Psychosocial burden and associated factors among nurses in care homes during the COVID-19 pandemic: findings from a retrospective survey in Germany

Background: Care homes were hit hard by the COVID-19 pandemic. Although high levels of psychosocial burden (i.e., anxiety, depression and stress) during the pandemic have been described for healthcare workers in hospitals, evidence on the psychosocial burden for nurses in care homes during the pandemic is scarce. Methods: A total of 811 nurses participated in a retrospective online survey between November 2020 and February 2021. Information about the COVID-19 situation (i.e., working demands, COVID-19 cases in their facility, and COVID-19-related burden) of nurses in German care homes during the first wave of the pandemic (March 2020 to June 2020) was gathered. The Stress Scale of the Depression Anxiety and Stress Scales (SDASS-21), the Generalized Anxiety Disorder Scale-2 (GAD-2), the Patients-Health-Questionnaire-2 (PHQ-2), and the Copenhagen Psychosocial Questionnaire (COPSOQ) were used to screen for psychosocial burden. Results: Among nurses, 94.2% stated that working demands since the COVID-19 pandemic increased. Further, 59.1% showed clinically relevant levels of either stress, anxiety, and/or depression. Multiple regression analysis showed significant associations between COVID-19-related burden and qualification (p < .01), dissatisfaction with COVID-19 management of care home manager (p < .05), COVID-19-related anxiety (p < .001), and dementia as a focus of care (p < .05). Stress, depression, and anxiety showed associations with COVID-19 related burden at work (p < .01), COVID-19-related anxiety (p < .001), social support (p < .01), and sense of community (p < .05). Stress was also associated with COVID-19 cases among residents (p < .05), and size of care home (p < .05). Conclusion: Short- and long-term strategies (i.e., psychosocial counseling, mandatory team meetings, more highly qualified nurses, additional training) in the work environment of nursing, in crises, but beyond, should be encouraged to reduce the burden on nursing staff in care homes

Refining multiple sequence alignments with conserved core regions

Accurate multiple sequence alignments of proteins are very important to several areas of computational biology and provide an understanding of phylogenetic history of domain families, their identification and classification. This article presents a new algorithm, REFINER, that refines a multiple sequence alignment by iterative realignment of its individual sequences with the predetermined conserved core (block) model of a protein family. Realignment of each sequence can correct misalignments between a given sequence and the rest of the profile and at the same time preserves the family's overall block model. Large-scale benchmarking studies showed a noticeable improvement of alignment after refinement. This can be inferred from the increased alignment score and enhanced sensitivity for database searching using the sequence profiles derived from refined alignments compared with the original alignments. A standalone version of the program is available by ftp distribution () and will be incorporated into the next release of the Cn3D structure/alignment viewer

General practitioner care in nursing homes during the first wave of the COVID-19 pandemic in Germany: a retrospective survey among nursing home managers

Background: Though evidence on the detrimental impact of the COVID-19 pandemic in nursing homes is vast, research focusing on general practitioners' (GP) care during the pandemic in nursing homes is still scarce. Methods: A retrospective online survey among 1,010 nursing home managers in Germany was conducted during the first wave of the COVID-19 pandemic between November 2020 and February 2021. Associations between perceived deficits in GP care (routine and acute visits) and both general and COVID-19-related characteristics of nursing homes were analysed using multiple logistic regression analyses. Results: The majority of nursing home managers reported no deficits in GP care (routine visits, 84.3%; acute visits, 92.9%). Logistic regression analyses revealed that deficits in GP care (routine visits) were significantly associated with visiting restrictions for GPs and nursing home size. Small nursing homes (1-50 residents) were significantly more likely to report deficits in GP care (routine visits) compared to medium (51-100 residents) and large nursing homes (> 100 residents). Further, deficits in GP care (acute visits) were significantly associated with dementia as a focus of care and the burden of insufficient testing for SARS-CoV-2 among residents. Moreover, visiting restrictions for GPs were significantly associated with dementia as the focus of care and the COVID-19 incidence at the federal state level. Finally, COVID-19 cases in nursing homes were significantly associated with size of nursing homes, COVID-19-incidence on the federal state level and the burden of insufficient testing capacities for SARS-CoV-2 among residents. Conclusion: We found structural factors associated with GP care deficits during the pandemic. New concepts for GP care should be implemented in pandemic preparedness plans to ensure high quality, consistent, and reliable GP care as well as effective infection prevention measures in nursing homes

Effect of Perioperative Lipid Status on Clinical Outcomes after Cardiac Surgery

Abstract Patients undergoing cardiac surgery are at increased cardiovascular risk, which includes altered lipid status. However, data on the effect of cardiac surgery and cardiopulmonary bypass (CPB) on plasma levels of key lipids are scarce. We investigated potential effects of CPB on plasma lipid levels and associations with early postoperative clinical outcomes. This is a prospective bio-bank study of patients undergoing elective cardiac surgery at our center January to December 2019. The follow-up period was 1 year after surgery. Blood sampling was performed before induction of general anesthesia, upon weaning from cardiopulmonary bypass (CPB), and on the first day after surgery. Clinical end points included the incidence of postoperative stroke, myocardial infarction, and death of any cause at 30 days after surgery as well as 1-year all-cause mortality. A total of 192 cardiac surgery patients (75% male, median age 67.0 years (interquartile range 60.0–73.0), median BMI 26.1 kg/m2 (23.7–30.4)) were included. A significant intraoperative decrease in plasma levels compared with preoperative levels (all p < 0.0001) was observed for total cholesterol (TC) (Cliff’s delta d: 0.75 (0.68–0.82; 95% CI)), LDL-Cholesterol (LDL-C) (d: 0.66 (0.57–0.73)) and HDL-Cholesterol (HDL-C) (d: 0.72 (0.64–0.79)). At 24h after surgery, the plasma levels of LDL-C (d: 0.73 (0.650.79)) and TC (d: 0.77 (0.69–0.82)) continued to decrease compared to preoperative levels, while the plasma levels of HDL-C (d: 0.46 (0.36–0.55)) and TG (d: 0.40 (0.29–0.50)) rebounded, but all remained below the preoperative levels (p < 0.001). Mortality at 30 days was 1.0% (N = 2/192), and 1-year mortality was 3.8% (N = 7/186). Postoperative myocardial infarction occurred in 3.1% of patients (N = 6/192) and postoperative stroke in 5.8% (N = 11/190). Adjusting for age, sex, BMI, and statin therapy, we noted a protective effect of postoperative occurrence of stroke for pre-to-post-operative changes in TC (adjusted odds ratio (OR) 0.29 (0.07–0.90), p = 0.047), in LDL-C (aOR 0.19 (0.03–0.88), p = 0.045), and in HDL-C (aOR 0.01 (0.00–0.78), p = 0.039). No associations were observed between lipid levels and 1-year mortality. In conclusion, cardiac surgery induces a significant sudden drop in levels of key plasma lipids. This effect was pronounced during the operation, and levels remained significantly lowered at 24 h after surgery. The intraoperative drops in LDL-C, TC, and HDL-C were associated with a protective effect against occurrence of postoperative stroke in adjusted models. We demonstrate that the changes in key plasma lipid levels during surgery are strongly correlated, which makes attributing the impact of each lipid to the clinical end points, such as postoperative stroke, a challenging task. Large-scale analyses should investigate additional clinical outcome measures

Per- and Polyfluoroalkyl Substances (PFAS) in PubChem: 7 Million and Growing.

peer reviewedPer- and polyfluoroalkyl substances (PFAS) are of high concern, with calls to regulate them as a class. In 2021, the Organisation for Economic Co-operation and Development (OECD) revised the definition of PFAS to include any chemical containing at least one saturated CF2 or CF3 moiety. The consequence is that one of the largest open chemical collections, PubChem, with 116 million compounds, now contains over 7 million PFAS under this revised definition. These numbers are several orders of magnitude higher than previously established PFAS lists (typically thousands of entries) and pose an incredible challenge to researchers and computational workflows alike. This article describes a dynamic, openly accessible effort to navigate and explore the >7 million PFAS and >21 million fluorinated compounds (September 2023) in PubChem by establishing the "PFAS and Fluorinated Compounds in PubChem" Classification Browser (or "PubChem PFAS Tree"). A total of 36500 nodes support browsing of the content according to several categories, including classification, structural properties, regulatory status, or presence in existing PFAS suspect lists. Additional annotation and associated data can be used to create subsets (and thus manageable suspect lists or databases) of interest for a wide range of environmental, regulatory, exposomics, and other applications

Open and FAIR transformation product data for improved suspect/non-target screening: REFTPs in the NORMAN-SLE, PubChem and patRoon

peer reviewedPresentation given at ICCE, Venice, 11 - 15 June 2023

Universality and its Origins at the Amorphous Solidification Transition

Systems undergoing an equilibrium phase transition from a liquid state to an amorphous solid state exhibit certain universal characteristics. Chief among these are the fraction of particles that are randomly localized and the scaling functions that describe the order parameter and (equivalently) the statistical distribution of localization lengths for these localized particles. The purpose of this Paper is to discuss the origins and consequences of this universality, and in doing so, three themes are explored. First, a replica-Landau-type approach is formulated for the universality class of systems that are composed of extended objects connected by permanent random constraints and undergo amorphous solidification at a critical density of constraints. This formulation generalizes the cases of randomly cross-linked and end-linked macromolecular systems, discussed previously. The universal replica free energy is constructed, in terms of the replica order parameter appropriate to amorphous solidification, the value of the order parameter is obtained in the liquid and amorphous solid states, and the chief universal characteristics are determined. Second, the theory is reformulated in terms of the distribution of local static density fluctuations rather than the replica order parameter. It is shown that a suitable free energy can be constructed, depending on the distribution of static density fluctuations, and that this formulation yields precisely the same conclusions as the replica approach. Third, the universal predictions of the theory are compared with the results of extensive numerical simulations of randomly cross-linked macromolecular systems, due to Barsky and Plischke, and excellent agreement is found.Comment: 10 pages, including 3 figures (REVTEX

MMDB: annotating protein sequences with Entrez's 3D-structure database

Three-dimensional (3D) structure is now known for a large fraction of all protein families. Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a sequence database with an arbitrary query sequence. Depending on the extent of similarity, such neighbor relationships may allow one to infer biological function and to identify functional sites such as binding motifs or catalytic centers. Entrez's 3D-structure database, the Molecular Modeling Database (MMDB), provides easy access to the richness of 3D structure data and its large potential for functional annotation. Entrez's search engine offers several tools to assist biologist users: (i) links between databases, such as between protein sequences and structures, (ii) pre-computed sequence and structure neighbors, (iii) visualization of structure and sequence/structure alignment. Here, we describe an annotation service that combines some of these tools automatically, Entrez's ‘Related Structure’ links. For all proteins in Entrez, similar sequences with known 3D structure are detected by BLAST and alignments are recorded. The ‘Related Structure’ service summarizes this information and presents 3D views mapping sequence residues onto all 3D structures available in MMDB ()