Profiling of Copy Number Alterations Using Low-Coverage Whole-Genome Sequencing Informs Differential Diagnosis and Prognosis in Primary Cutaneous Follicle Center Lymphoma.

Primary cutaneous follicle center lymphoma (PCFCL) has an excellent prognosis using local treatment, whereas nodal follicular lymphoma (nFL), occasionally presenting with cutaneous spread, often requires systemic therapy. Distinction of the 2 diseases based on histopathology alone might be challenging. Copy number alterations (CNAs) have scarcely been explored on a genome-wide scale in PCFCL; however, they might serve as potential biomarkers during differential diagnosis and risk stratification. Low-coverage whole-genome sequencing is a robust, high-throughput method for genome-wide copy number profiling. In this study, we analyzed 28 PCFCL samples from 20 patients and compared the copy number profiles with a cohort of diagnostic samples of 64 nFL patients. Although the copy number profile of PCFCL was similar to that of nFL, PCFCL lacked amplifications of 18q, with the frequency peaking at 18q21.33 in nFL cases involving the BCL2 locus (PCFCL: 5.0% vs nFL: 31.3%, P = .018, Fisher exact test). Development of distant cutaneous spread was significantly associated with higher genomic instability including the proportion of genome altered (0.02 vs 0.13, P = .033) and number of CNAs (2 vs 9 P = .017), as well as the enrichment of 2p22.2-p15 amplification involving REL and XPO1 (6.3% vs 60.0%, P = .005), 3q23-q24 amplification (0.0% vs 50.0%, P = .004), 6q16.1-q23.3 deletion (6.3% vs 50.0%, P = .018), and 9p21.3 deletion covering CDKN2A and CDKN2B loci (0.0% vs 40.0%, P = .014, all Fisher exact test) in PCFCL. Analysis of sequential tumor samples in 2 cases harboring an unfavorable clinical course pointed to the acquisition of 2p amplification in the earliest common progenitor underlining its pivotal role in malignant transformation. By performing genome-wide copy number profiling on the largest patient cohort to date, we identified distinctive CNA alterations conceivably facilitating the differential diagnosis of PCFCL and secondary cutaneous involvement of nFL and potentially aiding the risk stratification of patients with PCFCL in the future.

Combined immunosuppression for acquired hemophilia A: CyDRi is a highly effective low-toxicity regimen.

Acquired hemophilia A (AHA) is a rare severe autoimmune bleeding disorder with significant morbidity and mortality. Although critical for disease control, there is no consensus for the best immunosuppressive regimen. Most authors use steroids first line, followed by other agents for steroid failures. Upfront combined regimens offer the advantage of reduced steroid exposure and toxicity as well as increased efficacy. We retrospectively analyzed data from 32 patients with AHA treated on an identical such institutional protocol: cyclophosphamide 1000 mg on days 1 and 22, dexamethasone 40 mg on days 1, 8, 15, and 22, and rituximab 100 mg on days 1, 8, 15, and 22 (the regimen was termed CyDRi). All patients received at least 1 cycle of CyDRi. If necessary, CyDRi was repeated until remission, no sooner than day 43 of the previous cycle. Bleeding control was rapidly achieved. The median time for bleeding control was 15.5 days (range, 0-429 days; interquartile range, 2.5-29.5 days). Thirty-one (96.8%) of 32 patients achieved durable complete remission (CR); 29 (90.6%) of 32 patients were alive at last follow-up, all of them in CR. The median time to reach first CR was 77 days (range, 19-939 days; interquartile range, 31-115 days). Toxicity and side effects were acceptable and milder than those of commonly used, prolonged steroid therapies. In conclusion, the CyDRi regimen produced markedly higher CR rates and overall survival than currently used sequential regimens. Taken together, CyDRi proved to be an attractive option for the immunosuppression of elderly patients with AHA.

Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.

Fertilization in angiosperms involves the germination of pollen on the stigma, followed by the extrusion of a pollen tube that elongates through the style and delivers two sperm cells to the embryo sac. Sexual selection could occur throughout this process when male gametophytes compete for fertilization. The strength of sexual selection during pollen competition should be affected by the number of genotypes deposited on the stigma. As increased self-fertilization reduces the number of mating partners, and the genetic diversity and heterozygosity of populations, it should thereby reduce the intensity of sexual selection during pollen competition. Despite the prevalence of mating system shifts, few studies have directly compared the molecular signatures of sexual selection during pollen competition in populations with different mating systems. Here we analyzed whole-genome sequences from natural populations of Arabis alpina, a species showing mating system variation across its distribution, to test whether shifts from cross- to self-fertilization result in molecular signatures consistent with sexual selection on genes involved in pollen competition. We found evidence for efficient purifying selection on genes expressed in vegetative pollen, and overall weaker selection on sperm-expressed genes. This pattern was robust when controlling for gene expression level and specificity. In agreement with the expectation that sexual selection intensifies under cross-fertilization, we found that the efficacy of purifying selection on male gametophyte-expressed genes was significantly stronger in genetically more diverse and outbred populations. Our results show that intra-sexual competition shapes the evolution of pollen-expressed genes, and that its strength fades with increasing self-fertilization rates.

Culture-negative Capnocytophaga canimorsus meningitis diagnosed by 16s ribosomal RNA polymerase chain reaction in an immunocompetent veterinarian and a review of the literature.

Capnocytophaga canimorsus is a fastidious, capnophilic and facultative anaerobic Gram-negative rod found commonly in the oral flora of dogs that may cause zoonotic infections such as cellulitis and eye infections. In immunocompromised patients, it may cause fulminant sepsis. Meningitis due to C. canimorsus is, however, a rare manifestation. This is the first reported case of C. canimorsus meningitis in Australia in an immunocompetent veterinarian diagnosed by 16s ribosomal RNA polymerase chain reaction.

Dean-Flow Affected Lateral Focusing and Separation of Particles and Cells in Periodically Inhomogeneous Microfluidic Channels.

The purpose of the recent work is to give a better explanation of how Dean vortices affect lateral focusing, and to understand how cell morphology can alter the focusing position compared to spherical particles. The position and extent of the focused region were investigated using polystyrene fluorescent beads with different bead diameters (Ø = 0.5, 1.1, 1.97, 2.9, 4.8, 5.4, 6.08, 10.2, 15.8, 16.5 µm) at different flow rates (0.5, 1, 2 µL/s). Size-dependent focusing generated a precise map of the equilibrium positions of the spherical beads at the end of the periodically altering channels, which gave a good benchmark for focusing multi-dimensional particles and cells. The biological samples used for experiments were rod-shaped Escherichia coli (E. coli), discoid biconcave-shaped red blood cells (RBC), round or ovoid-shaped yeast, Saccharomyces cerevisiae, and soft-irregular-shaped HeLa cancer-cell-line cells to understand how the shape of the cells affects the focusing position at the end of the channel.

Selection on Accessible Chromatin Regions in Capsella grandiflora.

Accurate estimates of genome-wide rates and fitness effects of new mutations are essential for an improved understanding of molecular evolutionary processes. Although eukaryotic genomes generally contain a large noncoding fraction, functional noncoding regions and fitness effects of mutations in such regions are still incompletely characterized. A promising approach to characterize functional noncoding regions relies on identifying accessible chromatin regions (ACRs) tightly associated with regulatory DNA. Here, we applied this approach to identify and estimate selection on ACRs in Capsella grandiflora, a crucifer species ideal for population genomic quantification of selection due to its favorable population demography. We describe a population-wide ACR distribution based on ATAC-seq data for leaf samples of 16 individuals from a natural population. We use population genomic methods to estimate fitness effects and proportions of positively selected fixations (α) in ACRs and find that intergenic ACRs harbor a considerable fraction of weakly deleterious new mutations, as well as a significantly higher proportion of strongly deleterious mutations than comparable inaccessible intergenic regions. ACRs are enriched for expression quantitative trait loci (eQTL) and depleted of transposable element insertions, as expected if intergenic ACRs are under selection because they harbor regulatory regions. By integrating empirical identification of intergenic ACRs with analyses of eQTL and population genomic analyses of selection, we demonstrate that intergenic regulatory regions are an important source of nearly neutral mutations. These results improve our understanding of selection on noncoding regions and the role of nearly neutral mutations for evolutionary processes in outcrossing Brassicaceae species.

Comparative Assessment of the Inhibitory Potential of the Herbicide Glyphosate and Its Structural Analogs on RGD-Specific Integrins Using Enzyme-Linked Immunosorbent Assays.

Transmembrane glycoprotein integrins play crucial roles in biochemical processes, and by their inhibition or activation, different signal pathways can be disrupted, leading to abnormal physiological functions. We have previously demonstrated the inhibitory effect of glyphosate herbicide's active ingredient on cell adhesion and its αvß3 integrin antagonist effect. Therefore, it appeared particularly exciting to investigate inhibition of glyphosate and its metabolites on a wider range of Arg-Gly-Asp (RGD) binding integrins, namely αvß3, α5ß1 and αllbß3. Thus, the purpose of this study was to assess how extended the inhibitory effect observed for glyphosate on the integrin αvß3 is in terms of other RGD integrins and other structurally or metabolically related derivatives of glyphosate. Five different experimental setups using enzyme-linked immunosorbent assays were applied: (i) αvß3 binding to a synthetic polymer containing RGD; (ii) αvß3 binding to its extracellular matrix (ECM) protein, vitronectin; (iii) α5ß1 binding to the above polymer containing RGD; (iv) αllbß3 binding to its ECM protein, fibrinogen and (v) αvß3 binding to the SARS-CoV-2 spike protein receptor binding domain. Total inhibition of αvß3 binding to RGD was detected for glyphosate and its main metabolite, aminomethylphosphonic acid (AMPA), as well as for acetylglycine on α5ß1 binding to RGD.

Accelerated treatment of endocarditis-The POET II trial: Rationale and design of a randomized controlled trial.

BACKGROUND: The optimal antibiotic treatment length for infective endocarditis (IE) is uncertain. International guidelines recommend treatment duration of up to 6 weeks for patients with left-sided IE but are primarily based on historical data and expert opinion. Efficacies of modern therapies, fast recovery seen in many patients with IE, and complications to long hospital stays challenge the rationale for fixed treatment durations in all patients. OBJECTIVE: The objective was to conduct a noninferiority randomized controlled trial (acronym POET II) investigating the safety of accelerated (shortened) antibiotic therapy as compared to standard duration in patients with left-sided IE. METHODS: The POET II trial is a multicenter, multinational, open-label, noninferiority randomized controlled trial. Patients with definite left-sided IE due to Streptococcus spp, Staphylococcus aureus, or Enterococcus faecalis will be eligible for enrolment. Each patient will be randomized to accelerated antibiotic treatment or standard-length treatment (1:1) following clinical stabilization as defined by clinical parameters, laboratory values, and transesophageal echocardiography findings. Accelerated treatment will be between 2 and 4 weeks, whereas standard-length treatment will be between 4 and 6 weeks, depending on microbiologic etiology, complications, need for valve surgery, and prosthetic versus native valve endocarditis. The primary outcome is a composite of all-cause mortality, unplanned cardiac surgery, relapse of bacteremia, or embolization within 6 months of randomization. CONCLUSIONS: The POET II trial will investigate the safety of accelerated antibiotic therapy for patients with left-sided IE caused by Streptococcus spp, Staphylococcus aureus, or Enterococcus faecalis. The results of the POET II trial will improve the evidence base of treatment recommendations, and clinical practice may be altered.

Oxidization increases the binding of EGCG to serum albumin revealed by kinetic data from label-free optical biosensor with reference channel.

Epigallocatechin-gallate (EGCG) is the main polyphenol ingredient of green tea. This compound is a strong antioxidant and oxidizes easily. Numerous studies demonstrated its beneficial effects on the human health, for example its anticancer and anti-inflammatory activity. In the body, EGCG is transported by serum albumin. EGCG easily oxidizes and the interactions of the oxidized form presumably present significant differences. However, the presence of oxidized EGCG is usually neglected in the literature and its effects have not been investigated in detail. Here, we applied the label-free grating coupled interferometry method that performs dual-channel measurements. The measured kinetic signal can be compensated with a signal of a reference channel at each measurement time. By testing both hydrophilic and hydrophobic platforms, we found that EGCG can bind to a wide range of surfaces. Exploiting the dual-channel referencing ability as well as the unique sensitivity and throughput of the employed label-free technique, the experiments revealed the specific interactions between bovine serum albumin (BSA) and EGCG and determined the characteristic dissociation constant (Kd) of the binding equilibrium. The obtained binding constants were compared to literature values, showing reasonable agreement with NMR data. Besides the native EGCG, the oxidized form of EGCG was also examined, whose binding behaviors to serum albumins have never been studied. Overstoichiometric binding obtained; BSA has stronger and weaker binding sites, which could be characterized by two separate Kd values. Furthermore, EGCG oxidization increased the bound amount.

Biomimetic Dextran-Based Hydrogel Layers for Cell Micropatterning over Large Areas Using the FluidFM BOT Technology.

Micropatterning of living single cells and cell clusters over millimeter-centimeter scale areas is of high demand in the development of cell-based biosensors. Micropatterning methodologies require both a suitable biomimetic support and a printing technology. In this work, we present the micropatterning of living mammalian cells on carboxymethyl dextran (CMD) hydrogel layers using the FluidFM BOT technology. In contrast to the ultrathin (few nanometers thick in the dry state) CMD films generally used in label-free biosensor applications, we developed CMD layers with thicknesses of several tens of nanometers in order to provide support for the controlled adhesion of living cells. The fabrication method and detailed characterization of the CMD layers are also described. The antifouling ability of the CMD surfaces is demonstrated by in situ optical waveguide lightmode spectroscopy measurements using serum modeling proteins with different electrostatic properties and molecular weights. Cell micropatterning on the CMD surface was obtained by printing cell adhesion mediating cRGDfK peptide molecules (cyclo(Arg-Gly-Asp-d-Phe-Lys)) directly from aqueous solution using microchanneled cantilevers with subsequent incubation of the printed surfaces in the living cell culture. Uniquely, we present cell patterns with different geometries (spot, line, and grid arrays) covering both micrometer and millimeter-centimeter scale areas. The adhered patterns were analyzed by phase contrast microscopy and the adhesion process on the patterns was real-time monitored by digital holographic microscopy, enabling to quantify the survival and migration of cells on the printed cRGDfK arrays.

Single-cell expression noise and gene-body methylation in Arabidopsis thaliana.

Gene-body methylation (gbM) refers to an increased level of methylated cytosines specifically in a CG sequence context within genes. gbM is found in plant genes with intermediate expression level, which evolve slowly, and is often broadly conserved across millions of years of evolution. Intriguingly however, some plants lack gbM, and thus it remains unclear whether gbM has a function. In animals, there is support for a role of gbM in reducing erroneous transcription and transcription noise, but so far most studies in plants have tested for an effect of gbM on expression level, not noise. Here, we therefore tested whether gbM was associated with reduced expression noise in Arabidopsis thaliana, using single-cell transcriptome sequencing data from root quiescent centre cells. We find that gbM genes have lower expression noise levels than unmethylated genes. However, an analysis of covariance revealed that, if other genomic features are taken into account, this association disappears. Nonetheless, gbM genes were more consistently expressed across single-cell samples, supporting previous inference that gbM genes are constitutively expressed. Finally, we observed that fewer RNAseq reads map to introns of gbM genes than to introns of unmethylated genes, which indicates that gbM might be involved in reducing erroneous transcription by reducing intron retention.

Biophysical characteristics of proteins and living cells exposed to the green tea polyphenol epigallocatechin-3-gallate (EGCg): review of recent advances from molecular mechanisms to nanomedicine and clinical trials.

Herbs and traditional medicines have been applied for thousands of years, but researchers started to study their mode of action at the molecular, cellular and tissue levels only recently. Nowadays, just like in ancient times, natural compounds are still determining factors in remedies. To support this statement, the recently won Nobel Prize for an anti-malaria agent from the plant sweet wormwood, which had been used to effectively treat the disease, could be mentioned. Among natural compounds and traditional Chinese medicines, the green tea polyphenol epigallocatechin gallate (EGCg) is one of the most studied active substances. In the present review, we summarize the molecular scale interactions of proteins and EGCg with special focus on its limited stability and antioxidant properties. We outline the observed biophysical effects of EGCg on various cell lines and cultures. The alteration of cell adhesion, motility, migration, stiffness, apoptosis, proliferation as well as the different impacts on normal and cancer cells are all reviewed. We also handle the works performed using animal models, microbes and clinical trials. Novel ways to develop its utilization for therapeutic purposes in the future are discussed too, for instance, using nanoparticles and green tea polyphenols together to cure illnesses and the combination of EGCg and anticancer compounds to intensify their effects. The limitations of the employed experimental models and criticisms of the interpretation of the obtained experimental data are summarized as well.

A case of disseminated Mycobacterium bovis 2 years post-intravesicular Bacillus Calmette-Guérin therapy for superficial urinary bladder cancer.

Disseminated Mycobacterium bovis is an uncommon side-effect of intravesical Bacillus Calmette-Guérin (BCG) therapy that may be mediated through Mycobacteraemia. This case report, of a 77-year-old man with a history of intravesical BCG therapy and recent cardiac surgery, highlights the need for patients with similar features on history, presenting with generalised symptoms, to have mycobacterial cultures included in their workup.

Plasmon-enhanced two-channel in situ Kretschmann ellipsometry of protein adsorption, cellular adhesion and polyelectrolyte deposition on titania nanostructures.

Plasmon-enhanced in situ spectroscopic ellipsometry was realized using the Kretschmann geometry. A 10-µL flow cell was designed for multi-channel measurements using a semi-cylindrical lens. Dual-channel monitoring of the layer formation of different organic structures has been demonstrated on titania nanoparticle thin films supported by gold. Complex modeling capabilities as well as a sensitivity of ~40 pg/mm2 with a time resolution of 1 s was achieved. The surface adsorption was enhanced by the titania nanoparticles due to the larger specific surface and nanoroughness, which is consistent with our previous results on titanate nanotubes.

Comparison of Changes in Tensile Strength in Three Different Flexible Epidural Catheters Under Various Conditions.

BACKGROUND: Rarely, epidural catheters may fracture upon removal or insertion. Understanding some of the mechanical properties of epidural catheters, such as their tensile strength and how external factors (including temperature) can influence their strength, will aid physicians in making decisions if faced with an entrapped catheter. In the present study, we evaluated the impact in tensile strength when catheters are exposed to 37 ± 1°C, after the removal of the inner metal coil and after the injection of sterile saline through the catheter. METHODS: We analyzed the tensile strength of a total of 120 catheters (19-gauge) from 3 different brands and materials. The reinforced epidural catheters were affixed to opposing, specially designed tensile test fixtures and then installed in an Applied Test System tensile test apparatus. We evaluated the strength of 10 catheters from different brands and materials for each of the following variables: at room temperature (control group), after the removal of the inner wire present in all the flexible catheters tested, injection of normal saline, and at 37 ± 1°C. RESULTS: When compared with their control groups, the Arrow catheter (2.85 kg) was shown to be superior to B-Braun (2.17 kg; P < 0.0001) and Smith catheters (2.33 kg; P < 0.0005). No statistical difference was noted between the Smith and B-Braun catheters (P = 0.39). When comparing catheters after wire removal against their respective control group, no statistical difference was noted. A decrease in tensile strength was noted in the B-Braun catheters (1.53 kg) when tested at 37°C (P ≤ 0.0001). In contrast, the Smith and the Arrow catheters did not show a statistically significant change when tested at 37°C (P = 1.0 and P = 0.063, respectively). After the injection of normal saline, the Arrow (2.33 kg) and the B-Braun (1.58 kg) catheters showed a decrease in tensile strength (P = 0.0010 and P = 0.0001, respectively). CONCLUSIONS: The current recommendation of injecting saline through an entrapped catheter resulted in a decrease in tensile strength of the Arrow and B-Braun catheters. A decrease in tensile strength also was noted in the B-Braun catheters when tested at 37°C. There is no benefit, at least in terms of tensile strength, in removing the wire or inner coil from any of the tested brands. The Smith catheter was the most resilient, showing no decrease in tensile strength at 37°C and after the injection of normal saline when compared with control.

Assistive products and the Sustainable Development Goals (SDGs).

The Sustainable Development Goals (SDGs) have placed great emphasis on the need for much greater social inclusion, and on making deliberate efforts to reach marginalized groups. People with disabilities are often marginalized through their lack of access to a range of services and opportunities. Assistive products can help people overcome impairments and barriers enabling them to be active, participating and productive members of society. Assistive products are vital for people with disabilities, frailty and chronic illnesses; and for those with mental health problems, and gradual cognitive and physical decline characteristic of aging populations. This paper illustrates how the achievement of each of the 17 SDGs can be facilitated by the use of assistive products. Without promoting the availability of assistive products the SDGs cannot be achieved equitably. We highlight how assistive products can be considered as both a mediator and a moderator of SDG achievement. We also briefly describe how the Global Cooperation on Assistive Technology (GATE) is working to promote greater access to assistive products on a global scale.

Label-free in situ optical monitoring of the adsorption of oppositely charged metal nanoparticles.

The mechanism of alternating deposition of oppositely charged gold nanoparticles (AuNPs) was investigated by optical waveguide lightmode spectroscopy (OWLS). OWLS allows monitoring of the kinetics of layer-by-layer (LbL) adsorption of positively and negatively charged nanoparticles in real time without using any labels so that the dynamics of layer formation can be revealed. Positively charged NPs that are already deposited on a negatively charged glass substrate strongly facilitate the adsorption of the negatively charged particles. The morphology of the adsorbed layer was also investigated with atomic force microscopy (AFM). AFM revealed that the interaction between oppositely charged particles results in the formation of NP clusters with sizes varying between 100 and 6000 NPs. The cluster size distribution is found to be an exponentially decaying function, and we propose a simple theory to explain this finding.