Spin Coupling Effect on Geometry-Dependent X-Ray Absorption of Diradicals.

We theoretically investigate the influence of diradical electron spin coupling on the time-resolved X-ray absorption spectra of the photochemical ring opening of furanone. We predict geometry-dependent carbon K-edge signals involving transitions from core orbitals to both singly and unoccupied molecular orbitals. The most obvious features of the ring opening come from the carbon atom directly involved in the bond breaking through its transition to both the newly formed singly occupied and the available lowest unoccupied molecular orbitals (SOMO and LUMO, respectively).

FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases.

The majority of disease-associated variants identified through genome-wide association studies are located outside of protein-coding regions. Prioritizing candidate regulatory variants and gene targets to identify potential biological mechanisms for further functional experiments can be challenging. To address this challenge, we developed FORGEdb ( https://forgedb.

Femtosecond symmetry breaking and coherent relaxation of methane cations via x-ray spectroscopy.

Understanding the relaxation pathways of photoexcited molecules is essential to gain atomistic-level insight into photochemistry. We performed a time-resolved study of ultrafast molecular symmetry breaking through geometric relaxation (Jahn-Teller distortion) on the methane cation. Attosecond transient absorption spectroscopy with soft x-rays at the carbon K-edge revealed that the distortion occurred within 10 ± 2 femtoseconds after few-femtosecond strong-field ionization of methane.

Ultrafast X-ray Spectroscopy of Intersystem Crossing in Hexafluoroacetylacetone: Chromophore Photophysics and Spectral Changes in the Face of Electron-Withdrawing Groups.

Intersystem crossings between singlet and triplet states represent a crucial relaxation pathway in photochemical processes. Herein, we probe the intersystem crossing in hexafluoro-acetylacetone with ultrafast X-ray transient absorption spectroscopy at the carbon K-edge. We observe the excited state dynamics following excitation with 266 nm UV light to the ππ* (S) state with element and site-specificity using a broadband soft X-ray pulse produced by high harmonic generation.

Correction: Jahn-Teller distortion and dissociation of CCl by transient X-ray spectroscopy simultaneously at the carbon K- and chlorine L-edge.

[This corrects the article DOI: 10.1039/D2SC02402K.].

Jahn-Teller distortion and dissociation of CCl by transient X-ray spectroscopy simultaneously at the carbon K- and chlorine L-edge.

X-ray Transient Absorption Spectroscopy (XTAS) and theoretical calculations are used to study CCl prepared by 800 nm strong-field ionization. XTAS simultaneously probes atoms at the carbon K-edge (280-300 eV) and chlorine L-edge (195-220 eV). Comparison of experiment to X-ray spectra computed by orbital-optimized density functional theory (OO-DFT) indicates that after ionization, CCl undergoes symmetry breaking driven by Jahn-Teller distortion away from the initial tetrahedral structure (T) in 6 ± 2 fs.

Associations Between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants and Risk of Coronavirus Disease 2019 (COVID-19) Hospitalization Among Confirmed Cases in Washington State: A Retrospective Cohort Study.

Background: The coronavirus disease 2019 (COVID-19) pandemic is dominated by variant viruses; the resulting impact on disease severity remains unclear. Using a retrospective cohort study, we assessed the hospitalization risk following infection with 7 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants.

Methods: Our study includes individuals with positive SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) in the Washington Disease Reporting System with available viral genome data, from 1 December 2020 to 14 January 2022.

Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations.

Background: Genome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) are known to preferentially co-locate to active regulatory elements in tissues and cell types relevant to disease aetiology. Further characterisation of associated cell type-specific regulation can broaden our understanding of how GWAS signals may contribute to disease risk.

Results: To gain insight into potential functional mechanisms underlying GWAS associations, we developed FORGE2 ( https://forge2.

Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study.

Background: The COVID-19 pandemic is dominated by variant viruses; the resulting impact on disease severity remains unclear. Using a retrospective cohort study, we assessed the hospitalization risk following infection with seven SARS-CoV-2 variants.

Methods: Our study includes individuals with positive SARS-CoV-2 RT-PCR in the Washington Disease Reporting System with available viral genome data, from December 1, 2020 to January 14, 2022.

X-ray transient absorption reveals the A (nπ*) state of pyrazine in electronic relaxation.

Electronic relaxation in organic chromophores often proceeds via states not directly accessible by photoexcitation. We report on the photoinduced dynamics of pyrazine that involves such states, excited by a 267 nm laser and probed with X-ray transient absorption spectroscopy in a table-top setup. In addition to the previously characterized B (ππ*) (S) and B (nπ*) (S) states, the participation of the optically dark A (nπ*) state is assigned by a combination of experimental X-ray core-to-valence spectroscopy, electronic structure calculations, nonadiabatic dynamics simulations, and X-ray spectral computations.

Accurate prediction of core-level spectra of radicals at density functional theory cost via square gradient minimization and recoupling of mixed configurations.

State-specific orbital optimized approaches are more accurate at predicting core-level spectra than traditional linear-response protocols, but their utility had been restricted due to the risk of "variational collapse" down to the ground state. We employ the recently developed square gradient minimization [D. Hait and M.

Global reference mapping of human transcription factor footprints.

Combinatorial binding of transcription factors to regulatory DNA underpins gene regulation in all organisms. Genetic variation in regulatory regions has been connected with diseases and diverse phenotypic traits, but it remains challenging to distinguish variants that affect regulatory function. Genomic DNase I footprinting enables the quantitative, nucleotide-resolution delineation of sites of transcription factor occupancy within native chromatin.

Index and biological spectrum of human DNase I hypersensitive sites.

DNase I hypersensitive sites (DHSs) are generic markers of regulatory DNA and contain genetic variations associated with diseases and phenotypic traits. We created high-resolution maps of DHSs from 733 human biosamples encompassing 438 cell and tissue types and states, and integrated these to delineate and numerically index approximately 3.6 million DHSs within the human genome sequence, providing a common coordinate system for regulatory DNA.

Integrated epigenomic profiling reveals endogenous retrovirus reactivation in renal cell carcinoma.

Background: Transcriptional dysregulation drives cancer formation but the underlying mechanisms are still poorly understood. Renal cell carcinoma (RCC) is the most common malignant kidney tumor which canonically activates the hypoxia-inducible transcription factor (HIF) pathway. Despite intensive study, novel therapeutic strategies to target RCC have been difficult to develop.

Clinical outcomes with a systolic blood pressure lower than 120 mmHg in older patients with high disease burden.

Background: The target blood pressure in older patients is controversial. Recent studies provided clinical evidence supporting a target systolic blood pressure <120 mmHg in patients >50 years at high risk of cardiovascular events.

Methods: Retrospective study of 380 consecutive patients ≥60 years with stages 1-5 pre-dialysis chronic kidney disease seen between January 2013 and November 2015.

52 Genetic Loci Influencing Myocardial Mass.

Background: Myocardial mass is a key determinant of cardiac muscle function and hypertrophy. Myocardial depolarization leading to cardiac muscle contraction is reflected by the amplitude and duration of the QRS complex on the electrocardiogram (ECG). Abnormal QRS amplitude or duration reflect changes in myocardial mass and conduction, and are associated with increased risk of heart failure and death.

Rare Variants of the Serotonin Transporter Are Associated With Psychiatric Comorbidity in Irritable Bowel Syndrome.

Alterations in serotonin signaling are suspected in the pathophysiology of irritable bowel syndrome (IBS). By modulating the extracellular reuptake of serotonin, the serotonin transporter (SERT) acts as a key regulator of the bioavailability of serotonin. This study is the first to investigate the impact of rare SERT variants (i.

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo.

The function of human regulatory regions depends exquisitely on their local genomic environment and on cellular context, complicating experimental analysis of common disease- and trait-associated variants that localize within regulatory DNA. We use allelically resolved genomic DNase I footprinting data encompassing 166 individuals and 114 cell types to identify >60,000 common variants that directly influence transcription factor occupancy and regulatory DNA accessibility in vivo. The unprecedented scale of these data enables systematic analysis of the impact of sequence variation on transcription factor occupancy in vivo.

Avoidance of polypharmacy and excessive blood pressure control is associated with improved renal function in older patients.

Background: Elderly patients are particularly susceptible to polypharmacy. The present study evaluated the renal effects of optimizing potentially nephrotoxic medications in an older population.

Methods: Retrospective study of patients' ≥ 60 years treated between January of 2013 and February of 2015 in a Nephrology Clinic.

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.

To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I-hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS maps from orthologous compartments. We found that the mouse and human genomes have undergone extensive cis-regulatory rewiring that combines branch-specific evolutionary innovation and loss with widespread repurposing of conserved DHSs to alternative cell fates, and that this process is mediated by turnover of transcription factor (TF) recognition elements.

Conservation of trans-acting circuitry during mammalian regulatory evolution.

The basic body plan and major physiological axes have been highly conserved during mammalian evolution, yet only a small fraction of the human genome sequence appears to be subject to evolutionary constraint. To quantify cis- versus trans-acting contributions to mammalian regulatory evolution, we performed genomic DNase I footprinting of the mouse genome across 25 cell and tissue types, collectively defining ∼8.6 million transcription factor (TF) occupancy sites at nucleotide resolution.

A comparative encyclopedia of DNA elements in the mouse genome.

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization.