Efficacy of ImageJ in the assessment of apoptosis

<p>Abstract</p> <p>Objective</p> <p>To verify the efficacy of ImageJ 1.43 n in determining the extent of apoptosis which is a complex and multistep process.</p> <p>Study Design</p> <p>Cisplatin in different concentrations was used to induce apoptosis in cultured Hep2 cells. Cell viability assay and nuclear image analysis of stained Hep2 cells were used to discriminate apoptotic cells and cells suspected to be undergoing apoptosis from control cells based on parameters such as nuclear area, circularity, perimeter and nuclear area factor (NAF), in association with visual morphology.</p> <p>Results</p> <p>Image analysis revealed a progressive and highly significant decrease in nuclear area factor detected in apoptotic cells and in cells suspected of undergoing apoptosis compared to the control cells (P-values < 0.01). Some of the other studied parameters showed also the same trend. This decrease was assumed to indicate DNA loss. Image analysis results correlated positively and significantly with the results obtained by cell viability assay (R = 0.958, P-value = 0.042). NAF was the most reliable parameter in assessment of apoptosis.</p> <p>Conclusion</p> <p>Nuclear area factor can be calculated using powerful free and open-source software. Consequently, a quantitative measure of apoptosis can be obtained that is linked to morphological changes. ImageJ 1.43 n may therefore provide a useful tool for the assessment and discrimination of apoptotic cells.</p> <p>Virtual slides</p> <p>The virtual slide(s) for this article can be found here:</p> <p><url>http://www.diagnosticpathology.diagnomx.eu/vs/5929043086367338</url></p

Comment on "On the subtleties of searching for dark matter with liquid xenon detectors"

In a recent manuscript (arXiv:1208.5046) Peter Sorensen claims that XENON100's upper limits on spin-independent WIMP-nucleon cross sections for WIMP masses below 10 GeV "may be understated by one order of magnitude or more". Having performed a similar, though more detailed analysis prior to the submission of our new result (arXiv:1207.5988), we do not confirm these findings. We point out the rationale for not considering the described effect in our final analysis and list several potential problems with his study.Comment: 3 pages, no figure

Coating mechanisms of single-walled carbon nanotube by linear polyether surfactants: insights from computer simulations

The noncovalent coating of carbon-based nanomaterials, such as carbon nanotubes, has important applications in nanotechnology and nanomedicine. The molecular modeling of this process can clarify its mechanism and provide a tool for the design of novel materials. In this paper, the coating mechanism of single-walled carbon nanotubes (SWCNT) in aqueous solutions by 1,2-dimethoxyethane oxide (DME), 1,2-dimethoxypropane oxide (DMP), poly(ethylene oxide) (PEO), poly(propylene oxide) (PPO) pentamers, and L64 triblock copolymer chains have been studied using molecular dynamics (MD) simulations. The results suggest a preferential binding to the SWCNT surface of the DMP molecules with respect to DME mainly driven by their difference in hydrophobicity. For the longer pentamers, it depends by the chain conformation. PPO isomers with radius of gyration larger than PEO pentamers bind more tightly than those with more compact conformation. In the case of the L64 triblock copolymer, the coating of the SWCNT surface produces a shell of PPO blocks with the PEO chains protruding into bulk water as expected from the so-called nonwrapping binding mechanism of SWCNT. In addition, the polymer coating, in qualitative agreement with experimental evidence on the poor capability of the L64 to disperse SWCNT, do not prevent the formation of CNT aggregates

Geochemical detection of carbon dioxide in dilute aquifers

<p>Abstract</p> <p>Background</p> <p>Carbon storage in deep saline reservoirs has the potential to lower the amount of CO₂emitted to the atmosphere and to mitigate global warming. Leakage back to the atmosphere through abandoned wells and along faults would reduce the efficiency of carbon storage, possibly leading to health and ecological hazards at the ground surface, and possibly impacting water quality of near-surface dilute aquifers. We use static equilibrium and reactive transport simulations to test the hypothesis that perturbations in water chemistry associated with a CO₂gas leak into dilute groundwater are important measures for the potential release of CO₂to the atmosphere. Simulation parameters are constrained by groundwater chemistry, flow, and lithology from the High Plains aquifer. The High Plains aquifer is used to represent a typical sedimentary aquifer overlying a deep CO₂storage reservoir. Specifically, we address the relationships between CO₂flux, groundwater flow, detection time and distance. The CO₂flux ranges from 10³to 2 × 10⁶t/yr (0.63 to 1250 t/m²/yr) to assess chemical perturbations resulting from relatively small leaks that may compromise long-term storage, water quality, and surface ecology, and larger leaks characteristic of short-term well failure.</p> <p>Results</p> <p>For the scenarios we studied, our simulations show pH and carbonate chemistry are good indicators for leakage of stored CO₂into an overlying aquifer because elevated CO₂yields a more acid pH than the ambient groundwater. CO₂leakage into a dilute groundwater creates a slightly acid plume that can be detected at some distance from the leak source due to groundwater flow and CO₂buoyancy. pH breakthrough curves demonstrate that CO₂leaks can be easily detected for CO₂flux ≥ 10⁴t/yr within a 15-month time period at a monitoring well screened within a permeable layer 500 m downstream from the vertical gas trace. At lower flux rates, the CO₂dissolves in the aqueous phase in the lower most permeable unit and does not reach the monitoring well. Sustained pumping in a developed aquifer mixes the CO₂-affected water with the ambient water and enhances pH signal for small leaks (10³t/yr) and reduces pH signal for larger leaks (≥ 10⁴t/yr).</p> <p>Conclusion</p> <p>The ability to detect CO₂leakage from a storage reservoir to overlying dilute groundwater is dependent on CO₂solubility, leak flux, CO₂buoyancy, and groundwater flow. Our simulations show that the most likely places to detect CO₂are at the base of the confining layer near the water table where CO₂gas accumulates and is transported laterally in all directions, and downstream of the vertical gas trace where groundwater flow is great enough to transport dissolved CO₂laterally. Our simulations show that CO₂may not rise high enough in the aquifer to be detected because aqueous solubility and lateral groundwater transport within the lower aquifer unit exceeds gas pressure build-up and buoyancy needed to drive the CO₂gas upwards.</p

Dark Matter Results from 225 Live Days of XENON100 Data

We report on a search for particle dark matter with the XENON100 experiment, operated at the Laboratori Nazionali del Gran Sasso (LNGS) for 13 months during 2011 and 2012. XENON100 features an ultra-low electromagnetic background of (5.3 \pm 0.6) \times 10^-3 events (kg day keVee)^-1 in the energy region of interest. A blind analysis of 224.6 live days \times 34 kg exposure has yielded no evidence for dark matter interactions. The two candidate events observed in the pre-defined nuclear recoil energy range of 6.6-30.5 keVnr are consistent with the background expectation of (1.0 \pm 0.2) events. A Profile Likelihood analysis using a 6.6-43.3 keVnr energy range sets the most stringent limit on the spin-independent elastic WIMP-nucleon scattering cross section for WIMP masses above 8 GeV/c^2, with a minimum of 2 \times 10^-45 cm^2 at 55 GeV/c^2 and 90% confidence level.Comment: 6 pages, 5 figures. Matches version accepted by PRL. Includes limits up to 10 TeV/c^2, published as supplementary material: http://prl.aps.org/supplemental/PRL/v109/i18/e181301 Please cite high mass limits as "Phys. Rev. Lett. 109, 181301 (2012), online supplementary material.

Pseudoneoplastic lesions of the testis and paratesticular structures

Pseudotumors or tumor-like proliferations (non-neoplastic masses) and benign mimickers (non-neoplastic cellular proliferations) are rare in the testis and paratesticular structures. Clinically, these lesions (cysts, ectopic tissues, and vascular, inflammatory, or hyperplastic lesions) are of great interest for the reason that, because of the topography, they may be relevant as differential diagnoses. The purpose of this paper is to present an overview of the pseudoneoplasic entities arising in the testis and paratesticular structures; emphasis is placed on how the practicing pathologist may distinguish benign mimickers and pseudotumors from true neoplasia. These lesions can be classified as macroscopic or microscopic mimickers of neoplasia

Fecal Microbiota Transplantation Is Safe and Effective in Patients With Clostridioides difficile Infection and Cirrhosis

Background & Aims Clostridioides difficile infection (CDI) harms a large proportion of patients with cirrhosis. Fecal microbiota transplantation (FMT) is recommended for recurrent CDI, but its effects in patients with cirrhosis have not been established. We performed a multicenter observational study to evaluate the efficacy and safety of FMT for CDI in patients with cirrhosis. Methods We performed a retrospective study of 63 adults with cirrhosis (median model for end-stage liver disease score, 14.5; 24 patients with decompensated cirrhosis) who underwent FMT for CDI from January 2012 through November 2018 at 8 academic centers in the United States, Canada, and Italy. We collected data on patient demographics and characteristics of cirrhosis, CDI, and FMT from medical records and compared differences among patients with different severities of cirrhosis, and FMT successes vs failures at the 8-week follow-up evaluation. We also obtained data on adverse events (AEs) and severe AEs within 12 weeks of FMT. Results Patients underwent FMT for recurrent CDI (55 of 63; 87.3%), severe CDI (6 of 63; 9.5%), or fulminant CDI (2 of 63; 3.2%) primarily via colonoscopy (59 of 63; 93.7%) as outpatients (47 of 63; 76.8%). FMT success was achieved for 54 patients (85.7%). Among FMT failures, a higher proportion used non-CDI antibiotics at the time of FMT (44.4% vs 5.6%; P < .001), had Child–Pugh scores of B or C (100% vs 37.7%; P < .001), used probiotics (77.8% vs 24.1%; P = .003), had pseudomembranes (22.2% vs 0; P = .018), and underwent FMT as inpatients (45.5% vs 19%; P = .039), compared with FMT successes. In multivariable analysis, use of non-CDI antibiotics at the time of FMT (odds ratio, 17.43; 95% CI, 2.00–152.03; P = .01) and use of probiotics (odds ratio, 11.9; 95% CI, 1.81–78.3; P = .01) were associated with a greater risk of FMT failure. FMT-related AEs occurred in 33.3% of patients (21 of 63)—most were self-limited abdominal cramps or diarrhea. There were only 5 severe AEs that possibly were related to FMT; none involved infection or death. Conclusions In a retrospective study, we found FMT to be safe and effective for the treatment of CDI in patients with cirrhosis