A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis

Single particle analysis (SPA) in cryo-electron microscopy (cryo-EM) is highly used to obtain the near-atomic structure of biological macromolecules. The current methods allow users to produce high-resolution maps from many samples. However, there are still challenging cases that require extra processing to obtain high resolution. This is the case when the macromolecule of the sample is composed of different components and we want to focus just on one of them. For example, if the macromolecule is composed of several flexible subunits and we are interested in a specific one, if it is embedded in a viral capsid environment, or if it has additional components to stabilize it, such as nanodiscs. The signal from these components, which in principle we are not interested in, can be removed from the particles using a projection subtraction method. Currently, there are two projection subtraction methods used in practice and both have some limitations. In fact, after evaluating their results, we consider that the problem is still open to new solutions, as they do not fully remove the signal of the components that are not of interest. Our aim is to develop a new and more precise projection subtraction method, improving the performance of state-of-the-art methods. We tested our algorithm with data from public databases and an in-house data set. In this work, we show that the performance of our algorithm improves the results obtained by others, including the localization of small ligands, such as drugs, whose binding location is unknown a priori.

Identification of COVID-19 patients at risk of hospital admission and mortality: a European multicentre retrospective analysis of mid-regional pro-adrenomedullin

Background

Mid-Regional pro-Adrenomedullin (MR-proADM) is an inflammatory biomarker that improves the prognostic assessment of patients with sepsis, septic shock and organ failure. Previous studies of MR-proADM have primarily focussed on bacterial infections. A limited number of small and monocentric studies have examined MR-proADM as a prognostic factor in patients infected with SARS-CoV-2, however there is need for multicenter validation. An evaluation of its utility in predicting need for hospitalisation in viral infections was also performed.

Methods

An observational retrospective analysis of 1861 patients, with SARS-CoV-2 confirmed by RT-qPCR, from 10 hospitals across Europe was performed. Biomarkers, taken upon presentation to Emergency Departments (ED), clinical scores, patient demographics and outcomes were collected. Multiclass random forest classifier models were generated as well as calculation of area under the curve analysis. The primary endpoint was hospital admission with and without death.

Results

Patients suitable for safe discharge from Emergency Departments could be identified through an MR-proADM value of ≤ 1.02 nmol/L in combination with a CRP (C-Reactive Protein) of ≤ 20.2 mg/L and age ≤ 64, or in combination with a SOFA (Sequential Organ Failure Assessment) score < 2 if MR-proADM was ≤ 0.83 nmol/L regardless of age. Those at an increased risk of mortality could be identified upon presentation to secondary care with an MR-proADM value of > 0.85 nmol/L, in combination with a SOFA score ≥ 2 and LDH > 720 U/L, or in combination with a CRP > 29.26 mg/L and age ≤ 64, when MR-proADM was > 1.02 nmol/L.

Conclusions

This international study suggests that for patients presenting to the ED with confirmed SARS-CoV-2 infection, MR-proADM in combination with age and CRP or with the patient’s SOFA score could identify patients at low risk where outpatient treatment may be safe.

Circulating MR-proADM levels, as an indicator of endothelial dysfunction, for early risk stratification of mid-term mortality in COVID-19 patients

Objectives

Thromboinflammation, resulting from a complex interaction between thrombocytopathy, coagulopathy, and endotheliopathy, contributes to increased mortality in COVID-19 patients. MR-proADM, as a surrogate of adrenomedullin system disruption, leading to endothelial damage, has been reported as a promising biomarker for short-term prognosis. We evaluated the role of MR-proADM in the mid-term mortality in COVID-19 patients.

Methods

A prospective, observational study enrolling COVID-19 patients from August to October 2020. A blood sample for laboratory test analysis was drawn on arrival in the emergency department. The primary endpoint was 90-day mortality. The area under the curve (AUC) and Cox regression analyses were used to assess discriminatory ability and association with the endpoint.

Results

A total of 359 patients were enrolled, and the 90-day mortality rate was 8.9%. ROC AUC for MR-proADM predicting 90-day mortality was 0.832. An optimal cutoff of 0.80 nmol/L showed a sensitivity of 96.9% and a specificity of 58.4%, with a negative predictive value of 99.5%. Circulating MR-proADM levels (inverse transformed), after adjusting by a propensity score including eleven potential confounders, were an independent predictor of 90-day mortality (HR: 0.162 [95% CI: 0.043-0.480])

Conclusions

Our data confirm that MR-proADM has a role in the mid-term prognosis of COVID-19 patients and might assist physicians with risk stratification.

The effect of dexamethasone on disruption of ovarian steroid levels and receptors in female rats

This study was conducted to investigate if the injection of a single dose of dexamethasone may cause disruption of adult female rat gonadal function in terms of plasma and ovarian level of both androgen and estrogen, ovarian morphology, and changes in localization of androgen, estrogen and glucocorticoid receptors. Adult female Long Evans rats (n=50, 250-300 g) were used. At day 0 rats received subcutaneously 1 ml of saline (n=25; control group) or dexamethasone at 0.1 mg/kg (n=25, treated group). Rats were sacrificed in groups of five on days 10, 15, 20, 25 and 30 after injection. Blood samples and one ovary were collected to analyze dexamethasone, 17beta-estradiol (E2), testosterone (T) and androstenedione (A4) concentrations by amplified EIA. The remaining ovary was removed and processed for histopathology and immunocytochemistry. Differences between individual means were analyzed by Pairwise t-test and Bonferroni post test to asses whether values presented statistical significance. Increased E2, T and A4 levels were observed both in plasma and ovary samples in treated group when comparing with control (p< 0.01) at all days post-injection even when dexamethasone was undetectable. Ovarian morphology of treated group showed features compatible with female infertility. Inmmunolocalization of androgen and estrogen receptors showed that both were negative in treated group while controls showed highest positivity (AR +++, ER ++). Glucocorticoid receptor showed higher positivity in dexamethasone treated rats (GR ++) than in controls (GR +). Obtained results showed clear evidence that a single dose of dexamethasone may disrupt gonadal function in rats, and that possibly leads to infertility.

Dietary pharmacological or excess zinc and phytase effects on tissue mineral concentrations, metallothionein, and apparent mineral retention in the newly weaned pig

Feeding pharmacological zinc (Zn) to weaned pigs improves growth, and dietary phytase improves P and Zn availability. Metallothionein (MT) increases in the duodenum, kidney, and liver of pigs fed 1000 mg Zn/kg with phytase or 2000 mg Zn/kg with or without phytase when fed for 14 d postweaning. The goal of this study was to determine the effects of feeding pharmacological Zn and phytase on tissue minerals, MT, mineral excretion, and apparent retention. Twenty-four newly weaned pigs (20 d; 7.2 kg) were individually fed twice daily, a basal diet supplemented with 0, 1000, or 4000 mg Zn/kg as Zn oxide, without or with phytase (500 phytase units [FTU]/kg) for 14 d, followed by a basal diet (100 mg Zn/kg) without phytase for 7 d. Pigs fed 4000 mg Zn/kg without phytase had higher (p=0.01) plasma, hepatic, renal Zn, renal Cu, and hepatic, renal, and jejunal MT than pigs fed the basal diet or 1000 mg Zn/kg. Duodenal MT was higher (p=0.0001) in pigs fed 1000 and 4000 mg Zn/kg than in pigs fed the basal diet. In pigs fed 1000 and 4000 mg Zn/kg, Zn loading occurred during the first 11 d of supplementation; by d 14, excess Zn was being excreted in the feces.

Nematocidal activity of natural polyphenols from bryophytes and their derivatives

The nematocidal in vitro activity of three natural perotetins (phenolic bisbibenzyiethers) and eleven diphenyl ethers used as synthetic precursors has been assayed using two different experimental models, Caenorhabditis elegans and Nippostrongylus brasiliensis. Nine compounds showed some activity against C. elegans and nine against N. brasiliensis. For the former model, three compounds displayed an activity similar to that of the standards, whereas for N. brasiliensis none of the tested compounds was as active as the standards. From the in vitro results, five compounds (3, 4, 8, 9, 13) could be selected as lead compounds to continue the search for improved activity.

The effect of clenbuterol on adrenal function in rats

The use of anabolic agents is illegal in the European Community but the effect of these agents on animal welfare is not well documented. The aim of this study was to evaluate whether the administration of anabolic agents, such as clenbuterol, causes stressful effects in rats, as reflected by the adrenal function. Anabolic doses of clenbuterol (1 mg kg-1, 99% purity) were administered orally by stomach tube daily for 45 d to female Long Evans rats (250-300 g, n = 50). Twenty-five animals were used as controls. Blood samples were collected from the jugular vein in anaesthetised animals (ketamine and xylazine). At the end of the experiment, the animals were sacrificed and the adrenal glands were removed. Hormonal levels were measured by an enzyme immunoassay previously validated for this species. Hormonal levels of cortisol and corticosterone, and histopathological analysis, were used as indicators of the adrenal function. Increased corticosterone and cortisol secretion was found in the treated group (p < 0.001), both in adrenal homogenates and peripheral blood samples, compared with control animals. Higher relative adrenal gland weight (adrenal gland-to-body weight ratio) was also found in the treated group (p < 0.01). The major histopathological finding was the presence of hyperplasia in the adrenocortical cells. It was concluded that the administration of an anabolic dose of clenbuterol causes a hyperstimulation of adrenal gland secretion that could adversely affect animal welfare.

[Septic arthritis caused by Streptococcus pneumoniae]

BACKGROUND

Streptococcus pneumoniae is an uncommon agent of infective arthritis. In this report three cases of pneumococcal arthritis are described.

METHODS

Retrospective review of synovial fluids processed in our laboratory yielding bacteria. The study period was from January 1991 to December 1995. The clinical records of patients with the clinical and microbiological diagnosis of septic arthritis were reviewed.

RESULTS

Twenty-eight out of a total of 43 clinical records had the clinical and microbiological diagnosis of septic arthritis and three (11%) were caused by Streptococcus pneumoniae. The infective source in two of these three cases was probably the respiratory tract, and the most common location was the knee.

CONCLUSIONS

In our cases immunosuppression seemed to be the major risk factor involved in the development of pneumococcal arthritis.

Evaluation of different techniques in the diagnosis of Toxoplasma encephalitis

This study evaluated the detection of antibodies, circulating antigens and parasite DNA by polymerase chain reaction (PCR) in the diagnosis of toxoplasma encephalitis. The detection of antibody classes and IgG avidity were not useful diagnostically. The detection of circulating antigens by the ELISA system described was not sufficiently sensitive. The detection of DNA by PCR was the most useful test especially in untreated patients, with a sensitivity of 62% overall, 81% in untreated patients and only 20% in treated patients. The use of non-isotopic probes makes the use of this technique feasible in routine diagnostic parasitology laboratories.

[Immunoglobulins, beta-2 microglobulin and lymphocyte subpopulations in patients addicted to parenteral drugs (IVDA)]

Disorders in serum immunoglobulins, beta-2 microglobulin and lymphocyte subpopulations in parenterally drug-addict patients (PDAP) are analyzed. The study is divided in three parts. In the first one, a group of 33 HIV-negative PDAP without intercurrent diseases is compared with a control group of healthy non-addict persons. In the second part, the differences between a group of 58 HIV-negative PDAP and a group of 95 HIV-positive PDAP are studied. In the third part, the differences between the group of HIV-negative PDAP without associated procedures and a subgroup of HIV-positive patients including 31 asymptomatic carriers in phase II, are studied. No statistically significant differences were detected between the control group and the HIV-negative PDAP group. The HIV-positive PDAP group showed lymphocytes CD3, CD4 and a CD4/CD3 ratio statistically lower than the HIV-negative group, as well as a significant increase of the immunoglobulin IgG and beta-2 microglobulin. The same results were obtained when the subgroup of HIV-positive patients in phase II was compared with the group of HIV-negative PDAP without intercurrent diseases. According to these results, we conclude that the immunological disorders detected in PDAP patients seem to be more related with the infection by the human immunodeficiency virus and with other associated infections than with the drug-addiction itself.