GMQN: A Reference-Based Method for Correcting Batch Effects and Probe Bias in HumanMethylation BeadChip

The Illumina HumanMethylation BeadChip is one of the most cost-effective methods to quantify DNA methylation levels at single-base resolution across the human genome, which makes it a routine platform for epigenome-wide association studies. It has accumulated tens of thousands of DNA methylation array samples in public databases, providing great support for data integration and further analysis. However, the majority of public DNA methylation data are deposited as processed data without background probes which are widely used in data normalization. Here, we present Gaussian mixture quantile normalization (GMQN), a reference based method for correcting batch effects as well as probe bias in the HumanMethylation BeadChip. Availability and implementation: https://github.com/MengweiLi-project/gmqn.

XIII RISA Convention: Intercultural Communication Section

On October 15–16 the 13th Russian International Studies Association Convention took place in MGIMO, Moscow. The Department of Philosophy named after A. F. Shishkin and the editorial board of the journal Concept: Philosophy, Religion, Culture hosted the Intercultural Communication section with the great support of the organizers of the Convention. Researchers that took part in the Section represented many countries such as Abkhazia, Bosnia and Herzegovina, Egypt, Spain, Iran, Moldova, Serbia and the USA, and many Russian cities — Moscow, Saint Petersburg, Chita, Rostov-on-Don, Vladimir, Nizhny Novgorod, and Irkutsk. Online streaming gathered a wide audience from all over the world from Russia to Uruguay and Japan. Specialists from various academic backgrounds in social and cultural studies discussed intercultural communication in several sessions. Philosophers, linguists, political and cultural reseactors, specialists in arts, media, and regional studies were engaged in active debates on the presented reports and talks. The exchange of viewpoints and perspectives is beneficial for both experts in their field and interdisciplinary research: it introduces inspiring ideas, impressive results, and new visions. Moreover, the dialogue itself was an example of intercultural communication with the academic community involved in a fruitful and engaging conversation on the most exciting topics in the field.

Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RSCB PDB) provides a wide range of digital data regarding biology and biomedicine. This huge internet resource involves a wide range of important biological data, obtained from experiments around the globe by different scientists. The Worldwide Protein Data Bank (wwPDB) represents a brilliant collection of 3D structure data associated with important and vital biomolecules including nucleic acids (RNAs and DNAs) and proteins. Moreover, this database accumulates knowledge regarding function and evolution of biomacromolecules which supports different disciplines such as biotechnology. 3D structure, functional characteristics and phylogenetic properties of biomacromolecules give a deep understanding of the biomolecules’ characteristics. An important advantage of the wwPDB database is the data updating time, which is done every week. This updating process helps users to have the newest data and information for their projects. The data and information in wwPDB can be a great support to have an accurate imagination and illustrations of the biomacromolecules in biotechnology. As demonstrated by the SARS-CoV-2 pandemic, rapidly reliable and accessible biological data for microbiology, immunology, vaccinology, and drug development are critical to address many healthcare-related challenges that are facing humanity. The aim of this paper is to introduce the readers to wwPDB, and to highlight the importance of this database in biotechnology, with the expectation that the number of scientists interested in the utilization of Protein Data Bank’s resources will increase substantially in the coming years.

Applications of the Columbus steerable guidewire

The Columbus steerable guidewire (Rapid Medical, Israel) is a 0.014 inch guidewire with a remotely controlled deflectable tip intended for neuronavigational purposes. 1 The tip can be shaped by pulling or pushing the handle. Pulling the handle decreases the radius (from 4 mm to 2 mm) and curves the tip, while pushing the handle increases the curvature radius and straightens the tip until it bends in the opposite direction. The amount of deflection is at the discretion of the operator. Video 1 The response of the Columbus guidewire to rotational movements is inferior to that of standard wires, and the tip is very soft and malleable but brings great support when bent. We present two cases where the Columbus guidewire was used. In the first case, the Columbus enabled us to probe a posterior cerebral artery arising from a giant basilar tip aneurysm without wall contact. In the second case, the Columbus was used as a secondary wire to help cannulate the pericallosal artery in a patient with a recurrent anterior complex aneurysm; this subsequently permitted successful stent-assisted coiling of the aneurysm.Video 1

Destigmatising Schizophrenia: An Investigation into the Effects of Different Causal Explanations upon Stigma

<p>While many people with mental illnesses are stigmatised, those with schizophrenia are the most severely stigmatised group (Crisp, Gelder, Rix, Meltzer, & Rowlands, 2000; Marie & Miles, 2008; Pescosolido et al., 1999). A vast body of psychology research has been devoted to investigating how education – particularly education about the causes of schizophrenia – can reduce this stigma that is attached to schizophrenia. While there is great support for the notion that education in general can reduce stigma (e.g. Costin & Kerr, 1962; Griffiths, Christensen, Jorm, Evans, & Groves, 2004; Ritterfeld & Jin, 2006), there is still disagreement regarding exactly which set of causal factors the general public should be educated about – biogenetic or psychosocial? Until now, only three previous studies (Lincoln, Arens, Berger, & Rief, 2008; Schlier, Schmick, & Lincoln, 2014; Walker & Read, 2002) have experimentally compared teaching a purely biogenetic causal explanation to teaching a purely psychosocial causal explanation. The results of this research appear to be somewhat contradictory leading to the need for another, more robustly designed experiment. In the present research, two experiments were conducted in which participants’ level of stigma was measured after they were given a biogenetic causal explanation of schizophrenia, a psychosocial explanation, or given no causal explanation. It was predicted that participants given a causal explanation would show reduced levels of stigma compared to participants given no causal information, and that there would be a significant difference in the stigma reduction effectiveness between types of causal explanation. Contrary to these expectations, the results of Experiment One showed no reduction in stigma when participants were given a causal explanation compared to no causal explanation, and revealed no significant differences in stigma reduction efficacy between the biogenetic and psychosocial causal explanations. Experiment Two utilised the same basic paradigm as Experiment One but with the addition of more convincing causal explanations and a manipulation check. The results of Experiment Two gave evidence that both a biogenetic and psychosocial causal explanation successfully reduces discrimination compared to giving no information on the causes of schizophrenia. In addition, a purely biogenetic causal explanation was also found to successfully reduce belief in other stereotypes compared to a psychosocial causal explanation or no causal explanation. Thus, I conclude that stigma can be effectively reduced by providing education about the causes of schizophrenia, and that a biogenetic causal explanation is a more effective stigma reduction tool as it reduces multiple types of stigma. Strengths, limitations, implications and future directions are discussed.</p>

Destigmatising Schizophrenia: An Investigation into the Effects of Different Causal Explanations upon Stigma

<p>While many people with mental illnesses are stigmatised, those with schizophrenia are the most severely stigmatised group (Crisp, Gelder, Rix, Meltzer, & Rowlands, 2000; Marie & Miles, 2008; Pescosolido et al., 1999). A vast body of psychology research has been devoted to investigating how education – particularly education about the causes of schizophrenia – can reduce this stigma that is attached to schizophrenia. While there is great support for the notion that education in general can reduce stigma (e.g. Costin & Kerr, 1962; Griffiths, Christensen, Jorm, Evans, & Groves, 2004; Ritterfeld & Jin, 2006), there is still disagreement regarding exactly which set of causal factors the general public should be educated about – biogenetic or psychosocial? Until now, only three previous studies (Lincoln, Arens, Berger, & Rief, 2008; Schlier, Schmick, & Lincoln, 2014; Walker & Read, 2002) have experimentally compared teaching a purely biogenetic causal explanation to teaching a purely psychosocial causal explanation. The results of this research appear to be somewhat contradictory leading to the need for another, more robustly designed experiment. In the present research, two experiments were conducted in which participants’ level of stigma was measured after they were given a biogenetic causal explanation of schizophrenia, a psychosocial explanation, or given no causal explanation. It was predicted that participants given a causal explanation would show reduced levels of stigma compared to participants given no causal information, and that there would be a significant difference in the stigma reduction effectiveness between types of causal explanation. Contrary to these expectations, the results of Experiment One showed no reduction in stigma when participants were given a causal explanation compared to no causal explanation, and revealed no significant differences in stigma reduction efficacy between the biogenetic and psychosocial causal explanations. Experiment Two utilised the same basic paradigm as Experiment One but with the addition of more convincing causal explanations and a manipulation check. The results of Experiment Two gave evidence that both a biogenetic and psychosocial causal explanation successfully reduces discrimination compared to giving no information on the causes of schizophrenia. In addition, a purely biogenetic causal explanation was also found to successfully reduce belief in other stereotypes compared to a psychosocial causal explanation or no causal explanation. Thus, I conclude that stigma can be effectively reduced by providing education about the causes of schizophrenia, and that a biogenetic causal explanation is a more effective stigma reduction tool as it reduces multiple types of stigma. Strengths, limitations, implications and future directions are discussed.</p>

The ability of cash flows to predict the earning: Evidence from Jordan

This study aims to investigate the ability of cash flows components to predict the earning and to know the extent of the relationship between accounting profits and cash flow measures. The study sample consisted of 77 industrial companies listed on the Amman Stock Exchange in Jordan for the period from 2006 to 2019. This study relied on the regression method to test the relationship between the study variables. The study findings showed that the cash flows from operating, investing, and financial activities have a statistically significant impact on predicting future earnings. The study also examined the effect of length of operating cycle and company’s size on the predictive ability of cash flows regarding future earnings. The main results for this aspect are that large companies and short operating cycle companies have higher prediction ability for future earnings than small and long operating cycle companies. This paper provides evidence of the information content of cash flows for future earnings in emerging markets like Jordan and is important for Jordanian shareholders by enabling them to evaluate company’s performance. AcknowledgmentsI would like to thank Amman Arab University for its great support, and for funding this study.

Language Acquisition and Cultural Identity Among Modern Chinese Minority College Students

This research attempts to have an empirical analysis on the relationship between the acquisition of language and the cultural identity among modern Chinese minority college students，and try to show an empirical view of how the acquisition of language matters with the cultural identity from one side as well as the mutual influences reflected from the relationship between language acquisition and cultural identity from the other side. The research employs mainly three analytical methods including method of theoretical analysis, method of comparative analysis and method of questionnaire to acquire a full understanding of the relationship between the acquisition of language and the cultural identity among modern Chinese minority college students. The current study data shows that compared with the local language, modern Chinese minority college students use Mandarin more in most of the time and occasions. At the same time, while acknowledging the importance of their local language, modern Chinese minority students also strongly advocate the promotion of Mandarin and English. Conclusion: Language acquisition and cultural identity are closely related. This is mainly reflected in the fact that language acquisition deeply reflects the elements of cultural identity, while cultural identity deeply reciprocally affects the way of language acquisition. The cultural identity of modern Chinese minority college students has determined the series of characteristics and methods they exhibit in the process of their language acquisition. The close relationship between language acquisition and cultural identity has provided great support and enlightenment both theoretically and practically for the majority of language educators.

Editorial

Dear Readers, Welcome to the ninth issue in 2021. I am very pleased to mention that the access statistics show a steady growth and also the interest in our journal is increasing. This success is only possible because of the great support from all of you. Thus, on behalf of the J.UCS team, I would like to thank all authors for their sound research contributions, the reviewers for their very helpful suggestions, and the consortium members for their financial support. Your commitment and dedicated work have contributed significantly to the overall success of J.UCS. In this regular issue, I am very pleased to present three accepted papers from five different countries and 10 involved authors. Armando Cruz, Hugo Paredes, Leonel Morgado and Paulo Martins from Portugal investigate in their work non-verbal aspects of collaboration in virtual worlds in the context of the presence dimension. In a collaborative research between Chile and Japan, Paul Leger, Hiroaki Fukuda and Ismael Figueroa present a JavaScript package that allows developers to write event handlers that need nested callbacks in a synchronous style, avoiding the so-called &lsquo;callback hell&rsquo;. In another collaboration between Indonesia and the UK, Riri Fitri Sari, Asri Samsiar Ilmananda, and Daniela M. Romano discuss their research on a social trust-based blockchain-enabled social media news verification system. Enjoy Reading!

Characterisation and Prioritization of Micro Watersheds Using Geospatial Techniques: A Case Study on river Bharathapuzha, Kerala

Watershed based interventions are essential for the sustainable land and water management of any region. Watershed prioritisation is a must for the efficient utilisation of available monetary and human resources. One of the most common means of prioritisation is through morphometric analysis as hydrological processes or watershed responses depend on morphometric characteristics of the watersheds. The study contains morphometric analysis of a few number of micro watersheds of river Bharathapuzha of Kerala state. With the help of ArcGIS software and SRTM DEM, all the basic morphometric characteristics and derived morphometric characteristics of 10 micro watersheds are determined and then scores are assigned to the parameters. Finally, combined parameter scores are determined and ranking of each micro watershed is done. The priority scores between watersheds show considerable variation which is an indication of the efficacy of the methods employed. Once the ranking of the micro watersheds are done objectively and scientifically it would be a great support to the soil and water conservationist and planners. This study gives an insight into the applicability of the method to a mid land region in the state of Kerala, India.