nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Nonlinear Iterative Partial Least Squares.

Summary: With the increased reliance on multi-omics data for bulk and single cell analyses, the availability of robust approaches to perform unsupervised learning for clustering, visualization, and feature selection is imperative. We introduce nipalsMCIA, an implementation of multiple co-inertia analysis (MCIA) for joint dimensionality reduction that solves the objective function using an extension to Non-linear Iterative Partial Least Squares (NIPALS). We applied nipalsMCIA to both bulk and single cell datasets and observed significant speed-up over other implementations for data with a large sample size and/or feature dimension.

CHUWD-H v1.0: a comprehensive historical hourly weather database for U.S. urban energy system modeling.

Reliable and continuous meteorological data are crucial for modeling the responses of energy systems and their components to weather and climate conditions, particularly in densely populated urban areas. However, existing long-term datasets often suffer from spatial and temporal gaps and inconsistencies, posing great challenges for detailed urban energy system modeling and cross-city comparison under realistic weather conditions. Here we introduce the Historical Comprehensive Hourly Urban Weather Database (CHUWD-H) v1.

Putting computational models of immunity to the test - an invited challenge to predict vaccination outcomes.

Systems vaccinology studies have been used to build computational models that predict individual vaccine responses and identify the factors contributing to differences in outcome. Comparing such models is challenging due to variability in study designs. To address this, we established a community resource to compare models predicting booster responses and generate experimental data for the explicit purpose of model evaluation.

Square-planar imido complexes of cobalt: synthesis, reactivity and computational study.

Treatment of [Co(N)(PNP)] (PNP = anion of 2,5-bis(di--butylphosphinomethyl)pyrrole) with one equivalent of an aryl azide generates the four-coordinate imido complexes [Co(NAr)(PNP)] (Ar = mesityl, phenyl, or 4-Bu-phenyl). X-ray crystallographic analysis of the compounds shows an unusual square-planar geometry about cobalt with nearly linear imido units. In the presence of the hydrogen atom donor, TEMPOH, [Co(NPh)(PNP)] undergoes addition of the H atom to the imido nitrogen to generate the corresponding amido complex, [Co(NHPh)(PNP)], whose structure and composition were verified by independent synthesis.

nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Non-linear Iterative Partial Least Squares.

Motivation: With the increased reliance on multi-omics data for bulk and single cell analyses, the availability of robust approaches to perform unsupervised analysis for clustering, visualization, and feature selection is imperative. Joint dimensionality reduction methods can be applied to multi-omics datasets to derive a global sample embedding analogous to single-omic techniques such as Principal Components Analysis (PCA). Multiple co-inertia analysis (MCIA) is a method for joint dimensionality reduction that maximizes the covariance between block- and global-level embeddings.

Loop Catalog: a comprehensive HiChIP database of human and mouse samples.

HiChIP enables cost-effective and high-resolution profiling of regulatory and structural loops. To leverage the increasing number of publicly available HiChIP datasets from diverse cell lines and primary cells, we developed the Loop Catalog (https://loopcatalog.lji.

A multi-omics systems vaccinology resource to develop and test computational models of immunity.

Systems vaccinology studies have identified factors affecting individual vaccine responses, but comparing these findings is challenging due to varying study designs. To address this lack of reproducibility, we established a community resource for comparing Bordetella pertussis booster responses and to host annual contests for predicting patients' vaccination outcomes. We report here on our experiences with the "dry-run" prediction contest.

Impacts of climate change, population growth, and power sector decarbonization on urban building energy use.

Climate, technologies, and socio-economic changes will influence future building energy use in cities. However, current low-resolution regional and state-level analyses are insufficient to reliably assist city-level decision-making. Here we estimate mid-century hourly building energy consumption in 277 U.

A systems vaccinology resource to develop and test computational models of immunity.

Computational models that predict an individual's response to a vaccine offer the potential for mechanistic insights and personalized vaccination strategies. These models are increasingly derived from systems vaccinology studies that generate immune profiles from human cohorts pre- and post-vaccination. Most of these studies involve relatively small cohorts and profile the response to a single vaccine.

Daily SARS-CoV-2 Nasal Antigen Tests Miss Infected and Presumably Infectious People Due to Viral Load Differences among Specimen Types.

In a recent household transmission study of SARS-CoV-2, we found extreme differences in SARS-CoV-2 viral loads among paired saliva, anterior nares swab (ANS), and oropharyngeal swab specimens collected from the same time point. We hypothesized these differences may hinder low-analytical-sensitivity assays (including antigen rapid diagnostic tests [Ag-RDTs]) by using a single specimen type (e.g.

Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft.

Changes in the three-dimensional (3D) structure of the genome are an emerging hallmark of cancer. Cancer-associated copy number variants and single nucleotide polymorphisms promote rewiring of chromatin loops, disruption of topologically associating domains (TADs), active/inactive chromatin state switching, leading to oncogene expression and silencing of tumor suppressors. However, little is known about 3D changes during cancer progression to a chemotherapy-resistant state.

Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods.

SARS-CoV-2 viral-load measurements from a single-specimen type are used to establish diagnostic strategies, interpret clinical-trial results for vaccines and therapeutics, model viral transmission, and understand virus-host interactions. However, measurements from a single-specimen type are implicitly assumed to be representative of other specimen types. We quantified viral-load timecourses from individuals who began daily self-sampling of saliva, anterior-nares (nasal), and oropharyngeal (throat) swabs before or at the incidence of infection with the Omicron variant.

A global comparison of building decarbonization scenarios by 2050 towards 1.5-2 °C targets.

Buildings play a key role in the transition to a low-carbon-energy system and in achieving Paris Agreement climate targets. Analyzing potential scenarios for building decarbonization in different socioeconomic contexts is a crucial step to develop national and transnational roadmaps to achieve global emission reduction targets. This study integrates building stock energy models for 32 countries across four continents to create carbon emission mitigation reference scenarios and decarbonization scenarios by 2050, covering 60% of today's global building emissions.

A comparison of attitudes toward remote learning during the COVID-19 pandemic between students attending a Chinese and an Australian campus.

The COVID-19 pandemic has been a strong driver for moving more teaching and learning activities online. Border restrictions have had a severe impact on international students either hoping to enroll in courses offered in Australia or continue with such courses if they are already enrolled. The online learning experience is likely different between students onshore and offshore.

Evaluation of the Inclusion of the Green Seaweed as an Ingredient in Feeds for Gilthead Sea Bream () and European Sea Bass ().

This study evaluated the use of as an ingredient in feeds for aquaculture in three different experiments. Experiment 1 was oriented to confirm the negative effect of on fish digestion. Experiment 2 assessed the effect on growth, feed efficiency, and immune status of juvenile sea bass () fed on diets including , previously treated or not with carbohydrases used to partially hydrolyze indigestible polysaccharides.

Establishment of a multidisciplinary fetal center streamlines approach for congenital lung malformations.

Purpose: Fetuses with a diagnosis of congenital lung malformations (CLM) on prenatal imaging are commonly referred to a multi-disciplinary specialty team for prenatal assessment and postnatal management. The net effect of such services is broadly stated to improve the outcomes of affected newborns. However, these claims are relatively unsubstantiated.

Impact of Additional Anomalies on Postnatal Outcomes in Congenital Lung Malformations.

Background: Approximately 20% of fetuses diagnosed with congenital lung malformations (CLMs) are found to have additional anomalies. We aim to determine if additional anomalies have an impact on postnatal outcomes for patients with CLMs.

Methods: After institutional review board approval, we performed a retrospective review of live-born patients with CLMs from 2008 to 2018.

Twelve Tips for COVID-19 friendly learning design in medical education.

This article was migrated. The article was marked as recommended. The COVID-19 pandemic has caused educational institutions around the world to close their doors and move their teaching and learning into the online space.

Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease.

The MHC region is highly associated with autoimmune and infectious diseases. Here we conduct an in-depth interrogation of associations between genetic variation, gene expression and disease. We create a comprehensive map of regulatory variation in the MHC region using WGS from 419 individuals to call eight-digit HLA types and RNA-seq data from matched iPSCs.

Coronary Artery Dilation in Children with Febrile Exanthematous Illness without Criteria for Kawasaki Disease.

Background: Coronary dilatation is the most important complication of Kawasaki disease (KD) and, in addition to some clinical characteristics, is common to KD and febrile exanthematous illnesses (FEIs).

Objective: To assess whether children with FEI, who do not meet the criteria for KD, have changes in coronary arteries dimensions.

Methods: Echocardiography was performed within the first two weeks of the disease in patients < 10 years with fever and exanthema without other KD criteria.

Non-Invasive Method to Estimate Red Blood Cell in Blood.

This work proposes a non-invasive method to estimate the number of red blood cells in the blood. To achieve the development of this research, first, a photosensitive device was designed, which is formed by a phototransistor with a transparent casing allowing the red light coming from a red LED to penetrate the sensor. This means, that when the intensity of the light varies, the amount of current flowing through the sensor also changes.

A key to the North American genera of Stipeae (Poaceae, Pooideae) with descriptions and taxonomic names for species of , , , and five new genera: , ×, , , and .

Based on earlier molecular DNA studies we recognize 14 native Stipeae genera and one intergeneric hybrid in North America. We provide descriptions, new combinations, and 10 illustrations for species of , , , , , , , and × The following 40 new combinations are made: , , , , , , , , , , , , E.lemmoniissp.

Evidence for Transient Receptor Potential (TRP) Channel Contribution to Arthritis Pain and Pathogenesis.

Based on clinical and preclinical evidence, Transient Receptor Potential (TRP) channels have emerged as potential drug targets for the treatment of osteoarthritis, rheumatoid arthritis, and gout. This review summarizes the relevant data supporting a role for various TRP channels in arthritis pain and pathogenesis, as well as the current state of pharmacological efforts to ameliorate arthritis symptoms in patient populations.