A Stop Codon in Xeroderma Pigmentosum Group C Families in Turkey and Italy: Molecular Genetic Evidence for a Common Ancestor

Xeroderma pigmentosum family G from Van, Turkey had two severely affected children: a son with multiple skin cancers who died at age 10 (XP67TMA), and an 8 y old daughter who began developing skin cancer before 3 y of age (XP68TMA). XP67TMA and XP68TMA cells were hypersensitive to killing by ultraviolet and the post-ultraviolet DNA repair level was 12–16% of normal. Host cell reactivation of an ultraviolet-treated reporter plasmid cotransfected with a vector expressing wild-type XPC cDNA assigned XP67TMA to xeroderma pigmentosum complementation group C. The XPC mRNA level was markedly reduced. Sequencing of the 3.5 kb XPC cDNA from XP67TMA showed a C–T mutation in XPC exon 8 at base pair 1840. This mutation converts the CGA codon of arginine at amino acid 579 to a UGA stop codon resulting in marked truncation of the 940 amino acid xeroderma pigmentosum C protein. Restriction fragment length polymorphism analysis of XPC exon 8 DNA in XP67TMA and XP68TMA showed that both affected children had a homozygous mutation and that both parents had heterozygous normal and mutated sequences at the same position consistent with a history of consanguinity in the family. The mutated allele also contained two XPC single nucleotide polymorphisms. The same mutated XPC allele was reported in an Italian family. Studies of 19 microsatellite markers flanking the XPC gene on chromosome 3 suggest that the XPC allele passed between Italy and Turkey approximately 300–500 y ago. This XPC allele containing a nonsense mutation is associated with severe clinical disease with multiple skin cancers and early death

Desert Farming Benefits from Microbial Potential in Arid Soils and Promotes Diversity and Plant Health

BACKGROUND: To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known. METHODOLOGY/PRINCIPAL FINDINGS: We studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt). Using a polyphasic methodological approach to analyse microbial communities in soil as well as associated with cultivated plants, drastic effects caused by 30 years of agriculture were detected. Analysing bacterial fingerprints, we found statistically significant differences between agricultural and native desert soil of about 60%. A pyrosequencing-based analysis of the 16S rRNA gene regions showed higher diversity in agricultural than in desert soil (Shannon diversity indices: 11.21/7.90), and displayed structural differences. The proportion of Firmicutes in field soil was significantly higher (37%) than in the desert (11%). Bacillus and Paenibacillus play the key role: they represented 96% of the antagonists towards phytopathogens, and identical 16S rRNA sequences in the amplicon library and for isolates were detected. The proportion of antagonistic strains was doubled in field in comparison to desert soil (21.6%/12.4%); disease-suppressive bacteria were especially enriched in plant roots. On the opposite, several extremophilic bacterial groups, e.g., Acidimicrobium, Rubellimicrobium and Deinococcus-Thermus, disappeared from soil after agricultural use. The N-fixing Herbaspirillum group only occurred in desert soil. Soil bacterial communities were strongly driven by the a-biotic factors water supply and pH. CONCLUSIONS/SIGNIFICANCE: After long-term farming, a drastic shift in the bacterial communities in desert soil was observed. Bacterial communities in agricultural soil showed a higher diversity and a better ecosystem function for plant health but a loss of extremophilic bacteria. Interestingly, we detected that indigenous desert microorganisms promoted plant health in desert agro-ecosystems

Meta-analysis of real-time fMRI neurofeedback studies using individual participant data: How is brain regulation mediated?

An increasing number of studies using real-time fMRI neurofeedback have demonstrated that successful regulation of neural activity is possible in various brain regions. Since these studies focused on the regulated region(s), little is known about the target-independent mechanisms associated with neurofeedback-guided control of brain activation, i.e. the regulating network. While the specificity of the activation during self-regulation is an important factor, no study has effectively determined the network involved in self-regulation in general. In an effort to detect regions that are responsible for the act of brain regulation, we performed a post-hoc analysis of data involving different target regions based on studies from different research groups. We included twelve suitable studies that examined nine different target regions amounting to a total of 175 subjects and 899 neurofeedback runs. Data analysis included a standard first- (single subject, extracting main paradigm) and second-level (single subject, all runs) general linear model (GLM) analysis of all participants taking into account the individual timing. Subsequently, at the third level, a random effects model GLM included all subjects of all studies, resulting in an overall mixed effects model. Since four of the twelve studies had a reduced field of view (FoV), we repeated the same analysis in a subsample of eight studies that had a well-overlapping FoV to obtain a more global picture of self-regulation. The GLM analysis revealed that the anterior insula as well as the basal ganglia, notably the striatum, were consistently active during the regulation of brain activation across the studies. The anterior insula has been implicated in interoceptive awareness of the body and cognitive control. Basal ganglia are involved in procedural learning, visuomotor integration and other higher cognitive processes including motivation. The larger FoV analysis yielded additional activations in the anterior cingulate cortex, the dorsolateral and ventrolateral prefrontal cortex, the temporo-parietal area and the visual association areas including the temporo-occipital junction. In conclusion, we demonstrate that several key regions, such as the anterior insula and the basal ganglia, are consistently activated during self-regulation in real-time fMRI neurofeedback independent of the targeted region-of-interest. Our results imply that if the real-time fMRI neurofeedback studies target regions of this regulation network, such as the anterior insula, care should be given whether activation changes are related to successful regulation, or related to the regulation process per se. Furthermore, future research is needed to determine how activation within this regulation network is related to neurofeedback success

Exclusive J/ψ detection and physics with ECCE

The file available on this institutional repository is an arXiv preprint which may not have been certified by peer review. The definitive version of record published by Elsevier is available at https://doi.org/10.48550/arXiv.2207.10356.Copyright © The Authors 2023. The EIC Comprehensive Chromodynamics Experiment (ECCE) detector has been recommended as a reference design for the proposed Electron-Ion Collider (EIC) program. This paper presents simulation studies of exclusive J/ψ detection and selected physics impact results in EIC using the projected ECCE detector concept. Exclusive quarkonium photoproduction is one of the most popular processes in EIC, which has a large cross section and a simple final state. Due to the gluonic nature of the exchange Pomeron, this process can be related to the gluon distributions in the nucleus. Preliminary results estimate the excellent statistics benefited from the large cross section of J/ψ photoproduction and superior performance of ECCE detector concept. The precise measurement of exclusive J/ψ photoproduction at EIC will help us to more deeply understand nuclear gluon distributions, near threshold production mechanism and nucleon mass structure.X. Li and W. Zha are supported by the National Natural Science Foundation of China (12005220, 12175223) and MOST (2018YFE0104900). The authors would like to thank the ECCE Consortium for performing a full simulation of their detector design, for providing up-to-date information on EIC run conditions, and for suggestions and comments on the manuscript. X. Li and W. Zha would like to thank Y. Zhou for useful suggestions and discussions related to this analysis. W. Zha is supported by Anhui Provincial Natural Science Foundation No. 2208085J23 and Youth Innovation Promotion Association of Chinese Academy of Sciences. AANL group are supported by the Science Committee of RA , in the frames of the research project 21AG-1C028

Design and Simulated Performance of Calorimetry Systems for the ECCE Detector at the Electron Ion Collider

We describe the design and performance the calorimeter systems used in the ECCE detector design to achieve the overall performance specifications cost-effectively with careful consideration of appropriate technical and schedule risks. The calorimeter systems consist of three electromagnetic calorimeters, covering the combined pseudorapdity range from -3.7 to 3.8 and two hadronic calorimeters. Key calorimeter performances which include energy and position resolutions, reconstruction efficiency, and particle identification will be presented.Comment: 19 pages, 22 figures, 5 table

AI-assisted Optimization of the ECCE Tracking System at the Electron Ion Collider

The Electron-Ion Collider (EIC) is a cutting-edge accelerator facility that will study the nature of the "glue" that binds the building blocks of the visible matter in the universe. The proposed experiment will be realized at Brookhaven National Laboratory in approximately 10 years from now, with detector design and R&D currently ongoing. Notably, EIC is one of the first large-scale facilities to leverage Artificial Intelligence (AI) already starting from the design and R&D phases. The EIC Comprehensive Chromodynamics Experiment (ECCE) is a consortium that proposed a detector design based on a 1.5T solenoid. The EIC detector proposal review concluded that the ECCE design will serve as the reference design for an EIC detector. Herein we describe a comprehensive optimization of the ECCE tracker using AI. The work required a complex parametrization of the simulated detector system. Our approach dealt with an optimization problem in a multidimensional design space driven by multiple objectives that encode the detector performance, while satisfying several mechanical constraints. We describe our strategy and show results obtained for the ECCE tracking system. The AI-assisted design is agnostic to the simulation framework and can be extended to other sub-detectors or to a system of sub-detectors to further optimize the performance of the EIC detector.Comment: 16 pages, 18 figures, 2 appendices, 3 table

ECCE Sensitivity Studies for Single Hadron Transverse Single Spin Asymmetry Measurements

We performed feasibility studies for various single transverse spin measurements that are related to the Sivers effect, transversity and the tensor charge, and the Collins fragmentation function. The processes studied include semi-inclusive deep inelastic scattering (SIDIS) where single hadrons (pions and kaons) were detected in addition to the scattered DIS lepton. The data were obtained in {\sc pythia}6 and {\sc geant}4 simulated e+p collisions at 18 GeV on 275 GeV, 18 on 100, 10 on 100, and 5 on 41 that use the ECCE detector configuration. Typical DIS kinematics were selected, most notably $Q^2 > 1$ GeV$^2$, and cover the $x$ range from $10^{-4}$ to $1$. The single spin asymmetries were extracted as a function of $x$ and $Q^2$, as well as the semi-inclusive variables $z$, and $P_T$. They are obtained in azimuthal moments in combinations of the azimuthal angles of the hadron transverse momentum and transverse spin of the nucleon relative to the lepton scattering plane. The initially unpolarized MonteCarlo was re-weighted in the true kinematic variables, hadron types and parton flavors based on global fits of fixed target SIDIS experiments and $e^+e^-$ annihilation data. The expected statistical precision of such measurements is extrapolated to 10 fb$^{-1}$ and potential systematic uncertainties are approximated given the deviations between true and reconstructed yields. The impact on the knowledge of the Sivers functions, transversity and tensor charges, and the Collins function has then been evaluated in the same phenomenological extractions as in the Yellow Report. The impact is found to be comparable to that obtained with the parameterized Yellow Report detector and shows that the ECCE detector configuration can fulfill the physics goals on these quantities.Comment: 22 pages, 22 figures, to be submitted to joint ECCE proposal NIM-A volum

Open Heavy Flavor Studies for the ECCE Detector at the Electron Ion Collider

The ECCE detector has been recommended as the selected reference detector for the future Electron-Ion Collider (EIC). A series of simulation studies have been carried out to validate the physics feasibility of the ECCE detector. In this paper, detailed studies of heavy flavor hadron and jet reconstruction and physics projections with the ECCE detector performance and different magnet options will be presented. The ECCE detector has enabled precise EIC heavy flavor hadron and jet measurements with a broad kinematic coverage. These proposed heavy flavor measurements will help systematically study the hadronization process in vacuum and nuclear medium especially in the underexplored kinematic region.Comment: Open heavy flavor studies with the EIC reference detector design by the ECCE consortium. 11 pages, 11 figures, to be submitted to the Nuclear Instruments and Methods

ECCE unpolarized TMD measurements

We performed feasibility studies for various measurements that are related to unpolarized TMD distribution and fragmentation functions. The processes studied include semi-inclusive Deep inelastic scattering (SIDIS) where single hadrons (pions and kaons) were detected in addition to the scattered DIS lepton. The single hadron cross sections and multiplicities were extracted as a function of the DIS variables $x$ and $Q^2$, as well as the semi-inclusive variables $z$, which corresponds to the momentum fraction the detected hadron carries relative to the struck parton and $P_T$, which corresponds to the transverse momentum of the detected hadron relative to the virtual photon. The expected statistical precision of such measurements is extrapolated to accumulated luminosities of 10 fb$^{-1}$ and potential systematic uncertainties are approximated given the deviations between true and reconstructed yields.Comment: 12 pages, 9 figures, to be submitted in joint ECCE proposal NIM-A volum