Network medicine-based epistasis detection in complex diseases: ready for quantum computing

Most heritable diseases are polygenic. To comprehend the underlying genetic architecture, it is crucial to discover the clinically relevant epistatic interactions (EIs) between genomic single nucleotide polymorphisms (SNPs)1-3. Existing statistical computational methods for EI detection are mostly limited to pairs of SNPs due to the combinatorial explosion of higher-order EIs. With NeEDL (network-based epistasis detection via local search), we leverage network medicine to inform the selection of EIs that are an order of magnitude more statistically significant compared to existing tools and consist, on average, of five SNPs. We further show that this computationally demanding task can be substantially accelerated once quantum computing hardware becomes available. We apply NeEDL to eight different diseases and discover genes (affected by EIs of SNPs) that are partly known to affect the disease, additionally, these results are reproducible across independent cohorts. EIs for these eight diseases can be interactively explored in the Epistasis Disease Atlas (https://epistasis-disease-atlas.com). In summary, NeEDL is the first application that demonstrates the potential of seamlessly integrated quantum computing techniques to accelerate biomedical research. Our network medicine approach detects higher-order EIs with unprecedented statistical and biological evidence, yielding unique insights into polygenic diseases and providing a basis for the development of improved risk scores and combination therapies.

Dynamic interplay between metal nanoparticles and oxide support under redox conditions

The dynamic interactions between noble metal particles and reducible metal-oxide supports can depend on redox reactions with ambient gases. Transmission electron microscopy revealed that the strong metal-support interaction (SMSI)-induced encapsulation of platinum particles on titania observed under reducing conditions is lost once the system is exposed to a redox-reactive environment containing oxygen and hydrogen at a total pressure of ~1 bar. Destabilization of the metal-oxide interface and redox-mediated reconstructions of titania lead to particle dynamics and directed particle migration that depend on nanoparticle orientation. A static encapsulated SMSI state was reestablished when switching back to purely oxidizing conditions. This work highlights the difference between reactive and nonreactive states and demonstrates that manifestations of the metal-support interaction strongly depend on the chemical environment.

A massive rock and ice avalanche caused the 2021 disaster at Chamoli, Indian Himalaya

On 7 February 2021, a catastrophic mass flow descended the Ronti Gad, Rishiganga, and Dhauliganga valleys in Chamoli, Uttarakhand, India, causing widespread devastation and severely damaging two hydropower projects. More than 200 people were killed or are missing. Our analysis of satellite imagery, seismic records, numerical model results, and eyewitness videos reveals that ~27 × 10⁶ cubic meters of rock and glacier ice collapsed from the steep north face of Ronti Peak. The rock and ice avalanche rapidly transformed into an extraordinarily large and mobile debris flow that transported boulders greater than 20 meters in diameter and scoured the valley walls up to 220 meters above the valley floor. The intersection of the hazard cascade with downvalley infrastructure resulted in a disaster, which highlights key questions about adequate monitoring and sustainable development in the Himalaya as well as other remote, high-mountain environments.

Recent advances in the use of nanoparticles for allergen-specific immunotherapy

The number of patients suffering from allergic asthma and rhinoconjunctivitis has increased dramatically within the last decades. Allergen-specific immunotherapy (AIT) is the only available cause-oriented therapy so far. AIT reduces symptoms, but has also a disease-modifying effect. Disadvantages are a long-lasting procedure, and in a few cases potential systemic adverse reactions. Encapsulation of allergens or DNA vaccines into nanostructures may provide advantages compared to the conventional AIT with noncapsulated allergen extracts: The protein/DNA molecule can be protected from degradation, higher local concentrations and targeted delivery to the site of action appear possible, and most importantly, recognition of encapsulated allergen by the immune system, especially by IgE antibodies, is prevented. AIT with nanoparticles (NPs) may offer a safer and potentially more efficient way of treatment for allergic diseases. In this review, we summarize the use of biodegradable NPs consisting of synthetic or natural polymers, liposomes, and virus-like particles as well as nonbiodegradable NPs like dendrimers, and carbon- or metal-based NPs for AIT. More or less successful applications of these NPs in prophylactic as well as therapeutic vaccination approaches in rodents or other animals as well as first human clinical trials are discussed in detail.

Biodegradable hyperbranched polyether-lipids with in-chain pH-sensitive linkages

Hyperbranched polyether-based lipids with cleavable acetal units were obtained via copolymerization of the epoxide inimer 1-(glycidyloxy)ethyl ethylene glycol ether (GEGE) and glycidol, using anionic ring-opening polymerization.

Intrinsic superoxide dismutase activity of MnO nanoparticles enhances the magnetic resonance imaging contrast

MnO nanoparticles decompose superoxide and hydrogen peroxide in an enzyme-like manner leading to enhanced MRI contrast.

Enhanced immunogenicity of multivalent MUC1 glycopeptide antitumour vaccines based on hyperbranched polymers

A fully synthetic multivalent MUC1 glycopeptide vaccine based on a hyperbranched polyglycerol core induced IgG antibodies which strongly recognise epithelial tumour cells.

Extended magnetic reconnection across the dayside magnetopause

The extent of where magnetic reconnection (MR), the dominant process responsible for energy and plasma transport into the magnetosphere, operates across Earth's dayside magnetopause has previously been only indirectly shown by observations. We report the first direct evidence of X-line structure resulting from the operation of MR at each of two widely separated locations along the tilted, subsolar line of maximum current on Earth's magnetopause, confirming the operation of MR at two or more sites across the extended region where MR is expected to occur. The evidence results from in-situ observations of the associated ion and electron plasma distributions, present within each magnetic X-line structure, taken by two spacecraft passing through the active MR regions simultaneously.

Appropriate replacement dose of thyroxine in primary hypothyroidism

An ultrasensitive thyrotropin (TSH) assay was used to determine how many of 65 patients with primary hypothyroidism on thyroxine (T4) replacement therapy had suppressed serum TSH. In 13 patients (20%) TSH levels less than or equal to 0.1 mIU/l were found, indicating an overdose of thyroxine. After correction of the dose, 48 patients had normal TSH values. Their mean dose of thyroxine was 119 micrograms/24 hours, and the appropriate replacement dose tended to decline with advancing age. The serum level of thyroid hormones during replacement therapy with thyroxine very imperfectly reflected serum TSH values. It is concluded that overdose of thyroxine is common when suppressed serum TSH is used as an end point. Biochemical follow-up of replacement therapy with thyroxine in primary hypothyroidism therefore requires the use of an ultrasensitive TSH assay in order to detect such suppression. Serum levels of thyroxine or triiodothyronine (T3) during thyroxine therapy are poor indicators of pituitary TSH secretion and are therefore not useful as parameters of adequate thyroxine dosage.

Effects of synthetic corticotropin-releasing factor in normal individuals and in patients with hypothalamic-pituitary-adrenocortical disorders

Plasma adrenocortical hormone (ACTH) and cortisol response to four dose levels (25, 50, 100 and 300 micrograms) corticotropin-releasing factor (CRF) were studied in 5 healthy men, and the response to 100 micrograms CRF in 12 patients with various disorders of the hypothalamic-pituitary-adrenocortical function. In normals, mean plasma ACTH and cortisol concentration rose at all dose levels of CRF and peaked at 30 and 60 min respectively. The increment in plasma cortisol at 60 and 90 min was significantly higher on 100 and 300 micrograms CRF than on 25 micrograms, but the total cortisol concentration was not. Seven patients had Cushing's syndrome. In 2 patients with adrenocortical carcinoma the basal plasma ACTH was suppressed. After CRF a small increase was seen in plasma ACTH and cortisol in one patient successfully treated with mitotane, while the other patient did not respond. In 1 patient with ectopic ACTH syndrome an increase in plasma ACTH 15 min after CRF was not accompanied by any increase in plasma cortisol. One patient with bilateral multinodular adrenocortical hyperplasia did not respond to CRF. The plasma ACTH and cortisol response to CRF was supernormal in 2 patients with Cushing's disease, while a third patient responded in the normal range. In 2 patients with Nelson's syndrome the plasma ACTH response was excessive. Two out of three hypophysectomized patients did not respond to CRF, while one patient with a slightly positive response to hypoglycemia also responded (subnormally) to CRF. Our data indicate that CRF in doses of 50-100 micrograms will be a valuable substance in the differential diagnosis of Cushing's syndrome. Some overlap in the response is, however, seen between patients with Cushing's disease and other patients with Cushing' syndrome. CRF will possibly be of value also for the diagnosis of secondary adrenocortical failure.

Spondylolisthesis and posterior instability

We present the case of a patient with a spondylolisthesis of L5 on S1 due to spondylolysis at the level L5/S1. The vertebral slip was fixed and no anterior instability was found. Using functional magnetic resonance imaging (MRI) in an upright MRI scanner, posterior instability at the level of the spondylolytic defect of L5 was demonstrated. A structure, probably the hypertrophic ligament flava, arising from the spondylolytic defect was displaced toward the L5 nerve root, and a bilateral contact of the displaced structure with the L5 nerve root was shown in extension of the spine. To our knowledge, this is the first case described of posterior instability in patients with spondylolisthesis. The clinical implications of posterior instability are unknown; however, it is thought that this disorder is common and that it can only be diagnosed using upright MRI.

Real-time elastography--an advanced method of ultrasound: First results in 108 patients with breast lesions

OBJECTIVES

To evaluate whether real-time elastography, a new, non-invasive method for the diagnosis of breast cancer, improves the differentiation and characterization of benign and malignant breast lesions.

METHODS

Real-time elastography was carried out in 108 potential breast tumor patients with cytologically or histologically confirmed focal breast lesions (59 benign, 49 malignant; median age, 53.9 years; range, 16-84 years). Tumor and healthy tissue were differentiated by measurement of elasticity based on the correlation between tissue properties and elasticity modulus. Evaluation was performed using the three-dimensional (3D) finite element method, in which the information is color-coded and superimposed on the B-mode ultrasound image. A second observer evaluated the elastography images, in order to improve the objectivity of the method. The results of B-mode scan and elastography were compared with those of histology and previous sonographic findings. Sensitivities and specificities were calculated, taking histology as the gold standard.

RESULTS

B-mode ultrasound had a sensitivity of 91.8% and a specificity of 78%, compared with sensitivities of 77.6% and 79.6% and specificities of 91.5% and 84.7%, respectively, for the two observers evaluating elastography. Agreement between B-mode ultrasound and elastography was good, yielding a weighted kappa of 0.67.

CONCLUSIONS

Our initial clinical results suggest that real-time elastography improves the specificity of breast lesion diagnosis and is a promising new approach for the diagnosis of breast cancer. Elastography provides additional information for differentiating malignant BI-RADS (breast imaging reporting and data system) category IV lesions.

Contrast-Enhanced Endoscopic Ultrasound with Low Mechanical Index: A New Technique

AIM

Recent advances in technology have supported the development of new endoscopic ultrasound systems making it possible to use low MI contrast-enhanced imaging techniques (wide band harmonic imaging done with endoscopic ultrasound is currently at a preliminary stage). We now report on the first use of contrast-enhanced, low mechanical index, real-time endoscopic ultrasound (CELMI-EUS) in six patients using prototype technology.

MATERIALS AND METHODS

CELMI-EUS was performed using an electronic echo-endoscope HITACHI/Pentax EG-3830UT and adapted dynamic contrast harmonic wide-band pulsed inversion software with low mechanical index (MI = 0.09 - 0.25) before and up to 180 seconds after injection of SonoVue (4.8 mL) in six patients.

RESULTS

Adequate visualisation of the arterial and portal venous phases was achieved in all patients. The pancreas and liver were studied thereafter. In contrast to the satisfactory visualisation of these vessels, enhancement of the left liver lobe was sufficient only in 4 patients. In the remaining 2 patients with liver cirrhosis, the enhancement was less pronounced in contrast to the strong enhancement of the hepatic artery and portal vein.

CONCLUSION

Recent advances in technology have supported the development of new echo-endoscopic systems making it possible to use real-time, low mechanical index, contrast-enhanced imaging techniques with endoscopic ultrasound. We have preliminarily shown that arterial, portal venous and parenchymal contrast enhancement is possible.

Realtime-Elastographie

It is well known that some diseases, such as cancer, lead to a change of tissue hardness (i.e. the so-called elasticity modulus). The reconstruction of tissue elasticity provides the sonographer with important additional information which can be applied for the diagnosis of these diseases. Elasticity imaging has recently attracted attention as a technique which directly reveals the physical property of tissue and enables us to determine the change of tissue hardness caused by diseases. The elasticity modulus, i.e. the tissue elasticity distribution can be calculated from the strain and the stress of the examined structures. While the strain field can be estimated from the RF signals returned from tissue structures before and after compression, it is impossible to measure the stress field directly within the tissue. Another problem is that the compression of harder tissue structures is often followed by a lateral displacement of these structures. It is nearly impossible to represent the volume of this sideslip with conventional 2D methods but its calculation is indispensable for an accurate determination of the tissue elasticity of the examined structures. To overcome these problems, we propose the so-called Extended CA-method (Extended Combined Autocorrelation Method) which allows the reconstruction of the tissue elasticity of the examined structures on the basis of the 3-dimensional finite element model. The new technique enables a highly accurate estimation of the tissue elasticity distribution and the adequate compensation of sideslips. The realtime elasticity imaging described in this article, can easily be performed with the SonoElastography module that can be integrated into the platform of the HITACHI EUB-8500 system. Like colour Doppler examinations, tissue elasticity imaging can easily be performed with conventional ultrasound probes and does not require additional instruments (e.g. for measuring pressure or vibrations). The calculation of tissue elasticity distribution is performed in realtime and the examination results are represented in colour over the conventional B-mode image. The results of the simulations and phantom experiments performed verify that with the information obtained by the new realtime elasticity imaging method, lesions can be detected and represented more rapidly and with higher accuracy than with conventional methods based on the 2D Model, and that even lesions invisible on B-mode images can be detected.

Reversible posterior leukoencephalopathy after combination chemotherapy

We describe a young woman with Burkitt's lymphoma, treated with intravenous adriamycine and cyclophosphamide and intrathecal cytarabine. She developed a reversible posterior leukoencephalopathy syndrome (RPLS) with typical MRI findings. Diffusion-weighted images during the first days after the onset of symptoms predicted a small irreversible lesion in the frontal lobe, verified on T2-weighted images 1 month later. The patient showed full recovery after high-dose steroid treatment.

Dipeptidyl carboxypeptidase 1 (DCP1) and butyrylcholinesterase (BCHE) gene interactions with the apolipoprotein E epsilon4 allele as risk factors in Alzheimer's disease and in Parkinson's disease with coexisting Alzheimer pathology

Alzheimer's disease (AD) and Parkinson's disease (PD) are genetically heterogeneous. Dipeptidyl carboxypeptidase 1 (DCP1) and butyrylcholinesterase (BCHE) genes may modify the risk of these disorders. We investigated whether common polymorphisms present in these genes operate as risk factors for AD and PD in Finnish subjects, independently or in concert with the apolipoprotein E epsilon4 allele (APOE epsilon4). Eighty late onset sporadic AD patients, 53 PD patients (34 of whom had concomitant AD pathology), and 67 control subjects were genotyped for the insertion (I)/deletion (D) polymorphism of DCP1 and the K variant of BCHE. In logistic regression analysis, the DCP1 *I allele in combination with APOE epsilon4 significantly increased the risk of AD (OR 30.0, 95% CI 7.3-123.7), compared to subjects carrying neither of the alleles. Similar analysis showed that the risk of AD was significantly increased in subjects carrying both the BCHE wild type (*WT/*WT) genotype and epsilon4 (OR 9.9, 95% CI 2.9-33.8), compared to those without this BCHE genotype and epsilon4. Further, the risk of PD with AD pathology was significantly increased for carriers of DCP1 *I and epsilon4 (OR 8.0, 95% CI 2.1-31.1). We thus conclude that, in Finns, interaction between DCP1 *I and epsilon4 increases the risk of AD as well as of PD with coexisting Alzheimer pathology, which underlines the importance of the DCP1 I/D polymorphism in the development of Alzheimer neuropathology, whereas the wild type BCHE genotype in combination with epsilon4 had a combined effect with regard to the risk of AD.

3D real-time imaging of the fetal heart

OBJECTIVE

The aim of this study was to evaluate the clinical utility of a novel 3D scanner system for real-time 3D fetal echocardiography.

METHOD

In a prospective study, 13 single, healthy 20- to 24-week-old fetuses were examined with conventional 2D and real-time 3D echocardiography. The visualization rates and imaging quality of standard cardiac views were compared between both methods.

RESULTS

The visualization rates of standard cardiac planes were found to be slightly increased and more easily obtainable in 3D imaging whereas the image quality showed better results with conventional 2D echocardiography.

CONCLUSION

Our data show that real-time 3D fetal echocardiography can be considered a useful tool in the evaluation of the fetal heart with the necessity for further refinement of the resolution quality

Controlling the growth of polymer trees: concepts and perspectives for hyperbranched polymers

This article summarizes basic principles and recent progress in the field of cascade-branched polymers. Methods for the preparation of macromolecules with hyperbranched structures are presented and compared concerning the extent of control over molecular weights and polydispersity. Step-growth and recently developed chain-growth strategies as well as enzyme and transition metal catalyzed polymerizations are discussed with respect to mechanism and future potential.

Dendrimers: relationship between structure and biocompatibility in vitro, and preliminary studies on the biodistribution of 125I-labelled polyamidoamine dendrimers in vivo

Dendrimers are highly branched macromolecules of low polydispersity that provide many exciting opportunities for design of novel drug-carriers, gene delivery systems and imaging agents. They hold promise in tissue targeting applications, controlled drug release and moreover, their interesting nanoscopic architecture might allow easier passage across biological barriers by transcytosis. However, from the vast array of structures currently emerging from synthetic chemistry it is essential to design molecules that have real potential for in vivo biological use. Here, polyamidoamine (PAMAM, Starburst), poly(propyleneimine) with either diaminobutane or diaminoethane as core, and poly(ethylene oxide) (PEO) grafted carbosilane (CSi-PEO) dendrimers were used to study systematically the effect of dendrimer generation and surface functionality on biological properties in vitro. Generally, dendrimers bearing -NH(2) termini displayed concentration- and in the case of PAMAM dendrimers generation-dependent haemolysis, and changes in red cell morphology were observed after 1 h even at low concentrations (10 microg/ml). At concentrations below 1 mg/ml CSi-PEO dendrimers and those dendrimers with carboxylate (COONa) terminal groups were neither haemolytic nor cytotoxic towards a panel of cell lines in vitro. In general, cationic dendrimers were cytotoxic (72 h incubation), displaying IC(50) values=50-300 microg/ml dependent on dendrimer-type, cell-type and generation. Preliminary studies with polyether dendrimers prepared by the convergent route showed that dendrimers with carboxylate and malonate surfaces were not haemolytic at 1 h, but after 24 h, unlike anionic PAMAM dendrimers they were lytic. Cationic 125I-labelled PAMAM dendrimers (gen 3 and 4) administered intravenously (i.v.) to Wistar rats ( approximately 10 microg/ml) were cleared rapidly from the circulation (<2% recovered dose in blood at 1 h). Anionic PAMAM dendrimers (gen 2.5, 3.5 and 5.5) showed longer circulation times ( approximately 20-40% recovered dose in blood at 1 h) with generation-dependent clearance rates; lower generations circulated longer. For both anionic and cationic species blood levels at 1 h correlated with the extent of liver capture observed (30-90% recovered dose at 1 h). 125I-Labelled PAMAM dendrimers injected intraperitoneally were transferred to the bloodstream within an hour and their subsequent biodistribution mirrored that seen following i.v. injection. Inherent toxicity would suggest it unlikely that higher generation cationic dendrimers will be suitable for parenteral administration, especially if they are to be used at a high dose. In addition it is clear that dendrimer structure must also be carefully tailored to avoid rapid hepatic uptake if targeting elsewhere (e.g. tumour targeting) is a primary objective.