bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applications of 2D and 3D-Dynamic Representations of DNA/RNA
Sequences for a Description of Genome Sequences of Viruses
Authors: Bielińska-Wąż Dorota , Wąż Piotr , Panas Damian 
Published: August 2021

:
The aim of the studies is to show that graphical bioinformatics methods are good tools
for the description of genome sequences of viruses. A new approach to the identification of
unknown virus strains, is proposed.

Methods:
Biological sequences have been represented graphically through 2D and 3D-Dynamic
Representations of DNA/RNA Sequences - theoretical methods for the graphical representation of
the sequences developed by us previously. In these approaches, some ideas of the classical
dynamics have been introduced to bioinformatics. The sequences are represented by sets of
material points in 2D or 3D spaces. The distribution of the points in space is characteristic of the
sequence. The numerical parameters (descriptors) characterizing the sequences correspond to the
quantities typical of classical dynamics.

Results:
Some applications of the theoretical methods have been briefly reviewed. 2D-dynamic
graphs representing the complete genome sequences of SARS-CoV-2 are shown.

Conclusion:
It is proved that the 3D-Dynamic Representation of DNA/RNA Sequences, coupled
with the random forest algorithm, classifies successfully the subtypes of influenza A virus strains.
Role of Potential COVID-19 Immune System Associated Genes and the
Potential Pathways Linkage with Type-2 Diabetes
Authors: Mobashir Mohammad , Helmi Nawal , Alammari Dalia 
Published: August 2021

Background:
Coronavirus is an enclosed positive-sense RNA virus with club-like
spikes extending from its surface. It is most typically associated with acute respiratory infections in
humans, but its capacity to infect many host species and cause multiple illnesses makes it a complicated
pathogen. The frequent encounters between wild animals and humans are a typical cause
of infection. The zoonotic infections SARS-CoV and MERS-CoV are among the most common
causes of serious respiratory illnesses in humans.

Aim:
The main goal of this research was to look at gene expression profiles in human samples that
were either infected with coronavirus or were not, and compare the varied expression patterns and
their functional implications.

Methods:
The previously researched samples were acquired from a public database for this purpose,
and the study was conducted, which included gene expression analysis, pathway analysis,
and network-level comprehension. The results for differentially expressed genes, enriched pathways,
and networks for prospective genes and gene sets are presented in the analysis. In terms of
COVID-19 gene expression and its relationship to type 2 diabetes.

Results:
We see a lot of genes that have different gene expression patterns than normal for coronavirus
infection, but in terms of pathways, it appears that there are only a few sets of functions that
are affected by altered gene expression, and they are related to infection, inflammation, and the
immune system.

Conclusions:
Based on our study, we conclude that the potential genes which are affected due to
infection are NFKBIA, MYC, FOXO3, BIRC3, ICAM1, IL8, CXCL1/2/5, GADD45A, RELB,
SGK1, AREG, BBC3, DDIT3/4, EGR1, MTHFD2, and SESN2 and the functional changes are
mainly associated with these pathways: TNF, cytokine, NF-kB, TLR, TCR, BCR, Foxo, and TGF
signaling pathways are among them and there are additional pathways such as hippo signaling,
apoptosis, estrogen signaling, regulating pluropotency of stem cells, ErbB, Wnt, p53, cAMP,
MAPK, PI3K-AKT, oxidative phosphorylation, protein processing in endoplasmic reticulum, prolactin
signaling, adipocytokine, neurotrophine signaling, and longevity regulating pathways.
SMARCD3, PARL, GLIPR1, STAT2, PMAIP1, GP1BA, and TOX genes and PI3K-Akt, focal adhesion,
Foxo, phagosome, adrenergic, osteoclast differentiation, platelet activation, insulin, cytokine-
cytokine interaction, apoptosis, ECM, JAK-STAT, and oxytocin signaling appear as the linkage
between COVID-19 and Type-2 diabetes.
Nature-Derived Hit, Lead, and Drug-Like Small Molecules: Current Status
and Future Aspects Against Key Target Proteins of Coronaviruses
Authors: Junaid Md. , Akter Yeasmin , Siddika Aysha , Nayeem S. M. Abdul , Nahrin Afsana , Afrose Syeda Samira , Ezaj Md. Muzahid Ahmed , Alam Muhammad Shaiful 
Published: August 2021

Background:
COVID-19 pandemic, the most unprecedented event of the year 2020, has
brought millions of scientists worldwide in a single platform to fight against it. Though several drugs
are now in the clinical trial, few vaccines are available on the market already, but the lack of an effect
of those is making the situation worse.

Aim of the study:
In this review, we demonstrated comprehensive data of natural antiviral products
showing activities against different proteins of Human Coronaviruses (HCoV) that are responsible for
its pathogenesis. Furthermore, we categorized the compounds into the hit, lead, and drug based on the
IC50/EC50 value, drug-likeness, and lead-likeness test to portray their potentiality to be a drug. We also
demonstrated the present status of our screened antiviral compounds with respect to clinical trials and
reported the lead compounds that can be promoted to clinical trial against COVID-19.

Methods:
A systematic search strategy was employed focusing on Natural Products (NPs) with proven
activity (in vitro, in vivo, or in silico) against human coronaviruses, in general, and data were gathered
from databases like PubMed, Web of Science, Google Scholar, SciVerse, and Scopus. Information
regarding clinical trials retrieved from the Clinical Trial Database.

Results:
Total "245" natural compounds were identified initially from the literature study. Among
them, Glycyrrhizin, Caffeic acid, Curcumin is in phase 3, and Tetrandrine, Cyclosporine, Tacrolimus,
Everolimus are in phase 4 clinical trial. Except for Glycyrrhizin, all compounds showed activity
against COVID-19.

Conclusions:
In summary, our demonstrated specific small molecules with lead and drug-like capabilities
clarified their position in the drug discovery pipeline and proposed future research against
COVID-19.
Recent Advances of using Personal Glucose Meter as a Biosensor Readout
for Non-glucose Targets
Authors: Zhang Songbai , Li Shuang , Yan Rixin , Zhou Zhiyun , Wu Yuting , Lu Yi 
Published: August 2021

Background:
Personal Glucose Meter (PGM) has become the most successful biosensor
in past decades due to its advantages of small size, convenient operation, and low cost. To take
advantage of many years of research and development of PGMs, new signal transduction methods
have been developed to expand the PGM from simple monitoring of blood glucose to the detection
of numerous non-glucose targets.

Objectives:
This review summarizes recent advances of PGM-based biosensors for non-glucose
targets, including signal transduction, signal amplification, and target molecule recognition and
analysis. Current challenges and future directions are also discussed.

Conclusion:
PGM can be used as a biosensor readout to detect various non-glucose targets from
metal ion, small molecules to protein and even living organisms such as bacteria and other pathogens
by using different signal transduction elements such as invertase and amylase, and different
signal amplification methods such as nanomaterials, nucleic acid reaction, liposome encapsulation,
hydrogel trapping, DNAzyme amplification and biotin-streptavidin reaction.
Stem Cell-based Treatment Strategies for Degenerative Diseases of the
Retina
Authors: Nair Deepthi S. Rajendran , Thomas Biju B. 
Published: August 2021

Background:
The main cause of progressive vision impairment in retinal degenerative diseases is the dysfunction of photoreceptors and the underlying retinal pigment epithelial cells. The inadequate regenerative capacity of the neural retina and lack of established therapeutic options demand the development of clinical grade protocols to halt degenerative process in the eye or to replace the damaged cells by using stem cell derived products. Recently, stem cell-based regenerative therapies are at the forefront of clinical investigations for retinal dystrophies.

Objective:
This article will review different stem cell-based therapies currently employed for retinal degenerative diseases, recent clinical trials, and major challenges in the translation of these therapies from bench to bedside.

Methodology:
A systematic literature review was carried out to identify potentially relevant articles published in MEDLINE/PubMed, Embase, ClinicalTrials.gov, Drugs@FDA, European Medicines Agency, World Health Organization International Clinical Trials Registry Platform and CENTRAL

Result:
Transplantation of healthy cells to replace the damaged cells in the outer retina is a clinically relevant concept because the inner retina that communicates with the visual areas of the brain remains functional even after the photoreceptors are completely lost. Different methods have been established for the differentiation of pluripotent stem cells into different retinal cell types that can be used for therapies. Factors released from transplanted somatic stem cells showed trophic support and photoreceptor rescue during early stages of the disease. Several preclinical and phase I/II clinical studies using terminally differentiated photoreceptor/ retinal pigment epithelial cells derived from pluripotent stem cells have shown proof of concept for visual restoration in Age-related macular degeneration (AMD), Stargardt disease and Retinitis pigmentosa (RP).

Conclusion:
Cell replacement therapy has great potential for vision restoration. The results obtained from the initial clinical trials are encouraging and indicates its therapeutic benefits. The current status of the therapies suggests that there is a long way to go before these results can be applied to routine clinical practice. Input from the ongoing multicentre clinical trials will give a more refined idea for the future design of clinical- grade protocols to transplant GMP level HLA matched cells.
Structural Activity Relationship based Medicinal Perspectives of Pyrimidine
Derivatives as Anti-Alzheimer’s Agents: A Comprehensive Review
Authors: Ahmed Bahar , Joseph Alex , Das Subham , Akbar Saleem , Dewangan Rikeshwar Prasad , Iqubal Ashif , Pottoo Faheem Hyder 
Published: August 2021

:
Pyrimidine is an aromatic and heterocyclic organic compound containing a 6-membered
ring consisting of four carbon and two nitrogen atoms on alternative positions. Pyrimidine scaffolds
described their existence in the medicinal chemist’s cause for their synthesizing practicability
and nonpoisonous nature. However, the reason behind neurological disorders is still an open challenge
for scientific research and development organizations. Efficacy voids are widespread before
researchers, despite high throughput research in the field of anti-Alzheimer's drugs.Researchers
have constantly investigated all the probabilities for restraining the unwanted adverse effects of the
anti-Alzheimer’s agents and are focusing more extensively to rehabilitate neurological disorders.
The scientific literature on drug development has been an aspiration to medicinal chemists and
other researchers to facilitate further research. Therefore, this review emphasizes the structure-activity
relationship (SAR) based approach and the pharmacological advancements of pyrimidine
moiety in the new era of therapeutics as anti-Alzheimer’s agents.
Identifying and Responding to Health Misinformation on Reddit Dermatology Forums With Artificially Intelligent Bots Using Natural Language Processing: Design and Evaluation Study
Authors: Sager Monique A , Kashyap Aditya M , Tamminga Mila , Ravoori Sadhana , Callison-Burch Christopher , Lipoff Jules B 
Published: August 2021

BackgroundReddit, the fifth most popular website in the United States, boasts a large and engaged user base on its dermatology forums where users crowdsource free medical opinions. Unfortunately, much of the advice provided is unvalidated and could lead to the provision of inappropriate care. Initial testing has revealed that artificially intelligent bots can detect misinformation regarding tanning and essential oils on Reddit dermatology forums and may be able to produce responses to posts containing misinformation.ObjectiveTo analyze the ability of bots to find and respond to tanning and essential oil–related health misinformation on Reddit’s dermatology forums in a controlled test environment.MethodsUsing natural language processing techniques, we trained bots to target misinformation, using relevant keywords and to post prefabricated responses. By evaluating different model architectures across a held-out test set, we compared performances.ResultsOur models yielded data test accuracies ranging 95%-100%, with a Bidirectional Encoder Representations from Transformers (BERT) fine-tuned model resulting in the highest level of test accuracy. Bots were then able to post corrective prefabricated responses to misinformation in a test environment.ConclusionsUsing a limited data set, bots accurately detected examples of health misinformation within Reddit dermatology forums. Given that these bots can then post prefabricated responses, this technique may allow for interception of misinformation. Providing correct information does not mean that users will be receptive or find such interventions persuasive. Further studies should investigate this strategy’s effectiveness to inform future deployment of bots as a technique in combating health misinformation.
Information Retrieval in an Infodemic: The Case of COVID-19 Publications
Authors: Teodoro Douglas , Ferdowsi Sohrab , Borissov Nikolay , Kashani Elham , Vicente Alvarez David , Copara Jenny , Gouareb Racha , Naderi Nona , Amini Poorya 
Published: August 2021

Background
The COVID-19 global health crisis has led to an exponential surge in published scientific literature. In an attempt to tackle the pandemic, extremely large COVID-19–related corpora are being created, sometimes with inaccurate information, which is no longer at scale of human analyses.

Objective
In the context of searching for scientific evidence in the deluge of COVID-19–related literature, we present an information retrieval methodology for effective identification of relevant sources to answer biomedical queries posed using natural language.

Methods
Our multistage retrieval methodology combines probabilistic weighting models and reranking algorithms based on deep neural architectures to boost the ranking of relevant documents. Similarity of COVID-19 queries is compared to documents, and a series of postprocessing methods is applied to the initial ranking list to improve the match between the query and the biomedical information source and boost the position of relevant documents.

Results
The methodology was evaluated in the context of the TREC-COVID challenge, achieving competitive results with the top-ranking teams participating in the competition. Particularly, the combination of bag-of-words and deep neural language models significantly outperformed an Okapi Best Match 25–based baseline, retrieving on average, 83% of relevant documents in the top 20.

Conclusions
These results indicate that multistage retrieval supported by deep learning could enhance identification of literature for COVID-19–related questions posed using natural language.
O PROCESSO FORMATIVO NA EDUCAÇÃO PROFISSIONAL E TECNOLÓGICA: CONTRIBUIÇÕES DA ERGOLOGIA E DA TEORIA DIALÓGICA DA LINGUAGEM
Authors: Freire Jocélia da Silva Gurgel , Sampaio Maria Cristina Hennes 
Published: August 2021

O objetivo do presente estudo é discutir alguns conceitos postulados pela Ergologia e pela Teoria Dialógica da Linguagem que são relevantes quando se objetiva desenvolver uma discussão acerca de uma formação discente na Educação Profissional e Tecnológica – EPT, numa perspectiva crítica e autônoma. Para esse fim, recorremos ao campo conceitual proposto pelo filósofo e ergologista francês Yves Schwartz (1996; 2006; 2010; 2011); e às discussões mobilizadas pelo filósofo russo Mikhail Bakhtin (2010; 2011). Quanto aos postulados ergológicos, discutimos conceitos como: atividade industriosa, trabalho prescrito e trabalho real, renormalizações, saberes instituídos e saberes investidos, entre outros. No que diz respeito às discussões bakhtinianas, trabalhamos, em especial, com as noções de dialogismo, alteridade e exotopia.
PALAVRAS-CHAVES: Dialogismo; Educação Profissional e Tecnológica; Formação humana integral; Trabalho.
O ÓCIO E O DEVER: DISCURSOS SOBRE O TRABALHO EM O CORUJA, DE ALUÍSIO AZEVEDO, COMO EXEMPLO DE ROMANCE PSICOLÓGICO
Authors: Oliveira Marina Rodrigues de , Fuza Ângela Francine , Melo Lívia Chaves de 
Published: August 2021

O coruja (1890), de Aluísio Azevedo, aborda a representação do trabalho docente e do ócio, por meio de duas personagens principais que os representam, respectivamente, André e Teobaldo, cujas diferentes trajetórias tornam-se patentes, ao longo da referida obra, através do diálogo; devido à grande importância deste instrumento e compreendendo-o dentro de uma realidade histórica, este artigo, adotando o conceito do romance psicológico, de Bakhtin, analisa como o narrador azevediano problematiza a questão servil em nosso país e como se encontra diretamente relacionada ao aspecto sócio-econômico, durante a transição secular em voga. Para isso, o estudo contempla tanto as considerações apresentadas pela Crítica Literária como pela Linguística. A categoria de romance psicológico, empregada por Bakhtin, corrobora para refletir as questões sociais por mostrar que aqueles que, de alguma forma, encontram-se à margem da sociedade, assim o permanecem, uma vez que não conseguem se adequar à lógica capitalista.
PARTISIPASI, TRANSPARANSI DAN AKUNTABILITAS PERENCANAAN DAN PENGANGGARAN DANA DESA
Authors: Hendrawati Erna , Pramudianti Mira 
Published: August 2021

Penelitian ini bertujuan untuk mengetahui bagaimana pelaksanaan partisipasi, transparansi dan akuntabilitas dalam perencanaan dan penganggaran dana desa. Teknik Pengumpulan data dengan observasi, wawancara dan dokumentasi. Responden penelitian ini adalah perangkat desa, BPD dan perwakilan masyarakat di desa Setro, kecamatan Menganti Gresik. Teknik pengolahan data dengan editing, interprestasi. Partisipasi RPJMDesa dan RKPDesa, musyawarah perencanaan pembangunan desa melibatkan perangkat desa, BPD, LPMD, tokoh masyarakat, organisasi kemasyarakatan, RT,RW, kepala dusun. Transparansi, adanya mekanisme dan akses masyarakat dalam penyampaian pendapat, mengajukan tanggapan, kritik terhadap pemerintahan desa, keterbukaan dokumen RKPDesa Setro sebagai dasar penyusunan APBDesa. Akuntanbilitas, RPJMDesa sebagai acuan dan arah perencanaan penyusunan RKPDesa, dokumen RKPDesa sebagai dasar penyusunan APBDesa. Bentuk partisipasi APBDesa Setro tahun 2017, musyawarah antara tim Penyusun APBDesa dengan BPD, LPMD sebaggai perwakilan masyarakat. Transparansi APBDesa Setro, dibuat banner informasi tentang APBDesa desa Setro tahun 2017 di lokasi pelaksanaan program pembangunan, Akuntabilitas APBDesa Setro, penyusunan laporan pertanggungjawaban sebagai bentuk pertanggungjawaban penggunaan dana.
A PH LEVEL MONITORING IN HYDROPONIC SYSTEM USING ARDUINO
Authors: Ramli Stevanus Adi , Herawati Rosita 
Published: August 2021

Hydroponic is one of growing plant method without soil. It uses water as the planting media. As of this writing, hydroponic method is quite popular in Indonesia because it is more hygienic, more results, more environmentally friendly at a lower cost production. Hydroponic life depends on the nutrients in the water. One of the most important of the hydroponic method is pH level of the water. The standard of pH level which used to grow a plant is in the range of 5.5 to 6.5.
To balance the standard of pH level, liquid for increasing and decreasing pH level are needed, but it is difficult to measure the pH level on the standard range while adding the water. Based on this problem, this project will develop an automated device for mixing pH up and pH down liquid so the level of pH will be keep in the desire range using pH sensor and Arduino microcontroller.
Ability of Architects to See Autopoietic Environmental Features
Authors: Petrušonis Vytautas 
Published: August 2021

Abstract
This article discusses the way of rating the competency of architects through their ability to recognize the autopoietic properties of architecture in developed urban projects. The following theoretical methods were used: abstraction, analogy, generalization and reasoning. Metalanguage of consideration (opposite to directive metalanguage) embedded in projects displays the fact, that a person is able to recognize such autopoietic features as connotations, memory traces, that are important for continuity of locus cultural identity.
Pengaruh Persentase Penambahan Bubuk Daun Stevia rebaudiana Bertoni dan Lama Penyeduhan terhadap Karakteristik Minuman Kunyit Asam
Authors: Julianto Aman , Mulyani Sri , Wartini Ni Made 
Published: August 2021

The leaves of the Stevia rebaudiana Bertoni plant have glycoside compounds including stevioside and rebaudioside A which can be used as natural sweeteners to replace the artificial sweeteners such as aspartame. This sweetener has a sweetness level of 200-300 times that of sucrose, so it can be used as a non-calorie sweetener. One way to take advantage of these leaves is to brew directly on certain products. This study aims to determine the effect of the addition percentage and the duration of brewing stevia leaves on the characteristics of tamarind turmeric drink and determine the appropriate treatment to produce the best tamarind drink. This study used a randomized block design with two factors. The first factor is the percentage of addition of stevia leaves with 4 levels, namely 15, 20, 25 and 30%. The second factor is the length of brewing with 3 levels, namely 2, 3 and 4 minutes. The results showed that the treatment of the percentage of addition of stevia leaves had an effect on vitamin C levels and antioxidant activity of IC50. The treatment duration of brewing had an effect on the level of vitamin C, while the interaction between the percentage of addition and the duration of brewing had an effect on the ranking of sweetness and the preference for sour turmeric drink.. The addition of 15% stevia leaf powder by brewing for 2 minutes resulted in the best tamarind turmeric drink with the characteristics of IC50 namely 15.78 + 0.38 mg/ml, vitamin C level specifically 14.02 + 1.15 mg AAE/g extracts and ph was 3.33 + 0.18 and the sweet and hedonic taste ratings are slightly sweet and slightly likable, respectively.
Keywords : Brewing time, stevia addition, turmeric-tamarind drink
Mixing ARMA Models with EGARCH Models and Using it in Modeling and Analyzing the Time Series of Temperature
Authors: Ali Mudhir Abduljabbar 
Published: August 2021

In this article our goal is mixing ARMA models with EGARCH models and composing a mixed model ARMA(R,M)-EGARCH(Q,P) with two steps, the first step includes modeling the data series by using EGARCH model alone interspersed with steps of detecting the heteroscedasticity effect and estimating the model's parameters and check the adequacy of the model. Also we are predicting the conditional variance and verifying it's convergence to the unconditional variance value. The second step includes mixing ARMA with EGARCH and using the mixed (composite) model in modeling time series data and predict future values then asses the prediction ability of the proposed model by using prediction error criterions.