How to build the virtual cell with artificial intelligence: Priorities and opportunities.

Cells are essential to understanding health and disease, yet traditional models fall short of modeling and simulating their function and behavior. Advances in AI and omics offer groundbreaking opportunities to create an AI virtual cell (AIVC), a multi-scale, multi-modal large-neural-network-based model that can represent and simulate the behavior of molecules, cells, and tissues across diverse states. This Perspective provides a vision on their design and how collaborative efforts to build AIVCs will transform biological research by allowing high-fidelity simulations, accelerating discoveries, and guiding experimental studies, offering new opportunities for understanding cellular functions and fostering interdisciplinary collaborations in open science.

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities.

The cell is arguably the most fundamental unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent advances in artificial intelligence (AI), combined with the ability to generate large-scale experimental data, present novel opportunities to model cells.

Biomimetic Optical-Filter Sensor System for Discrimination of Infrared Chemical Signatures Against a Cold Sky Background.

Passive infrared (IR) systems enable rapid detection of chemical vapors but are limited by size, weight, cost, and power. Previously, the authors reported a novel passive sensor that utilizes multiple IR filter/detector combinations to discriminate between different chemical vapors based on their unique IR absorption spectra in the same manner the human eye uses to generate colors. This approach enables a very small, compact, and low-power sensor system with the capability to discriminate between chemical vapors of interest and background chemicals.

Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline.

Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the CZ ID AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data.

Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline.

Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data.

Evaluation of Transmission Near the Christiansen Wavelength for Dynamic Sand Samples.

Many optical applications, including free-space optical communications, lidar, and astronomical measurements, are impacted by the presence of light-scattering particles also known as obscurants. Scattering from particles consisting of sand, dust, dirt, and other substances can significantly degrade optical signals. For many obscurants, the index of refraction is dependent on the wavelength of light, and there exists a Christiansen wavelength (λ) at which scattering is at a minimum.

Measurement of the Optical Constants of Sand Samples Using Ellipsometry on Sand-Adhesive Composites.

In order to model the propagation of light through a sand cloud, it is critical to have accurate data for the optical constants of the sand particles that comprise it. The same holds true for modeling propagation through particles of any type suspended in a medium. Few methods exist, however, to measure these quantities with high accuracy.

Intraoperative Inversion of the Left Atrial Appendage Following Ligation.

• Intraoperative TEE improves the diagnosis of LAA inversion. • Excess negative pressure causes inversion at predictable points in cardiac surgery. • Structural characteristics of the LAA may influence inversion susceptibility.

The Relationship Between an Individual's Birthday and Admission for Traumatic Injury.

Background: Birthdays provide an opportunity to celebrate; however, they can also be associated with various adverse medical events. This is the first study to examine the association between birthdays and in-hospital trauma team evaluation.

Methods: This retrospective study analyzed trauma registry patients 19-89 years of age, who were evaluated by in-hospital trauma services from 1/1/2011 to 12/31/2021.

The Impact of Relocating a Trauma Center: Retrospective Observations on Payer Demographics and Cost-Analysis.

Background: Standardization of trauma centers improves quality of care, yet that comes with financial challenges. The decision to designate a trauma center typically focuses on access, quality of care, and the needs of the local community, but less often considers the financial viability of the trauma center. A level-1 trauma center was relocated in 2017 and this presented an opportunity to compare financial data at two separate locations in the same city.

The Impact of Relocating a Trauma Center: Observations on Patient Injury Demographics and Resident Volumes.

Introduction Changing the physical zip code location of an academic trauma center may affect the distribution and surgical volume of its trauma patients. General surgical residency case log requirements may also be affected. This study describes the impact of moving a level I trauma center to a different zip code location, on the hospital and resident trauma case volumes.

Takotsubo Cardiomyopathy and Trauma: The Role of Injuries as Physical Stressors.

Introduction: Physical stressors are common predisposing factors for takotsubo cardiomyopathy (TTC). However, the role of traumatic injuries in TTC has not been well defined. This study describes the characteristics of TTC in the broad spectrum of traumatic injuries using the information available in the National Trauma Data Bank (NTDB).

In-hospital outcomes of intercostal nerve cryoablation and surgical stabilization of rib fractures.

Background: Severe pain and pulmonary complications commonly follow rib fractures, both of which may be improved by surgical stabilization of rib fractures (SSRFs). However, significant postoperative pain still persists which may negatively impact in-hospital outcomes. Combining intercostal nerve cryoablation (INCA) with SSRF may improve those outcomes by further decreasing postoperative pain, opioid consumption, and pulmonary complications.

Spectral Considerations for Standoff Infrared Detection of RDX on Reflective Aluminum.

This paper examines infrared spectroscopic effects for the standoff detection of an explosive material, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), inkjet printed on an aluminum surface. Results of a spectroscopic study are described, using multiple optical setups. These setups were selected to explore how variations in the angles of incidence and collection from the surface of the material result in corresponding variations in the spectral signatures.

Peri-operative antibiotics acutely and significantly impact intestinal microbiota following bariatric surgery.

Bariatric surgery is the most effective treatment for weight loss. Vertical sleeve gastrectomy (VSG) involves the resection of ~ 80% of the stomach and was conceived to purely restrict oral intake. However, evidence suggests more complex mechanisms, particularly postoperative changes in gut microbiota, in facilitating weight loss and resolving associated comorbidities.

Adherence to Multiple Treatment Recommendations in Adolescents and Young Adults with Cancer: A Mixed Methods, Multi-Informant Investigation.

This mixed methods study sought to assess adolescent and young adult (AYA) adherence to three cancer treatment recommendations (medications, diet, physical activity), and determine the individual, family, and health system factors associated with suboptimal adherence. In Stage 1, 72 AYA-caregiver dyads completed a validated adherence interview and surveys about individual and family functioning. Matched providers ( = 34 who reported on 61 AYAs) completed global adherence ratings through survey.

Behavior of the Reststrahlen Band in the 17-25 m Spectral Region in the Diffuse Reflection Spectra of Sand and Silt Mixtures.

Studies on the reflectance spectra of different mixtures of sand and silt were performed in the infrared spectral region of 7-25 µm to explore the behavior of a second reststrahlen band occurring between 17 and 25 µm with respect to different mixtures of sand and silt. The reflectance spectrum of all samples exhibited reststrahlen bands within both the long wavelength infrared (LWIR) and the very long wavelength infrared (VLWIR) regions of the reflectance spectrum. Results demonstrate that both LWIR and VLWIR reststrahlen bands increase in area as the fraction of sand increases to 80%.

Demonstration of a Human Color Vision Mimic in the Infrared.

Color vision results from the interaction of retinal photopigments with reflected or transmitted visible light. The International Commission on Illumination (CIE) developed the CIE color-matching chart, which separates colors on the basis of the interaction of their spectral profiles with three retinal photopigments in the human eye. We report the development of an infrared chromaticity (CIE-IR) chart, which mimics the CIE chart, in order to discriminate between different chemicals on the basis of the interactions of their IR signatures with three different IR optical filters, instead of the retinal photopigments in the human eye.

Correction to: Partitioning of adipose lipid metabolism by altered expression and function of PPAR isoforms after bariatric surgery.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Discrimination Between Explosive Materials and Isomers Using a Human Color Vision-Inspired Sensing Method.

This paper describes the application of a human color vision approach to infrared (IR) chemical sensing for the discrimination between multiple explosive materials deposited on aluminum substrates. This methodology classifies chemicals using the unique response of the chemical vibrational absorption bands to three broadband overlapping IR optical filters. For this effort, Fourier transform infrared (FT-IR) spectroscopy is first used to computationally examine the ability of the human color vision sensing approach to discriminate between three similar explosive materials, 1,3,5,-Trinitro-1,3,5-triazinane (RDX), 2,2-Bis[(nitrooxy)methyl]propane-1,3,-diyldinitrate (PETN), and 1,3,5,7-Tetranitro-1,3,5,7-tetrazocane (HMX).

Predictors of discharge destination in patients with major traumatic injury: Analysis of Oklahoma Trauma Registry.

Background: The ability to predict the need for discharge of trauma patients to a facility may help shorten hospital stay. This study aimed to determine the predictors of discharge to a facility and develop and validate a predictive scoring model, utilizing the Oklahoma Trauma Registry (OTR).

Methods: A multivariate analysis of the OTR 2005-2013 determined independent predictors of discharge to a facility.

Analytical procedure to assess the performance characteristics of a non-spectroscopic infrared optical sensor for discrimination of chemical vapors.

An optical-filter-based sensor that was designed to mimic human color vision was recently developed. This sensor uses three mid-infrared optical filters to discriminate between chemicals with similar, strongly overlapping mid-infrared absorption bands. This non-spectroscopic technique requires no spectral scanning.

Infrared Reflectance Spectroscopic Evaluation of Inkjet Printed Standards of Cyclotrimethylenetrinitramine (RDX) on Aluminum Substrates.

The Department of Defense (DOD) and first responder communities are evaluating and developing optical systems for the detection and identification of explosives and components used for assembling homemade explosives (HMEs). Emerging detection technologies must be evaluated with authentic hazard material concentrations to ensure their accurate and reliable use in the field. In this work, infrared (IR) reflectance spectra over the spectral rage of 1000-1700 cm were collected for different concentrations of inkjet-printed RDX (cyclotrimethylenetrinitramine) samples deposited onto aluminum substrates.

Humidity as a non-pharmaceutical intervention for influenza A.

Influenza is a global problem infecting 5-10% of adults and 20-30% of children annually. Non-pharmaceutical interventions (NPIs) are attractive approaches to complement vaccination in the prevention and reduction of influenza. Strong cyclical reduction of absolute humidity has been associated with influenza outbreaks in temperate climates.