bluuebunny/crossref_metadata_2025 huggingface dataset:
Assisted Psychedelic Psychotherapy: Rethinking the Paradigms of Psychiatric Care?
Authors: Mea Eliana , Clemente Paola
Published: December 2024

Can psychedelic-assisted psychotherapy (PAT) serve as a paradigm for describing and navigating a profound transformative experience of the self? This model of therapy has ignited an intense debate in recent years that seems aimed at calling into question, more than the various currents of psychotherapy, the model of psychiatric care that has lost over time the real capacity to address the psychological distress of people and to interpret the psychological phenomena observed, too often reducing itself to an aseptic prescription of drugs in which the therapeutic relationship has progressively become emptied of meaning. In this work, we will examine the current schools of thought that animate the debate on PAT and the psychodynamic aspects that allow us to better understand the functioning of this specific psychotherapeutic approach. According to the psycholytic paradigm, psychedelic substances are capable of inducing regression to states of consciousness different from its ordinary state. In such states, fundamental conflicts may emerge in the early years of life that have led to the development of an ego that has realized the adaptive functions to the external environment with various more or less functional configurations. Is it possible through this type of therapeutic approach to access states of temporary psychic deintegration and then arrive at new integrative modalities that broaden the subject’s self-awareness?
Dark Matter and Dark Energy in Galaxies Via Gravitational Field Self-Interaction
Authors: Oliveira Firmin
Published: December 2024

The gravitational redshift theory (GRST) is defined in terms of the gravitational and cosmological redshifts of the gravitational field by means of the self-interaction of the field. The concept is applied to spiral galaxy rotation and to elliptical galaxies acting in the form of gravitational lensing. These field effects which are due solely to the baryonic mass in the galaxy are sufficient to account for the missing mass needed to match the observed rotation velocities without the need for other forms of matter. It is claimed that these effects which are described by the GRST, being purely relativistic in nature, are non-electromagnetic and act by gravity via the relativistic increase of the galaxy mass, and are responsible for the manifestations that have been attributed to dark matter and dark energy.
Age Management for Healthy and Active Aging: Analysis of the Impact on Employment Status and Household Composition in the Czech Republic and Selected Eurozone Countries
Authors: Jasova Emilie
Published: December 2024

The book chapter applies the concept of age management to promote active and healthy ageing of the population in the Czech Republic and in selected Eurozone countries, especially with regard to the resilience of the pension system. Ageing should be understood as a lifelong process. In addition to activities to prevent age discrimination, the employment of older people should also be promoted, for example, by developing a corporate culture that is friendly to all age groups, raising awareness of the principles of age management among employers, and increasing interest in implementing it in practice. The principles of age management are represented by the concept of work ability. International and domestic research has located the impact of age management measures on published labour market indicators and family by labour market status and composition. Regression analysis was applied to confirm these conclusions using data from the Czech Republic and the Eurozone. In the area of labour status and household composition, for example, the analysis confirms an above-average, statistically significant, undesirable effect of the indicator % of enterprises with a collective agreement between social partners out of all enterprises with 250 or more employees.
Guidelines for the governance of digital platforms: safeguarding freedom of expression and access to information through a multi-stakeholder approach (nep)
Authors:   UNESCO
Published: December 2024

Drafted through extensive consultations, these Guidelines aim to safeguard the right to freedom of expression and access to information in the context of the governance of digital platforms. They present a multistakeholder approach outlining key responsibilities for States and digital platforms to fulfill theirhuman rights obligations and define roles for intergovernmentalorganizations, civil society, media, academia, the technical community, and other stakeholders.
Vadlīnijas digitālo platformu pārvaldībai: Vārda brīvības un informācijas piekļuves nodrošināšana, izmantojot daudzpušu pieeju
Authors:   UNESCO
Published: December 2024

Drafted through extensive consultations, these Guidelines aim to safeguard the right to freedom of expression and access to information in the context of the governance of digital platforms. They present a multistakeholder approach outlining key responsibilities for States and digital platforms to fulfill theirhuman rights obligations and define roles for intergovernmentalorganizations, civil society, media, academia, the technical community, and other stakeholders.
Pemanfaatan Wireless Sensor Netwrok Untuk Monitoring Parameter Kualitas Air Kolam Budidaya Ikan Tawar di SMKN 2 Ketapang Kalimantan Barat
Authors: Wahyudi Eka , Darmanto Darmanto , Indah Pradasari Novi
Published: December 2024

Tujuan dari kegiatan Penelitian ini adalah membangun sistem monitoring parameter kualitas air kolam budidaya ikan tawar di Lab APAT SMKN 2 Ketapang. Hasil penelitian ini diharapkan mampu menyumbangkan kajian ilmiah dalam bidang perancangan dan pengembangan sistem informasi. Pada sistem monitoring nantinya siswa dan guru dapat melakukan kontrol parameter kualitas air yaitu suhu dan pH tanpa harus mengecek satu per satu kolam budidaya. Sistem ini menyediakan fitur pengontrolan suhu dan pH memanfaatkan Wireless Sensor Netwrok (WSN) sehingga apabila terdapat kolam budidaya yang mengalami kenaikan maupun penurunan parameter kualitas air langsung dapat diketahui dan dapat segera diberi perlakuan khusus. Sistem monitoring memanfaatkan WSN dibuat untuk membantu proses kontrol parameter kualitas air yang pada awalnya harus dilakukan secara manual dengan membutukan waktu sekitar 30 menit sampai dengan 1 jam untuk mengecek masing-masing kolam. Diharapkan dengan adanya sistem tersebut kegiatan mengecek parameter kualitas air menjadi lebih hemat waktu maupun tenaga serta dapat meningkatkan keakuratan dalam pemeriksaan parameter kualitas air dan sistem tersebut dapat membantu para taruna/taruni maupun guru untuk monitoring dari jarak jauh tanpa harus datang ke kolam budidaya. Sistem kontrol parameter kualitas air tersebut dibuat berbasis Android agar dapat diakses dan terjangkau selama prosesmonitoring. Monitoring dilakukan agar semua data informasi yang diperoleh dari hasil pengamatan tersebut dapat menjadi landasan dalam mengambil keputusan tindakan selanjutnya yang diperlukan.
Türkiye’de Transfer Harcamaları İle Gelir Dağılımı Arasındaki İlişki
Authors: Yalçın Ebru
Published: December 2024

Gelir dağılımında eşitsizliği ve yoksulluğu azaltmak amacıyla kullanılan maliye politikası araçlarından biri olan transfer harcamalarının bütçe içindeki payının yıllar itibariyle arttığı görülmektedir. Bu çalışmada,  hane halkına yapılan transferler ve sosyal yardımların gelir dağılımı üzerinde etkisini değerlendirmek üzere Granger nedensellik analizi uygulanmıştır. Elde edilen bulgular, transfer harcamalarından Gini katsayısına doğru tek yönlü bir nedensellik bulunduğunu göstermektedir. Bu kapsamda, doğru hedeflenmiş transfer harcamalarının, sosyo-ekonomik dengeyi sağlanma ve gelir eşitsizliğini azaltma potansiyeline sahip olduğu görülmektedir.
Bridging Traditions and Modernity: Cross-Cultural Adaptation of Pingle Guo’s Bone Setting in Global Healthcare
Authors:   Institute of International Education, New Era University College, Kajang, Malaysia., Guan Xiaoyin , Lim Lian Seng ,   Institute of International Education, New Era University College, Kajang, Malaysia., Lew Siew Boon ,   Institute of International Education, New Era University College, Kajang, Malaysia., Tey Shi Bin ,   Institute of International Education, New Era University College, Kajang, Malaysia., Li Hongxia ,   Shenzhen Pingle Orthopedic Hospital (Shenzhen Pingshan Traditional Chinese Medicine Hospital), Shenzhen, China., Sun Peng ,   School of Management, Jinan University (JNU), Guangzhou, China., Li Wei ,   Shenzhen Pingle Orthopedic Hospital (Shenzhen Pingshan Traditional Chinese Medicine Hospital), Shenzhen, China.
Published: December 2024

This study investigates the cross-cultural dissemination of traditional medical practices in the globalized world, focusing on the Pingle Guo’s Bone Setting Method (PGBS), a distinctive practice rooted in traditional Chinese medicine (TCM). Originating from Luoyang, China, PGBS has transcended cultural and geographical boundaries, gaining recognition in various international healthcare systems. Using a multi-method approach, including in-depth interviews, document analysis, and comparative case studies, this research examines the mechanisms of PGBS’s internationalization. Key aspects explored include cultural adaptation, the role of cultural brokers, institutional collaboration, and the negotiation of medical paradigms. The study reveals that PGBS’s success lies in balancing cultural authenticity with necessary adaptations to fit diverse healthcare systems, such as in the United States, Japan, and South Korea. Furthermore, it highlights challenges in the global dissemination of traditional practices, particularly regarding standardization, regulatory approval, and institutional recognition. The findings contribute to cross-cultural healthcare management by offering insights into how traditional knowledge can be integrated into global health systems. This research also provides valuable implications for policymakers, healthcare providers, and scholars interested in the future of traditional medicine in a globalized world.
Nilai Filsafat Keadilan Dalam Putusan Pidana Terhadap Pelaku Human Trafficking
Authors: Candra M. Dewi , Syihabuddin Syihabuddin
Published: December 2024

Penelitian ini bertujuan untuk menganalisis isu perdagangan manusia yang marak di Indonesia, dimulai dengan konsep dan tipologi perdagangan manusia. Metode yang digunakan adalah studi literatur sistematis, menganalisis 1.229 artikel dari database Scopus. Hasil penelitian menunjukkan bahwa definisi perdagangan manusia sangat kompleks dan belum ada kesepakatan di kalangan akademisi mengenai definisi yang paling representatif. Untuk memahami konsep ini, akademisi perlu memperhatikan karakteristik spesifik dan kontekstual dari tipologi perdagangan orang. Banyak faktor internal dan eksternal yang mempengaruhi pilihan imigrasi korban ke dalam kejahatan ini, sehingga pembuat kebijakan perlu memahami isu-isu penting terkait referensi korban. Ada tiga tema utama yang diidentifikasi dalam perdagangan manusia: (1) pengembangan model dan strategi yang lebih efektif untuk memerangi perdagangan manusia, (2) eksplorasi faktor sosial dan budaya yang mendasari perdagangan manusia di berbagai kawasan, dan (3) pengembangan kapasitas serta penerapan kebijakan untuk melindungi korban. Tinjauan literatur ini memberikan informasi rinci tentang aliran penelitian perdagangan manusia dalam ilmu sosial. Perdagangan manusia adalah bentuk intimidasi terhadap nilai kebebasan dan hak dasar manusia. Teori keadilan bermartabat, yang menjunjung nilai Pancasila, menekankan pentingnya pertanggungjawaban pidana bagi pelaku human trafficking. Penerapan sanksi pidana dalam kasus Tindak Pidana Perdagangan Orang (TPPO) dianggap rendah, dan setiap sanksi harus mencerminkan prinsip peradilan pidana yang objektif dan sesuai prosedur.
Conceptual Cost Estimation In Green Buildings By Using Regression Analysis And Artificial Neural Network Methods To Improve Accuracy
Authors: Isvara Wisnu , Kamilah Fauziyah
Published: December 2024

Conceptual cost estimation is a critical task during the early stages of a construction project, especially for green buildings, which present unique sustainability challenges and design complexities. Traditional methods such as regression analysis are widely used but often rely on experienced estimators and are time-consuming, while Artificial Neural Networks (ANN) offer a modern alternative but are limited by the quality and quantity of available data. This study aims to develop a hybrid model combining regression analysis and ANN to improve the accuracy of conceptual cost estimation for green and conventional high-rise buildings in Indonesia. Using data from 22 high-rise building projects (13 conventional and 9 green buildings), the study employed regression analysis, ANN techniques, and a combination of the two, with eight key variables selected for modeling. The hybrid model demonstrated the highest accuracy, achieving a Mean Absolute Percentage Error (MAPE) of 15.09%, within the acceptable range for conceptual cost estimation (+10–30%) as per AACE standards, outperforming standalone regression and ANN models. These findings highlight that integrating regression analysis and ANN provides a robust tool for early-stage cost estimation, supporting sustainable construction practices and informed decision-making.
Exploration of Work Accident Prevention Behavior Among Technical Service Personnel In the Implementation of The 'One Pict Saves You' Movement at PT PLN (Persero) Customer Service Unit Bireuen
Authors: Gunawan Ricky , W. Saputra Bobby
Published: December 2024

This study aims to explore the work accident prevention behaviors of technical service officers in response to the implementation of the "One Pict Saves You" initiative at PT PLN (Persero) Customer Service Unit in Bireuen. This initiative was introduced to improve compliance with the use of personal protective equipment (PPE) as a preventive measure to reduce workplace accidents. The methodology used in this study is a qualitative approach with thematic analysis techniques. Data was obtained through in-depth interviews with supervisors, management, and technical service officers, as well as an analysis of the company's safety documents. Interview questions focused on officers' awareness of the importance of PPE, compliance with safety procedures, and behavioral changes following the implementation of the "One Pict Saves You" initiative. The results indicate that the implementation of this initiative successfully increased awareness and compliance with PPE use. Most officers recognized the importance of PPE in protecting their own safety and felt encouraged by consistent visual monitoring. Additionally, the data demonstrated positive changes in safety behavior, including voluntary compliance and enhanced awareness of safety procedures. However, challenges remain in overcoming factors that inhibit consistent compliance, such as occasional PPE availability issues and ingrained habits. The managerial implications of this research highlight the importance of developing an app-based monitoring system, improving internal communication regarding safety procedures, and providing incentives for officers who comply with safety protocols. The company is advised to continue periodic safety training and awareness programs to ensure that behavioral changes remain sustainable.
The Influence of Brand Image, Product Innovation, and Social Media Marketing Activities on Iphone Purchasing Decisions In Jakarta
Authors: Ponikasari Ponikasari , Sibarani Mentiana
Published: December 2024

This study aims to analyze the influence of brand image, product innovation and social media marketing activities on iPhone purchasing decisions in DKI Jakarta. This study is included in quantitative research. The population in this study were former iPhone users in DKI Jakarta who are currently or have used iPhone cellphones. The number of samples using the Cochran formula so that 100 respondents were obtained. The analysis method used is multiple linear regression. The results of the study show that brand image has a significant effect on iPhone purchasing decisions in DKI Jakarta, product innovation has a significant effect on iPhone purchasing decisions in DKI Jakarta, and social media marketing activities have a significant effect on iPhone purchasing decisions. Then, brand image, product innovation and social media marketing activities simultaneously (together) have a significant effect on iPhone purchasing decisions in DKI Jakarta. It is recommended that Apple can utilize platforms such as Instagram and TikTok to display user stories that illustrate how the iPhone supports their lifestyle. Local content that is tailored to trends in Jakarta, such as sustainability issues or urban productivity needs, can also increase appeal.
The Influence of Social Media, Search Engine Optimization, and Influencer Marketing On Brand Awareness of Siloam Hospitals
Authors: Kurniadi Kenny , W. Saputra Bobby
Published: December 2024

This study aims to measure the influence of social media usage, search engine optimization (SEO), and influencer marketing on the brand awareness of Siloam Hospital. The study sample consists of 120 respondents selected through purposive sampling from individuals who have used or plan to use hospital services. Multiple linear regression analysis is used to test the research hypotheses. The results show that the SEO variable has a significant positive effect on Siloam Hospital's brand awareness. This indicates that search engine optimization efforts are an effective strategy for increasing the hospital’s visibility to the public. In contrast, social media and influencer marketing variables do not have a significant impact on brand awareness. These findings suggest that, in the context of Siloam Hospital, SEO is the most dominant factor in enhancing brand awareness. The practical implication of this research is the importance for Siloam Hospital to continuously improve website content quality, optimize keywords, and build backlinks from relevant websites. This study contributes to understanding effective digital marketing strategies in the healthcare sector, particularly for hospitals. However, further research with a larger sample and the inclusion of additional variables is needed to achieve more generalized results.
Psychological Capital as a Predictor of Organizational Citizenship Behaviour in the Personnel and Human Resources Development Agency employees in West Kalimantan
Authors: Maulida Rahman Riki , Endang Kusmaryani Rosita
Published: December 2024

This research starts from an indication of the low Organizational Citizenship Behavioral (OCB) of government agency employees at the Personnel and Human Resources Development Agency (BKPSDM) in West Kalimantan. Previous research explains that the predictor of employee OCB level is psychological capital. Therefore, this study aims to determine psychological capital as a predictor of organizational citizenship behavior in the Civil Service Agency and Human Resources Development employees in West Kalimantan. This research uses quantitative with ex-post facto type. The sample used was 52 BKPSDM employees in West Kalimantan. The instrument validation technique uses construct validation and previous research reliability. The data analysis technique uses descriptive and inferential analysis consisting of classical assumption tests and hypothesis testing. The results of this study indicate inferential analysis in the simultaneous test (F test) psychological capital variables become predictors of OCB. Then a partial test (T test) the hope dimension had no effect, the optimism dimension had no effect, the resilience dimension had no effect, and the self-efficacy dimension was the only predictor of psychological capital on OCB.
Geopolitical Influence of Afghanistan’s Neighbors on the Country's Domestic and Foreign Policies
Authors: Wafa Noorani , Mazloum Yar Fayaz Gul
Published: December 2024

This paper examines the impact of Afghanistan’s neighbors on the country’s domestic and foreign policies. Afghanistan shares borders with Pakistan, Iran, China, India, and the Central Asian republics, and its unique geographical location has made it a focal point in regional and global geopolitics. Using a mixed-methods research approach that incorporates both quantitative and qualitative data, this study analyzes the economic, cultural, security, and political effects of Afghanistan’s neighboring countries on its policies. The findings reveal that economic and trade cooperation with China and Pakistan has contributed to Afghanistan’s infrastructure and economic development. Additionally, cultural and historical ties with Iran and India have played a significant role in strengthening Afghanistan’s political and social relationships. Furthermore, security and intelligence collaborations with Central Asian countries and China have helped mitigate security threats and promote regional stability. This research also proposes strategies to improve Afghanistan's relations and strengthen its domestic and foreign policies with its neighbors.
AIDS in Women Caused by Human Immunodeficiency Virus: A Comprehensive Review
Authors:   School of Applied Health Sciences Kampala International University Uganda, Mwendwa G. Fabiola
Published: December 2024

HIV/AIDS remains a significant global health challenge, disproportionately affecting women, especially in resource-limited regions like sub-Saharan Africa. This comprehensive review explores the complex factors contributing to the feminization of the HIV/AIDS epidemic, focusing on biological, social, cultural, and economic vulnerabilities that heighten women’s risk of infection. Biological factors such as increased mucosal susceptibility, along with gender-based violence, economic dependency, and restrictive cultural norms, compound women’s vulnerability. Prevention and treatment strategies, including condom use, Pre-exposure Prophylaxis (PrEP), and mother-to-child transmission prevention (PMTCT), are examined alongside structural barriers that limit their efficacy. The review also highlights the importance of integrating HIV services with sexual and reproductive health, addressing the root causes of gender inequality, and expanding research to include gender-sensitive approaches. By empowering women economically, socially, and legally, tailored interventions can mitigate the impact of HIV/AIDS and improve health outcomes for women worldwide.

Keywords: HIV/AIDS, women, feminization of HIV, gender-based violence, PrEP, PMTCT, sexual and reproductive health, sub-Saharan Africa.
Media Trials: The Intersection of Law and Public Opinion
Authors:   Department of Publication and Extension Kampala International University, Uganda, Nnenna Ugwu Jovita
Published: December 2024

Media trials, characterized by the extensive media coverage of legal proceedings, play a complex role at the intersection of law and public opinion. While media serves as a vital tool for public transparency, it also introduces risks of prejudice and bias, threatening the impartiality of judicial processes. This paper investigates the historical evolution of media trials, their ethical implications, and the impact of sensational coverage on judicial outcomes. Case studies are examined to illustrate the dual-edged nature of media involvement in high-profile cases. The paper highlights regulatory frameworks and best practices to balance freedom of expression and the right to a fair trial. Ultimately, it argues for a nuanced approach to mitigate media influence while preserving the integrity of both legal systems and democratic ideals.

Keywords: Media Trials, Public Opinion, Judicial Impartiality, Fair Trial, Sensationalism, Ethical Journalism, Media Regulation.
Prevalence and Risk Factors of Anemia among Women in Uganda: A Comprehensive Review
Authors:   School of Natural and Applied Sciences Kampala International University Uganda, Moses H. Mugo
Published: December 2024

Anemia is a prevalent public health issue among women in Uganda, with significant implications for their health and socio-economic well-being. This comprehensive review examines the prevalence and risk factors of anemia among women, especially those of reproductive age, and identifies the multifaceted contributors to this condition. Nutritional deficiencies, particularly iron deficiency, are primary causes, exacerbated by limited access to iron-rich foods and food insecurity. Infectious diseases, such as malaria, hookworm, and HIV/AIDS, also contribute substantially to anemia by inducing red blood cell loss or impairing their production. Socioeconomic determinants, including education level, income, and access to healthcare, significantly impact anemia prevalence, as do reproductive factors like early pregnancies and high parity. This review synthesizes research on anemia among Ugandan women to highlight the urgent need for targeted interventions, including improved nutritional programs, enhanced malaria and deworming campaigns, and policy measures addressing socioeconomic barriers. By addressing the underlying determinants of anemia in Uganda, stakeholders can work toward mitigating its impact on women’s health, productivity, and community participation.

Keywords: Anemia, prevalence, risk factors, Uganda, women’s health, iron deficiency, reproductive health.
Steroid-Induced Immunomodulation in Clinical Practice: Navigating the Fine Line between Therapeutic Benefits and Immunosuppression Risks
Authors:   School of Natural and Applied Sciences Kampala International Uganda, Mwaura F. Maina
Published: December 2024

Steroids, particularly glucocorticoids, are integral in managing a broad spectrum of clinical conditions due to their potent anti-inflammatory and immunosuppressive properties. This review explores the mechanisms through which steroids modulate immune function, offering therapeutic benefits in autoimmune diseases, respiratory disorders, organ transplantation, and cancer therapy. However, the immunosuppressive effects of steroids pose risks such as increased susceptibility to infections, reactivation of latent infections, osteoporosis, and metabolic disturbances. Balancing therapeutic efficacy and immunosuppressive risks is a major clinical challenge. Strategies such as tailored dosing regimens, steroid-sparing agents, prophylactic measures, and the development of selective glucocorticoid receptor modulators (SEGRMs) are discussed as potential solutions for optimizing patient outcomes while minimizing adverse effects. This review highlights the need for ongoing research to refine steroid therapy, ensuring a careful balance between therapeutic benefits and immunosuppression risks in clinical practice.

Keywords: Steroid-induced immunomodulation, glucocorticoids, autoimmune diseases, immunosuppression, infections.
Mapping Malaria: Trends in Malaria Prevalence and Incidence Rates: A Comparative Study of West and East Africa from 2000 to 2024tilizing Geographic Information Systems (GIS) for Spatial Analysis of Transmission Hotspots in West and East Africa
Authors:   faulty of Medicine Kampala International University Uganda, Bina K Nalongo
Published: December 2024

Malaria remains a major public health challenge in sub-Saharan Africa, with West and East Africa carrying a significant burden. This comparative study evaluates trends in malaria prevalence and incidence rates from 2000 to 2024, analyzing regional differences shaped by factors such as climate, socioeconomic conditions, healthcare access, and public health interventions. The study identifies progress in both regions due to the widespread adoption of insecticide-treated nets (ITNs), indoor residual spraying (IRS), and artemisinin-based combination therapies (ACTs). However, West Africa faces higher malaria rates, largely influenced by limited healthcare access, insecticide resistance, and socioeconomic disparities. East Africa, particularly in urban areas, has seen more significant reductions in malaria prevalence. Despite advances, challenges like insecticide and antimalarial drug resistance, healthcare accessibility in rural areas, and the need for innovative interventions persist. The study underscores the importance of integrated resistance management, research on new treatments, healthcare system strengthening, and public-private partnerships to sustain progress and move towards malaria elimination in both regions.

Keywords: Malaria trends, prevalence, incidence, West Africa, East Africa, insecticide-treated nets.
Computational Genomics Journal Club, Monday Feb 8
Authors: Turner Stephen
Published: December 2024

We're restarting the PCG Journal Club again Monday February 8 at 4pm in the CHGR conference room. Most of you who usually attend are familiar with the format, but if not, bring any papers you've read recently and give a brief (i.e. 2 minute) overview of the paper and why you thought it was interesting. No slides allowed.
Gene Prospector
Authors: Turner Stephen
Published: December 2024

This abstract in BMC Bioinformatics was presented in our Computational Genetics Journal Club a few weeks back: "Gene Prospector: An evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases."As described by the authors at CDC, Gene Prospector is a bioinformatics tool designed to sort, rank, and display information about genes in relation to human diseases, risk factors and other
PLATO, an Alternative to PLINK
Authors:   Unknown
Published: December 2024

Since the near beginning of genome-wide association studies, the PLINK software package (developed by Shaun Purcell’s group at the Broad Institute and MGH) has been the standard for manipulating the large-scale data produced by these studies.
Microbial Genomics: the State of the Art in 2015
Authors: Turner Stephen
Published: December 2024

Current Opinion in Microbiology

recently published a special issue in genomics. In an excellent editorial overview, “Genomics: The era of genomically-enabled microbiology”, Neil Hall and Jay Hinton give an overview of the state of the field in microbial genomics, summarize recent contributions, and give a great synopsis of each of the reviews in this issue.
What's the Right Analysis for this Data?
Authors:   Unknown
Published: December 2024

If you've ever had trouble getting started doing a data analysis, you are certainly not alone. Should I run an ANOVA, MANOVA, ANCOVA, or MANCOVA? Should that have been a McNemar's test, a Kruskal-Wallis, or a Mann-Whitney U?To at least pin down the statistical test you should run, consult these excellent flowcharts by Marylyn Ritchie, Jason Moore, and Tricia Thornton-Wells.
Scotty, We Need More Power! Power, Sample Size, and Coverage Estimation for RNA-Seq
Authors: Turner Stephen
Published: December 2024

Two of the most common questions at the beginning of an RNA-seq experiments are "how many reads do I need?" and "how many replicates do I need?". This paper describes a web application for designing RNA-seq applications that calculates an appropriate sample size and read depth to satisfy user-defined criteria such as cost, maximum number of reads or replicates attainable, etc.
Ditch Excel for AWK!
Authors:   Unknown
Published: December 2024

How often have you needed to extract a certain column from a file, or strip out only a few individuals from a ped file? This is often done with Excel, but that requires loading the data, manipulating it, then saving it back into a format that is acceptable, which may require converting tabs to spaces or other aggravating things.
Coursera Specializations: Data Science, Systems Biology, Python Programming
Authors: Turner Stephen
Published: December 2024

I first mentioned Coursera about a year ago, when I hired a new analyst in my core. This new hire came in as a very competent Python programmer with a molecular biology and microbial ecology background, but with very little experience in statistics.
Awk Command to Count Total, Unique, and the Most Abundant Read in a FASTQ file
Authors: Turner Stephen
Published: December 2024

I was reading through a paper on comparative ChIP-Seq when I found this awk gem that lets you get some very basic stats very quickly on next generation sequencing reads. To use, simply cat the fastq file (or gunzip -c) and pipe that to this awk command: cat myfile.fq | awk '((NR-2)%4==0){read=$1;total++;count[read]++}END{for(read in count){if(!max||count[read]>max) {max=count[read];maxRead=read};if(count[read]==1){unique++}};print
Seminar announcement: A Multivariate Methodology for Analyzing Genome-wide Association Studies
Authors: Turner Stephen
Published: December 2024

This looks interesting. Department of Biostatistics Seminar/Workshop Series: A Multivariate Methodology for Analyzing Genome-wide Association Studies, by Janice Brodsky, PhD, UCLA.
R package to convert statistical analysis objects to tidy data frames
Authors: Turner Stephen
Published: December 2024

I talked a little bit about tidy data my recent post about dplyr, but you should really go check out Hadley’s paper on the subject. R expects inputs to data analysis procedures to be in a tidy format, but the model output objects that you get back aren’t always tidy. The reshape2, tidyr, and dplyr are meant to take data frames, munge them around, and return a data frame.
A Mitochondrial Manhattan Plot
Authors:   Unknown
Published: December 2024

Manhattan plots have become the standard way to visualize results for genetic association studies, allowing the viewer to instantly see significant results in the rough context of their genomic position.  Manhattan plots are typically shown on a linear X-axis (although the circos package can be used for radial plots), and this is consistent with the linear representation of the genome in online genome browsers.
Covcalc: Shiny App for Calculating Coverage Depth or Read Counts for Sequencing Experiments
Authors: Turner Stephen
Published: December 2024

How many reads do I need? What's my sequencing depth?

These are common questions I get all the time. Calculating how much sequence data you need to hit a target depth of coverage, or the inverse, what's the coverage depth given a set amount of sequencing, are both easy to answer with some basic algebra. Given one or the other, plus the genome size and read length/configuration, you can calculate either.
Learn R and Python, and Have Fun Doing It
Authors: Turner Stephen
Published: December 2024

If you need to catch up on all those years you spent

not

learning how to code (you

need

to know how to code), here are a few resources to help you quickly learn R and Python, and have a little fun doing it. First, the free online Coursera course

Computing for Data Analysis

just started.
PCG Journal Club Articles, 6/24
Authors:   Unknown
Published: December 2024

Here are citations for the articles discussed at our most recent meeting (June 24). Our next meeting is scheduled for July 17.~JuliaChoi Y, Wijsman EM, Weir BS. Case-control association testing in the presence of unknown relationships.

Genet Epidemiol

. 2009 Mar 30. [Epub ahead of print]Gao X, Becker LC, Becker DM, Starmer JD, Province MA. Avoiding the high Bonferroni penalty in genome-wide association studies.

Genet Epidemiol

.
Illumina: $10,000 genome sequence with HiSeq 2000
Authors: Turner Stephen
Published: December 2024

Illumina just unveiled their latest sequencing machine, the HiSeq 2000, capable of sequencing two human genomes to 30x coverage in a single run for less than $10,000 each. Using reversible terminator-based sequencing by synthesis chemistry, the HiSeq 2000 is capable of quickly generating a flood of data: 200 Gb per run, 2 x 100 bp read length, up to 25 Gb per day, two billion paired-end reads/run.
Getting help with R
Authors: Turner Stephen
Published: December 2024

There's no doubt that by now you've noticed that we're big fans of R around here.
Webinar: Genomic Networks - Resolving Biomarkers from a Cloud of Data
Authors: Turner Stephen
Published: December 2024

Kevin White from the University of Chicago will be giving a special guest lecture at NCI next week on systems biology approaches to mine genomics data for biomarkers and therapeutic targets. The lecture will be available online as a videocast.
Noteworthy Blog: The Spittoon
Authors: Turner Stephen
Published: December 2024

For those of you who attend our computational genetics journal club every other week, you've all heard about this. Say what you will about the "consumer genetics" enterprise, 23andMe maintains an excellent blog. In their "SNPwatch" category, The Spittoon surveys and summarizes the latest findings in human genetics research before they hit the press.
NYT: SAS threatened by R
Authors: Turner Stephen
Published: December 2024

The New York Times had an interesting piece yesterday about how SAS is facing several business threats from companies like the recently IBM-acquired SPSS, and from burgeoning interest in open-source software like R.
How To Install BioPerl Without Root Privileges
Authors: Turner Stephen
Published: December 2024

I've seen this question asked and partially answered all around the web. As with anything related to Perl, I'm sure there is more than one way to do it. Here's how I do it with Perl 5.10.1 on CentOS 6.4. First, install local::lib with bootstrapping method as described here.
PDF tutorial from R course (Introduction to R)
Authors: Turner Stephen
Published: December 2024

Writing from the previously mentioned intro to R course at the Kennedy Center. If you couldn't make it you can download all the course materials from Theresa Scott's website, under the "Current Teaching Material" heading. Here is a direct link to the PDF for the overview materials that we're going over today, along with the R code from the examples in this guide.
Genotyping Portal: A comprehensive (and freely available) online resource about methods for DNA genotyping, screening and sequencing
Authors: Turner Stephen
Published: December 2024

Diego Forero has compiled a comprehensive list of primary publications on commonly used SNP genotyping and DNA sequencing technologies (including SNP arrays, Sequenom, TaqMan, Pyrosequencing, Molecular Beacons, FP-TDI, Invader, xMAP, SNaPshot, SNPlex, Sanger, 454, Illumina, Helicos, SOLiD, Complete Genomics, Bisulfite sequencing, and others).
Papers from March 8, 2010 Journal Club
Authors:   Unknown
Published: December 2024

Here are the papers we talked about in yesterday's Journal Club:Genome Biol. 2009; 10(11): R134Searching for SNPs with cloud computing.Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL.Table of Contents, Nature Methods, Visualization Supplement.Am J Hum Genet.
Annotated LD-Plots
Authors:   Unknown
Published: December 2024

Often when presenting statistics from a candidate gene study, or a region of interest from a genome-wide association study, it is useful to see various SNP-wise values in the context of linkage disequilibrium patterns.
GNU datamash
Authors: Turner Stephen
Published: December 2024

GNU datamash is a command-line utility that offers simple calculations (e.g. count, sum, min, max, mean, stdev, string coalescing) as well as a rich set of statistical functions, to quickly assess information in textual input files or from a UNIX pipe.
Formulação de escoamento plástico: aspectos de natureza computacional e aplicação a processos de forjamento
Authors: Alves M. L. , Rodrigues Jorge Manuel da Conceição , Martins Paulo António Firme
Published: December 2024

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Development of Site-Specific Nutrient Management (SSNM) Recommendations for Irrigated Rice in Region VI (Capiz, Aklan, and Antique)
Authors: Gabinete Greta , Peñaranda Hector , Gutierrez Benjamin , Buresh Roland
Published: December 2024

Site-specific nutrient management (SSNM) is a plant-need-based approach for optimized application of nitrogen, phosphorus, and potassium fertilizers. This study developed and evaluated SSNM recommendations for irrigated rice in Aklan, Antique, and Capiz. Field trials using the nutrient omission plot technique provided information to calibrate Nutrient Manager for Rice, a computer-based decision tool. Additional field trials compared SSNM-based fertilizer recommendations of Nutrient Manager with farmer's fertilizer practices. Measured soil properties were not well related to rice yields measured in nutrient omission plots suggesting soil properties are not good predictors of nutrient supply in rice soils. Relationships of yield in nutrient omission plots with yield in full fertilized plots were comparable to relationships from other regions of the Philippines already used in Nutrient Manager. This provides confidence that Nutrient Manager is well adapted for Region 6. Fertilizer management based on Nutrient Manager increased yield by 370 kg per hectare per season. Results suggest an increased income of PhP 4500 per hectare per season is a realistic target with Nutrient Manager. When factors other than nutrients - such as pests, diseases, or poor crop management - limit rice yield, improved nutrient management should be combined with practices to overcome these constraints.
Response of Anthurium to the Different Planting Containers
Authors: Penpillo Rubin , Ballano Monica
Published: December 2024

One hundred twenty ready-to-bloom anthurium of different varieties were planted in clay pots and plastic bags using chopped coconut husk as planting media. The objectives were to compare the agronomic characteristics of anthurium cv. grown in clay pots and plastic bags, and to determine the cost and return of each treatment. The treatments used are the following Factor A Four varieties of Anthurium : Baguio Red(V₁) Manila Red (V₂) Baguio White(V₃), Lady Jean (V₄) and Factor B two kinds of container; Clay pot (C₁) and Plastic bag (C₂). The experiment was laid out in factorial (4 x 2) in a Randomized Complete Block Design (RCBD) replicated 3 times with 5 pots per treatment per replicate. Results showed that the number of suckers harvested for five-year period, Baguio White and Lady Jean both planted in plastic bags gave the highest (102.00) and lowest (42.40) number of suckers, respectively. The most prolific year of sucker production was observed in the third year and decline in the fourth year due to cutting back of the main stem of the plant as they become tall and easily toppled down if left untouched. In flower production, the highest peak was during the third year and the lowest during the first year. On the average over the five-year period, Manila Red in plastic bags (15.16) and Baguio Red in clay pots (13.6) gave the highest and the lowest number of flowers per year, respectively. Lady Jean in clay pots and plastic bags and Manila Red in plastic bags appeared to show stability in flower production in 5 year period. Lady Jean both planted in clay pots and plastic bags gave the highest return of investment of 125.11 and 114.83, respectively.
Yield Improvement of Volvariella volvacea in Composted Banana Peels Under Indoor Conditions
Authors: Lopez Crisanto , Armada Esperanza , Roxas George Fredrick
Published: December 2024

Mushroom, Vovariella volvacea, was grown on green banana peels composted at different length of time. The objectives of the study were to assess the potential of the substrate in terms of mycelial growth and pin-head development. Much more, it was also the objective of the study to provide added value to the waste banana peels by using as substrate in mushroom production and at the same time mitigating the burgeoning issue of environmental problem. The study was done in the laboratory and is composed of two phases, the assessment of mycelial growth and the pinhead development under laboratory conditions. Results showed that 15-day composting showed a significant result compared to other treatments of 0-day and 30-day composting in terms of vegetative growth as well as pin-head development.
Bamban (Donax cannaeformis K. Schum) as an Alternative Source of Livelihood for Upland Communities in Panay Island, Philippines
Authors: Alli Roel , Labramonte Louella , Roncesvalles Leah
Published: December 2024

A survey was conducted on the production, processing, utilization, and marketing of Bamban products in Panay Island, Philippines. One hundred fifty-five respondents in four provinces, namely: Aklan, Antique, Capiz, and Iloilo categorized into four groups, namely, (a) those who harvested Bamban culms, processed into splits and sold in the market, (b) those who wove Bamban and bought by customers, (c) those who wove and sold products to the households in different parts of the province, and (d) those who were involved in buy-and-sell of Bamban products.
Respondents were mostly males and married. About 50% had no formal education, with only 6% having high school. Main occupation was farming and about 44.5% were involved in paid labor. The mean age was 39.53 years old, with an average household size of 6 members and an estimated annual income of PhP26,236.77. Estimated annual income earned from Bamban production was PhP12,605.68.
IMPLEMENTATION OF CANVA-BASED INTERACTIVE GAMES IN INCREASING STUDENTS' INTEREST IN LEARNING ARABIC AT MTSN 1 MEDAN-NORTH SUMATERA
Authors: Rawi Nasution Fadlan , Khalisa Nayla , Dwi Maulana Arjuna , Nasution Sakholid
Published: December 2024

The low interest in learning Arabic is one of the problems in learning Arabic. Interest in learning Arabic has a very important role in supporting the abilities of the four maharah in Arabic. The purpose of this study is to provide a solution to the low interest in learning Arabic of class VII-D MTsn 1 Medan students through the implementation of interactive games based on canva. The research method used in this study is a qualitative method with a descriptive qualitative approach, while data collection techniques use interviews, observations and documentation. The results of the study indicate that the implementation of interactive games based on canva has a very important role in increasing the interest in learning Arabic of class VII-D MTsn 1 Medan students, through the implementation of interactive games based on canva students become more active and enthusiastic in learning Arabic this is shown through the results of observations and interviews with students and Arabic teachers.
AN OVERVIEW OF PHONETICS, PHONEMICS, AND GRAPHEMES
Authors: Naqsyah Ibnu Dwi , Husna Fadhilatul
Published: December 2024

Phonetics explores how humans produce speech sounds, focusing on their physical creation and articulation. Phonemics, a subset of phonology, examines how sounds function within a language, particularly their role in distinguishing meaning. Graphemes, on the other hand, are the smallest meaningful units of written language that can differentiate words. This research aims to delve into the interaction between spoken sounds and written symbols and their contribution to linguistic communication. The study employs a descriptive qualitative approach, analyzing data from books, journals, and other relevant literature on phonetics, phonemics, and graphemics. Data collection involves library research and content analysis, which are interpreted to understand the production of language sounds, their role in conveying meaning, and their representation in writing. Findings indicate that phonetics focuses on sound production, phonemics deals with sound units such as phonemes and their variations (allophones), and graphemics examines a language's writing system, including its basic units (graphemes). In conclusion, phonetics, phonemics, and graphemics are interconnected branches of linguistics that collectively address the role of sounds and symbols in communication.