Learning from each other: Cross-cutting diagnostic development activities between magnetic and inertial confinement fusion (invited).

Inertial Confinement Fusion and Magnetic Confinement Fusion (ICF and MCF) follow different paths toward goals that are largely common. In this paper, the claim is made that progress can be accelerated by learning from each other across the two fields. Examples of successful cross-community knowledge transfer are presented that highlight the gains from working together, specifically in the areas of high-resolution x-ray imaging spectroscopy and neutron spectrometry. Opportunities for near- and mid-term collaboration are identified, including in chemical vapor deposition diamond detector technology, using gamma rays to monitor fusion gain, handling neutron-induced backgrounds, developing radiation hard technology, and collecting fundamental supporting data needed for diagnostic analysis. Fusion research is rapidly moving into the igniting and burning regimes, posing new opportunities and challenges for ICF and MCF diagnostics. This includes new physics to probe, such as alpha heating; increasingly harsher environmental conditions; and (in the slightly longer term) the need for new plant monitoring diagnostics. Substantial overlap is expected in all of these emerging areas, where joint development across the two subfields as well as between public and private researchers can be expected to speed up advancement for all.

UAV Path Optimization for Precision Agriculture Wireless Sensor Networks.

The use of monitoring sensors is increasingly present in the context of precision agriculture. Usually, these sensor nodes (SNs) alternate their states between periods of activation and hibernation to reduce battery usage. When employing unmanned aerial vehicles (UAVs) to collect data from SNs distributed over a large agricultural area, we must synchronize the UAV route with the activation period of each SN. In this article, we address the problem of optimizing the UAV path through all the SNs to reduce its flight time, while also maximizing the SNs' lifetime. Using the concept of timeslots for time base management combined with the idea of flight prohibition list, we propose an efficient algorithm for discovering and reconfiguring the activation time of the SNs. Experimental results were obtained through the development of our own simulator-UAV Simulator. These results demonstrate a considerable reduction in the distance traveled by the UAV and also in its flight time. In addition, the model provides a reduction in transmission time by SNs after reconfiguration, thus ensuring a longer lifetime for the SNs in the monitoring environment, as well as improving the freshness and continuity of the gathered data, which support the decision-making process.

Turbulence and jet-driven zonal flows: Secondary circulation in rotating fluids due to asymmetric forcing.

We report on experiments and modeling on a rotating confined liquid that is forced by circumferential jets coaxial with the rotation axis, wherein system-scale secondary flows are observed to emerge. The jets are evenly divided in number between inlets and outlets and have zero net mass transport. For low forcing strengths the sign of this flow depends on the sign of a sloped end cap, which simulates a planetary ß plane. For increased forcing strengths the secondary flow direction is insensitive to the slope sign, and instead appears to be dominated by an asymmetry in the forcing mechanism, namely, the difference in radial divergence between the inlet and outlet jet profiles. This asymmetry yields a net radial velocity that is affected by the Coriolis force, inducing secondary zonal flow.

A multi-species powder dropper for magnetic fusion applications.

We present a device for controlled injection of a variety of materials in powder form. The system implements four independent feeder units, arranged to share a single vertical drop tube. Each unit consists of a 80 ml reservoir, coupled to a horizontal linear trough, where a layer of powder is advanced by piezo-electric agitation at a speed proportional to the applied voltage, until it falls into a drop tube. The dropper has been tested with a number of impurities of low (B, BN, C), intermediate (Si, SiC), and high Z (Sn) and a variety of microscopic structures (flakes, spheres, rocks) and sizes (5-200 µm). For low Z materials, drop rates ∼2-200 mg/s have been obtained showing good repeatability and uniformity. A calibrated light-emitting diode (LED)-based flowmeter allows measuring and monitoring the drop rate during operation. The fast time-response of the four feeders allows combination of steady and pulsed injections, providing a flexible tool for controlled-dose, real-time impurity injection in fusion plasmas.

Design and implementation of a Thomson parabola for fluence dependent energy-loss measurements at the Neutralized Drift Compression eXperiment.

The interaction of ion beams with matter includes the investigation of the basic principles of ion stopping in heated materials. An unsolved question is the effect of different, especially higher, ion beam fluences on ion stopping in solid targets. This is relevant in applications such as in fusion sciences. To address this question, a Thomson parabola was built for the Neutralized Drift Compression eXperiment (NDCX-II) for ion energy-loss measurements at different ion beam fluences. The linear induction accelerator NDCX-II delivers 2 ns short, intense ion pulses, up to several tens of nC/pulse, or 1010-1011 ions, with a peak kinetic energy of ∼1.1 MeV and a minimal spot size of 2 mm FWHM. For this particular accelerator, the energy determination with conventional beam diagnostics, for example, time of flight measurements, is imprecise due to the non-trivial longitudinal phase space of the beam. In contrast, a Thomson parabola is well suited to reliably determine the beam energy distribution. The Thomson parabola differentiates charged particles by energy and charge-to-mass ratio, through deflection of charged particles by electric and magnetic fields. During first proof-of-principle experiments, we achieved to reproduce the average initial helium beam energy as predicted by computer simulations with a deviation of only 1.4%. Successful energy-loss measurements with 1 µm thick silicon nitride foils show the suitability of the accelerator for such experiments. The initial ion energy was determined during a primary measurement without a target, while a second measurement, incorporating the target, was used to determine the transmitted energy. The energy-loss was then determined as the difference between the two energies.

Abundance of small mammals in the Atlantic Forest (ASMAF): a data set for analyzing tropical community patterns.

Local abundance results from the interaction between populational and environmental processes. The abundance of the species in a community is also one of the most basic descriptors of its structure. Despite its importance, information about species abundances is fragmentary, creating a knowledge gap about species abundances known as the Prestonian Shortfall. Here we present a comprehensive data set of small mammal abundance in the Atlantic Forest. Data were extracted from 114 published sources and from unpublished data collected by our research groups spanning from 1943 to 2017. The data set includes 1,902 records of at least 111 species in 155 localities, totaling 42,617 individuals represented. We selected studies that (1) were conducted in forested habitats of the Atlantic Forest, (2) had a minimum sampling effort of at least 500 trap-nights, and (3) contained species abundance data in detail. For each study, we recorded (1) latitude and longitude, (2) name of the locality, (3) employed sampling effort, (4) type of traps used, (5) study year, (6) country, and (7) species name with (8) its respective abundances. For every locality, we also obtained information regarding its (9) ecoregion, (10) predominant vegetation type, and (11) biogeographic subdivision. Whenever necessary, we also (12) updated the species names as new species were described and some genera suffered taxonomic revision since the publication. The localities are spread across the Atlantic Forest and most of the small mammal species known to occur in Atlantic Forest are present in the data set, making it representative of communities of the entire biome. This data set can be used to address various patterns in community ecology and geographical ecology, as the relation between local abundance and environmental suitability, hypothesis regarding local and regional factors on community structuring, species abundance distributions (SAD), functional and phylogenetic mechanisms on community assembling.

Vocal patterns of adult females and juveniles Caiman yacare (Crocodilia: Alligatoridae) in Brazilian Pantanal wetland.

The Paraguayan caiman (Caiman yacare) is the main Caimaninae species occurring in the Brazilian Pantanal Wetland. Despite the relative availability of works focused on biology and conservation of the Paraguayan caiman, almost nothing is known about its vocal structure and behavior. We recorded aggressive calls of adult caiman females guarding nests and, afterwards, the distress calls of the new born juvenile caimans in seasonally flooded areas of the Nhecolândia (Southern Pantanal). The results of both observations and sonographic analyses diverged from studies with other crocodilian species. Aggressive vocalization of adult females of the Paraguayan caiman was longer and more complex than the same vocalization of larger Alligatoridae species. Vocalizations of the young caimans presented interspecific differences with other crocodilian offsprings. Moreover, we found statistically significant intraspecific variation in the distress call structure among different pods, even separated by few kilometers. Differences in distress call structure were tested by Canonical Discriminant Analysis (CDA). We obtained the squared Mahalanobis distances between the acoustic multivariate spaces of each pod provided by the CDA and compared with the geographic distance between the bays of origin of each pod through Mantel Test. The geographic distance by itself did not explain the differences found in the structure of the vocalization of young caimans from different pods. The adult females of Paraguayan caiman positively responded to playbacks of calls from juvenile caimans from pods of other regions, as well as to rough imitations of distress call. Since the adult caimans showed protective responses to quite heterogeneous vocalizations of distress by juveniles, we hypothesized that the variation in the distress call pattern may be associated to a low specificity in sound recognition by adult caimans.

Vocal patterns of adult females and juveniles Caiman yacare (Crocodilia: Alligatoridae) in Brazilian Pantanal wetland / Patrones de vocalización de jóvenes y hembras adultas de Caiman yacare (Crocodilia: Alligatoridae) en el Pantanal de Brasil

The Paraguayan caiman (Caiman yacare) is the main Caimaninae species occurring in the Brazilian Pantanal Wetland. Despite the relative availability of works focused on biology and conservation of the Paraguayan caiman, almost nothing is known about its vocal structure and behavior. We recorded aggressive calls of adult caiman females guarding nests and, afterwards, the distress calls of the new born juvenile caimans in seasonally flooded areas of the Nhecolândia (Southern Pantanal). The results of both observations and sonographic analyses diverged from studies with other crocodilian species. Aggressive vocalization of adult females of the Paraguayan caiman was longer and more complex than the same vocalization of larger Alligatoridae species. Vocalizations of the young caimans presented interspecific differences with other crocodilian offsprings. Moreover, we found statistically significant intraspecific variation in the distress call structure among different pods, even separated by few kilometers. Differences in distress call structure were tested by Canonical Discriminant Analysis (CDA). We obtained the squared Mahalanobis distances between the acoustic multivariate spaces of each pod provided by the CDA and compared with the geographic distance between the bays of origin of each pod through Mantel Test. The geographic distance by itself did not explain the differences found in the structure of the vocalization of young caimans from different pods. The adult females of Paraguayan caiman positively responded to playbacks of calls from juvenile caimans from pods of other regions, as well as to rough imitations of distress call. Since the adult caimans showed protective responses to quite heterogeneous vocalizations of distress by juveniles, we hypothesized that the variation in the distress call pattern may be associated to a low specificity in sound recognition by adult caimans.

Poco se conoce sobre la estructura vocal del Caiman yacare del Pantanal brasileño. Llamadas agresivas de hembras adultas que cuidaban de los nidos fueron registradas durante enero y febrero y llamadas de socorro de caimanes jóvenes, en abril de 1992. Hembras adultas de C. yacare presentaron una vocalización agresiva más larga y compleja que en otras especies más grandes de Alligatoridae. Las vocalizaciones de los jóvenes caimanes también presentaron diferencias interespecíficas con otros cocodrilos y variaciones intraespecíficas entre grupos separados por pocos kilómetros. Se utilizó la Prueba de Mantel para comparar las distancias de Mahalanobis entre la estructura de las vocalizaciones de los jóvenes de acuerdo con sus grupos y las distancias geográficas donde ellos estaban. La distancia geográfica en sí no explica las diferencias en las vocalizaciones de jóvenes de diferentes grupos. Hembras adultas de C. yacare han respondido a grabaciones de llamadas de caimanes de grupos de otras regiones, así como a imitaciones de llamada de socorro. Se postula que las variaciones en las llamadas de socorro pueden estar asociadas con una baja especificidad en el reconocimiento de sonido por caimanes adultos que han respondido de la misma forma protectora a las más heterogéneas expresiones de peligro de los jóvenes.

PARP1 is activated at telomeres upon G4 stabilization: possible target for telomere-based therapy.

New anti-telomere strategies represent important goals for the development of selective cancer therapies. In this study, we reported that uncapped telomeres, resulting from pharmacological stabilization of quadruplex DNA by RHPS4 (3,11-difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl]acridinium methosulfate), trigger specific recruitment and activation of poly-adenosine diphosphate (ADP) ribose polymerase I (PARP1) at the telomeres, forming several ADP-ribose polymers that co-localize with the telomeric repeat binding factor 1 protein and are inhibited by selective PARP(s) inhibitors or PARP1-specific small interfering RNAs. The knockdown of PARP1 prevents repairing of RHPS4-induced telomere DNA breaks, leading to increases in chromosome abnormalities and eventually to the inhibition of tumor cell growth both in vitro and in xenografts. More interestingly, the integration of a TOPO1 inhibitor on the combination treatment proved to have a high therapeutic efficacy ensuing a complete regression of the tumor as well as a significant increase in overall survival and cure of mice even when treatments started at a very late stage of tumor growth. Overall, this work reveals the unexplored link between the PARP1 and G-quadruplex ligands and demonstrates the excellent efficacy of a multi-component strategy based on the use of PARP inhibitors in telomere-based therapy.

Large telomerase RNA, telomere length heterogeneity and escape from senescence in Candida glabrata.

Telomerase, the key enzyme essential for the maintenance of eukaryotic chromosome ends, contains a reverse transcriptase and an RNA that provides the template for the synthesis of telomeric repeats. Here, we characterize the telomerase subunits in the hemiascomycete yeast Candida glabrata. We propose a secondary structure model for the telomerase RNA that is the largest described to date. Telomerase deletion mutants show a progressive shortening of telomeres and a modest loss of viability. Frequent post-senescence survivors emerge that possess long telomeric repeat tracts. We suggest that the high telomere length heterogeneity accounts for this distinct senescence phenotype.

TRF2 inhibition promotes anchorage-independent growth of telomerase-positive human fibroblasts.

Although telomere instability is observed in human tumors and is associated with the development of cancers in mice, it has yet to be established that it can contribute to the malignant transformation of human cells. We show here that in checkpoint-compromised telomerase-positive human fibroblasts an episode of TRF2 inhibition promotes heritable changes that increase the ability to grow in soft agar, but not tumor growth in nude mice. This transforming activity is associated to a burst of telomere instability but is independent of an altered control of telomere length. Moreover, it cannot be recapitulated by an increase in chromosome breaks induced by an exposure to gamma-radiations. Since it can be revealed in the context of telomerase-proficient human cells, telomere dysfunction might contribute to cancer progression even at late stages of the oncogenesis process, after the telomerase reactivation step.

Drift compression of an intense neutralized ion beam.

Longitudinal compression of a velocity-tailored, intense neutralized beam at 300 keV, 25 mA has been demonstrated. The compression takes place in a 1-2 m drift section filled with plasma to provide space-charge neutralization. An induction cell produces a head-to-tail velocity ramp that longitudinally compresses the neutralized beam, enhancing the beam peak current by a factor of 50 and producing a pulse duration of about 3 ns. This measurement has been confirmed independently with two different diagnostic systems.

A haploid-specific transcriptional response to irradiation in Saccharomyces cerevisiae.

Eukaryotic cells respond to DNA damage by arresting the cell cycle and modulating gene expression to ensure efficient DNA repair. We used global transcriptome analysis to investigate the role of ploidy and mating-type in inducing the response to damage in various Saccharomyces cerevisiae strains. We observed a response to DNA damage specific to haploid strains that seemed to be controlled by chromatin regulatory proteins. Consistent with these microarray data, we found that mating-type factors controlled the chromatin-dependent silencing of a reporter gene. Both these analyses demonstrate the existence of an irradiation-specific response in strains (haploid or diploid) with only one mating-type factor. This response depends on the activities of Hdf1 and Sir2. Overall, our results suggest the existence of a new regulation pathway dependent on mating-type factors, chromatin structure remodeling, Sir2 and Hdf1 and independent of Mec1 kinase.

Telomere maintenance, function and evolution: the yeast paradigm.

Telomeres are multifunctional genetic elements that cap chromosome ends, playing essential roles in genome stability, chromosome higher-order organization and proliferation control. The telomere field has largely benefited from the study of unicellular eukaryotic organisms such as yeasts. Easy cultivation in laboratory conditions and powerful genetics have placed mainly Saccharomyces cerevisiae, Kluveromyces lactis and Schizosaccharomyces pombe as crucial model organisms for telomere biology research. Studies in these species have made it possible to elucidate the basic mechanisms of telomere maintenance, function and evolution. Moreover, comparative genomic analyses show that telomeres have evolved rapidly among yeast species and functional plasticity emerges as one of the driving forces of this evolution. This provides a precious opportunity to further our understanding of telomere biology.

Quadrupole-induced resonant-particle transport in a pure electron plasma.

Small transverse magnetic quadrupole fields sharply degrade the confinement of non-neutral plasmas held in Malmberg-Penning traps. For example, a quadrupole magnetic field of only 0.02 G/cm doubles the diffusion rate in a trap with a 100 G axial magnetic field. Larger quadrupole fields noticeably change the shape of the plasma. The transport is greatest at an orbital resonance. These results cast doubt on plans to use magnetic quadrupole neutral atom traps to confine antihydrogen atoms created in double-well positron/antiproton Malmberg-Penning traps.

The set1Delta mutation unveils a novel signaling pathway relayed by the Rad53-dependent hyperphosphorylation of replication protein A that leads to transcriptional activation of repair genes.

SET domain proteins are present in chromosomal proteins involved in epigenetic control of transcription. The yeast SET domain protein Set1p regulates chromatin structure, DNA repair, and telomeric functions. We investigated the mechanism by which the absence of Set1p increases DNA repair capacities of checkpoint mutants. We show that deletion of SET1 induces a response relayed by the signaling kinase Rad53p that leads to the MEC1/TEL1-independent hyperphosphorylation of replication protein A middle subunit (Rfa2p). Consequently, the binding of Rfa2p to upstream repressing sequences (URS) of repair genes is decreased, thereby leading to their derepression. Our results correlate the set1Delta-dependent phosphorylation of Rfa2p with the transcriptional induction of repair genes. Moreover, we show that the deletion of the amino-terminal region of Rfa2p suppresses the sensitivity to ultraviolet radiation of a mec3Delta checkpoint mutant, abolishes the URS-mediated repression, and increases the expression of repair genes. This work provides an additional link for the role of Rfa2p in the regulation of the repair capacity of the cell and reveals a role for the phosphorylation of Rfa2p and unveils unsuspected connections between chromatin, signaling pathways, telomeres, and DNA repair.

Protosilencers in Saccharomyces cerevisiae subtelomeric regions.

Saccharomyces cerevisiae subtelomeric repeats contain silencing elements such as the core X sequence, which is present at all chromosome ends. When transplaced at HML, core X can enhance the action of a distant silencer without acting as a silencer on its own, thus fulfilling the functional definition of a protosilencer. Here we show that an ACS motif and an Abf1p-binding site participate in the silencing capacity of core X and that their effects are additive. In addition, in a variety of settings, core X was found to bring about substantial gene repression only when a low level of silencing was already detectable in its absence. Adjoining an X-STAR sequence, which naturally abuts core X in subtelomeric regions, did not improve the silencing capacity of core X. We propose that protosilencers play a major role in a variety of silencing phenomena, as is the case for core X, which acts as a silencing relay, prolonging silencing propagation away from telomeres.

An activation-independent role of transcription factors in insulator function.

Chromatin insulators are defined as transcriptionally neutral elements that prevent negative or positive influence from extending across chromatin to a promoter. Here we show that yeast subtelomeric anti-silencing regions behave as boundaries to telomere-driven silencing and also allow discontinuous propagation of silent chromatin. These two facets of insulator activity, boundary and silencing discontinuity, can be recapitulated by tethering various transcription activation domains to tandem sites on DNA. Importantly, we show that these insulator activities do not involve direct transcriptional activation of the reporter promoter. These findings predict that certain promoters behave as insulators and partition genomes in functionally independent domains.

Ku-deficient yeast strains exhibit alternative states of silencing competence.

In Saccharomyces cerevisiae, efficient silencer function requires telomere proximity, i.e. compartments of the nucleoplasm enriched in silencing factors. Accordingly, silencers located far from telomeres function inefficiently. We show here that cells lacking yKu balance between two mitotically stable states of silencing competence. In one, a partial delocalization of telomeres and silencing factors throughout the nucleoplasm correlates with enhanced silencing at a non-telomeric locus, while in the other, telomeres retain their focal pattern of distribution and there is no repression at the non-telomeric locus, as observed in wild-type cells. The two states also differ in their level of residual telomeric silencing. These findings indicate the existence of a yKu-independent pathway of telomere clustering and Sir localization. Interestingly, this pathway appears to be under epigenetic control.