Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular cytogenetic identification and nutritional composition evaluation of newly synthesized Triticum turgidum-Triticum boeoticum amphiploids (AABBAbAb)

Triticum boeoticum Boiss. (AbAb, 2n = 2x = 14) is a wheat-related species with the blue aleurone trait. In this study, 18 synthetic Triticum turgidum-Triticum boeoticum amphiploids were identified, which were derived from crosses between T. boeoticum and T. turgidum. Three probes (Oligo-pTa535, Oligo-pSc119.2, and Oligo-pTa713) for multicolor fluorescence in situ hybridization (mc-FISH) were combined with genomic in situ hybridization (GISH) to identify chromosomal composition. Seven nutritional indices (anthocyanins, protein, total essential amino acids TEAA, Fe, Zn, Mn and Cu) were measured, and the nutritional components of 18 synthetic amphiploids were comprehensively ranked by principal component analysis (PCA). The results showed that all three synthetic amphiploids used for cytological identification contained 42 chromosomes, including 14 A, 14 B, and 14 Ab chromosomes. The average anthocyanin content was 82.830 μg/g to 207.606 μg/g in the whole meal of the 17 blue-grained lines (Syn-ABAb-1 to Syn-ABAb-17), which was obviously higher than that in the yellow-grained line Syn-ABAb-18 (6.346 μg/g). The crude protein content was between 154.406 and 180.517 g/kg, and the EAA content was 40.193-63.558 mg/g. The Fe, Zn, Mn and Cu levels in the 17 blue-grained lines were 60.55 to 97.41 mg/kg, 60.55-97.41 mg/kg, 35.11 to 65.20 mg/kg and 5.74 to 7.22 mg/kg, respectively, which were higher than those in the yellow-grained line. The contribution of the first three principal components reached 84%. The first principal component was mainly anthocyanins, Fe, Zn and Mn. The second principal component contained protein and amino acids, and the third component contained only Cu. The top 5 Triticum turgidum-Triticum boeoticum amphiploids were Syn-ABAb-11, Syn-ABAb-17, Syn-ABAb-5, Syn-ABAb-8 and Syn-ABAb-4. These amphidiploids exhibited the potential to serve as candidates for hybridization with common wheat, as indicated by comprehensive score rankings, toward enhancing the nutritional quality of wheat.
Effects of Per2 overexpression on growth inhibition and metastasis, and on MTA1, nm23-H1 and the autophagy-associated PI3K/PKB signaling pathway in nude mice xenograft models of ovarian cancer

The aim of the present study was to evaluate the association between Period2 (Per2) and the occurrence and development of ovarian cancer, in addition to evaluating the effect of this gene on the growth and metastasis of ovarian cancer in nude mice xenograft models. The detection of Per2 by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blotting methods at various stages of ovarian cancer in tumor tissue samples was conducted. Nude mice xenograft models of ovarian cancer were constructed using an ovarian cancer cell line and, using a gene transfection technique, exogenous infusion of the recombinant gene, Per2, was performed. To assess for the successful and stable expression of Per2 in the tumor tissue, levels of Per2 expression in the nude mice xenograft models were detected by RT-qPCR. During the experimental period, the tumor volumes were measured every three days. Two weeks following treatment cessation, the nude mice were sacrificed and the tumor weight and volume were measured. Furthermore, detection of the changes in expression levels of metastasis-associated gene 1 (MTA-1) and tumor metastasis suppressor gene, non-metastasis protein 23-H1 (nm23-H1), and the expression change of autophagy-associated signal transduction pathway, phosphatidylinositol 3-kinase (PI3K)/protein kinase B (PKB) kinase were analyzed. The findings demonstrated that with ovarian cancer stage development, the expression of Per2 gradually reduced or ceased. In addition, exogenous Per2 was successfully and stably expressed in nude mice tumor tissue samples. Furthermore, in the Per2 overexpression group, MTA-1 protein expression was significantly reduced when compared with the phosphate-buffered saline (PBS) control and empty plasmid groups, while nm23-H1 protein expression was significantly higher when compared with those two groups. The expression levels of PI3K and PKB kinase, which are marker proteins of the autophagy associated signaling pathway PI3K/PKB, were significantly downregulated, when compared with the PBS control and empty plasmid groups (P<0.001). Thus, it was demonstrated that Per2 is closely associated with the development of ovarian cancer, and late-stage ovarian cancer is associated with Per2 mutation or deletion. Per2 overexpression, via exogenous infusion reduced the ovarian cancer growth rate, which was demonstrated by a significant increase in the tumor inhibition rate. In addition, Per2 may inhibit the expression of MTA-1 and promote the expression of nm23-H1 to restrict ovarian tumor growth and metastasis. Finally, it is hypothesized that Per2 affects autophagy by interfering with the PI3K/PKB signaling pathway, causing inhibition of tumor angiogenesis in order to inhibit tumor growth.
World Journal of Diabetes

The complication of diabetes, which is known as diabetic foot ulcer (DFU), is a significant concern due to its association with high rates of disability and mortality. It not only severely affects patients’ quality of life, but also imposes a substantial burden on the healthcare system. In spite of efforts made in clinical practice, treating DFU remains a challenging task. While mesenchymal stem cell (MSC) therapy has been extensively studied in treating DFU, the current efficacy of DFU healing using this method is still inadequate. However, in recent years, several MSCs-based drug delivery systems have emerged, which have shown to increase the efficacy of MSC therapy, especially in treating DFU. This review summarized the application of diverse MSCs-based drug delivery systems in treating DFU and suggested potential prospects for the future research.
A protocol for systematic review and network meta-analysis

Background:To compare and rank the clinical effects of different acupuncture and acupuncture-related therapies on patients with poststroke cognitive impairment. Methods:We evaluated the direct and indirect evidence from relevant studies using network meta-analysis. Eight databases were examined in order to find randomized controlled trials of acupuncture-related therapies for individuals with poststroke cognitive impairment. After 2 researchers independently scanned the literature, extracted the data, and assessed the risk of bias in the included studies, the data were analyzed using RevMan5.4, Stata15.0, and WinBUGS1.4. 3 software. Results: We assess the benefits and drawbacks of various acupuncture-related therapies, rank the efficacy of various acupuncture-related therapies in the treatment of poststroke cognitive impairment, and describe the best acupuncture intervention approaches or combinations based on the available data. Conclusion: This study will contribute to the existence of data on the safety and efficacy of acupuncture-related therapies in the treatment of poststroke cognitive impairment, and it may aid clinical guideline makers in selecting the best acupuncture treatment for poststroke cognitive impairment. Registration Number: INPLASY2021120117. Abbreviations: NMA = network meta-analysis, PSCI = poststroke cognitive impairment, PSCIND = poststroke cognitive impairment no dementia, PSD = poststroke dementia.
Localization of whistler wave and turbulent spectra in the magnetotail region

Observations show that whistler waves play a very crucial role both in magnetic reconnection and turbulence. In this context, linear and nonlinear dynamical equations of whistler wave have been derived and further these equations have been solved numerically as well as semianalytically. For application purpose, magnetotail parameters have been chosen. The obtained results reveal that the nonlinearity as well as field perturbation results in the formation of localized structures. These structures contribute to the turbulence and lead to the formation of current sheets in the magnetotail. Finally, the power spectrum has been evaluated and compared with the observed spectra in the magnetotail ion diffusion region as reported.
Evolutionary Stages and Dynamic Mechanisms of Thematic Cultural Tourist Areas: A Case Study of Lingshan Scenic Area in Wuxi

With the seasonal adjustment of Tramo/Seats and multi-peak fitting methods,this paper analyses the evolutionary stages and fluctuant characteristics of Wuxi Lingshan Scenic Area from 1998 to 2008.Some conclusions can be drawn as follows.1) In terms of the tourist evolutionary stages of Lingshan,it has entered the mature stage after the preliminary and upgrading evolutionary stages.2) The stage evolution has always been a key component of a thematic cultural tourist area in its life cycle,which displays the tendency phase division in the long term and the fluctuant variations in the short term.3) The key dynamic factors that affect the evolutionary stages of thematic cultural tourist areas may include cultural resources,market demand,tourist investment,product improvement,etc.Furthermore,based on the theory of the tourist destination life cycle,we establish a theoretic model of the development and evolution of thematic cultural tourist areas.Therefore,the life cycle of a thematic cultural tourist area can be divided into five stages,i.e.,the exploration and starting stage,the substantial development stage,the fast development stage,the balanced development stage and the follow-up(declining or recessing) development stage.Influenced by more factors than one,the evolution of a thematic cultural tourist area is jointly motivated under the interactions and phase transformations of various dynamic factors,and also led to its stage evolution and fluctuant growth.Finally,a thematic cultural tourist area can maintain sustained development by enhancing its cultural characteristic,strengthening the cultural driving force,cultivating the overall development power and shaping its multi-dynamic growth mechanism.
The geology of the Gryphon Oil Field

The Gryphon Oil Field is located 320 km northeast of Aberdeen in UK Ninth Round Block 9/18b. The field was discovered by Well 9/18b-7 in 1987. This well proved the prognosed Eocene/Paleocene submarine fan system. To date, Kerr-McGee has drilled 13 wells and 10 sidetracks on the field. In 1990 a 3D seismic survey was acquired over the whole trend, in Blocks 9/18a, 9/18b, 9/23a and 9/23b. The field is a complex combination structural/stratigraphic trap formed on the northerly plunging nose of the Crawford Ridge. The principal reservoir sands are of the Balder Formation (latest Paleocene-earliest Eocene) and consist of thick, massive, well-sorted, high porosity sands deposited from high-density gravity flows. Water-escape and soft sediment deformation features are common and no primary sedimentary structures are preserved. These sands formed a 9Lowstand Fan9 complex within a lowstand systems tract. Areas of sand deposition were determined by the sea floor topography, which was controlled by basement structure, soft sediment deformation and the disposition of older sandbodies. In order to establish accurate time lines, it is important to identify the relative ages of these sands correctly. This was achieved using detailed biostratigraphy combined with the innovative techniques of 9desanding9 and petrophysical analysis of the Balder Tuff. Overlying the Balder sequence is the earliest Eocene interbedded claystone, silt and sand sequence of the Frigg Formation. These sediments were deposited within the 9Lowstand Wedge9 channel/levee complex which built out across the previously deposited Balder Fan. Oil and gas migrated into the structure via the ridge fault system from the mature Kimmeridge Clay source in the deep graben to the north and east.
A Two-Step Mechanism for Creating Stable, Condensed Chromatin with the Polycomb Complex PRC1

The Drosophila PRC1 complex regulates gene expression by modifying histone proteins and chromatin architecture. Two PRC1 subunits, PSC and Ph, are most implicated in chromatin architecture. In vitro, PRC1 compacts chromatin and inhibits transcription and nucleosome remodeling. The long disordered C-terminal region of PSC (PSC-CTR) is important for these activities, while Ph has little effect. In cells, Ph is important for condensate formation, long range chromatin interactions, and gene regulation, and its polymerizing Sterile alpha motif (SAM) is implicated in these activities. In vitro, truncated Ph containing the SAM and two other conserved domains (mini-Ph) undergoes phase separation with chromatin, suggesting a mechanism for SAM-dependent condensate formation in vivo. How the distinct activities of PSC and Ph on chromatin function together in PRC1 is not known. To address this question, we analyzed structures formed with large chromatin templates and PRC1 in vitro. PRC1 bridges chromatin into extensive fibrillar networks. Ph, its SAM, and SAM polymerization activity have little effect on these structures. Instead, the PSC-CTR controls their growth, and is sufficient for their formation. To understand how phase separation driven by Ph SAM intersects with the chromatin bridging activity of the PSC-CTR, we used mini-Ph to form condensates with chromatin and then challenged them with PRC1 lacking Ph (PRC1ΔPh). PRC1ΔPh converts mini-Ph chromatin condensates into clusters of small non-fusing condensates and bridged fibers. These condensates retain a high level of chromatin compaction and do not intermix. Thus, phase separation of chromatin by mini-Ph, followed by the action of the PSC-CTR creates a unique chromatin organization with regions of high nucleosome density and extraordinary stability. We discuss how this coordinated sequential activity of two proteins found in the same complex may occur and the possible implications of stable chromatin architectures in maintaining transcription states.
Petrological and structural significance of the Santa Elena-Nicoya ophiolitic complex in Costa Rica and geodynamic implications

Detailed structural and petrological investigations were carried out on the Santa Elena-Nicoya ophiolitic complex in Costa Rica, which is represented by a classic association of mantle tectonites (Santa Elena Peninsula), a cumulitic gabbroic-plagiogranite sequence, and basaltic volcanics and sills (Matapalo and Esperanza Units of the Nicoya Peninsula), with discontinuous radiolarian covers. Despite biostratigraphically different ages (Late Jurassic for Matapalo and Mid-Late Cretaceous for Esperanza) in both units, the major and trace element data, Sr-Nd isotope systematics, and mineral phase crystallization order show identical tholeiitic fractionation trends, where the marked Fe-Ti enrichment of the volcanics is reflected in the gabbroic-Fe gabbroic-plagiogranite intrusives which, in turn, represent the cumulitic counterparts of an essentially analogous magmatic system. Parental basaltic magmas for the Nicoya complex share geochemical features with both Pacific MORB and oceanic plateaus, as indicated by the characteristic flat REE patterns, Zr/Y and Zr/Nb ratios, and Sr-Nd isotopic data ( 87 Sr/ 86 Sr: 0.70295-0.70323; 144 Nd/ 143 Nd: 0.51309-0.51275). On the other hand, basalts and gabbros from Santa Elena display typical N-MORB affinity, as shown by their LREE-depleted patterns. These data, together with the unusual abundance of Fe-Ti differentiated rocks, suggest that the Santa Elena-Nicoya ophiolites may have been generated at oceanic spreading centres in a mantle plume region, analogous to the present Galapagos ridge/hot spot system. The present fore-arc structural setting of the deformed Costa Rica ophiolites is the result of several tectogenetic events recorded by three main ductile deformation phases (from Late Cretaceous to Tertiary): the oldest d1 related to W-E convergent tectonics, followed by d2 related to N-S compression, and the youngest d3 related to NE-SW convergence. The oceanic lithosphere represented by the Costa Rica ophiolites may have been generated at the westernmost termination of the spreading system, leading to the formation of the Caribbean plateau, and later involved in complicated intra-oceanic convergence and rotation processes. These resulted in the progressive building and insertion of the Chorotega block (present Costa Rica) between the Maya-Chortis and Choco-South America continental blocks.
Queuosine Salvage in Bartonella henselae Houston 1: A Unique Evolutionary Path

Queuosine (Q) stands out as the sole tRNA modification that can be synthesized via salvage pathways. Comparative genomic analyses identified specific bacteria that showed a discrepancy between the projected Q salvage route and the predicted substrate specificities of the two identified salvage proteins: 1) the distinctive enzyme tRNA guanine-34 transglycosylase (TGT), responsible for inserting precursor bases into target tRNAs; and 2) Queuosine Precursor Transporter (QPTR), a transporter protein that imports Q precursors. Organisms like the facultative intracellular pathogen Bartonella henselae, which possess only TGT and QPTR but lack predicted enzymes for converting preQ1 to Q, would be expected to salvage the queuine (q) base, mirroring the scenario for the obligate intracellular pathogen Chlamydia trachomatis. However, sequence analyses indicate that the substrate-specificity residues of their TGTs resemble those of enzymes inserting preQ1 rather than q. Intriguingly, mass spectrometry analyses of tRNA modification profiles in B. henselae reveal trace amounts of preQ1, previously not observed in a natural context. Complementation analysis demonstrates that B. henselae TGT and QPTR not only utilize preQ1, akin to their E. coli counterparts, but can also process q when provided at elevated concentrations. The experimental and phylogenomic analyses suggest that the Q pathway in B. henselae could represent an evolutionary transition among intracellular pathogens—from ancestors that synthesized Q de novo to a state prioritizing the salvage of q. Another possibility that will require further investigations is that the insertion of preQ1 has fitness advantages when B. henselae is growing outside a mammalian host. Author summary Transfer RNAs (tRNAs) are adaptors that deliver amino acids to ribosomes during translation of messenger RNAs (mRNAs) into proteins. tRNA molecules contain specially-modified nucleotides that affect many aspects of translation including regulation of translational efficiency, as modified nucleotides primarily occur near the portion of tRNA (anticodon) that directly interacts with the coding sequence (codon) of the mRNA while it is associated with a ribosome. Queuosine (Q) is a modified tRNA nucleotide located in the anticodon that can be synthesized or uniquely imported from the environment as Q or a precursor using a salvage mechanism. Free-living bacteria, e.g., E. coli, can synthesize Q or salvage precursors from the environment, but many obligate intracellular pathogens, e.g., Chlamydia trachomatis, cannot synthesize Q and must import a precursor from eukaryotic hosts. In this study, we determined that Bartonella henselae, a facultative intracellular bacterial pathogen of vascular cells, falls somewhere in the middle, as it is unable to synthesize Q but can salvage Q or certain precursors. The unusual nature of Bartonella’s system suggests different evolutionary scenarios. It could be a snapshot of the transition from Q synthesis to strict Q salvage or represent a unique adaptation to a complex multi-host lifestyle.
Neuronal connectivity, behavioral, and transcriptional alterations associated with the loss of MARK2

Neuronal connectivity is essential for adaptive brain responses and can be modulated by dendritic spine plasticity and the intrinsic excitability of individual neurons. Dysregulation of these processes can lead to aberrant neuronal activity, which has been associated with numerous neurological disorders including autism, epilepsy, and Alzheimer’s disease. Nonetheless, the molecular mechanisms underlying aberrant neuronal connectivity remains unclear. We previously found that the serine/threonine kinase Microtubule Affinity Regulating Kinase 2 (MARK2), also known as Partitioning Defective 1b (Par1b), is important for the formation of dendritic spines in vitro. However, despite its genetic association with several neurological disorders, the in vivo impact of MARK2 on neuronal connectivity and cognitive functions remains unclear. Here, we demonstrate that loss of MARK2 in vivo results in changes to dendritic spine morphology, which in turn leads to a decrease in excitatory synaptic transmission. Additionally, loss of MARK2 produces substantial impairments in learning and memory, anxiety, and social behavior. Notably, MARK2 deficiency results in heightened seizure susceptibility. Consistent with this observation, RNAseq analysis reveals transcriptional changes in genes regulating synaptic transmission and ion homeostasis. These findings underscore the in vivo role of MARK2 in governing synaptic connectivity, cognitive functions, and seizure susceptibility.
TGF-beta dynamically controls epithelial identity in a 3D model of human epiblast

Pluripotency is the ability to give rise to all cell types of the body and is first observed in a mass of disorganised cells of the embryo. Upon implantation, pluripotent cells form a columnar epithelium and undergo lumenogenesis. At gastrulation, a portion of the pluripotent epiblast will undergo epithelial to mesenchymal transition (EMT), forming the primitive streak (PS). It still remains unclear what molecular mechanism supports the epithelial identity of the pluripotent epiblast before gastrulation. Here we developed an optimised, chemically defined 3D model of human pluripotent epiblast formation in which conventional pluripotent stem cells (PSCs) self-organise into a columnar epithelium with a lumen in 48 hours. From 72 hours we observed spontaneous symmetry breaking and specification of PS-like cells, as confirmed by single-cell RNA sequencing. We found that Insulin and FGF signalling are both required for the proliferation and survival of the pluripotent epiblast model. Conversely, TGF-beta signalling maintains epithelial identity. Epithelial identity appears uncoupled from the expression of canonical pluripotency markers OCT4, NANOG and PRDM14, but under the control of ZNF398. Once the pluripotent epithelium is established, TGF-beta inhibition is inconsequential, and stimulation with Activin A leads to highly efficient PS induction. We conclude that TGF-beta dynamically orchestrates epithelial identity of human pluripotent cells.
Emergent Haldane phase in the S =1 bilinear-biquadratic Heisenberg model on the square lattice

Infinite projected entangled pair states simulations of the S=1 bilinear-biquadratic Heisenberg model on the square lattice reveal an emergent Haldane phase in between the previously predicted antiferromagnetic and three-sublattice 120∘ magnetically ordered phases. This intermediate phase preserves SU(2) spin and translational symmetry but breaks lattice rotational symmetry, and it can be adiabatically connected to the Haldane phase of decoupled S=1 chains. Our results contradict previous studies which found a direct transition between the two magnetically ordered states.
2-Phase model for population growth

We discuss the 2-component model of population growth when different types of dynamics are attributed to rural and urban population respectively. We suppose the birth rate to be higher for rural areas, and death rate to dominate for cities. The flow between areas compensates these effects. This approach can reduce the number of parameters usually used for population growth behavior. We also discuss the socio-economic aspects of the model: the ability to control population size by adjusting the flow of people from the city to the countryside, and the trends in the urban and rural population. Finally the Earth population model is proposed.