Hengzongshu/ArticleAgent huggingface dataset:
Despite the rapid development of approaches aimed to precisely control transcription of exogenous genes in time and space, design of systems providing similar tight regulation of endogenous gene expression is much more challenging. However, finding ways to control the activity of endogenous genes is absolutely necessary for further progress in safe and effective gene therapies and regenerative medicine. In addition, such systems are of particular interest for genetics, molecular and cell biology. An ideal system should ensure tunable and reversible spatio-temporal control over transcriptional activity of a gene of interest. Although there are drug-inducible systems for transcriptional regulation of endogenous genes, optogenetic approaches seem to be the most promising for the gene therapy applications, as they are noninvasive and do not exhibit toxicity in comparison with druginducible systems.

Moreover, they are not dependent on chemical inducer diffusion rate or pharmacokinetics and exhibit fast activation-deactivation switching. Among optogenetic tools, long-wavelength light-controlled systems are more preferable for use in mammalian tissues in comparison with tools utilizing shorter wavelengths, since far-red/near-infrared light has the maximum penetration depth due to lower light scattering caused by lipids and reduced tissue autofluorescence at wavelengths above 700 nm. Here, we review such light-inducible systems, which are based on synthetic factors that can be targeted to any desired DNA sequence and provide activation or repression of a gene of interest. The factors include zinc finger proteins, transcription activator-like effectors (TALEs), and the CRISPR/Cas9 technology.

We also discuss the advantages and disadvantages of these DNA targeting tools in the context of the light-inducible gene regulation systems.
A theoretical description of pulsed reaction yield detected magnetic resonance (RYDMR) is proposed. In RYDMR, magnetic resonance spectra of radical pairs (RPs) are indirectly detected by monitoring their recombination yield. Such a detection method is significantly more sensitive than conventional electron paramagnetic resonance (EPR), but design of appropriate pulse sequences for RYDMR requires additional effort because of a different observable. In this work various schemes for generating spin-echo like signals and detecting them by RYDMR are treated. Specifically, we consider refocusing of zero-quantum coherences (ZQCs) and single-quantum coherences (SQCs) by selective as well as by non-selective pulses and formulate a general analytical approach to pulsed RYDMR, which makes an efficient use of the product operator formalism. We anticipate that these results are of importance for RYDMR studies of elusive paramagnetic particles, notably, in organic semiconductors.
Myelodysplastic syndromes are a group of clonal diseases of hematopoietic stem cells and are characterized by multilineage dysplasia, ineffective hematopoiesis, peripheral blood cytopenias, genetic instability and a risk of transformation to acute myeloid leukemia. Some patients with non-Hodgkin lymphomas (NHLs) may have developed secondary myelodysplasia before therapy. Bone marrow (BM) hematopoiesis is regulated by a spectrum of epigenetic factors, among which microRNAs (miRNAs) are special.

The aim of this work is to profile miRNA expression in BM cells in untreated NHL patients with secondary myelodysplasia. A comparative analysis of miRNA expression levels between the NHL and non-cancer blood disorders samples revealed that let-7a-5p was upregulated, and miR-26a-5p, miR-199b-5p, miR-145-5p and miR-150-5p were downregulated in NHL with myelodysplasia (p < 0.05).

We for the first time developed a profile of miRNA expression in BM samples in untreated NHL patients with secondary myelodysplasia. It can be assumed that the differential diagnosis for blood cancers and secondary BM conditions based on miRNA expression profiles will improve the accuracy and relevance of the early diagnosis of cancerous and precancerous lesions in BM.
local earthquake travel‐time tomography (LET) model previously applied for the same station network

We present a three‐dimensional model of the distribution of S‐wave velocity in the upper crust to a depth of 20 km beneath Central Java based on the analysis of seismic ambient noise data recorded by more than 100 seismic stations in 2004 associated with the MERAMEX project. To invert the Rayleigh wave dispersion curves to construct 2‐D group‐velocity maps and 3‐D distributions of S‐wave velocity, we have used a new tomographic algorithm based on iterative linearized inversion. We have performed a series of synthetic tests that demonstrate significantly higher resolution in the upper crust with this model compared to the local earthquake travel‐time tomography (LET) model previously applied for the same station network.

Beneath the southern flank of Merapi, we identify a large low‐velocity anomaly that can be split into two layers. The upper layer reflects the ∼1 km thick sedimentary cover of volcanoclastic deposits. The deeper anomaly at depths of ∼4–8 km may represent a magma reservoir with partially molten rock that feeds several volcanoes in Central Java. Beneath the Merapi summit, we observe another low‐velocity anomaly as deep as 8 km that may be associated with the active magma reservoir that feeds the eruptive activity of Merapi. In the southern portion of the study area, in the lower crust, we identify a low‐velocity anomaly that may represent the top of the pathways of volatiles and melts ascending from the slab that was previously inferred from the LET model results. We observe that this anomaly is clearly separate from the felsic magma reservoirs in the upper crust.
Актуальность исследования обусловлена получением новых данных по изотопной геохимии сверхкрепких рассолов Сибирской платформы. Цель: выявить особенности генезиса рассолов и растворенной в них углекислоты, а также взаимодействия вод с окружением.

Методы. Полевое опробование проведено в соответствии с общепринятыми методиками. Химико-аналитические исследования выполнены методами титриметрии, ионной хроматографии и масс-спектрометрии с индуктивно связанной плазмой. Определение δD, δ18O, δ13С проводилось на приборе Isotope Ratio Mass Spectrometer FinniganTM MAT 253, снабженном приставками пробоподготовки H/Device (для анализа δD) и GasBench II (для анализа δ18O и δ13СDIC). Изотопные отношения 87Sr86/Sr и 87Rb/86Sr изучались на масс-спектрометре MI 1201T в двухленточном режиме с регистрацией на одном коллекторе.

Результаты. Представлены новые изотопно-геохимические данные по сверхкрепким рассолам Сибирской платформы широкого стратиграфического диапазона (от рифея до ордовика). Для изученных рассолов характерен широкий интервал относительных концентраций дейтерия и кислорода-18: от –133 до –17,5 ‰ для δD и от –17,0 до –2,5 ‰ для δ18O. На основании значений кислородных и водородных дельт рассолов предполагается их седиментационно-метаморфический генезис. Значения δ13С для DIC рассолов варьируют в диапазоне от –31 до +12,7 ‰. Предполагается биогенное (бактериальное) происхождение растворенной в водах углекислоты. В среднем переход от более молодых комплексов к более древним сопровождается обогащением DIC легким изотопом углерода. Стронциевые отношения изученных рассолов делят их на две группы: с отношениями 87Sr/86Sr, близкими к значениям в водах современного океана, и со значениями 87Sr/86Sr, существенно их превышающими. Предполагается, что для рассолов второй группы захоронение вод происходило в присутствии обломочного материала выветривания континентальной коры, обогащенного радиоактивным 87Rb.
The Helmholtz decomposition of the vector field of probability fluxes in a two-dimensional space of collective variables makes it possible to introduce a potential for the driving force of protein folding [Chekmarev, J. Chem. Phys. 139 (2013) 145103]. The potential has two components: one component (Φ) is responsible for the source and sink of the folding flow, which represent, respectively, the unfolded and native state of the protein, and the other (Ψ) accounts for the flow vorticity inherently generated at the periphery of the flow field and provides the canalization of the flow between the source and sink. Both components obey Poisson's equations with the corresponding source/sink terms. In the present paper, we consider how the shape of the potential changes depending on the scenario of protein folding. To mimic protein folding dynamics projected onto a two-dimensional space of collective variables, the two-dimensional Müller and Brown potential is employed. Three characteristic scenarios are considered: a single pathway from the unfolded to the native state without intermediates, two parallel pathways without intermediates, and a single pathway with an off-pathway intermediate. To determine the probability fluxes, the hydrodynamic description of the folding reaction is used, in which the first-passage folding is viewed as a steady flow of the representative points of the protein from the unfolded to the native state. We show that despite the possible complexity of the folding process, the Φ-component is simple and universal in shape. The Ψ-component is more complex and reveals characteristic features of the process of folding. The present approach is potentially applicable to other complex reactions, for which the transition from the reactant to the product can be described in a space of two (collective) variables.
The sources were identified among collection samples characterized by highly pronounced economic and valuable features, which allows new geographically remote source material to be taken to the regional breeding practices. This research aims to assess the agronomic traits (duration of the growing period, lodging resistance and plant height, 1000-grain weight, grain weight and yield) in soft spring wheat varieties of different ecological and geographical origin. Estimation was carried out by a 9-point system of expression of the trait during the study, which allows identifying samples with the greatest expression of the trait in the years of study with respect to the average experience. 5439 samples have been studied over 28 years, with 1106 of them, over two years or more. The study was carried out according to the methods of VIR on plots of 2 m2. It was shown that the samples mainly had no correlation between the yield and the duration of the growing period, while the average dependence (г = 0.6) was revealed between the yield and the height of the plants. Varieties forming the intermediate (4.5-5 points) and above average (6-7) yield in a short growing period (69-85 days) were identified (Lutescens 675, Irkut-skaya 49, Simbirca, Hybrid F3 S-141, Hybrid F4, Hybrid F3 S-289 and Hybrid F4 S-2300 and Pamyati Vavenko-va). A high average score (8.6-9) at 1000 grains weight was shown for 16 varieties with variation from 37 g (N43 and IAO-9) to 56 g (Hofed 1). A high average score (8-9) in the evaluation of grain weight was shown for Pamyati Leont'eva, Ekada 70, Simbirtsit, Don Jose, Yong-Liang 4 and Long-Mai 11, which formed ears with an average weight from 0.96 to 2.30 g. A consistently high score (9) reflecting the yield was in the varieties Condestavel, PF 843025, Prilenskaya 19, Pamyati Leont'eva, Omskaya Krasa.
Receptors of the leukocyte receptor cluster (LRC) play a range of important functions in the human immune system. However, the evolution of the LRC remains poorly understood, even in mammals not to mention nonmammalian vertebrates.

We conducted a comprehensive bioinformatics analysis of the LRC-related genes in the publicly available genomes of six species that represent eutherian, marsupial, and monotreme lineages of mammals.

These findings have for the first time provided a solid basis for inference of the LRC phylogeny across mammals. Our analysis suggests that the mammalian LRC family likely derived from two ancestral genes, which evolved in a lineage-specific manner by expansion/contraction, extensive exon shuffling, and sequence divergence. The striking structural and functional diversity of eutherian LRC molecules appears largely lineage specific. The only family member retained in all the three mammalian lineages is a collagen-binding receptor OSCAR. Strong sequence conservation of a transmembrane domain known to associate with FcRγ suggests an adaptive role of this domain subtype in the LRC evolution.
An unprecedented silver-centered P-tetracapped [Ag@Ag4(μ3-P)4] tetrahedron inscribed within a N12 icosahedral cage has been discovered in the novel family of luminescent clusters. The latter are easily self-assembled by reacting AgI salts with tris(2-pyridyl)phosphine (Py3P).
Increasing complexity of modern laser systems, mostly originated from the nonlinear dynamics of radiation, makes control of their operation more and more challenging, calling for development of new approaches in laser engineering. Machine learning methods, providing proven tools for identification, control, and data analytics of various complex systems, have been recently applied to mode-locked fiber lasers with the special focus on three key areas: self-starting, system optimization and characterization. However, the development of the machine learning algorithms for a particular laser system, while being an interesting research problem, is a demanding task requiring arduous efforts and tuning a large number of hyper-parameters in the laboratory arrangements. It is not obvious that this learning can be smoothly transferred to systems that differ from the specific laser used for the algorithm development by design or by varying environmental parameters.

Here we demonstrate that a deep reinforcement learning (DRL) approach, based on trials and errors and sequential decisions, can be successfully used for control of the generation of dissipative solitons in mode-locked fiber laser system. We have shown the capability of deep Q-learning algorithm to generalize knowledge about the laser system in order to find conditions for stable pulse generation. Region of stable generation was transformed by changing the pumping power of the laser cavity, while tunable spectral filter was used as a control tool. Deep Q-learning algorithm is suited to learn the trajectory of adjusting spectral filter parameters to stable pulsed regime relying on the state of output radiation.

Our results confirm the potential of deep reinforcement learning algorithm to control a nonlinear laser system with a feed-back. We also demonstrate that fiber mode-locked laser systems generating data at high speed present a fruitful photonic test-beds for various machine learning concepts based on large datasets.
Eukaryotic chromosomes are spatially segregated into topologically associating domains (TADs). Some TADs are attached to the nuclear lamina (NL) through lamina-associated domains (LADs). Here, we identified LADs and TADs at two stages of Drosophila spermatogenesis – in bamΔ86 mutant testes which is the commonly used model of spermatogonia (SpG) and in larval testes mainly filled with spermatocytes (SpCs). We found that initiation of SpC-specific transcription correlates with promoters’ detachment from the NL and with local spatial insulation of adjacent regions. However, this insulation does not result in the partitioning of inactive TADs into sub-TADs. We also revealed an increased contact frequency between SpC-specific genes in SpCs implying their de novo gathering into transcription factories. In addition, we uncovered the specific X chromosome organization in the male germline. In SpG and SpCs, a single X chromosome is stronger associated with the NL than autosomes. Nevertheless, active chromatin regions in the X chromosome interact with each other more frequently than in autosomes. Moreover, despite the absence of dosage compensation complex in the male germline, randomly inserted SpG-specific reporter is expressed higher in the X chromosome than in autosomes, thus evidencing that non-canonical dosage compensation operates in SpG.
Oedaleus decorus is a widely distributed species over the Eurasian semi-arid territories, from the Atlantic coast to the Pacific one. In many semi-arid territories, O. decorus was and is the important pest. In the south-eastern part of West Siberian Plain, until the 1960s it was not considered a pest. We compared two sets of data on the acridid distribution in the region: until the 1950s and from the 1960s until 2019. Until the 1960s the species occurred mainly in the southern steppes. Since the 1960s its distribution changed significantly. Nowadays it occupies almost all local steppes and the southern part of the forest-steppes and was also found on the eastern side of the Ob River. These shifts may be explained by both climatic changes and changes in human activities. During upsurges the densities of O. decorus were often more than 1–2 adults per square meter. It was and is often abundant in the same habitats and in the same periods as the Italian locust (Calliptamus italicus) – one of the most important pest. This means during joint outbreaks these two species can simultaneously damage almost all spectrum of plants.
A positive list (list of positive integers) is protographic if its merger with all but finitely many positive graphic lists is graphic. Define the family ${\cal P}_s$ of $s$-protogaphic lists by letting ${\cal P}_0$ be the family of positive graphic lists and letting ${\cal P}_s$ for $s>0$ be the family of positive lists whose merger with all but finitely many lists in ${\cal P}_{s-1}$ is in ${\cal P}_{s-1}$.

The main result is that $X\in{\cal P}_s$ if and only if $t(X)\in {\cal P}_{s-1}$, where $t(X)$ is the list obtained from $X$ by subtracting one from each term of $X$ (deleting those that become $0$) and appending a 1 for each term of $X$.

A corollary is that the maximum number of iterations to reach a graphic list from an $n$-term even list with sum $2k$ is $k-n+1$ (when $k\ge n$), achieved by the unique such list having one term larger than 1.
The present study examines the effects of serotonin (5-HT) 1A receptor ligands on humoral immune response in two rat lines selected for over 75 generations for the enhancement or elimination of aggression.

Activation of presynaptic 5-HT1A receptors with a low dose of the selective 5-HT1A receptor agonist 8-OH-DPAT (0.1 mg/kg) or the blockade of postsynaptic 5-HT1A receptors with the antagonist WAY-100635 (1.0 mg/kg) did not affect the numbers of IgM-antibody forming cells (IgM-AFC) in the spleen of highly aggressive rats. On the other hand, the same doses of 8-OH-DPAT and WAY-100635, as well as a higher dose of 8-OH-DPAT (1.0 mg/kg), which is known to activate postsynaptic 5-HT1A receptors, produce immunostimulation in nonaggressive rats. However, only the highest dose of 8-OH-DPAT (5.0 mg/kg) was able to cause immunosuppression in nonaggressive rats that was mainly dependent on stimulation of postsynaptic 5-HT1A receptors. In contrast to nonaggressive rats, the dose of 1.0 mg/kg 8-OH-DPAT was sufficient to produce a decrease in the numbers of IgM-AFC in highly aggressive rats.

Thus, pharmacological activation of pre- and postsynaptic 5-HT1A receptors, as well as the blockade of postsynaptic 5-HT1A receptors, produced different effects on the immune response in two lines of rats selected for high level of aggression or its absence. These data may have implications for more efficient treatments of a number of mental disorders associated with abnormal aggression.
The unexpected formation of a highly strained polycyclic amine was observed in a one-pot synthesis from cyclopentanone, dimethyl fumarate and ammonium acetate. This multistep reaction includes 1,3-dipolar cycloaddition of dimethyl fumarate to the cyclic azomethine ylide formed in situ from cyclopentanone and ammonia. The polycyclic amine product was easily converted into a sterically shielded polycyclic nitroxide. The EPR spectra and spin relaxation behavior of the nitroxide were studied in solution. The spin relaxation seems well suited for the use as a biological spin label and are comparable with those of cyclic nitroxides with two spirocyclic moieties adjacent to the N–O · group.
A bstract The isospin asymmetries of B → K (∗) μ + μ − decays and the partial branching fractions of B 0 → K 0 μ + μ − and B + → K ∗+ μ + μ − are measured as a function of the di-muon mass squared q 2 using an integrated luminosity of 1.0 fb −1 collected with the LHCb detector. The B → Kμ + μ − isospin asymmetry integrated over q 2 is negative, deviating from zero with over 4 σ significance. The B → K ∗ μ + μ − decay measurements are consistent with the Standard Model prediction of negligible isospin asymmetry. The observation of the decay B 0 → K S μ + μ − is reported with 5.7 σ significance. Assuming that the branching fraction of B 0 → K 0 μ + μ − is twice that of B 0 → K S μ + μ − , the branching fractions of B 0 → K 0 μ + μ − and B → K ∗+ μ + μ − are found to be (0 . 31 −0.06 ) × 10 −6 and (1 . 16 ± 0 . 19) × 10 −6 , respectively.
Apurinic/apyrimidinic (AP) endonucleases play critical roles in the repair of abasic sites and strand breaks in DNA. Complete genome sequences of Helicobacter pylori reveal that this bacterial specie has a single AP endonuclease. An H. pylori homolog of Xth (HpXth) is a member of exonuclease III family, which is represented by Escherichia coli Xth. Currently, it remains unknown whether this single AP endonuclease has DNA repair activities similar to those of its counterpart in E. coli and other bacteria. We report that HpXth possesses efficient AP site cleavage, 3'-repair phosphodiesterase, and 3'-phosphatase activities but not the nucleotide incision repair function. Optimal reaction conditions for HpXth's AP endonuclease activity are low ionic strength, high Mg2+ concentration, pH in the range 7–8, and temperature 30 °C. The kinetic parameters measured under steady-state conditions showed that HpXth removes the AP site, 3'-blocking sugar-phosphate, and 3'-terminal phosphate in DNA strand breaks with good efficiency (kcat/KM = 1240, 44, and 5,4 μM–1·min–1, respectively), similar to that of E. coli Xth. As expected, the presence of HpXth protein in AP endonuclease—deficient E. coli xth nfo strain significantly reduced the sensitivity to an alkylating agent and H2O2. Mutation of active site residue D144 in HpXth predicted to be essential for catalysis resulted in a complete loss of enzyme activities. Several important structural features of HpXth were uncovered by homology modeling and phylogenetic analysis. Our data show the DNA substrate specificity of H. pylori AP endonuclease and suggest that HpXth counteracts the genotoxic effects of DNA damage generated by endogenous and host-imposed factors.
The process of the liquid spray impact on the heated surface is studied experimentally using the IR-transparent sapphire plate method. The spatiotemporal distribution of the temperature field on the sapphire substrate surface during impacting spray is received. The obtained experimental data are an important step in a study of the local characteristics of heat transfer in the areas of the contact lines during liquid spray impact on the heated surface. Further, the local heat fluxes and heat transfer coefficients will be determined by solving the problem of thermal conductivity in the sapphire substrate.