Single Breaks Research Articles

An investigation of the potential effect of sperm nuclear vacuoles in human spermatozoa on DNA fragmentation using a neutral and alkaline Comet assay

Presence of vacuoles and degree of sperm DNA damage are considered to be the basic factors used for the assessment of sperm fertilization capacity. We aimed to investigate the link between these two parameters. According to our knowledge, this is the first study where the Comet assay was used to assess the degree of DNA fragmentation of sperm categorized by Motile Sperm Organelle Morphology Examination (MSOME) Grades. Semen samples from 10 patients were assessed. Spermatozoa were graded into four MSOME groups according to the Vanderzwalmen's criteria. A total of 3930 motile spermatozoa were selected one-by-one using an inverted microscope and transferred onto two different slides. The degree of DNA fragmentation was analyzed by alkaline and neutral Comet assay. Results of the neutral Comet assay showed that Grade I spermatozoa (absence of vacuoles) presented significantly lower dsDNA fragmentation level (mean: 3.13±1.17%) than Grade II (maximum of two small vacuoles; mean: 10.34±2.65%), Grade III (more than two small vacuoles or at least one large vacuole; mean: 23.88±8.37%), and Grade IV (large vacuoles associated with abnormal head shapes or other abnormalities; mean: 36.94±7.78%; p<0.05). Results of the alkaline Comet assay showed that Grade I spermatozoa had significantly lower DNA (ssDNA+dsDNA) fragmentation level (mean: 8.33±3.62%) than Grade III (mean: 25.64±9.15%) and Grade IV (mean: 40.10±9.10%, p<0.05), but not significantly lower than Grade II (mean: 12.73±5.06%; p>0.05). Probably, the vacuoles may be responsible for double strand DNA breaks rather than single strand DNA breaks (only 2.39% spermatozoa in MSOME Grade II, 1.76% in III, and 3.16% in IV has single strand breaks). The results demonstrate that lower MSOME grading correlates with lower sperm DNA fragmentation. Therefore, the observation of sperm nuclear vacuoles using real-time optical microscopy without precise DNA fragmentation examination is not sufficient for optimal sperm selection for intracytoplasmic sperm injection.

Uncovering hierarchical data structure in single molecule transport

Interpretation of single molecule transport data is complicated by the fact that all such data are inherently highly stochastic in nature. Features are often broad, seemingly unstructured and distributed over more than an order of magnitude. However, the distribution contains information necessary for capturing the full variety of processes relevant in nanoscale transport, and a better understanding of its hierarchical structure is needed to gain deeper insight into the physics and chemistry of single molecule electronics. Here, we describe a novel data analysis approach based on hierarchical clustering to aid in the interpretation of single molecule conductance-displacement histograms. The primary purpose of statistically partitioning transport data is to provide avenues for unbiased hypothesis generation in single molecule break junction experiments by revealing otherwise potentially hidden aspects in the conductance data. Our approach is generalizable to the analysis of a wide variety of other single molecule experiments in molecular electronics, as well as in single molecule fluorescence spectroscopy, force microscopy, and ion-channel conductance measurements.

Selected Techniques of Detecting Structural Breaks in Financial Volatility

We investigate several promising algorithms, proposed in literature, devised to detect sudden changes (structural breaks) in the volatility of financial time series. Comparative study of three techniques: ICSS, NPCPM and Cheng’s algorithm is carried out via numerical simulation in the case of simulated T-GARCH models and two real series, namely German and US stock indices. Simulations show that the NPCPM algorithm is superior to ICSS because is not over-sensitive either to heavy tails of market returns or to their serial dependence. Some signals generated by ICSS are falsely classified as structural breaks in volatility, while Cheng’s technique works well only when a single break occurs.

A pathway of targeted autophagy is induced by DNA damage in budding yeast

Autophagy plays a central role in the DNA damage response (DDR) by controlling the levels of various DNA repair and checkpoint proteins; however, how the DDR communicates with the autophagy pathway remains unknown. Using budding yeast, we demonstrate that global genotoxic damage or even a single unrepaired double-strand break (DSB) initiates a previously undescribed and selective pathway of autophagy that we term genotoxin-induced targeted autophagy (GTA). GTA requires the action primarily of Mec1/ATR and Rad53/CHEK2 checkpoint kinases, in part via transcriptional up-regulation of central autophagy proteins. GTA is distinct from starvation-induced autophagy. GTA requires Atg11, a central component of the selective autophagy machinery, but is different from previously described autophagy pathways. By screening a collection of ∼6,000 yeast mutants, we identified genes that control GTA but do not significantly affect rapamycin-induced autophagy. Overall, our findings establish a pathway of autophagy specific to the DNA damage response.

Photoprotective Potential of Glycolic Acid by Reducing NLRC4 and AIM2 Inflammasome Complex Proteins in UVB Radiation-Induced Normal Human Epidermal Keratinocytes and Mice

Exposure to UVB radiation induces inflammation and free radical-mediated oxidative stress through reactive oxygen species (ROS) that play a crucial role in the induction of skin cancer. Glycolic acid (GA) is frequently used in cosmetics and dermatology. The aim of the study was to analyze the photoprotective mechanisms through which GA retards UVB-induced ROS accumulation and inflammation in normal human epidermal keratinocytes (NHEKs) and mice skin, respectively. NHEK cell line and C57BL/6J mice were treated with GA (0.1 or 5 mM) for 24 h followed by UVB irradiation. ROS accumulation, DNA damage, and expression of inflammasome complexes (NLRP3, NLRC4, ASC, and AIM2) were measured in vitro. Epidermal thickness and inflammasome complex proteins were analyzed in vivo. GA significantly prevented UVB-induced loss of skin cell viability, ROS formation, and DNA damage (single and double strands DNA break). GA suppressed the mRNA expression levels of NLRC4 and AIM2 among the inflammasome complexes. GA also blocked interleukin (IL)-1β by reducing the activity of caspase-1 in the NHEKs. Treatment with GA (2%) inhibited UVB-induced inflammation marker NLRC4 protein levels in mouse dorsal skin. The photoprotective activity of GA was ascribed to the inhibition of ROS formation and DNA damage, as well as a reduction in the activities of inflammasome complexes and IL-1β. We propose that GA has anti-inflammatory and photoprotective effects against UVB irradiation. GA is potentially beneficial to the protection of human skin from UV damage.

Single Cas9 nickase induced generation of NRAMP1 knockin cattle with reduced off-target effects

BackgroundThe CRISPR-Cas9 system is a widely utilized platform for transgenic animal production in various species, although its off-target effects should be addressed. Several applications of this tool have been proposed in model animals but remain insufficient for transgenic livestock production.ResultsHere, we report the first application of single Cas9 nickase (Cas9n) to induce gene insertion at a selected locus in cattle. We identify the main binding sites of a catalytically inactive Cas9 (dCas9) protein in bovine fetal fibroblast cells (BFFs) with chromatin immunoprecipitation sequencing (ChIP-seq). Subsequently, we demonstrate that a single Cas9n-induced single-strand break can stimulate the insertion of the natural resistance-associated macrophage protein-1 (NRAMP1) gene with reduced, but still considerable, off-target effects. Through somatic cell nuclear transfer, we finally obtain transgenic cattle with increased resistance to tuberculosis.ConclusionsOur results contribute to the development of CRISPR-Cas9 system for agriculture applications.

Outcomes of Pneumatic Retinopexy for the Management of Rhegmatogenous Retinal Detachment at a Tertiary Care Center.

PURPOSE:The purpose of the study was to report the outcomes of pneumatic retinopexy (PR) for rhegmatogenous retinal detachment (RRD).METHODS:A retrospective chart review of all patients with RRD who were managed with PR at the King Khaled Eye Specialist Hospital between 2000 and 2014. Data were collected on preoperative ocular history, characteristics of the RRD, postoperative anatomical and visual outcomes, and secondary surgeries.RESULTS:Sixty-five eyes comprised the study sample with mean a follow-up of 42 months. Eighteen (27%) eyes had a history of ocular surgery and 5 (7.6%) had previous ocular trauma. Thirty-nine (60%) eyes had macula on RRD. Retinal detachment (RD) was caused by a single break in fifty (76.9%) eyes. Superior breaks were found in 56 (86.1%) eyes. Twelve (18%) eyes had posterior vitreous detachment. Fifty-one (78.5%) eyes underwent PR under local anesthesia and 9 (13.8%) underwent conjunctival peritomy. Octafluoropropane gas was used in 49 (75.4%) eyes and sulfur hexafluoride in 16 (24.6%) eyes. Cryotherapy was performed in 48 (73.8%) eyes and only laser photocoagulation in 8 (12.3%) eyes. Nine (13.8%) eyes underwent both cryotherapy and laser photocoagulation. Primary anatomical healing was achieved in 45 (69.2%) eyes, of which 20 (30.8%) required a second intervention. The final anatomical outcome was achieved in 100% of the eyes. At final visit, vision improved in 72% of eyes, was maintained in14.5%, and decreased in 9.7% (6).CONCLUSION:PR is a safe procedure for RRD repair. The final anatomical outcome was excellent in all cases including the recurrent RD after primary failure.

A surprising way to control the charge transport in molecular electronics: the subtle impact of the coverage of self-assembled monolayers of floppy molecules adsorbed on metallic electrodes

Inspired by earlier attempts in organic electronics aiming at controlling charge injection from metals into organic materials by manipulating the Schottky energy barrier using self-assembled monolayers (SAMs), recent experimental and theoretical work in molecular electronics showed that metal-organic interfaces can be controlled via changes in the metal work function that are induced by SAMs. In this paper we indicate a different route to achieve interface-driven control over the charge transfer/transport at the molecular scale. It is based on the fact that, in floppy molecule based SAMs, the molecular conformation can be tuned by varying the coverage of the adsorbate. We demonstrate this effect with the aid of benchmark molecules that are often used to fabricate nanojunctions and consist of two rings that can easily rotate relative to each other. We show that, by varying the coverage of the SAM, the twisting angle φ of the considered molecular species can be modified by a factor of two. Given the fact that the low bias conductance G scales as cos2 φ, this results in a change in G of over one order of magnitude for the considered molecular species. Tuning the twisting angle by controlling the SAM coverage may be significant, e.g., for current efforts to fabricate molecular switches. Conversely, the lack of control over the local SAM coverage may be problematic for the reproducibility and interpretation of the STM (scanning tunneling microscope) measurements on repeatedly forming single molecule break junctions.

Activation induced cell death (AICD) of human melanoma antigen-specific TCR engineered CD8 T cells involves JNK, Bim and p53

ABSTRACTObjectives: Adoptive cancer immunotherapy (ACT) with transgenic T cell receptor (TCR) engineered (TCReng) anti-tumor T cells has produced encouraging results, however, efficacy of these approaches need improvement. Since premature activation induced cell death (AICD) of adoptively administered T cells could be a major impediment, we examined the mechanism(s) underlying AICD in TCReng CD8+ cytolytic T lymphocytes (CTL).Methods: AICD in human tumor antigen-specific MHC class I restricted TCR engineered CD8+ CTL was induced by exposing them to cognate peptide epitope.Results: We show that TCReng CD8+ human primary CTL undergo AICD even upon encountering their cognate peptide epitope for the very first time. AICD in TCReng CTL is a death-receptor-independent, JNK activation-driven intrinsic processes, in which p53-mediated mitochondria-centric, non-transcription-dependent pathway plays an essential role. Activated JNK modulates mitochondrial membrane integrity in CTL undergoing AICD by directly interacting with Bcl family protein, Bim, and the mitochondrial membrane pore complex, voltage dependent anion channel (VDAC), leading to the release of caspase-independent death executioner, apoptosis inducing factor (AIF), accumulation of single strand DNA breaks and eventually to cell death.Conclusions: Our findings offer opportunities to interfere with AICD in TCReng CD8+ anti-tumor CTL for sustaining them longer for producing better clinical outcomes.

A fast algorithm for the elastic fields due to a single fiber break in a periodic fiber-reinforced composite

The stress state in a shear-lag model of a unidirectional fiber composite with an arbitrary configuration of fiber breaks is obtained by the weighted superposition of the stress state due to a single broken fiber. In a periodic patch comprised of N fibers located at the points of a regular lattice, a method to determine the stress state due to a single break was proposed by Landis et al. (J Mech Phys Solids 48(3):621–648, 2000). This method entails the determination of the eigenspace of an \(N\times N\) matrix, at a computational cost of \(O(N^3)\). In the present work, an alternative algorithm is proposed. This algorithm exploits the circulant structure of the matrix describing the inter-fiber interactions. The asymptotic computational complexity of the present algorithm equals that of the discrete Fourier transform: \({O}(N \log N)\). Run times of the present method with the eigensolution based method are compared, and shown to be very favorable for the present method, even for small N. Power-law scaling of the overloads due to a single break to much larger distances than previously possible has been verified using the present method.

Catheter-guided suprachoroidal buckling of rhegmatogenous retinal detachments secondary to peripheral retinal breaks.

To evaluate functional and anatomic outcomes of eyes undergoing suprachoroidal buckling (SCB) using a specially designed catheter for the management of rhegmatogenous retinal detachment (RRD) secondary to peripheral retinal breaks. Retrospective cohort study of 62 eyes of 62 patients. Subjects underwent SCB for the management of RRD secondary to single or multiple retinal breaks. Suprachoroidal indentation was achieved through the introduction of viscoelastic material in the suprachoroidal space overlying the break using an illuminated, 450μm-wide, flex-tip catheter. This allowed for the creation of a suprachoroidal dome and chorio-retinal apposition. Forty-seven eyes (80%) underwent SCB alone, while 15 eyes (20%) were combined with 25-G pars-plana vitrectomy. Cryopexy and laserpexy were used in 38 (61%) and 24 of eyes (39%) respectively. Mean pre-operative best-corrected visual acuity (BCVA) improved from logMAR 0.82 (20/132) to 0.22 (20/33) (p < 0.0001). The single surgery reattachment rate was 92% (57/62.) Final retinal reattachment was achieved in all eyes (100%). No significant difference was observed in single-surgery anatomic success rates when stratified by lens status, macular involvement, or break location. There were no major intra- or post-operative complications. Suprachoroidal buckling using a special-design, flexible catheter is a safe and effective procedure for the management of RRD secondary to peripheral retinal breaks.

Investigating the effect of applied strain rate in a single breakage event

For successful mechanistic modelling of any size reduction equipment, an understanding of the fundamentals of the breakage mechanisms is essential. This understanding will allow the comparison of breakage events and the quantification of the effect of key factors such as applied strain rate, particle size, and particle shape while they are isolated. This paper uses the concept of analysing breakage of a single particle as a multi-stage process to compare different breakage mechanisms and to quantify the effect of factors such as applied strain rate. This approach regards a single breakage event as a process affected by three sub-processes; first (or primary) fracture, capture and spatial distribution of fragments. The first fracture is assumed to be independent of breakage mechanism and to be a characteristic of the ore type. On the other hand, capture and spatial distribution are influenced by the characteristics of breakage environment, the kinetic energy of fragments and their brittleness. The focus of this paper is to examine how each sub-process of a breakage event is influenced by applied strain rate and its impact on the size distribution of progeny. In this work, three rock types of widely different strength and brittle behaviour, i.e. LKAB magnetite ore, Beaudesert silicate and Bundaberg quartz, were tested at various energy levels using the impact and compression breakage mechanisms. To isolate the effect of spatial distribution of fragments, particles were forced to remain in the breakage zone. In this condition, similar progeny size distributions were generated from compression and impact mechanisms at similar energy levels. However, allowing natural distribution of fragments produced coarser progeny from the compression of silicate.

Identification and estimation of a large factor model with structural instability

This paper tackles the identification and estimation of a high dimensional factor model with unknown number of latent factors and a single break in the number of factors and/or factor loadings occurring at unknown common date. First, we propose a least squares estimator of the change point based on the second moments of estimated pseudo factors and show that the estimation error of the proposed estimator is Op(1). We also show that the proposed estimator has some degree of robustness to misspecification of the number of pseudo factors. With the estimated change point plugged in, consistency of the estimated number of pre and post-break factors and convergence rate of the estimated pre and post-break factor space are then established under fairly general assumptions. The finite sample performance of our estimators is investigated using Monte Carlo experiments.

Experimental investigation of breakage and energy consumption characteristics of mixtures of different components in vertical spindle pulverizer

Complex interactions among components in the heterogeneous grinding have an influence on breakage and energy consumption characteristics of components in mixtures if compared with the single breakage. In this paper, a modified Hardgrove mill, with the addition of a power meter, is used to simulate the grinding process of vertical spindle pulverizer. Binary-component mixtures of coal and pyrite, or coal and calcite, in the size of −2.8+2mm, are prepared to study the heterogeneous breakage. For the mixture A of coal and pyrite, the fineness of pyrite progeny is higher than that from single-breakage. Instead, the coal in mixture A shows the opposite trend. Because of the relatively less difference in hardness between coal and calcite, size distributions of components are environment-independent. Breakage of mixture follows the first-order kinetics, as well as each component in mixtures. In order to describe the energy-size reduction of mixture, a modified model in the form t10=A(1-e-b·ECS/Hw), has been derived from modeling the mass weighted hardness index of mixture, and its predictions are highly fitted with experimental and supplemental data. In addition, energy split phenomena of components are discussed qualitatively using the modified model. Specific energies that need to yield the same product t10 of one component both in the single and mixture breakage are compared, and the interaction of one component on the breakage of another one in mixture grinding also has been analyzed. Size distributions of ground products using t10 are well predicted, which are critical to conduct the computation of size distribution of progenies at given specific energies.

Dynamic effects of single fiber break in unidirectional glass fiber-reinforced composites

In a unidirectional composite under static tensile loading, breaking of a fiber is shown to be a locally dynamic process that leads to stress concentrations in the interface, matrix and neighboring fibers that can propagate at high speed over long distances. To gain better understanding of this event, a fiber-level finite element model of a two-dimensional array of S2-glass fibers embedded in an elastic epoxy matrix with interfacial cohesive traction law is developed. The brittle fiber fracture results in release of stored strain energy as a compressive stress wave that propagates along the length of the broken fiber at speeds approaching the axial wave-speed in the fiber (6 km/s). This wave induces an axial tensile wave with a dynamic tensile stress concentration in adjacent fibers that diminishes with distance. Moreover, dynamic interfacial failure is predicted where debonding initiates, propagates and arrests at longer distances than predicted by models that assume quasi-static fiber breakage. In the case of higher strength fibers breaks, unstable debond growth is predicted. A stability criterion to define the threshold fiber break strength is derived based on an energy balance between the release of fiber elastic energy and energy absorption associated with interfacial debonding. A contour map of peak dynamic stress concentrations is generated at various break stresses to quantify the zone-of-influence of dynamic failure. The dynamic results are shown to envelop a much larger volume of the microstructure than the quasi-static results. The implications of dynamic fiber fracture on damage evolution in the composite are discussed.

Active School Lesson Breaks Increase Daily Vigorous Physical Activity, but Not Daily Moderate to Vigorous Physical Activity in Elementary School Boys.

Brief classroom-based episodes of physical activity (active lesson breaks, ALBs) have improved schoolchildren's classroom behaviors in some studies, and may also increase the likelihood of children meeting the recommended daily minutes of moderate to vigorous physical activity (MVPA). However, there is emerging evidence that increases in physical activity at particular times of the day may lead to compensatory declines at other times. This study explored evidence for compensatory declines in response to a 10 min ALB during the school day. Thirty-eight 12-year-old boys from a single elementary school completed intervention and control conditions in a cross-over design, with each phase lasting one week. The intervention consisted of a single 10-min active lesson break delivered on each of three days in the intervention week. Twenty-four hour accelerometry was used to quantify moderate and vigorous physical activity. ALBs increased in-school MVPA by 5.8 min (p < .0001), but overall daily MVPA was similar between intervention and control conditions (77.2 vs 77.4 min/d, p > .05), However, vigorous physical activity increased significantly over the whole day (11.2 vs 8.9 min, p = .0006). A brief episode of classroom-based play led to a modest increase in vigorous physical activity in elementary school students, but did not increase MVPA across the day.

Detecting structural changes under nonstationary volatility

This paper shows that the U-statistic for moment condition stability proposed by Juhl and Xiao (2013) can be used to test against structural changes in regression coefficients under nonstationary volatility. We investigate the power property under the alternative, and prove that the test is consistent against single break, multiple breaks and smooth structural changes. Finally, we advocate using a bootstrap method to improve its size performance in finite samples.

The random-walk hypothesis revisited: new evidence on multiple structural breaks in emerging markets

We examine whether stock prices in 18 emerging markets follow random-walk or mean-reversion processes in the presence of sudden and gradual multiple structural breaks. Our tests endogenously determined the structural shifts and are more powerful than either the traditional random-walk (unit root) tests or the single structural break tests. In all emerging markets, we find strong evidence for multiple structural breaks. When we use single break tests, the random-walk hypothesis is rejected. However, when we use tests of double level shifts in the mean and make due allowance for multiple structural breaks, the results are consistent with the random-walk hypothesis in the vast majority of the sampled markets. The evidence proves robust to using price indexes whether denominated in U.S. dollars, in local currencies or in real terms, and also to using fractional integration tests. Our results contradict some previous studies for emerging markets which restrict structural breaks to only one-time shift.

A phenomenological model of single particle breakage as a multi-stage process

Understanding ore breakage is the key for the development of appropriate breakage characterisation experiments. Hence, there has been significant effort to understand a single breakage event, both from the experimental and the modelling standpoints. One particularly interesting approach is to consider breakage of a particle, for instance in a drop weight tester, as a sequence of primary and secondary breakage components. Secondary breakage is defined as subsequent breakage of progeny that takes place after the primary fracture of the parent particle due to surplus energy that is provided by the comminution or breakage testing device. This influences the spatial distribution of fragments as well as their selection. Due to the complex nature of secondary breakage, most of the researches in the past have either been dedicated to understanding primary fracture as a basic element of every comminution process or to describe the breakage process as a whole. However, the progression of breakage may be modelled properly by incorporating the sequential breakage of fragments into a breakage process model. In the paper, a novel approach is proposed to describe a single breakage event by modelling it as a process through several stages of primary fracture while appreciating the effect of sequential fragmentation. The model has three main components: the primary breakage, the selection, and the classification functions. The data that served as the basis for demonstrating this model were a number of impact experiments in an impact load cell on quartz and apatite particles. The results indicate a good correspondence between experiments and model fit. Additionally, a sensitivity analysis to changes in selection and classification functions was performed, which indicated a strong dependency of a breakage event on its sub-processes. It is envisaged that this approach will allow decoupling the contributions of the ore and of the stressing conditions on the outcome of the breakage event.

A bubble breakage model for finite Reynolds number flows

ABSTRACTThe breakage frequency of bubbles in turbulent liquid flows is modeled as the inverse of the breakage time by Martinez-Bazan et al. [J. Fluid Mech. 401: 157–182; 1999]. In this definition of the breakage frequency, it is assumed that the breakage probability is unity and hence all bubbles will break. This assumption is reasonable in turbulent flows at extremely high Reynolds numbers in which the turbulence energy dissipation is very high. For systems characterized by finite Reynolds numbers the energy dissipation rate decreases rapidly and the breakage probability is reduced significantly. In the present study, the breakage frequency model by Martinez-Bazan et al. has been extended to include the effect that only a fraction of the bubbles breaks at finite Reynolds numbers. For this model extension, an adjusted version of the breakage probability formula proposed by Coulaloglou and Tavlarides [Chem. Eng. Sci. 32: 1289–1297; 1977] was employed. The extended breakage frequency model for finite Reynolds number flows has been evaluated by comparison to recent experimental single bubble breakage data. It can be concluded that extensive experimental analyses are required to gather sufficient experimental data for improved understanding of the physical phenomena and for model validation. In particular, the bubble breakage analysis must be performed simultaneously with the characterization of the local turbulence properties in the flow.