Dynamics of Pulsed X-Ray Radiation of a Plasma Micropinch Discharge

Plasma Physics Reports - A complex of diagnostic equipment has been created and a measurement procedure has been developed for a multi-channel scintillation X-ray spectrometer with nanosecond time...     

Results of the Preliminary Experiments with a Miniaturized Plasma Focus Device

Plasma Physics Reports - In this article, a miniaturized Mather-type Plasma Focus (PF) device is presented. This device operates at a very low energy range (0.3–3 J). Here, the results of the...     

Plasma Current Sheath Shape and Trapping Efficiency in the 2.2-kJ EAEA-PF1 Plasma Focus Device

Plasma Physics Reports - The plasma current sheath (PCS) shape and trapping efficiency η are investigated experimentally. The experiments are carried out at the 2.2-kJ Egyptian Atomic Energy...     

Experimental Study of the Effect of External Inductance on Pinch Characteristics and Neon Soft X-Ray Yield in Filippov-Type Plasma Focus Device

Plasma Physics Reports - So far, the detailed experimental effect of the inductance on the X-ray yield in the Filippov-type plasma focus devices has not been documented in literature. In this...     

Method to Improve Initial Azimutal Uniformity of a Current Shell in Devices with a Plasma Focus

Plasma Physics Reports - In a device with a plasma focus, the possibility of improving the initial azimuthal uniformity of the current plasma shell is realized by enhancing the stabilizing action...     

Features of a High-Current Pulse-Periodic Cesium Discharge as a Source of Visible Radiation

Plasma Physics Reports - A pulse-periodic cesium discharge is studied in a wide range of its parameters in two lamps with burners of the same diameter (5 mm), but with different interelectrode...     

Energy of Plasma Flows Accelerated in a Current Sheet as a Function of the Current Flowing through the Sheet

The energy of directed plasma flows accelerated in a current sheet is studied experimentally as a function of the current flowing through the sheet. It is found that the plasma flow energy rapidly increases with increasing current amplitude, nearly according to a power law with an exponent of 1.8–1.9. Using relations for the neutral current sheet and the concept of plasma acceleration under action of the Ampère forces, the energy of directed plasma flows is estimated as a function of the total current flowing through the sheet. It is shown that, as the current rises, the ion energy grows due to an increase in both the Ampère forces and the width of the current sheet within which plasma is accelerated.     

Phosphoprotein Secretome of Tumor Cells as a Source of Candidates for Breast Cancer Biomarkers in Plasma

Breast cancer is a heterogeneous disease whose molecular diversity is not well reflected in clinical and pathological markers used for prognosis and treatment selection. As tumor cells secrete proteins into the extracellular environment, some of these proteins reach circulation and could become suitable biomarkers for improving diagnosis or monitoring response to treatment. As many signaling pathways and interaction networks are altered in cancerous tissues by protein phosphorylation, changes in the secretory phosphoproteome of cancer tissues could reflect both disease progression and subtype. To test this hypothesis, we compared the phosphopeptide-enriched fractions obtained from proteins secreted into conditioned media (CM) derived from five luminal and five basal type breast cancer cell lines using label-free quantitative mass spectrometry. Altogether over 5000 phosphosites derived from 1756 phosphoproteins were identified, several of which have the potential to qualify as phosphopeptide plasma biomarker candidates for the more aggressive basal and also the luminal-type breast cancers. The analysis of phosphopeptides from breast cancer patient plasma and controls allowed us to construct a discovery list of phosphosites under rigorous collection conditions, and second to qualify discovery candidates generated from the CM studies. Indeed, a set of basal-specific phosphorylation CM site candidates derived from IBP3, CD44, OPN, FSTL3, LAMB1, and STC2, and luminal-specific candidates derived from CYTC and IBP5 were selected and, based on their presence in plasma, quantified across all cell line CM samples using Skyline MS1 intensity data. Together, this approach allowed us to assemble a set of novel cancer subtype specific phosphopeptide candidates for subsequent biomarker verification and clinical validation.Breast cancer (BC)¹ is a heterogeneous disease whose molecular complexity and diversity is not well reflected in current clinical and pathological markers. Therefore, there is a critical need to increase the number of clinically suitable biomarkers that better reflect the many molecular subtypes of BC (1–3). BC can be categorized by gene expression profiling and molecular pathology into three major clinical types, each with different natural histories and therapeutic recommendations, and exhibiting significant molecular and clinical heterogeneity. First, luminal estrogen receptor (ER) positive breast cancers exist in luminal A and B subtypes; they are the most numerous and clinically diverse of all breast cancers, with luminal A tumors having the more favorable prognosis because of their responsiveness to targeted endocrine therapy compared with the more proliferative luminal B tumors. Second, human epidermal growth factor receptor-2 (HER2/ErbB2) amplified breast cancers, despite having poor prognosis in the absence of any systemic adjuvant therapy, can now be successfully treated with HER2-targeted agents. Third, basal-like breast cancers are among the most aggressive tumors, and are further subdivided. Those with BRCA1-like features are modeled by basal-A breast cancer cell lines, and those with mesenchymal and stem/progenitor-cell features are modeled by basal-B breast cancer cell lines (4). This latter subtype of basal-like tumors include triple negative breast cancers (TNBC), lacking expression of ER, progesterone receptor (PR), and HER2, and therefore not susceptible to more advanced targeted treatment options and requiring aggressive chemotherapy with otherwise very poor prognosis (5).BC is the leading cause of adult female mortality worldwide, caused by recurrent spread of metastatic disease that is thought to have seeded prior to the time of primary tumor excision (6). Thus, blood-based biomarkers that are highly specific as well as capable of detecting BC prior to primary tumor diagnosis offer the potential to decrease BC morbidity as well as identify the most appropriate treatment options (7). As cancer cells are known to secrete proteins into the extracellular microenvironment that modify cell adhesion, intercellular communication, motility, and invasiveness (8), it is expected that some will enter the blood stream and become suitable targets for early noninvasive diagnosis or monitoring of treatment progression.It is well recognized that blood contains hormones, cytokines, and other nonhormonal proteins, as well as a tissue leakage products and secretions from diseased tissues and tumors (9). Secreted proteins are often in the low abundance range of plasma protein concentrations, and likely contain proteins specific for distinct tumor and/or tissue types. Because tumorogenesis is known to involve changes in cellular signaling pathways involving protein kinases, protein phosphorylation is a particularly promising target for the detection of such activated pathways in BC (10). For example, almost half of the tyrosine kinases of the human “kinome” are implicated in human cancers (11) as well as numerous serine-threonine kinases, including Akt and mTOR (12, 13). Kinases participating in signal transduction pathways phosphorylate their substrates altering their conformation, localization, and activity, which in turn modulates downstream protein effectors and alters cellular processes. Like other posttranslational modifications, changes in the phosphorylation status of a protein do not directly correlate with changes in expression, and are therefore not accounted for in most gene expression or protein array analyses (14). Therefore, we hypothesized that phosphoproteins secreted or shed by cancer cells constitute a largely overlooked source of biomarker candidates that could be correlated with BC subtypes and/or disease status (15, 16).To test this hypothesis, we analyzed the conditioned media (CM) from human cancer cell lines, a well-established model for the discovery of disease-specific biomarkers (17, 18). Breast cancer cell lines derived from primary tumors or pleural effusions are a good model of BC, mirroring molecular characteristics of primary breast tumors (19). The use of CM is also advantageous in that it provides sufficient amounts of sample to identify candidates that can subsequently be targeted in more limited breast cancer patient plasma samples. To examine the phosphorylation status of secreted proteins, we examined a panel of five luminal and five basal type BC cell lines thought to emulate the molecular characteristics of most primary breast tumor types, including four basal-B subtypes corresponding to TNBC (19). A mass spectrometry-based proteomic approach was used that employed HILIC fractionation, TiO₂ affinity enrichment of phosphopeptides, and final mass spectrometric analysis by reverse-phase liquid chromatography and label-free quantification (Fig. 1). MS1 Filtering in Skyline (20, 21) was used to quantify relative differences in site-specific protein phosphorylation between secretomes of BC cell lines derived from breast tumor subtypes to discern luminal or basal tumor specificity. Lastly, plasma obtained from breast cancer patients and controls were analyzed in an optimized workflow suitable to both preserve and identify phosphopeptides, and to qualify a subset of biomarker candidates selected from the CM analysis (Fig. 1). Overall, we identified 107 phosphorylation sites specific for basal-type tumors derived from 84 proteins and 95 phosphorylation sites specific for luminal-type tumors derived from 64 proteins. Moreover, we qualified the presence of seven basal type specific and two luminal specific phosphosites derived from eight phosphoproteins in BC patient and control plasma.

Table I

Luminal and basal breast cancer cell lines

Room temperature sterilization of surfaces and fabrics with a One Atmosphere Uniform Glow Discharge Plasma

We report the results of an interdisciplinary collaboration formed to assess the sterilizing capabilities of the One Atmosphere Uniform Glow Discharge Plasma (OAUGDP). This newly-invented source of glow discharge plasma (the fourth state of matter) is capable of operating at atmospheric pressure in air and other gases, and of providing antimicrobial active species to surfaces and workpieces at room temperature as judged by viable plate counts. OAUGDP exposures have reduced log numbers of bacteria, Staphylococcus aureus and Escherichia coli, and endospores from Bacillus stearothermophilus and Bacillus subtilis on seeded solid surfaces, fabrics, filter paper, and powdered culture media at room temperature. Initial experimental data showed a two-log₁₀ CFU reduction of bacteria when 2 × 10² cells were seeded on filter paper. Results showed ≥3 log₁₀ CFU reduction when polypropylene samples seeded with E. coli (5 × 10⁴) were exposed, while a 30 s exposure time was required for similar killing with S. aureus-seeded polypropylene samples. The exposure times required to effect ≥6 log₁₀ CFU reduction of E. coli and S. aureus on polypropylene samples were no longer than 30 s. Experiments with seeded samples in sealed commercial sterilization bags showed little or no differences in exposure times compared to unwrapped samples. Plasma exposure times of less than 5 min generated ≥5 log₁₀ CFU reduction of commercially prepared Bacillus subtilis spores (1 × 10⁶); 7 min OAUGDP exposures were required to generate a ≥3 log₁₀ CFU reduction for Bacillus stearothermophilus spores. For all microorganisms tested, a biphasic curve was generated when the number of survivors vs time was plotted in dose-response cures. Several proposed mechanisms of killing at room temperature by the OAUGDP are discussed. Received 06 June 1997/ Accepted in revised form 01 November 1997     

Seminal Plasma as a Source of Prostate Cancer Peptide Biomarker Candidates for Detection of Indolent and Advanced Disease

Background

Extensive prostate specific antigen screening for prostate cancer generates a high number of unnecessary biopsies and over-treatment due to insufficient differentiation between indolent and aggressive tumours. We hypothesized that seminal plasma is a robust source of novel prostate cancer (PCa) biomarkers with the potential to improve primary diagnosis of and to distinguish advanced from indolent disease.

Methodology/Principal Findings

In an open-label case/control study 125 patients (70 PCa, 21 benign prostate hyperplasia, 25 chronic prostatitis, 9 healthy controls) were enrolled in 3 centres. Biomarker panels a) for PCa diagnosis (comparison of PCa patients versus benign controls) and b) for advanced disease (comparison of patients with post surgery Gleason score <7 versus Gleason score >7) were sought. Independent cohorts were used for proteomic biomarker discovery and testing the performance of the identified biomarker profiles. Seminal plasma was profiled using capillary electrophoresis mass spectrometry. Pre-analytical stability and analytical precision of the proteome analysis were determined. Support vector machine learning was used for classification. Stepwise application of two biomarker signatures with 21 and 5 biomarkers provided 83% sensitivity and 67% specificity for PCa detection in a test set of samples. A panel of 11 biomarkers for advanced disease discriminated between patients with Gleason score 7 and organ-confined (<pT3a) or advanced (≥pT3a) disease with 80% sensitivity and 82% specificity in a preliminary validation setting. Seminal profiles showed excellent pre-analytical stability. Eight biomarkers were identified as fragments of N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase, prostatic acid phosphatase, stabilin-2, GTPase IMAP family member 6, semenogelin-1 and -2. Restricted sample size was the major limitation of the study.

Conclusions/Significance

Seminal plasma represents a robust source of potential peptide makers for primary PCa diagnosis. Our findings warrant further prospective validation to confirm the diagnostic potential of identified seminal biomarker candidates.     

A Study on the Improvement of Etch Uniformity in an Ion Beam Etcher with a Magnetized Inductively Coupled Plasma Source

Plasma Physics Reports - A magnetized inductively coupled plasma ion beam etcher (MICP-IBE) was designed by employing electromagnets around the etcher (IBE). A magnetic field can be set up such...     

Neutrophils as a Source of Chitinases and Chitinase-Like Proteins in Type 2 Diabetes

Purpose

The pathophysiological role of human chitinases and chitinase-like proteins (CLPs) is not fully understood. We aimed to determine the levels of neutrophil-derived chitotriosidase (CHIT1), acidic mammalian chitinase (AMCase) and chitinase 3-like protein 1 (YKL-40) in patients with type 2 diabetes (T2D) and verify their association with metabolic and clinical conditions of these patients.

Methods

Neutrophils were obtained from the whole blood by gradient density centrifugation from 94 T2D patients and 40 control subjects. The activities of CHIT1 and AMCase as well as leukocyte elastase (LE) were measured fluorometrically and concentration of YKL-40 immunoenzymatically. Also, routine laboratory parameters in serum/plasma were determined by standard methods.

Results

The levels of all three examined proteins were about 2-times higher in diabetic patients in comparison to control subjects. They were significantly correlated with the activity of LE and increased progressively across tertiles of LE activity. Moreover, the activities of CHIT1 and AMCase were significantly correlated with each other. Metabolic compensation of diabetes did not influence the levels of these proteins. In the subgroup of patients with inflammatory evidence only YKL-40 concentration was significantly higher compared to those without inflammation. The highest levels of all three proteins were observed in patients with macroangiopathies. Insulin therapy was associated with lower levels of examined proteins.

Conclusions

We revealed that neutrophils may be an important source of the increased levels of chitinases and CLPs in T2D, and these proteins may participate in inflammatory mechanisms in the course of the disease and consequent development of diabetic angiopathies.     

Growth of Pseudomonas fluorescens with Sodium Maleate as a Carbon Source

The growth of Pseudomonas fluorescens (ATCC 11150) on sodium maleate was observed, and the composition of the media was monitored in batch culture. Utilization of the maleate as the sole organic carbon source proceeded by stepwise conversion to fumarate and then to malate. Respiration rates of P. fluorescens on maleate, mixtures of maleate and fumarate salts, and mixtures of maleate and malate salts were measured. Complex effects, possibly due to a change in metabolic mechanism, were observed.     

A Relativistic Neutron Fireball from a Supernova Explosion as a Possible Source of Chiral Influence

We elaborate on a previously proposed idea that polarized electrons produced from neutrons, released in a supernova (SN) explosion, can cause chiral dissymmetry of molecules in interstellar gas-dust clouds. A specific physical mechanism of a relativistic neutron fireball with Lorentz factor of the order of 100 is assumed for propelling a great number of free neutrons outside the dense SN shell. A relativistic chiral electron–proton plasma, produced from neutron decays, is slowed down owing to collective effects in the interstellar plasma. As collective effects do not involve the particle spin, the electrons can carry their helicities to the cloud. The estimates show high chiral efficiency of such electrons. In addition to this mechanism, production of circularly polarized ultraviolet photons through polarized-electron bremsstrahlung at an early stage of the fireball evolution is considered. It is shown that these photons can escape from the fireball plasma. However, for an average density of neutrals in the interstellar medium of the order of 0.2 cm⁻³ and at distances of the order of 10 pc from the SN, these photons will be absorbed with a factor of about 10⁻⁷ due to the photoeffect. In this case, their chiral efficiency will be about five orders of magnitude less than that for polarized electrons.     

A Guide to Follow-on Biologics and Biosimilars with a Focus on Insulin

Objective: Many healthcare providers in the U.S. are not familiar with follow-on biologics and biosimilars nor with their critical distinctions from standard generics. Our aim is to provide a detailed review of both, with a focus on insulins in the U.S. regulatory system.Methods: Literature has been reviewed to provide information on various aspects of biosimilars and a follow-on biologic of insulin. This will include structure, efficacy, cost, switching, and legal issues.Results: Biologic products are large, complex molecules derived from living sources. Follow-on biologics are copies of the original innovator biologics. It is not possible to copy their structure exactly, leading to possible differences in efficacy and safety. Thus, regulations involving biologics are complex. Follow-on biologics are regulated under two Federal laws until March 23, 2020: the Public Health Service Act (PHS Act) and the Federal Food, Drug, and Cosmetic Act. Biosimilars are follow-on biologics which have been approved via the PHS Act. They consist of those which are “highly similar” to the reference drug and those which are “expected” to produce the same clinical result as the reference drug (interchangeable biosimilars). Interchangeable biosimilars have been determined by the U.S. Food and Drug Administration to be substitutable by the pharmacist “without the intervention” of the prescriber. From the patient perspective, switching to a follow-on biologic may necessitate a change in delivery device, which may create issues for patient adherence and dosing.Conclusion: Although they present several challenges in terms of regulation and acceptance, follow-on biologics have the potential to significantly reduce costs for patients requiring insulin therapy.Abbreviations:BLA = biologics license applicationEU = European UnionFDA = Food and Drug AdministrationFD&C = Food, Drug, and CosmeticHCPCS = Healthcare Common Procedure Coding SystemINN = internatinal nonproprietary nameNDA = new drug applicationPHS = Public Health Service     

Otitis Media: A Review, with a Focus on Alternative Treatments

Otitis media (OM) is the accumulation of fluids in the middle ear, with or without symptoms of inflammation. The infection is caused by dysfunction or obstruction of the eustachian tube and is most commonly diagnosed in children under the age of two. The microbiology of OM differs, with Streptococcus pneumoniae, non-typeable Haemophilus influenzae and Moraxella catarrhalis the most commonly isolated pathogens. The emergence of penicillin-resistant Strep. pneumoniae, β-lactamase-producing strains, Haem. influenzae and Mor. catarrhalis is a major concern and health care costs associated with treatment are substantial, especially in cases of unresponsive treatment as a result of incorrect diagnosis. Alternative treatments such as vaccines and a nasal spray containing α-haemolytic streptococci with antimicrobial activity against OM pathogens, have been developed. The rationale behind such treatments is to induce an appropriate immune response against the pathogens and decrease bacterial colonisation in the nasopharynx. Another approach may be treatment with bacteriocins (natural antimicrobial peptides) or bacteriocin-like inhibitory substances (BLIS) produced by lactic acid bacteria. We have recently described an antibacterial peptide produced by Enterococcus mundtii ST4SA and have published on bacteriocins (enterocins) with antibacterial and antiviral activity. This review discusses the condition OM, summarises current methods used to treat the infection, and suggests alternative safe and natural treatments that need to be explored.     

Reciprocal Regulation as a Source of Ultrasensitivity in Two-Component Systems with a Bifunctional Sensor Kinase

Two-component signal transduction systems, where the phosphorylation state of a regulator protein is modulated by a sensor kinase, are common in bacteria and other microbes. In many of these systems, the sensor kinase is bifunctional catalyzing both, the phosphorylation and the dephosphorylation of the regulator protein in response to input signals. Previous studies have shown that systems with a bifunctional enzyme can adjust the phosphorylation level of the regulator protein independently of the total protein concentrations – a property known as concentration robustness. Here, I argue that two-component systems with a bifunctional enzyme may also exhibit ultrasensitivity if the input signal reciprocally affects multiple activities of the sensor kinase. To this end, I consider the case where an allosteric effector inhibits autophosphorylation and, concomitantly, activates the enzyme''s phosphatase activity, as observed experimentally in the PhoQ/PhoP and NRII/NRI systems. A theoretical analysis reveals two operating regimes under steady state conditions depending on the effector affinity: If the affinity is low the system produces a graded response with respect to input signals and exhibits stimulus-dependent concentration robustness – consistent with previous experiments. In contrast, a high-affinity effector may generate ultrasensitivity by a similar mechanism as phosphorylation-dephosphorylation cycles with distinct converter enzymes. The occurrence of ultrasensitivity requires saturation of the sensor kinase''s phosphatase activity, but is restricted to low effector concentrations, which suggests that this mode of operation might be employed for the detection and amplification of low abundant input signals. Interestingly, the same mechanism also applies to covalent modification cycles with a bifunctional converter enzyme, which suggests that reciprocal regulation, as a mechanism to generate ultrasensitivity, is not restricted to two-component systems, but may apply more generally to bifunctional enzyme systems.     

Submarine Groundwater Discharge as a nitrogen source to the Ria Formosa studied with seepage meters

Submarine Groundwater Discharge (SGD) has been frequently ignored as a nutrient source to marine ecosystems because it is difficult to identify and quantify. However, recent studies show its ubiquity and ecological importance to the coastal zone, particularly when associated with contaminated continental aquifers. The Ria Formosa is a coastal lagoon located in the south of Portugal and surrounded by an intensely farmed area. Following a 12-month field study using seepage meters, we identified groundwater discharge in the intertidal zone of the lagoon. The seeping fluid was a mixture of two water types: one with low salinity and high nitrate concentration and another similar to local seawater. Based on the integration of monthly seepage rate measurements throughout the year, we estimate the mean discharge of submarine groundwater into the lagoon to be 3.6 m³ day⁻¹ per linear meter of coastline with freshwater contributions (per volume) ranging from 10% to 50%. The results of this study suggest a continental origin for the freshwater component, thus linking the biogeochemical cycles in the lagoon to anthropogenic activities taking place in the neighboring coastal plain. We further identify SGD as an important nutrient source to the Ria Formosa, estimating annual loads of 36.2 mol (0.507 kg) of Nitrogen, 1.1 mol (0.034 kg) of Phosphorus and 18.6 mol (0.522 kg) of Silicon per meter of coastline. Based on these results, we suggest that SGD is a potential contributor to the observed nutrification status of the Ria Formosa lagoon. All the authors were previously in Biogeochemistry Research Group, CIMA/IMAR (Centro de Investigacao Marinha e Ambiental/Instituto do Mar), Campus de Gambelas, 8000, Faro.