Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. `Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).Peer reviewe

Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.Peer reviewe

The screens culture: impact on ADHD

Children’s use of electronic media, including Internet and video gaming, has increased dramatically to an average in the general population of roughly 3 h per day. Some children cannot control their Internet use leading to increasing research on “internet addiction.” The objective of this article is to review the research on ADHD as a risk factor for Internet addiction and gaming, its complications, and what research and methodological questions remain to be addressed. The literature search was done in PubMed and Psychinfo, as well as by hand. Previous research has demonstrated rates of Internet addiction as high as 25% in the population and that it is addiction more than time of use that is best correlated with psychopathology. Various studies confirm that psychiatric disorders, and ADHD in particular, are associated with overuse, with severity of ADHD specifically correlated with the amount of use. ADHD children may be vulnerable since these games operate in brief segments that are not attention demanding. In addition, they offer immediate rewards with a strong incentive to increase the reward by trying the next level. The time spent on these games may also exacerbate ADHD symptoms, if not directly then through the loss of time spent on more developmentally challenging tasks. While this is a major issue for many parents, there is no empirical research on effective treatment. Internet and off-line gaming overuse and addiction are serious concerns for ADHD youth. Research is limited by the lack of measures for youth or parents, studies of children at risk, and studies of impact and treatment

Global Variation of Nutritional Status in Children Undergoing Chronic Peritoneal Dialysis : A Longitudinal Study of the International Pediatric Peritoneal Dialysis Network

While children approaching end-stage kidney disease (ESKD) are considered at risk of uremic anorexia and underweight they are also exposed to the global obesity epidemic. We sought to investigate the variation of nutritional status in children undergoing chronic peritoneal dialysis (CPD) around the globe. The distribution and course of body mass index (BMI) standard deviation score over time was examined prospectively in 1001 children and adolescents from 35 countries starting CPD who were followed in the International Pediatric PD Network (IPPN) Registry. The overall prevalence of underweight, and overweight/obesity at start of CPD was 8.9% and 19.7%, respectively. Underweight was most prevalent in South and Southeast Asia (20%), Central Europe (16.7%) and Turkey (15.2%), whereas overweight and obesity were most common in the Middle East (40%) and the US (33%). BMI SDS at PD initiation was associated positively with current eGFR and gastrostomy feeding prior to PD start. Over the course of PD BMI SDS tended to increase on CPD in underweight and normal weight children, whereas it decreased in initially overweight patients. In infancy, mortality risk was amplified by obesity, whereas in older children mortality was markedly increased in association with underweight. Both underweight and overweight are prevalent in pediatric ESKD, with the prevalence varying across the globe. Late dialysis start is associated with underweight, while enteral feeding can lead to obesity. Nutritional abnormalities tend to attenuate with time on dialysis. Mortality risk appears increased with obesity in infants and with underweight in older children.Peer reviewe

Ground observations of a space laser for the assessment of its in-orbit performance

The wind mission Aeolus of the European Space Agency was a groundbreaking achievement for Earth observation. Between 2018 and 2023, the space-borne lidar instrument ALADIN onboard the Aeolus satellite measured atmospheric wind profiles with global coverage which contributed to improving the accuracy of numerical weather prediction. The precision of the wind observations, however, declined over the course of the mission due to a progressive loss of the atmospheric backscatter signal. The analysis of the root cause was supported by the Pierre Auger Observatory in Argentina whose fluorescence detector registered the ultraviolet laser pulses emitted from the instrument in space, thereby offering an estimation of the laser energy at the exit of the instrument for several days in 2019, 2020 and 2021. The reconstruction of the laser beam not only allowed for an independent assessment of the Aeolus performance, but also helped to improve the accuracy in the determination of the laser beam's ground track on single pulse level. The results presented in this paper set a precedent for the monitoring of space lasers by ground-based telescopes and open new possibilities for the calibration of cosmic-ray observatories.Comment: 10 pages, 10 figure

The Pierre Auger Observatory Open Data

The Pierre Auger Collaboration has embraced the concept of open access to their research data since its foundation, with the aim of giving access to the widest possible community. A gradual process of release began as early as 2007 when 1% of the cosmic-ray data was made public, along with 100% of the space-weather information. In February 2021, a portal was released containing 10% of cosmic-ray data collected from 2004 to 2018, during Phase I of the Observatory. The Portal included detailed documentation about the detection and reconstruction procedures, analysis codes that can be easily used and modified and, additionally, visualization tools. Since then the Portal has been updated and extended. In 2023, a catalog of the 100 highest-energy cosmic-ray events examined in depth has been included. A specific section dedicated to educational use has been developed with the expectation that these data will be explored by a wide and diverse community including professional and citizen-scientists, and used for educational and outreach initiatives. This paper describes the context, the spirit and the technical implementation of the release of data by the largest cosmic-ray detector ever built, and anticipates its future developments.Comment: 19 pages, 8 figure

Radio Measurements of the Depth of Air-Shower Maximum at the Pierre Auger Observatory

The Auger Engineering Radio Array (AERA), part of the Pierre Auger Observatory, is currently the largest array of radio antenna stations deployed for the detection of cosmic rays, spanning an area of $17$ km$^2$ with 153 radio stations. It detects the radio emission of extensive air showers produced by cosmic rays in the $30-80$ MHz band. Here, we report the AERA measurements of the depth of the shower maximum ($X_\text{max}$), a probe for mass composition, at cosmic-ray energies between $10^{17.5}$ to $10^{18.8}$ eV, which show agreement with earlier measurements with the fluorescence technique at the Pierre Auger Observatory. We show advancements in the method for radio $X_\text{max}$ reconstruction by comparison to dedicated sets of CORSIKA/CoREAS air-shower simulations, including steps of reconstruction-bias identification and correction, which is of particular importance for irregular or sparse radio arrays. Using the largest set of radio air-shower measurements to date, we show the radio $X_\text{max}$ resolution as a function of energy, reaching a resolution better than $15$ g cm$^{-2}$ at the highest energies, demonstrating that radio $X_\text{max}$ measurements are competitive with the established high-precision fluorescence technique. In addition, we developed a procedure for performing an extensive data-driven study of systematic uncertainties, including the effects of acceptance bias, reconstruction bias, and the investigation of possible residual biases. These results have been cross-checked with air showers measured independently with both the radio and fluorescence techniques, a setup unique to the Pierre Auger Observatory.Comment: Submitted to Phys. Rev.

Demonstrating Agreement between Radio and Fluorescence Measurements of the Depth of Maximum of Extensive Air Showers at the Pierre Auger Observatory

We show, for the first time, radio measurements of the depth of shower maximum ($X_\text{max}$) of air showers induced by cosmic rays that are compared to measurements of the established fluorescence method at the same location. Using measurements at the Pierre Auger Observatory we show full compatibility between our radio and the previously published fluorescence data set, and between a subset of air showers observed simultaneously with both radio and fluorescence techniques, a measurement setup unique to the Pierre Auger Observatory. Furthermore, we show radio $X_\text{max}$ resolution as a function of energy and demonstrate the ability to make competitive high-resolution $X_\text{max}$ measurements with even a sparse radio array. With this, we show that the radio technique is capable of cosmic-ray mass composition studies, both at Auger and at other experiments.Comment: Submitted to Phys. Rev. Let