Spectral classification of short numerical exon and intron sequences

This research presents three new numerical representations for classifying short exon and intron sequences using discrete Fourier transform period-3 value. Based on the human genome, results indicate that the Complex Twin-Pair representation is attractive compared with other numerical representations and the approach has potential applications in genome annotation and read mapping

Decoding a Complex Visualization in a Science Museum -- An Empirical Study

This study describes a detailed analysis of museum visitors' decoding process as they used a visualization designed to support exploration of a large, complex dataset. Quantitative and qualitative analyses revealed that it took, on average, 43 seconds for visitors to decode enough of the visualization to see patterns and relationships in the underlying data represented, and 54 seconds to arrive at their first correct data interpretation. Furthermore, visitors decoded throughout and not only upon initial use of the visualization. The study analyzed think-aloud data to identify issues visitors had mapping the visual representations to their intended referents, examine why they occurred, and consider if and how these decoding issues were resolved. The paper also describes how multiple visual encodings both helped and hindered decoding and concludes with implications on the design and adaptation of visualizations for informal science learning venues.Comment: IEEE VIS (InfoVis/VAST/SciVis) 2019 ACM 2012 CCS - Human-centered computing, Visualization, Empirical studies in visualizatio

Sea of Genes: Combining Animation and Narrative Strategies to Visualize Metagenomic Data for Museums

We examine the application of narrative strategies to present a complex and unfamiliar metagenomics dataset to the public in a science museum. Our dataset contains information about microbial gene expressions that scientists use to infer the behavior of microbes. This exhibit had three goals: to inform (the) public about microbes' behavior, cycles, and patterns; to link their behavior to the concept of gene expression; and to highlight scientists' use of gene expression data to understand the role of microbes. To address these three goals, we created a visualization with three narrative layers, each layer corresponding to a goal. This study presented us with an opportunity to assess existing frameworks for narrative visualization in a naturalistic setting. We present three successive rounds of design and evaluation of our attempts to engage visitors with complex data through narrative visualization. We highlight our design choices and their underlying rationale based on extant theories. We conclude that a central animation based on a curated dataset could successfully achieve our first goal, i.e., to communicate the aggregate behavior and interactions of microbes. We failed to achieve our second goal and had limited success with the third goal. Overall, this study highlights the challenges of telling multi-layered stories and the need for new frameworks for communicating layered stories in public settings.Comment: This manuscript has been accepted to VIS 2020 and TVCG 9 pages 2 reference

Kebijakan Pajak Karbon Sebagai Strategi Pembangunan Ekonomi Berkelanjutan

The decline in the earth's climate was the cause for the birth of the 2015 Paris Agreement which was ratified by Indonesia through Law Number 16 of 2016 concerning the Paris Agreement on the United Nations Framework Convention on Climate Change as a form of commitment from the government to address climate problems in Indonesia. One of the strategic efforts made by the government is to implement a carbon tax policy to reduce the increase in carbon emissions which was accommodated in Article 13 of Law Number 7 of 2021 concerning Harmonization of Tax Regulations. The implementation of a carbon tax policy is an implementation of Pancasila economic principles which focus on creating sustainable economic development by harmonizing the balance between economic growth and improving environmental quality. The implementation of the carbon tax policy is also a manifestation of the fifth precept of Pancasila which aims to fulfill the constitutional rights of the people as stipulated in Article 28H paragraph (1) of the 1945 Constitution of the Republic of Indonesia by creating corrective justice in the economic and environmental fields. The purpose of this paper is to analyze the application of carbon tax policies in order to achieve the goals of sustainable economic development in Indonesia. The writing method used is juridical-normative using statutory and conceptual approaches. The data used is secondary data through literature study on primary, secondary, and tertiary legal materials. The results of this paper show that the implementation of carbon tax policies is in line with Pancasila economic principles and is a strategic effort in creating a green investment climate, as well as increasing state revenue from the tax sector. However, strengthening is needed in terms of substance, structure, and legal culture in implementing the policy

Short-Term Serial Sampling of Natriuretic Peptides in Patients Presenting With Chest Pain

ObjectivesThe purpose of this study was to characterize the diagnostic and prognostic utility of short-term dynamic changes in natriuretic peptides in patients presenting with chest pain.BackgroundAlthough single levels of natriuretic peptides in patients admitted for acute coronary syndromes (ACS) have important prognostic value, it is unclear whether serial sampling of natriuretic peptides might have both diagnostic and prognostic value in the setting of chest pain.MethodsWe followed 276 patients for 90 days who presented to the emergency department with chest pain. We sampled brain natriuretic peptide (BNP) and amino-terminal (NT)-proBNP up to 5 times within 24 h of presentation and again at discharge. Follow-up data was collected at 30 and 90 days after admission. Adverse events included emergency department visits for chest pain, cardiac readmission, and death. We assessed the prognostic and diagnostic value of baseline natriuretic peptide measurements with receiver-operating characteristic analyses.ResultsNatriuretic peptides were diagnostic for congestive heart failure (CHF) and new-onset CHF but less so for ACS. The prognostic utility of serial sampling was evaluated through testing the statistical contribution of each future time point (as well as variability over time) over and above the baseline values in logistic regression models.ConclusionsBaseline elevated BNP and NT-proBNP concentrations were predictive of adverse events at 30 and 90 days. Serial sampling did not improve the prognostic value of BNP or NT-proBNP

Mapping genomic and transcriptomic alterations spatially in epithelial cells adjacent to human breast carcinoma.

Almost all genomic studies of breast cancer have focused on well-established tumours because it is technically challenging to study the earliest mutational events occurring in human breast epithelial cells. To address this we created a unique dataset of epithelial samples ductoscopically obtained from ducts leading to breast carcinomas and matched samples from ducts on the opposite side of the nipple. Here, we demonstrate that perturbations in mRNA abundance, with increasing proximity to tumour, cannot be explained by copy number aberrations. Rather, we find a possibility of field cancerization surrounding the primary tumour by constructing a classifier that evaluates where epithelial samples were obtained relative to a tumour (cross-validated micro-averaged AUC = 0.74). We implement a spectral co-clustering algorithm to define biclusters. Relating to over-represented bicluster pathways, we further validate two genes with tissue microarrays and in vitro experiments. We highlight evidence suggesting that bicluster perturbation occurs early in tumour development

The Importance of Acquisition Learning on Nicotine and Varenicline Drug Substitution in a Drug-Discriminated Goal-Tracking Task

Nicotine and varenicline (Chantix®; the leading non-nicotine cessation pharmacotherapy) can come to control appetitive behaviors such as goal-tracking. We tested rats (N = 48) in a drug-discriminated goal-tracking (DGT) task where each rat received daily subcutaneous injections of either nicotine (0.4 mg/kg) or saline (0.9% [w/v]) interspersed across the acquisition phase (Phase 1). On saline days, sucrose was intermittently available. On nicotine days, sucrose was withheld. All rats acquired the discrimination with increased goal-tracking rates on saline days relative to nicotine days. Following acquisition, rats were separated into four groups to assess drug-substitution and discrimination reversal in Phase 2. The first group maintained the stimulus-reinforcer relation from acquisition (NIC−). The reversal group was now given access to sucrose on nicotine days (NIC+). The substitution group replaced nicotine with varenicline (1 mg/kg) while maintaining the acquisition stimulus-reinforcer relation (VAR−). The substitution and reversal group had nicotine replaced by varenicline and the stimulus-reinforcer relation reversed (VAR+). Rats in all groups learned or maintained their Phase 1 discriminations. For Phase 2, the reversal groups (+ conditions) acquired their discriminations within 10 sessions. The VAR−group displayed a pattern of disrupted discrimination at the outset of Phase 2 but was reestablished after continued training. In substitution testing, VAR groups received nicotine and NIC groups received varenicline. The NIC−and VAR−groups displayed full substitution of the test stimulus whereas the NIC+ and VAR+ groups displayed partial substitution of the test stimulus. Rats underwent nicotine extinction in Phase 3. Initial responding for each group mimicked Phase 2 training (i.e., higher responding by the reversal groups). All rats maintained similarly low levels of responding after six sessions. In conclusion, initial learning history with nicotine (i.e., + or −) influenced drug-stimulus substitution and the rate at which new learning (e.g., reversal) occurs with the varenicline and nicotine interoceptive stimuli

Maternal Choline Supplementation during Normal Murine Pregnancy Alters the Placental Epigenome: Results of an Exploratory Study

The placental epigenome regulates processes that affect placental and fetal development, and could be mediating some of the reported effects of maternal choline supplementation (MCS) on placental vascular development and nutrient delivery. As an extension of work previously conducted in pregnant mice, the current study sought to explore the effects of MCS on various epigenetic markers in the placenta. RNA and DNA were extracted from placentas collected on embryonic day 15.5 from pregnant mice fed a 1X or 4X choline diet, and were subjected to genome-wide sequencing procedures or mass-spectrometry-based assays to examine placental imprinted gene expression, DNA methylation patterns, and microRNA (miRNA) abundance. MCS yielded a higher (fold change = 1.63-2.25) expression of four imprinted genes (Ampd3, Tfpi2, Gatm and Aqp1) in the female placentas and a lower (fold change = 0.46–0.62) expression of three imprinted genes (Dcn, Qpct and Tnfrsf23) in the male placentas (false discovery rate (FDR) \u3c 0.05 for both sexes). Methylation in the promoter regions of these genes and global placental DNA methylation were also affected (p \u3c 0.05). Additionally, a lower (fold change = 0.3; Punadjusted = 2.05 x 10; FDR = 0.13) abundance of miR-2137 and a higher (fold change = 1.25–3.92; p \u3c 0.05) expression of its target genes were detected in the 4X choline placentas. These data demonstrate that the placental epigenome is responsive to maternal choline intake during murine pregnancy and likely mediates some of the previously described choline-induced effects on placental and fetal outcomes