E.PAGE: A curated database and enrichment tool to predict modules associated with gene-environment interactions

Aims/hypothesis: The purpose of this study is to manually and semi-automatically curate a database and develop an R package that will act as a comprehensive resource to understand how biological processes are dysregulated due to interactions with environmental factors. Methods: We followed a two-step process to achieve the objectives of this study. First, we conducted a systematic review of the existing gene expression datasets to identify the integrated genomic and environmental factors used in available studies. This enabled us to curate a comprehensive genomic-environmental database for four key environmental factors (smoking, diet, infections and toxic chemicals) associated with various autoimmune and chronic conditions. Second, we developed a statistical analysis package that allows users to understand the relationships between differentially expressed genes and environmental factors under different disease conditions. Results: The initial database search run on the Gene Expression Omnibus (GEO) and the Molecular Signature Database (MSigDB) retrieved a total of 90,018 articles. After title and abstract screening against pre-set criteria, a total of 186 studies were selected. From those, 243 individual sets of genes, or gene modules, were obtained. We then curated a database containing four environmental factors, namely cigarette smoking, diet, infections and toxic chemicals, along with a total of 25789 genes that had an association with one or more of these factors. In 6 case studies, the database and statistical analysis package were then tested with lists of differentially expressed genes obtained from the published literature related to type 1 diabetes, rheumatoid arthritis, small cell lung cancer, cobalt exposure, COVID-19 and smoking. On testing, we uncovered statistically enriched biological processes, which could help us understand the pathways associated with environmental factors and gene modules. Conclusions: A novel curated database and software tool is provided as an R Package. Users can enter a list of genes to discover associated environmental factors under various disease conditions.

Using Sentiment Analysis to Understand What Patients Are Saying About Hand Surgeons Online

Background: Physician review websites have influence on a patient’s selection of a provider. Written reviews are subjective and difficult to quantitatively analyze. Sentiment analysis of writing can quantitatively assess surgeon reviews to provide actionable feedback for surgeons to improve practice. The objective of this study is to quantitatively analyze large subset of written reviews of hand surgeons using sentiment analysis and report unbiased trends in words used to describe the reviewed surgeons and biases associated with surgeon demographic factors. Methods: Online written and star-rating reviews of hand surgeons were obtained from healthgrades.com and webmd.com . A sentiment analysis package was used to calculate compound scores of all reviews. Mann-Whitney U tests were performed to determine the relationship between demographic variables and average sentiment score of written reviews. Positive and negative word and word-pair frequency analysis was also performed. Results: A total of 786 hand surgeons’ reviews were analyzed. Analysis showed a significant relationship between the sentiment scores and overall average star-rated reviews ( r2 = 0.604, P ≤ .01). There was no significant difference in review sentiment by provider sex; however, surgeons aged 50 years and younger had more positive reviews than older ( P < .01). The most frequently used bigrams used to describe top-rated surgeons were associated with good bedside manner and efficient pain management, whereas those with the worst reviews are often characterized as rude and unable to relieve pain. Conclusions: This study provides insight into both demographic and behavioral factors contributing to positive reviews and reinforces the importance of pain expectation management.

The influence of drinkers on the affective status of representatives of their microsocial environment

The purpose of the work is to study the adverse influence of drinkers on the affective status of representatives of their microsocial environment. In four regions of Ukraine (Kharkiv, Lugansk and Zaporizhzhia regions, as well as the city of Kyiv), during 2018—2021, 1742 people were examined, who belonged to three qualitatively different comparison groups: patients with alcohol dependence (AD) (393 people); healthy relatives of alcohol-dependent patients (274 people) and representatives of the general population (1075 people). Of these surveyed, respondents were identified who had drinkers in the environment: 288 persons among healthy people and 121 persons among patients with AD. Further research focused on this particular contingent. The main research tool was the questionnaire of the international research consortium GENAHTO (Gender, Alcohol, and Harms to Others) and Hamilton Depression Rating Scale (HDRS). The obtained data were processed by methods of mathematical statistics (variance and cluster analysis) on a computer using Excel 2016 computational tables (with the Data Analysis package) and also the software package SPSS-15. It was shown that the presence of drinkers in environment of the women significantly increases the proportion of people with depressive disorders among them, while among the male respondents, this effect was not found. It was revealed that the presence of drinkers in environment of the women significantly increases the severity of such manifestations of depression as: insomnia, weight loss, sexual dysfunctions; suicidal tendencies and guilt. Using cluster analysis, the following typical symptom complexes (important for choosing the optimal therapeutic tactics) were established: insomnia-somatoform, hypochondriacal and anxiety-agitational (the latter — with a sense of guilt and an increased risk of suicidal activity).

Translation of Reflective Thinking Questionnaire: A Structural Equation Model

The purpose of this study is to translate, validate the reflective thinking questionnaire, and to explain the reflective thinking profile of UIN Mataram biology prospective teachers. A total 243 of UIN Mataram biology prospective teacher as voluntary respondents. The data analysis process was carried out using the JASP for windows analysis package. Structural equation model testing based on P-value, CFI, and RMSEA. The results of the confirmatory factor analysis, from 16 items were analyzed, only 11 items supported a fit model, with P-value= 0.225, CFI= 0.986, and RMSEA= 0.026. The 11 items reflect four categories of RT (understanding, reflection, habitual action, and critical reflection), show high internal consistency, and show good construct validity. The translation of the RT questionnaire was declared valid and could be used to measure RT.

Експериментальне визначення стану текстильних матеріалів десантної парашутної системи Д-5 серії 2 після тривалого зберігання. Повідомлення 2. Статистичні характеристики результатів вимірювання показників строп основного парашуту

The subject of the article is the analysis of the array of experimental data of loading and elongation at break of the slings of the main parachute landing parachute systems D-5 series 2 1973 and 1974 years of manufacture after long-term storage with zero (inexhaustible) resource. The current article attempts to determine the ratio of external factors related to the natural factors of aging of polymers, and internal, due to errors in the measurement process, based on statistical analysis of measurement results. Objective: to determine the degree of influence of internal and external factors on the process and result of measuring indicators. The following methods and equipment were used. An improved method of spot sampling of the samples under study of landing parachute systems D-5 series 2 for laboratory studies to determine the load at break and elongation at break of the slings of the main parachute. Measurements were performed on a machine of bursting brand ИР 5047-50M2C, accuracy class - 0.5 for the measurement range from 0.5 kN to 5 kN. The volume of the party was 25 parachute systems, only 250 elementary tests. The array of empirical data was processed by mathematical and statistical methods of the software package Descriptive statistics on the add-on of MS EXCEL Analysis Package. The following results were obtained. The relative error of the results of load measurement when breaking the slings of the domes of parachutes of 1973 production was ± 5.0%, for parachutes of 1974 production - ± 3.8%. The relative error of the results of measuring the elongation at the break of the slings of the domes of parachutes of 1973 manufacture was ± 2.9%, for parachutes of 1974 manufacture ± 3.3%. Given that the measuring instrument has an error of ± 0.29% in the passport, which can be considered systematic, the overall level of uncertainty is acceptable for conventional measurements in engineering. Conclusions. The main factors of accidental errors in the process of measuring the load at break and elongation at break of the slings of the main parachute are external factors due to the state of the cord structure and changes in the internal structure of the polymer.

The XFaster Power Spectrum and Likelihood Estimator for the Analysis of Cosmic Microwave Background Maps

We present the XFaster analysis package, a fast, iterative angular power spectrum estimator based on a diagonal approximation to the quadratic Fisher matrix estimator. It uses Monte Carlo simulations to compute noise biases and filter transfer functions and is thus a hybrid of both Monte Carlo and quadratic estimator methods. In contrast to conventional pseudo-C ℓ –based methods, the algorithm described here requires a minimal number of simulations and does not require them to be precisely representative of the data to estimate accurate covariance matrices for the bandpowers. The formalism works with polarization-sensitive observations and also data sets with identical, partially overlapping, or independent survey regions. The method was first implemented for the analysis of BOOMERanG data and also used as part of the Planck analysis. Here we describe the full, publicly available analysis package, written in Python, as developed for the analysis of data from the 2015 flight of the Spider instrument. The package includes extensions for self-consistently estimating null spectra and estimating fits for Galactic foreground contributions. We show results from the extensive validation of XFaster using simulations and its application to the Spider data set.

FARCI: Fast and Robust Connectome Inference

The inference of neuronal connectome from large-scale neuronal activity recordings, such as two-photon Calcium imaging, represents an active area of research in computational neuroscience. In this work, we developed FARCI (Fast and Robust Connectome Inference), a MATLAB package for neuronal connectome inference from high-dimensional two-photon Calcium fluorescence data. We employed partial correlations as a measure of the functional association strength between pairs of neurons to reconstruct a neuronal connectome. We demonstrated using in silico datasets from the Neural Connectomics Challenge (NCC) and those generated using the state-of-the-art simulator of Neural Anatomy and Optimal Microscopy (NAOMi) that FARCI provides an accurate connectome and its performance is robust to network sizes, missing neurons, and noise levels. Moreover, FARCI is computationally efficient and highly scalable to large networks. In comparison with the best performing connectome inference algorithm in the NCC, Generalized Transfer Entropy (GTE), and Fluorescence Single Neuron and Network Analysis Package (FluoroSNNAP), FARCI produces more accurate networks over different network sizes, while providing significantly better computational speed and scaling.

HARAPAN MAHATHIR KEPADA PENJAWAT AWAM MALAYSIA BAHARU: ANALISIS UCAPAN TUN DR. MAHATHIR MOHAMAD

The purpose of this article is to identify the aspects that Mahathir stressed on his first year of office as the 7th Prime Minister of Malaysia. The focus of this study is from the aspect of visionary leadership, namely the vision formation and vision delivery to civil servants through his speeches. This was done by content analyzing Mahathir's five speeches during the YAB Prime Minister's Monthly Meeting with the Public Servants in the Prime Minister's Department (JPM) from May 2018 to May 2019. Themes from the speech texts were analyzed using the NVivo12 qualitative analysis package. The results showed that there were four themes that are often emphasized in Mahathir's speech, namely civil servant responsibility, national recovery, values and loyalty. This study also showed that the combination of these themes formed by Mahathir has its own thoughts in uplifting the spirit of civil servants to restore the country. Keywords: Leadership communication, Mahathir’s speeches, Visionary leadership Abstrak: Matlamat artikel ini adalah untuk mengenalpasti aspek-aspek yang ditekankan oleh Mahathir dalam ucapan sepanjang tahun pertama beliau memegang jawatan sebagai Perdana Menteri Malaysia ke-7. Fokus kajian ini adalah dari segi kepimpinan bervisi, iaitu pembentukan dan penyampaian visi Mahathir kepada penjawat awam melalui ucapan beliau. Ini dilakukan dengan menganalisis kandungan lima ucapan Mahathir semasa Perhimpunan Bulanan YAB Perdana Menteri bersama Penjawat Awam di Jabatan Perdana Menteri (JPM) dari bulan Mei 2018 hingga Mei 2019. Tema dalam teks ucapan dianalisis menggunakan pakej analisis kualitatif NVivo12. Hasil kajian menunjukkan terdapat empat tema yang sering ditekankan dalam ucapan Mahathir, iaitu tanggungjawab penjawat awam, pemulihan negara, nilai murni dan kesetiaan. Kajian ini turut memperlihatkan bahawa kombinasi tema ini yang terbentuk daripada Mahathir mempunyai pemikiran tersendiri dalam menaikkan semangat penjawat awam memulihkan negara. Kata kunci: Komunikasi kepimpinan, Kepimpinan bervisi, Ucapan Mahathir

Correlation and regression analysis of the investment attractiveness of the petroleum refining industry

The article presents the results of the analysis of the investment attractiveness of the petroleum refining industry using correlation and regression methods. It has been suggested to evaluate the level of investment attractiveness of the petroleum refining industry through capital productivity. A system of indicators affecting the investment attractiveness of the petroleum refining has been formed in the context of resource and production, financial, economic and social groups of factors. This methodology of correlation and regression analysis for modeling factors affecting investment attractiveness has been presented. The methodology includes the construction of a pair correlation, the selection of factors, the construction of a generalised correlation matrix using the “Correlation” tool in the “Data Analysis” package Microsoft Excel, the regression analysis based on the finally selected factors, the construction of the regression equation, the justification of the obtained dependence using the “Regression” tool in the “Data Analysis” package MS Excel.According to the results of calculations for the type of economic activity “Production of coke and petroleum products” in the Russian Federation in dynamics for 2012 –2019, a strong correlation has been revealed between the output-capital ratio and such factors as the oil refining depth, profit from sales and labor productivity.The results of the study can be used to identify significant factors affecting the investment attractiveness of the petroleum refining industry in order to further optimise them.

Scrutinising the Exceptionalism of Young Rural NEETs: A Bibliometric Review

The situation of rural NEETs aged 15 to 24 remains understudied. However, transitions from adolescence to emerging adulthood are very demanding for those in the countryside. Our paper discusses this gap by characterising the scholarship focusing on rural NEETs. We undertook a bibliometric review based on 325 entries on Web of Science (WoS) using the Bibliometrix analysis package. Our approach included descriptive bibliometric analysis, co-citation networks assessment, and thematic analysis. Our findings show that the investigation efforts depicting younger rural NEET are recent and marginal in the larger context of international NEETs scholarship. The field is dominated by economy- and sociology-led networks. Concerns regarding health and employment issues are central in international publishing trends, showing a dominant youth-at-risk approach to this group. Still, themes associated with adolescent NEETs and relevant programs’ assessment are gaining traction. Our findings show a need for funding research initiatives to reduce the invisibility of young rural NEETs.