Hengzongshu/ArticleAgent huggingface dataset:
The Worldwide LHC Computing Grid (WLCG) is an innovative distributed environment which is deployed through the use of grid computing technologies in order to provide computing and storage resources to the LHC experiments for data processing and physics analysis. Following increasing demands of LHC computing needs toward high luminosity era, the experiments are engaging in an ambitious program to extend the capability of WLCG distributed environment, for instance including opportunistically used resources such as High-Performance Computers (HPCs), cloud platforms and volunteer computers.

In order to be effectively used by the LHC experiments, all these diverse distributed resources should be described in detail. This implies easy service discovery of shared physical resources, detailed description of service configurations and experiment-specific data structures is needed. In this contribution, we present a high-level information component of a distributed computing environment, the Computing Resource Information Catalogue (CRIC) which aims to facilitate distributed computing operations for the LHC experiments and consolidate WLCG topology information. In addition, CRIC performs data validation and provides coherent view and topology description to the LHC VOs for service discovery and configuration.

CRIC represents the evolution of ATLAS Grid Information System (AGIS) into the common experiment independent high-level information framework. CRIC's mission is to serve not just ATLAS Collaboration needs for the description of the distributed environment but any other virtual organization relying on large scale distributed infrastructure as well as the WLCG on the global scope. The contribution describes CRIC architecture, implementation of data model, collectors, user interfaces, advanced authentication and access control components of the system.
X-chromosome inactivation, which occurs in female eutherian mammals is controlled by a complex X-linked locus termed the X-inactivation center (XIC). Previously it was proposed that genes of the XIC evolved, at least in part, as a result of pseudogenization of protein-coding genes.

In this study we show that the key XIC gene Xist, which displays fragmentary homology to a protein-coding gene Lnx3, emerged de novo in early eutherians by integration of mobile elements which gave rise to simple tandem repeats. The Xist gene promoter region and four out of ten exons found in eutherians retain homology to exons of the Lnx3 gene. The remaining six Xist exons including those with simple tandem repeats detectable in their structure have similarity to different transposable elements.

Integration of mobile elements into Xist accompanies the overall evolution of the gene and presumably continues in contemporary eutherian species. Additionally we showed that the combination of remnants of protein-coding sequences and mobile elements is not unique to the Xist gene and is found in other XIC genes producing non-coding nuclear RNA.
Specialized quantitative MRI techniques allow identifying structural changes in individual muscles in inflammatory myopathies.

T2 mapping technique for assessing structural changes in muscle tissues was optimized for the Philips “Ingenia” 3.0T MR scanner. T2 relaxation (T2rt) time of the thigh and lower leg muscles (muscule rectus femoris, m. vastus lateralis, m. adductor magnus, m. soleus, m. tibialis anterior, medial and lateral head of m. gastrocnemius) was assessed in the control group (n = 9) and the study group (n = 6). Patients recruited in the study group suffered from dermatomyositis and polymyositis of various severity.

The sensitivity of the reported technique in the detection of sub-acute swelling of muscle tissue in the absence of significant changes in signal characteristics on routine MR sequences had been shown.
Raman lasing in a graded-index fiber (GIF) attracts now great deal of attention due to the opportunity to convert high-power multimode laser diode radiation into the Stokes wave with beam quality improvement based on the Raman clean-up effect. Here we report on the cascaded Raman generation of the 2nd Stokes order in the 1.1-km long GIF with 100-μm core directly pumped by 915-nm diodes. In the studied all-fiber scheme, the 1st Stokes order is generated at 950-954 nm in a linear cavity formed at GIF ends by two fiber Bragg gratings (FBGs) securing beam quality improvement from M
The sustainability of farming and animal welfare requires the reconsideration of current selection schemes. In particular, implementation of new selection criteria related to animal health and welfare should help to produce more robust animals and to reduce anti-microbial use. The hypothalamo-pituitary-adrenocortical (HPA) axis plays a major role in metabolic regulation and adaptation processes and its activity is strongly influenced by genetic factors. A positive association between HPA axis activity and robustness was recently described. To explore whether selecting pigs upon HPA axis activity could increase their robustness, a divergent selection experiment was carried out in the Large White pig breed. This allowed the generation of low (HPAlo) and high (HPAhi) responders to adrenocorticotropic hormone administration.In this study, we compared 23 hematologic and immune parameters of 6-week-old, HPAlo and HPAhi piglets and analysed their response to a low dose of lipopolysaccharide (LPS) two weeks later. At six weeks of age, HPAhi piglets displayed greater red blood cell and leucocyte number including CD8α+ γδ cells, cytotoxic T lymphocytes, naive T helper (Th) cells and B lymphocytes as compared to HPAlo individuals. The ability of blood cells to secrete TNFα in response to LPS ex vivo was higher for HPAhi pigs. At week eight, the inflammatory response to the LPS in vivo challenge was poorly affected by the HPA axis activity.Divergent selection upon HPA axis activity modulated hematologic and immune parameters in 6-week-old pigs, which may confer an advantage to HPAhi pigs at weaning. However, HPAlo and HPAhi piglets did not exhibit major differences in the parameters analysed two weeks later, i. e. in 8-week-old pigs. In conclusion, chronic exposure to high cortisol levels in HPAhi pigs does not negatively impact immunity.
BioUML (homepage: http://www.biouml.org, main public server: https://ict.biouml.org) is a web-based integrated environment (platform) for systems biology and the analysis of biomedical data generated by omics technologies. The BioUML vision is to provide a computational platform to build virtual cell, virtual physiological human and virtual patient.

BioUML spans a comprehensive range of capabilities, including access to biological databases, powerful tools for systems biology (visual modelling, simulation, parameters fitting and analyses), a genome browser, scripting (R, JavaScript) and a workflow engine. Due to integration with the Galaxy platform and R/Bioconductor, BioUML provides powerful possibilities for the analyses of omics data. The plug-in-based architecture allows the user to add new functionalities using plug-ins.

To facilitate a user focus on a particular task or database, we have developed several predefined perspectives that display only those web interface elements that are needed for a specific task. To support collaborative work on scientific projects, there is a central authentication and authorization system (https://bio-store.org). The diagram editor enables several remote users to simultaneously edit diagrams.
A setup has been created to study the drying of wet coals by microwave radiation with a frequency of 2.45 GHz.

Time dependences of humidity and surface temperature of brown coal samples from the Talovskoye deposit in Siberia are measured at an absorbed energy density of about 30 W g −1.

The analysis of the data obtained is carried out and the mechanisms of possible processes that explain the observed patterns are considered.
The process $e^+e^- \to K^+K^-$ has been studied using $1.7 \times 10^6$ events from a data sample corresponding to an integrated luminosity of 5.7 pb$^{-1}$ collected with the CMD-3 detector in the center-of-mass energy range 1010--1060 MeV. The cross section measured with an about 2\% systematic uncertainty and it is used to calculate the contribution to the anomalous magnetic moment of the muon $a_μ^{K^+K^-} = (19.33 \pm 0.40) \times 10^{-10}$, and to obtain the $ϕ(1020)$ meson parameters. We consider the relationship between the $e^+e^- \to K^+K^-$ and $e^+e^- \to K^0_SK^0_L$ cross sections and compare it to the theoretical expectations.
In the present work, we studied in detail the thermochemistry, thermal stability, mechanical sensitivity, and detonation performance for 20 nitro-, cyano-, and methyl derivatives of 1,2,5-oxadiazole-2-oxide (furoxan), along with their bis-derivatives.

For all species studied, we also determined the reliable values of the gas-phase formation enthalpies using highly accurate multilevel procedures W2-F12 and/or W1-F12 in conjunction with the atomization energy approach and isodesmic reactions with the domain-based local pair natural orbital (DLPNO) modifications of the coupled-cluster techniques. Apart from this, we proposed reliable benchmark values of the formation enthalpies of furoxan and a number of its (azo)bis-derivatives. Additionally, we reported the previously unknown crystal structure of 3-cyano-4-nitrofuroxan.

Among the monocyclic compounds, 3-nitro-4-cyclopropyl and dicyano derivatives of furoxan outperformed trinitrotoluene, a benchmark melt-cast explosive, exhibited decent thermal stability (decomposition temperature >200 °C) and insensitivity to mechanical stimuli while having notable volatility and low melting points. In turn, 4,4′-azobis-dicarbamoyl furoxan is proposed as a substitute of pentaerythritol tetranitrate, a benchmark brisant high explosive. Finally, the application prospects of 3,3′-azobis-dinitro furoxan, one of the most powerful energetic materials synthesized up to date, are limited due to the tremendously high mechanical sensitivity of this compound. Overall, the investigated derivatives of furoxan comprise multipurpose green energetic materials, including primary, secondary, melt-cast, low-sensitive explosives, and an energetic liquid.
A theoretical framework is proposed to describe the spin dynamics driven by coherent spin mixing at level anti-crossings (LACs). We briefly introduce the LAC concept and propose to describe the spin dynamics using a vector of populations of the diabatic eigenstates. In this description, each LAC gives rise to a pairwise redistribution of eigenstate populations, allowing one to construct the total evolution operator of the spin system. Additionally, we take into account that in the course of spin evolution a "rotation" of the eigenstate basis case take place. The approach is illustrated by a number of examples, dealing with magnetic field inversion, cross-polarization, singlet-state nuclear magnetic resonance and parahydrogen-induced polarization.
Dermal fibroblasts were obtained from a 55 year old male Сaucasian familial Alzheimer's disease (AD) patient carrying heterozygous V717I mutation in the APP gene.

The induced pluripotent stem cell (iPSC) lines ICGi008-A and ICGi008-B were generated from dermal fibroblasts using episomal vectors expressing pluripotency factors.

The generated iPSC lines maintained the original APP genotype, expressed pluripotency markers, exhibited a normal karyotype and retained the ability to differentiate into cell types of the three germ layers. The iPSC lines will be useful for the study of the AD molecular and cellular mechanisms and drug screening.
Single alkali-metal atoms in arrays of optical dipole traps represent a quantum register that can be used for quantum computation and simulation based on short-term Rydberg excitations, which switch the interactions between qubits. To load single atoms into optical dipole traps and then detect them by resonance fluorescence, lenses with a large numerical aperture (NA > 0.5) inside a vacuum chamber and expensive EMCCD cameras are commonly used. We present our recent experimental results on demonstrating the trapping of single 87 Rb atoms using a long-focus objective lens with a low numerical aperture (NA = 0.172) placed outside the vacuum chamber, and detecting single atoms with a low-cost sCMOS camera. We also present our current results on implementing a single-qubit gate based on optical pumping and subsequent microwave transition between two hyperfine sublevels of a single 87 Rb atom with fidelity near 95%.
The article presents the results of studies of petrophysical properties and the study of samples by the method of nuclear magnetic resonance (NMR).

The measurements were carried out on a collection of artificial core samples with different grain sizes. The procedure for preparing the samples is described, and the comparison of the results of measuring the petrophysical properties by different methods is given.

The quantitative relationships between the size of the sand grains from which the samples are made, the filtration-capacity properties and the distribution of the relaxation times of the NMR spectrum of the samples are investigated.
The goal was to determine clinical and anamnestic features of acne patients aged up to 18 years needing systemic isotretinoin treatment, and to assess the treatment dynamics. Materials and methods. The authors conducted a study of 27 patients with moderate to severe acne (with the mean age of 16.2 ± 1.2 years) receiving isotretinoin in the form of LIDOSE (Acnecutan) in the dose of 0.33 ± 0.06 mg/kg. Results. A steady improvement of the skin condition was observed when the dose of isotretinoin in the form of LIDOSE of 60.3 ± 2.8 mg/kg was used. Clinical recovery was observed in all of the patients (the cumulative dose amounted to 100 mg/kg). Teenagers demonstrated good tolerance to the drug and had no systemic adverse effects.
The myelodysplastic syndrome (MDS) holds a special place among blood cancers, as it represents a whole spectrum of hematological disorders with impaired differentiation of hematopoietic precursors, bone marrow dysplasia, genetic instability and is noted for an increased risk of acute myeloid leukemia. Both genetic and epigenetic factors, including microRNAs (miRNAs), are involved in MDS development. MicroRNAs are short non-coding RNAs that are important regulators of normal hematopoiesis, and abnormal changes in their expression levels can contribute to hematological tumor development. To assess the prognosis of the disease, an international assessment system taking into account a karyotype, the number of blast cells, and the degree of deficiency of different blood cell types is used. However, the overall survival and effectiveness of the therapy offered are not always consistent with predictions. The search for new biomarkers, followed by their integration into the existing prognostic system, will allow for personalized treatment to be performed with more precision. Additionally, this paper explains how miRNA expression levels correlate with the prognosis of overall survival and response to the therapy offered.
The cross section of the process e+e−→3(π+π−) has been measured using a data sample of 22pb−1 collected with the CMD-3 detector at the VEPP-2000 e+e− collider.

7956 signal events are selected in the center-of-mass energy range 1.5–2.0 GeV.

The measured cross section exhibits a sharp drop near the pp¯ threshold. A first study of dynamics of six-pion production has been performed.
Introduction : Increasingly, the emergence and evolution of our species is being tied to genetic exchange between divergent lineages within ~1Ma (e.g., Neanderthals, Denisovans). However, little is known about genetic exchange during earlier (pre-1Ma) human evolution and between more divergent lineages. Results : We present evidence of hybridization within human lineage, show that it likely happened between highly divergent (~4.5My) lineages, more than once. We use analysis of nuclear pseudogenes of mtDNA (“NUMTs”). NUMTs are considered “mtDNA fossils”, as they preserve sequences of ancient mtDNA because mutational rate in the nucleus is much lower than in mtDNA. We demonstrate that a NUMT on human chromosome 5, which is shared by chimpanzee and gorilla, had descended from a mitochondrial genome that had been divergent from our ancestor’s mtDNA by ~4.5% at the time of pseudogene insertion. This implies that this pseudogene should have been inserted in a hominid that at that time had been diverged by about 4.5My of evolution from the hominid that at that time carried our mtDNA lineage. In order for this pseudogene and our mtDNA to end up in the same body, these two hominids should have mated with each other. The large divergence implies a distant interspecies (or even inter-generic) hybridization. Additionally, analysis of two other NUMTs (on Chr11 and Chr7) suggests that hybridization events occurred repeatedly. To exclude the large ancestral population size effect we show that mtDNA divergence in extant ape populations does not depend on population size. Discussion : It is thought that within mammals, it takes ~2-4My to establish reproductive isolation. However, fertile inter-generic hybrids have been documented among several primates, separated by ca. 4My. Very recently, hybridization between Colobine genera separated by ~5 My was reported to involve a NUMT scenario similar to what we had proposed human ancestors. Interestingly, phylogenic analysis consistently places the chr5 NUMT insertion around the time of the Homo/Pan split. Intriguingly, certain hominin fossils of that epoch have been interpreted alternately as more human-like or more ape-like. Such morphological mosaicisity could potentially be explained by hybridization. Fixation of NUMTs in question within population should have been rather efficient, since these pseudogenes appear to have been fixed in more than one population. Thus their spread across populations might have been driven by selection. Indeed, NUMTs on chr5 and chr11 are located in 3’ regions of functional genes. Most intriguingly, Ps11 is located 3’ to the RNF141/ZNF230 gene, essential for spermatogenesis. NUMT might have served as an expression modifier for RNF141, resulting in reproductive advantage. Indeed, RNF141 demonstrates selectively driven expression shift in testis of the ancestor of hominines.
Anhydrobiosis represents an extreme example of tolerance adaptation to water loss, where an organism can survive in an ametabolic state until water returns.

Here we report the first comparative analysis examining the genomic background of extreme desiccation tolerance, which is exclusively found in larvae of the only anhydrobiotic insect, Polypedilum vanderplanki. We compare the genomes of P. vanderplanki and a congeneric desiccation-sensitive midge P. nubifer. Comparison of expression patterns of orthologues between two chironomid species provides evidence for the existence of desiccation-specific gene expression systems in P. vanderplanki.

We determine that the genome of the anhydrobiotic species specifically contains clusters of multi-copy genes with products that act as molecular shields. In addition, the genome possesses several groups of genes with high similarity to known protective proteins. However, these genes are located in distinct paralogous clusters in the genome apart from the classical orthologues of the corresponding genes shared by both chironomids and other insects. The transcripts of these clustered paralogues contribute to a large majority of the mRNA pool in the desiccating larvae and most likely define successful anhydrobiosis. The African chironomid midge, Polypedilum vanderplanki, is able to withstand extreme desiccation. Here the authors sequence the genomes of a desiccation-tolerant and desiccation-sensitive species of chironomid midge and pinpoint genes that may have a role in conferring resistance to desiccation.
Using our previously published Web service SNP_TATA_Comparator, we conducted a genome-wide study of single-nucleotide polymorphisms (SNPs) within core promoters of 68 human rheumatoid arthritis (RA)-related genes.

Using 603 SNPs within 25 genes clinically associated with RA-comorbid disorders, we predicted 84 and 70 candidate SNP markers for overexpression and underexpression of these genes, respectively, among which 58 and 96 candidate SNP markers, respectively, can relieve and worsen RA as if there is a neutral drift toward susceptibility to RA. Similarly, we predicted natural selection toward susceptibility to RA for 8 immunostimulatory genes (e.g., IL9R ) and 10 genes most often associated with RA (e.g., NPY ). On the contrary, using 25 immunosuppressive genes, we predicted 70 and 109 candidate SNP markers aggravating and relieving RA, respectively (e.g., IL1R2 and TGFB2 ), suggesting that natural selection can simultaneously additionally yield resistance to RA. We tested this hypothesis by means of public RNA-Seq data on 1740 differentially expressed genes (DEGs) of pets vs. wild animals (e.g., dogs vs. wolves). The difference in gene numbers is statistically significant as confirmed by binomial distribution ( p < 0.01), Pearson’s χ 2 ( p < 0.01), and Fisher’s exact test ( p < 0.05).

We concluded that disruptive natural selection of human immunostimulatory and immunosuppressive genes is concurrently elevating and reducing the risk of RA, respectively. So, we hypothesize that RA in human could be a self-domestication syndrome referring to evolution patterns in domestic animals. The number of DEGs in the domestic animals corresponding to worsened RA condition in humans was significantly larger than that in the related wild animals (10 vs. 3). Moreover, much less DEGs in the domestic animals were accordant to relieved RA condition in humans than those in the wild animals (1 vs. 8 genes). This indicates that the anthropogenic environment, in contrast to a natural one, affects gene expression across the whole genome (e.g., immunostimulatory and immunosuppressive genes) in a manner that likely contributes to RA. This allows us to propose RA as a candidate symptom within a self-domestication syndrome. Such syndrome might be considered as a human’s payment with health for the benefits received during evolution.
Background . Predominant use of the H1 and Gro1-4 genes of resistance to golden nematode (PGN) in potato breeding requires widening the gene pool of resistance to this pathogen. Materials and methods . Thirty-four genotypes of wild potatoes from North and South Americas, 14 interspecific hybrids, and 10 Russian potato cultivars were studied for PGN resistance. Screening for resistance to PGN pathotype Ro1 and molecular screening for the presence of H1 and Gro1-4 gene markers were performed. Amplification products of the Gro1-4 gene marker were sequenced. Results . Only seven among the studied 34 potato genotypes (two of S. brachystotrichum (Bitt.) Rydb., four of S. lesteri Hawkes et Hjerting, and one of S. kurtzianum Bitt. et Wittm.) were susceptible to PGN, while the rest demonstrated high or medium resistance. Molecular screening for the presence of H1 and Gro1-4 gene markers allowed us to identify Gro1-4 in 13 South American genotypes of S. alandiae Cárd., S. × doddsii Corr., S. kurtzianum , S. leptophyes Bitt., and S. yungasense Hawkes. The remaining 14 genotypes may supposedly contain resistance genes non-identical to H1 or Gro1-4 . Hybrids of S. tuberosum L. with medium-resistant wild accessions of S. kurtzianum , S. leptophyes , S. sparsipilum (Bitt.) Juz. et Buk., S. alandiae , and S. × doddsii inherited PGN resistance determined either by the Gro1-4 gene or genes non-identical to H1 or Gro1-4 . Sequencing a fragment of the Gro1-4 gene showed that changes in the structure of this fragment in orthologous genes did not affect the feature of resistance to PGN pathotype Ro1. Conclusion . For the first time, sources of resistance to PGN were found among the North American species S. brachystotrichum (k-23201) and S. lesteri (k-24475). Among the wild South American Solanum spp., sources of resistance determined by genes different from H1 or Gro1-4 were identified. Resistant interspecific hybrids can serve as donors of the Gro1-4 resistance gene or new resistance genes.