economic, but also common socio-political and spiritual interests and a vision of the common future of the EAEU.Tasks. To reveal the essence of the ideology of Eurasian nationalism, the value content of the concept of the Community of the Common Destiny of Humanity and the possibility of their complementary integrity in the ethno-political continuum of Greater Eurasia.Methods. Civilizational and concrete-historical approaches, as well as axiological discourse regarding the ideological choice in a multi-ethnic community.Results. The enduring value of the concepts of Eurasian nationalism, inverted in relation to modernity, and the Community of the Common Destiny of Mankind is substantiated. The main directions of the search for theoretical and axiological foundations are determined.Conclusion. On the agenda of Eurasian integration is the search for conditions for the rejection of libertarian ideology, serving the interests of international capital, and not peoples with a common historical destiny. It is necessary to search for its own kind of social-conservative synthesis, which combines the restoration of socialist ideology with the spiritual traditions of the Eurasian peoples.