Cryo-EM images of phase-separated lipid bilayer vesicles analyzed with a machine-learning approach.

Lateral lipid heterogeneity (i.e., raft formation) in biomembranes plays a functional role in living cells. Three-component mixtures of low- and high-melting lipids plus cholesterol offer a simplified experimental model for raft domains in which a liquid-disordered (Ld) phase coexists with a liquid-ordered (Lo) phase. Using such models, we recently showed that cryogenic electron microscopy (cryo-EM) can detect phase separation in lipid vesicles based on differences in bilayer thickness. However, the considerable noise within cryo-EM data poses a significant challenge for accurately determining the membrane phase state at high spatial resolution. To this end, we have developed an image-processing pipeline that utilizes machine learning (ML) to predict the bilayer phase in projection images of lipid vesicles. Importantly, the ML method exploits differences in both the thickness and molecular density of Lo compared to Ld, which leads to improved phase identification. To assess accuracy, we used artificial images of phase-separated lipid vesicles generated from all-atom molecular dynamics simulations of Lo and Ld phases. Synthetic ground-truth data sets mimicking a series of compositions along a tieline of Ld + Lo coexistence were created and then analyzed with various ML models. For all tieline compositions, we find that the ML approach can correctly identify the bilayer phase with >90% accuracy, thus providing a means to isolate the intensity profiles of coexisting Ld and Lo phases, as well as accurately determine domain-size distributions, number of domains, and phase-area fractions. The method described here provides a framework for characterizing nanoscopic lateral heterogeneities in membranes and paves the way for a more detailed understanding of raft properties in biological contexts.

Guidelines for medical management of nuclear/radiation emergencies.

Management of victim of radiation injury poses a wide spectrum of challenges to the health care provider starting with the evaluation of the damage, the kind of hospitalization and treatment and the regular monitoring of the patient. Undesirable clinical outcomes are probable if prodromal stage evolves rapidly and is severe. Critical systems like neurovascular, gastrointestinal, haematopoietic and cutaneous are afflicted in Acute Radiation Syndrome. Three main elements which are essential for assessment of prognosis and selection of treatment are vomiting onset time, kinetics of depletion of lymphocyte, and chromosome abnormalities. Larger incidents warrant, a well-structured national response system. Health care institutions must develop protocols to respond to radiation exposure related emergencies in tandem with the local response teams. Multidisciplinary approach between clinical specialists, nursing staff and psychological experts is of critical significance. External decontamination, estimation of dose and fluid and electrolyte replacements form part of support therapy. Reverse isolation, antacids, H2 blockers, use of reverse barrier nursing and prophylactic antimicrobials are part of the treatment plan. Patients with severe bone marrow damage will require blood products support. Increased recovery of neutrophils in radiationaccident victims is the rationale for the use of Colony Stimulating Factors. New directions are under evaluation which includes novel cytokine therapies like interleukin-7, keratinocyte growth factor, and thrombopoietin or its analogues. The final decision regarding allogenic haematopoietic stem cell transplant should be considered after considering the irradiation source, particularity of the situations or circumstances, associated injuries and disease.

Population-based incidence of diabetes in Australian youth aged 10-18 yr: increase in type 1 diabetes but not type 2 diabetes.

BACKGROUND: Global incidence of childhood type 2 diabetes has increased, with a greater rise amongst certain ethnic groups. OBJECTIVES: To examine the change in the incidence of type 1 and type 2 diabetes in Australian youth, aged 10-18 yr, in New South Wales, Australia. METHODS: Prospective population-based incidence study (2001-2008). Primary case ascertainment was from the Australasian Paediatric Endocrine Group Diabetes Register, secondary independent ascertainment from the National Diabetes Register. RESULTS: There were 202 incident cases of type 2 diabetes (96 boys, 48%). The mean age at diagnosis (±SD) was 14.6 ± 2.5 yr; 93% were overweight (International Obesity Taskforce Grade ≥1). Mean HbA1c was 8.8 ± 2.8%. Ethnicity was Caucasian 31%, Indigenous Australian 20%, Southeast Asian 11%, North African/Middle Eastern 9%, and NewZealander/Melanesian/Polynesian 8%. The mean annual incidence of type 2 diabetes was 3.0 per 100 000 per year (95% confidence interval (CI): 2.6-3.4) and did not change over time. The mean annual incidence of type 1 diabetes was 22.0 per 100 000 per year (95% CI: 20.8-23.1), and increased by 3.8% per year [incidence rate ratio IRR: 1.04, 95% CI: 1.02-1.06, p = 0.001]. Incidence was higher in Indigenous vs. non-Indigenous youth, IRR: 6.9 (95% CI: 4.7-10.2, p < 0.001). CONCLUSION: In 10-18 yr old youth, in Australia, the incidence of type 2 diabetes has remained steady during the last decade; however, the incidence of type 1 diabetes continues to rise. Most common diabetes in Australian youth is type 1 diabetes.

Reconstructing single hepatic artery with two arterial stumps: biliary complications in pediatric living donor liver transplantation.

INTRODUCTION: Liver grafts can at times have two hepatic arterial stumps. This can result in a dilemma whether to reconstruct single or both the arteries. Hepatic artery (HA) thrombosis is the most dreaded complication in pediatric living donor liver transplantation (LDLT) as it can result in biliary complications and subsequent graft loss. We herein report the feasibility of reconstructing single hepatic artery in pediatric living donor liver transplantation having two arterial stumps in the liver graft. MATERIALS AND METHODS: From 2008 to 2010, 87 pediatric patients undergoing LDLT were divided into three groups. Group 1 (n = 20): two HA stumps with two HA reconstruction, Group 2 (n = 22): two HA stumps with one HA reconstruction and Group 3 (n = 45): one HA stump with one HA reconstruction. The decision regarding the reconstruction of single or multiple HAs was made depending on the pre-operative radiological and intraoperative assessments. RESULTS: The incidence of HA thrombosis (p = 0.126) and biliary complications (p = 0.617), was similar in the three groups. CONCLUSION: Single HA reconstruction does not increase the risk of biliary strictures in pediatric LDLT recipients having dual hepatic arterial stumps in the liver graft.

Visualizing lipid membrane structure with cryo-EM: past, present, and future.

The development of electron cryomicroscopy (cryo-EM) has evolved immensely in the last several decades and is now well-established in the analysis of protein structure both in isolation and in their cellular context. This review focuses on the history and application of cryo-EM to the analysis of membrane architecture. Parallels between the levels of organization of protein structure are useful in organizing the discussion of the unique parameters that influence membrane structure and function. Importantly, the timescales of lipid motion in bilayers with respect to the timescales of sample vitrification is discussed and reveals what types of membrane structure can be reliably extracted in cryo-EM images of vitrified samples. Appreciating these limitations, a review of the application of cryo-EM to examine the lateral organization of ordered and disordered domains in reconstituted and biologically derived membranes is provided. Finally, a brief outlook for further development and application of cryo-EM to the analysis of membrane architecture is provided.

Multi-contrast high-field quality image synthesis for portable low-field MRI using generative adversarial networks and paired data.

Introduction: Portable low-field strength (64mT) MRI scanners promise to increase access to neuroimaging for clinical and research purposes, however these devices produce lower quality images compared to high-field scanners. In this study, we developed and evaluated a deep learning architecture to generate high-field quality brain images from low-field inputs using a paired dataset of multiple sclerosis (MS) patients scanned at 64mT and 3T. Methods: A total of 49 MS patients were scanned on portable 64mT and standard 3T scanners at Penn (n=25) or the National Institutes of Health (NIH, n=24) with T1-weighted, T2-weighted and FLAIR acquisitions. Using this paired data, we developed a generative adversarial network (GAN) architecture for low- to high-field image translation (LowGAN). We then evaluated synthesized images with respect to image quality, brain morphometry, and white matter lesions. Results: Synthetic high-field images demonstrated visually superior quality compared to low-field inputs and significantly higher normalized cross-correlation (NCC) to actual high-field images for T1 (p=0.001) and FLAIR (p<0.001) contrasts. LowGAN generally outperformed the current state-of-the-art for low-field volumetrics. For example, thalamic, lateral ventricle, and total cortical volumes in LowGAN outputs did not differ significantly from 3T measurements. Synthetic outputs preserved MS lesions and captured a known inverse relationship between total lesion volume and thalamic volume. Conclusions: LowGAN generates synthetic high-field images with comparable visual and quantitative quality to actual high-field scans. Enhancing portable MRI image quality could add value and boost clinician confidence, enabling wider adoption of this technology.

Elastography of soft materials and tissues by holographic imaging of surface acoustic waves.

We use optical interferometry to capture coherent surface acoustic waves for elastographic imaging. An inverse method is employed to convert multi-frequency data into an elastic depth profile. Using this method, we image elastic properties over a 55 mm range with <5 mm resolution. For relevance to breast cancer detection, we employ a tissue phantom with a tumor-like inclusion. Holographic elastography is also shown to be well-behaved in ex vivo tissue, revealing the subsurface position of a bone. Because digital holography can assess waves over a wide surface area, this constitutes a flexible new platform for large volume and non-invasive elastography.

Sensitivity of portable low-field magnetic resonance imaging for multiple sclerosis lesions.

Magnetic resonance imaging (MRI) is a fundamental tool in the diagnosis and management of neurological diseases such as multiple sclerosis (MS). New portable, low-field strength, MRI scanners could potentially lower financial and technical barriers to neuroimaging and reach underserved or disabled populations, but the sensitivity of these devices for MS lesions is unknown. We sought to determine if white matter lesions can be detected on a portable 64mT scanner, compare automated lesion segmentations and total lesion volume between paired 3T and 64mT scans, identify features that contribute to lesion detection accuracy, and explore super-resolution imaging at low-field. In this prospective, cross-sectional study, same-day brain MRI (FLAIR, T1w, and T2w) scans were collected from 36 adults (32 women; mean age, 50 ± 14 years) with known or suspected MS using Siemens 3T (FLAIR: 1 mm isotropic, T1w: 1 mm isotropic, and T2w: 0.34-0.5 × 0.34-0.5 × 3-5 mm) and Hyperfine 64mT (FLAIR: 1.6 × 1.6 × 5 mm, T1w: 1.5 × 1.5 × 5 mm, and T2w: 1.5 × 1.5 × 5 mm) scanners at two centers. Images were reviewed by neuroradiologists. MS lesions were measured manually and segmented using an automated algorithm. Statistical analyses assessed accuracy and variability of segmentations across scanners and systematic scanner biases in automated volumetric measurements. Lesions were identified on 64mT scans in 94% (31/33) of patients with confirmed MS. The average smallest lesions manually detected were 5.7 ± 1.3 mm in maximum diameter at 64mT vs 2.1 ± 0.6 mm at 3T, approaching the spatial resolution of the respective scanner sequences (3T: 1 mm, 64mT: 5 mm slice thickness). Automated lesion volume estimates were highly correlated between 3T and 64mT scans (r = 0.89, p < 0.001). Bland-Altman analysis identified bias in 64mT segmentations (mean = 1.6 ml, standard error = 5.2 ml, limits of agreement = -19.0-15.9 ml), which over-estimated low lesion volume and under-estimated high volume (r = 0.74, p < 0.001). Visual inspection revealed over-segmentation was driven venous hyperintensities on 64mT T2-FLAIR. Lesion size drove segmentation accuracy, with 93% of lesions > 1.0 ml and all lesions > 1.5 ml being detected. Using multi-acquisition volume averaging, we were able to generate 1.6 mm isotropic images on the 64mT device. Overall, our results demonstrate that in established MS, a portable 64mT MRI scanner can identify white matter lesions, and that automated estimates of total lesion volume correlate with measurements from 3T scans.

Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy.

The SARS-CoV-2 pandemic has differentially impacted populations across race and ethnicity. A multi-omic approach represents a powerful tool to examine risk across multi-ancestry genomes. We leverage a pandemic tracking strategy in which we sequence viral and host genomes and transcriptomes from nasopharyngeal swabs of 1049 individuals (736 SARS-CoV-2 positive and 313 SARS-CoV-2 negative) and integrate them with digital phenotypes from electronic health records from a diverse catchment area in Northern California. Genome-wide association disaggregated by admixture mapping reveals novel COVID-19-severity-associated regions containing previously reported markers of neurologic, pulmonary and viral disease susceptibility. Phylodynamic tracking of consensus viral genomes reveals no association with disease severity or inferred ancestry. Summary data from multiomic investigation reveals metagenomic and HLA associations with severe COVID-19. The wealth of data available from residual nasopharyngeal swabs in combination with clinical data abstracted automatically at scale highlights a powerful strategy for pandemic tracking, and reveals distinct epidemiologic, genetic, and biological associations for those at the highest risk.

Recent developments and strategies for the discovery of TACE inhibitors.

INTRODUCTION: TNF-α plays a central role in certain autoimmune diseases as well as in inflammation. The current strategy for excluding TNF-α from circulation is to selectively inhibit TNF-α converting enzyme (TACE), an enzyme that cleaves mTNF-α to active TNF-α. Various TACE inhibitors have been discovered by using different strategies to control inflammatory diseases, cancer, and cardiac hypertrophy. AREAS COVERED: The present article summarizes the design and discovery of novel TACE inhibitors that have been reported in the literature since 2012 onwards. It also includes some reports concerning the new role that TACE plays in cancer and cardiac hypertrophy. EXPERT OPINION: So far, undertaken studies that have looked to design and develop small TACE inhibitors have been discouraging due to the failure of any TACE inhibitors to hit the market. However, some of the latest developments, such as with tartrate-based inhibitors, has given hope to the potentiality of a viable novel selective TACE inhibitor therapeutic in the future. Indeed, some of the novel peptidomimetics and monoclonal antibodies have great potential to pave the way for an effective and safe therapy by selectively inhibiting TACE enzyme.

Effect of Seabuckthorn (Hippophae rhamnoides) flavone on immune system: an in-vitro approach.

There are several reports, which suggest that the consumption of foods rich in flavonoids is associated with a lower incidence of certain degenerative diseases, including cardiovascular disease. Flavones, of Seabuckthorn (SBT) (Hippophae rhamnoides L.) fruit berry can modulate the production and level of several signaling molecules associated with immune function and inflammation in vitro, including several cytokines. We have evaluated the immunomodulatory activity of ethanolic solution of SBT flavone (FLV) in human peripheral blood mononuclear cells (PBMCs). The SBT flavone was found to stimulate production of interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-alpha) in PBMCs. However, increased expressions of p-IkappaB, NF-kappaB, and p-p38 were found in flavone-treated human PBMCs with significantly suppressed expression of CD25 (IL-2R). There was no alteration found in the nitric oxide (NO) production in mouse macrophage cell line RAW 264.7. These observations suggest that stimulation of IL-6 and TNF-alpha secretion may contribute to the putative beneficial effects of dietary flavone against microbial infection.

Temperature- and concentration-dependence of urea permeability of human erythrocytes determined by NMR.

The temperature- and concentration-dependence of [13C]urea self-exchange across the human red cell membrane has been determined by NMR measurements of T1 (spin-lattice) relaxation times. T1 for intracellular label is 17 s, which is much longer than the urea exchange time across the cell membrane (about 0.5 s). T1 for urea in extracellular solution is quenched with 17 mM of impermeable Mn2+ in less than 2 ms. Hence the observed T1 (corrected for intracellular decay) is a measure of urea exchange across the cell membrane. The method is tested by showing both PCMBS and increasing concentrations of urea lengthen T1. Urea exchange permeability, defined as Purea = flux/conc, can be described by Purea = Vmax/(K1/2 + conc). Studies of temperature-dependence showed that activation energies were strongly dependent on both temperature and concentration. However, this apparently anomalous behavior was resolved into two well-behaved functions, K1/2 and Vmax, with linear Arrhenius plots and apparent 'activation energies' of 15.5 and 12.4 kcal/mol, respectively. These were used to construct an equation for calculating Purea at any concentration and temperature. Assuming a simple channel model with single binding, K1/2 becomes the dissociation equilibrium constant for the site with delta H degree = 15.5 kcal/mol and delta S degree = 51.8 cal/(mol.deg); dissociation is entropically driven.

Decreased androgen-responsive growth of human prostate cancer is associated with increased genetic alterations.

Genetic mechanisms involved in prostate tumor progression from the androgen-responsive to androgen-unresponsive stage are not well understood because of the tremendous heterogeneity in the tumor as well as the lack of suitable models. Using 165 repeat microsatellite DNA markers distributed equally over all of the chromosomes, we determined an association between genetic alterations and androgen-unresponsive growth in three stages of LNCaP cell model (C33: early, androgen-responsive; C51: mid, decreased androgen-responsive; and C81: late, androgen-unresponsive and increased tumorigenicity). Furthermore, the genetic alterations were confirmed in laser microdissected normal and cancerous tissues from 15 clinical samples of human prostatic adenocarcinomas using selected markers. A stem-line karyotype analysis exhibited an identical chromosomal pattern in both C33 and C81 stage cells except for the structural rearrangements of chromosome 3 and a gain of one copy of the Y chromosome in the androgen-unresponsive C81 stage cells. Nine microsatellite DNA markers on seven different chromosomes (1, 4, 5, 11, 17, 18, and 19) showed microsatellite instability (MSI) in both C51 and C81 stage cells. Additionally, 23 markers on 15 different chromosomes revealed MSI in C81 cells. Chromosomal regions demonstrating allelic loss (AL) include 1q, 3p, 5p, 8q, 9q, and 13q in C51 and C81 cells. In clinical human specimens, MSI was observed on chromosomes 1 (20%), 5 (23%), 17 (40%), and 19 (36%), whereas ALs were found 40% on chromosomal region 1q, 20% on 3p, 26% on 5p and 8q, and 33% on 13q. In conclusion, the LNCaP cell model showed the increasing number of genetic changes including MSI and AL. These increased genetic alterations may be associated with the development of the androgen-unresponsive phenotype.

Molecular evolution of the AMP-forming Acetyl-CoA synthetase.

Acetyl-CoA-Synthetase (ACS) is involved in the production of acetate, a major metabolite in numerous organisms. There are two forms of this enzyme: ADP-forming ACS and ATP-forming ACS. We focus mainly on the AMP-forming ACS gene, which is relatively well conserved in eubacteria, archeaebacteria, and eukaryotes. BLAST searches in databases showed 30 protein sequences significantly related to the ACS. Most of these sequences were identified as ACS but three of them, belonging to the mammalian species, were annotated as another gene named: the SA gene, which is involved in the essential hypertension. The ACS and SA genes probably derived from a duplication of an ancestral gene but have acquired different functions. Six conserved regions of the ACS protein were defined across the three domains of life. While the precise function of the conserved regions remains unknown, they are probably involved in the enzymatic activity. Among eukaryotes, we found a high variability with respect to the number and the position of introns. However, some positions are conserved between fungi and a nematode. A maximum likelihood tree based upon the conserved regions showed that all sequences except the one from B. subtilis, belong to two basic groups: one the SA-like group including sequences from Archaeoglobus fulgidus and Streptomyces coelicolor, and second, the ACS group. The later can be further divided in two parts: a prokaryotic one including eubacteria and an archaebacterium, and a eukaryotic group within which two proteobacterial sequences branch including ACS from the alpha-proteobacterium Rhodobacter capsulatus. Within the eukaryotic group, bootstrap support is very low, but overall the data are consistent with the view that eukaryotes acquired their ACS gene from the ancestors of mitochondria. The localization of this enzyme in eukaryotic mitochondria is the additional evidence in favor of this interpretation.

Chill-coma tolerance, a major climatic adaptation among Drosophila species.

Most drosophilid species can be classified either as temperate or tropical. Adults of species were submitted to a cold treatment (0 degrees C) and then brought back to ambient temperature. They generally exhibited a chill coma and the time needed to recover was measured. We found in a set of 26 temperate species that recovery was rapid (average 1.8 min, range 0.15-4.9). In contrast, a long recovery time (average 56 min, range 24-120) was observed for 48 tropical species. A few species, like Drosophila melanogaster, are cosmopolitan and can proliferate under temperate and tropical climates. In 9 of 10 such species, slight genetic differences were found: a shorter recovery in temperate than in tropical populations. Comparing physiological data to phylogeny suggests that chill-coma tolerance has been a recurrent adaptation that is selected for in cold climates but tends to disappear under a permanently warm environment. This major climatic adaptation, evidenced in drosophilids, seems to occur in other insect groups also.

The genetics of phenotypic plasticity. IX. Genetic architecture, temperature, and sex differences in Drosophila melanogaster.

We examined the genetic architecture of plasticity of thorax and wing length in response to temperature in Drosophila melanogaster. Reaction norms as a function of growth temperature were analyzed in 20 isofemale lines in a natural population collected from Grande Ferrade near Bordeaux (southern France) in two different years. We found evidence for a complex genetic architecture underlying the reaction norms and differences between males and females. Reaction norms were negative quadratics. Genetic correlations were moderately high between traits within environments. Among characteristic values, the magnitudes of genetic correlations varied among traits and sexes. We hypothesized that genetic correlations among environments would decrease as temperatures became more different. This expectation was upheld for only one trait, female thorax length. For males for both traits, the correlations were large for both very similar and very different temperatures. These correlations may constrain the evolution of the shape of the reaction norms. Whether the extent of independence implies specific regulatory genes or only a specific allelic regulation of trait genes can not be decided from our results.

Mucins in protozoan parasites.

Studies on host-pathogen interactions have led to the discovery of various cell surface associated and secretory molecules. Mucins and mucin-like molecules have recently been described in several protozoan parasites, at different stages of the life cycle. These share many structural and compositional features with mammalian mucins, but vary in several other aspects. It is now becoming evident that mucins in parasite are involved in cell-cell interaction and cell surface protection, thus helping the parasite to establish infection. A large number of mucin like genes from the parasite genome have been reported, and their expression differ during the developmental stages of the parasite. In this review, we describe the structure and functions of mucin and mucin-like molecules in parasitic protozoa.

Epithelioid cell nevus of the iris.

A 21-year-old woman had a progressively enlarging pigmented tumor of the iris and anterior chamber angle in the right eye. Because the lesion was suspected to be a malignant melanoma, it was removed by an iridocyclectomy. Histopathologic examination disclosed the tumor to be a benign epithelioid cell nevus. This article describes the clinical and pathologic features of this rare iris tumor.