A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry

We present here a review of the fundamental topics of Hartree-Fock theory in Quantum Chemistry. From the molecular Hamiltonian, using and discussing the Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock equations for the electronic problem. Special emphasis is placed in the most relevant mathematical aspects of the theoretical derivation of the final equations, as well as in the results regarding the existence and uniqueness of their solutions. All Hartree-Fock versions with different spin restrictions are systematically extracted from the general case, thus providing a unifying framework. Then, the discretization of the one-electron orbitals space is reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition of the basic underlying concepts related to the construction and selection of Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we close the review with a section in which the most relevant modern developments (specially those related to the design of linear-scaling methods) are commented and linked to the issues discussed. The whole work is intentionally introductory and rather self-contained, so that it may be useful for non experts that aim to use quantum chemical methods in interdisciplinary applications. Moreover, much material that is found scattered in the literature has been put together here to facilitate comprehension and to serve as a handy reference.Comment: 64 pages, 3 figures, tMPH2e.cls style file, doublesp, mathbbol and subeqn package

Symptom-based stratification of patients with primary Sjögren's syndrome: multi-dimensional characterisation of international observational cohorts and reanalyses of randomised clinical trials

Background Heterogeneity is a major obstacle to developing effective treatments for patients with primary Sjögren's syndrome. We aimed to develop a robust method for stratification, exploiting heterogeneity in patient-reported symptoms, and to relate these differences to pathobiology and therapeutic response. Methods We did hierarchical cluster analysis using five common symptoms associated with primary Sjögren's syndrome (pain, fatigue, dryness, anxiety, and depression), followed by multinomial logistic regression to identify subgroups in the UK Primary Sjögren's Syndrome Registry (UKPSSR). We assessed clinical and biological differences between these subgroups, including transcriptional differences in peripheral blood. Patients from two independent validation cohorts in Norway and France were used to confirm patient stratification. Data from two phase 3 clinical trials were similarly stratified to assess the differences between subgroups in treatment response to hydroxychloroquine and rituximab. Findings In the UKPSSR cohort (n=608), we identified four subgroups: Low symptom burden (LSB), high symptom burden (HSB), dryness dominant with fatigue (DDF), and pain dominant with fatigue (PDF). Significant differences in peripheral blood lymphocyte counts, anti-SSA and anti-SSB antibody positivity, as well as serum IgG, κ-free light chain, β2-microglobulin, and CXCL13 concentrations were observed between these subgroups, along with differentially expressed transcriptomic modules in peripheral blood. Similar findings were observed in the independent validation cohorts (n=396). Reanalysis of trial data stratifying patients into these subgroups suggested a treatment effect with hydroxychloroquine in the HSB subgroup and with rituximab in the DDF subgroup compared with placebo. Interpretation Stratification on the basis of patient-reported symptoms of patients with primary Sjögren's syndrome revealed distinct pathobiological endotypes with distinct responses to immunomodulatory treatments. Our data have important implications for clinical management, trial design, and therapeutic development. Similar stratification approaches might be useful for patients with other chronic immune-mediated diseases. Funding UK Medical Research Council, British Sjogren's Syndrome Association, French Ministry of Health, Arthritis Research UK, Foundation for Research in Rheumatology

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Microwave Oven Pretreatment of Carbonates for 14C Dating by Accelerator Mass Spectrometry

A microwave oven is used to pretreat carbonate samples prior to graphitisation and radiocarbon dating by accelerator mass spectrometry. The method reduces the risk of contamination of small carbonate samples and provides a fast and convenient method for the acid evolution of CO2.This material was digitized as part of a cooperative project between Radiocarbon and the University of Arizona Libraries.The Radiocarbon archives are made available by Radiocarbon and the University of Arizona Libraries. Contact [email protected] for further information.Migrated from OJS platform February 202

A decade of CH4, CO and N2O in situ measurements at Lauder, New Zealand: Assessing the long-term performance of a Fourier transform infrared trace gas and isotope analyser

We present a 10-year (January 2007-December 2016) time series of continuous in situ measurements of methane (CH4), carbon monoxide (CO) and nitrous oxide (N2O) made by an in situ Fourier transform infrared trace gas and isotope analyser (FTIR) operated at Lauder, New Zealand (45.04 S, 169.68 E, 370 m a. m. s. l.). Being the longest continuous deployed operational FTIR system of this type, we are in an ideal position to perform a practical evaluation of the multi-year performance of the analyser. The operational methodology, measurement precision, reproducibility, accuracy and instrument reliability are reported. We find the FTIR has a measurement repeatability of the order of 0.37 ppb (1σ standard deviation) for CH4, 0.31 ppb for CO and 0.12 ppb for N2O. Regular target cylinder measurements provide a reproducibility estimate of 1.19 ppb for CH4, 0.74 ppb for CO and 0.27 ppb for N2O. FTIR measurements are compared to co-located ambient air flask samples acquired at Lauder since May 2009, which allows a long-term assessment of the FTIR data set across annual and seasonal composition changes. Comparing FTIR and co-located flask measurements show that the bias (FTIR minus flask) for CH4 of −1.02 ± 2.61 ppb and CO of −0.43 ± 1.60 ppb are within the Global Atmospheric Watch (GAW)-recommended compatibility goals of 2 ppb. The N2O FTIR flask bias of −0.01 ± 0.77 ppb is within the GAW-recommended compatibility goals of 0.1 ppb and should be viewed as a serendipitous result due to the large standard deviation along with known systematic differences in the measurement sets. Uncertainty budgets for each gas are also constructed based on instrument precision, reproducibility and accuracy. In the case of CH4, systematic uncertainty dominates, whilst for CO and N2O it is comparable to the random uncertainty component. The long-term instrument stability, precision estimates and flask comparison results indicate the FTIR CH4 and CO time series meet the GAW compatibility recommendations across multiple years of operation (and instrument changes) and are sufficient to capture annual trends and seasonal cycles observed at Lauder. The differences between FTIR and flask N2O measurements need to be reconciled. Trend analysis of the 10-year time series captures seasonal cycles and the secular upward trend of CH4 and N2O. The CH4 and CO time series have the required precision and accuracy at a high enough temporal resolution to be used in inversion models in a data-sparse region of the world

Seasonal snapshots of the isotopic (14C, 13C) composition of tropospheric carbon monoxide at Niwot Ridge, Colorado

Clean continental air, collected near Niwot Ridge, Colorado (3.75 km altitude), over a two-year period (1991-1992), has been investigated for the composition of atmospheric carbon monoxide. Its chemical and isotopic signatures, distributed through time and space, along with a detailed look at gridded meteorological parameters, summarized in 5-day back-trajectories, have shed some light on the distribution of CO in tropospheric air and what the likely source regions are that contribute to background CO mixing ratios. The temporal distribution of CO and CO mixing ratios exhibit a seasonal trend with a maximum during the winter/spring and a minimum during the late summer. CO mixing ratios peak at about 19 molecules cm of air (at STP) with a minimum between years of about 9 molecules cm. A comparable seasonal pattern was observed for CO mixing ratios with a maximum of 240 nmol mol and a minimum of 100 nmol mol. An observed trend of increasing CO with increasing CO mixing ratios suggests an input of recycled living carbon. The δC data show a winter/spring peak in 1992; however, too few data points exist for 1991 to indicate a clear seasonal cycle. δC values range from -26.3‰ to -30.5‰ over the two years of data. The seasonally averaged CO and δC data show autumn values of 116 ± 11 (std. dev.) nmol mol and -27.85 ± 0.87‰, respectively; winter values 159 ± 19 nmol mol and -28.0 ± 1.7‰; spring values 181 ± 45 nmol mol and -27.1 ± 1.6‰; and summer values 142 ± 37 nmol mol and -29.4 ± 1.2‰. Five-day back trajectories and on-site meteorology for each sampling day show that, with some exceptions, winds were on average from the west or northwest. Potential CO sources on these dates were in the northwestern US. CO sampled during these periods may reflect continental CO sources such as oxidized vegetative emissions and biomass burning. On the other hand, there were days when the winds were either from the south and southwest or from northern Canada. Thus, urban air from the Boulder/Denver metropolitan area to the east and southeast was probably not sampled to any significant extent