Miracle-dz/UniFAR-FTUs huggingface dataset:
Long Noncoding RNA ANRIL Supports Proliferation of Adult T-Cell Leukemia Cells through Cooperation with EZH2

Human T-cell leukemia virus type 1 (HTLV-1) is the pathogen that causes adult T-cell leukemia (ATL), which is a unique malignancy of CD4+ T cells. A role for long noncoding RNA (lncRNA) in HTLV-1-mediated cellular transformation has not been described. In this study, we demonstrated that the lncRNA ANRIL was important for maintaining the proliferation of ATL cells in vitro and in vivo. ANRIL was shown to activate NF-κB signaling through forming a ternary complex with EZH2 and p65. Furthermore, epigenetic inactivation of p21/CDKN1A was involved in the oncogenic function of ANRIL. To the best of our knowledge, this is the first study to address the regulatory role of the lncRNA ANRIL in ATL and provides an important clue to prevent or treat HTLV-1-associated human diseases. ABSTRACT Adult T-cell leukemia (ATL) is a highly aggressive T-cell malignancy induced by human T-cell leukemia virus type 1 (HTLV-1) infection. Long noncoding RNA (lncRNA) plays a critical role in the development and progression of multiple human cancers. However, the function of lncRNA in HTLV-1-induced oncogenesis has not been elucidated. In the present study, we show that the expression level of the lncRNA ANRIL was elevated in HTLV-1-infected cell lines and clinical ATL samples. E2F1 induced ANRIL transcription by enhancing its promoter activity. Knockdown of ANRIL in ATL cells repressed cellular proliferation and increased apoptosis in vitro and in vivo. As a mechanism for these actions, we found that ANRIL targeted EZH2 and activated the NF-κB pathway in ATL cells. This activation was independent of the histone methyltransferase (HMT) activity of EZH2 but required the formation of an ANRIL/EZH2/p65 ternary complex. A chromatin immunoprecipitation assay revealed that ANRIL/EZH2 enhanced p65 DNA binding capability. In addition, we observed that the ANRIL/EZH2 complex repressed p21/CDKN1A transcription through H3K27 trimethylation of the p21/CDKN1A promoter. Taken together, our results implicate that the lncRNA ANRIL, by cooperating with EZH2, supports the proliferation of HTLV-1-infected cells, which is thought to be critical for oncogenesis. IMPORTANCE Human T-cell leukemia virus type 1 (HTLV-1) is the pathogen that causes adult T-cell leukemia (ATL), which is a unique malignancy of CD4+ T cells. A role for long noncoding RNA (lncRNA) in HTLV-1-mediated cellular transformation has not been described. In this study, we demonstrated that the lncRNA ANRIL was important for maintaining the proliferation of ATL cells in vitro and in vivo. ANRIL was shown to activate NF-κB signaling through forming a ternary complex with EZH2 and p65. Furthermore, epigenetic inactivation of p21/CDKN1A was involved in the oncogenic function of ANRIL. To the best of our knowledge, this is the first study to address the regulatory role of the lncRNA ANRIL in ATL and provides an important clue to prevent or treat HTLV-1-associated human diseases.
Coalitional Skill Games for Self-Interested robots with SVO

Robots in a multi-robot system cannot communicate with each other due to various reasons. The robots can only maximize their own individual performance without regard for the overall system performance. To guarantee high system revenue even when the robots are self-interested, an algorithm called the intermediary recruitment algorithm (IRA) is proposed. It imitates the operating mechanism of an intermediary recruitment market to allocate the tasks to the robots. The simulation results analyse the inﬂuence of the robots’ social value orientation (SVO) on the system revenue, where SVO is used to measure the degree of self-interest, and the eﬀectiveness of the IRA is also veriﬁed.
Imperfect magnetic field gradients in radial k‐space encoding—Quantification, correction, and parameter dependency

Sensitivity to imperfections of image‐encoding gradient fields may significantly impair widespread use of radial MR data acquisition. Such imperfections can cause individual echo shifts for each spoke acquired in the k‐space and may produce severe image artifacts. Therefore, fast and robust methods to quantify and correct for those echo shifts are required.
The Cocktail Effect of BMP-2 and TGF-β1 Loaded in Visible Light-Cured Glycol Chitosan Hydrogels for the Enhancement of Bone Formation in a Rat Tibial Defect Model

Bone tissue engineering scaffolds offer the merits of minimal invasion as well as localized and controlled biomolecule release to targeted sites. In this study, we prepared injectable hydrogel systems based on visible light-cured glycol chitosan (GC) hydrogels containing bone morphogenetic protein-2 (BMP-2) and/or transforming growth factor-beta1 (TGF-β1) as scaffolds for bone formation in vitro and in vivo. The hydrogels were characterized by storage modulus, scanning electron microscopy (SEM) and swelling ratio analyses. The developed hydrogel systems showed controlled releases of growth factors in a sustained manner for 30 days. In vitro and in vivo studies revealed that growth factor-loaded GC hydrogels have no cytotoxicity against MC3T3-E1 osteoblast cell line, improved mRNA expressions of alkaline phosphatase (ALP), type I collagen (COL 1) and osteocalcin (OCN), and increased bone volume (BV) and bone mineral density (BMD) in tibia defect sites. Moreover, GC hydrogel containing BMP-2 (10 ng) and TGF-β1 (10 ng) (GC/BMP-2/TGF-β1-10 ng) showed greater bone formation abilities than that containing BMP-2 (5 ng) and TGF-β1 (5 ng) (GC/BMP-2/TGF-β1-5 ng) in vitro and in vivo. Consequently, the injectable GC/BMP-2/TGF-β1-10 ng hydrogel may have clinical potential for dental or orthopedic applications.
Discovery of two skin-derived dermaseptins and design of a TAT-fusion analogue with broad-spectrum antimicrobial activity and low cytotoxicity on healthy cells

Two novel peptides belonging to the dermaseptin family, namely DRS-CA-1 and DRS-DU-1, were encoded from cDNA libraries derived from the skin secretions of Phyllomedusa camba and Callimedusa (Phyllomedusa) duellmani. Both natural peptides are highly-conserved and exhibited high potency against wild-type Gram-positive, Gram-negative bacteria, yeast and antibiotic-resistant bacteria (MRSA and Pseudomonas aeruginosa) (MICs 4–8 µM) with no obvious hemolytic activity. Collectively these results suggest that both peptides may have potential as novel antibiotics. Additionally, DRS-DU-1 exhibited selective cytotoxicity to tumor cells. The truncated analogue, DP-1 and TAT-fused DP-1 (namely DP-2) were subsequently synthesised. It showed that DP-1 had low antimicrobial activity, no hemolytic and cytotoxicity to tumor cells. However, DP-2 possessed strong antimicrobial activity and the similar selective, no obvious hemolytic activity and cytotoxicity on normal human cells, but enhanced cytotoxicity to tumor cells of DRS-DU-1. These findings indicate that the N-terminus of the dermaseptins may contribute to their bioactivity, and that addition of the TAT peptide can improve biological activity. The results provide a new insight for designing novel peptide-based antimicrobial or anticancer agents with low hemolytic activity and cytotoxicity.
GmLEA2-1, a Late Embryogenesis Abundant Protein Gene Isolated from Soybean (Glycine max (L.) Merr.), Confers Tolerance to Abiotic Stress

Late embryonic proteins (LEA) gene family was abundant mainly in higher plant embryos, which could protect the embryos from the damage caused by abiotic stress, especially drought and salt stresses. In the present study, GmLEA2-1 was cloned from soybean leaf tissue treated by 10% polyethylene glycol 6000 (PEG6000). The results of quantitative real-time PCR (qRT-PCR) revealed a variety of expression patterns of GmLEA2-1 in various tissues of soybean (root, stem, leaf, flower, pod, early embryo and late embryo). GmLEA2-1 gene shared a lower sequence similarity with other typical LEA genes of same group from different species, but similar functions. Overexpression of GmLEA2-1 in transgenic Arabidopsis thaliana conferred tolerance to drought and salt stresses. The fresh weight and dry weight of seedling, the primary root length and the lateral root density of transgenic Arabidopsis plants were higher than those of wild type Arabidopsis (WT) under drought and salt stresses. Cis -acting regulatory elements in the GmLEA2-1 promoter were also predicted. These data demonstrate that GmLEA2-1 protein play an important role in improving drought and salt tolerance in plants.
Residuum-Condition Diagram and Reduction of Over-Complete Endmember-Sets

Extracting reference spectra, or endmembers (EMs) from a given multi- or hyperspectral image, as well as estimating the size of the EM set, plays an important role in multispectral image processing. In this paper, we present condition-residuum-diagrams. By plotting the residuum resulting from the unmixing and reconstruction and the condition number of various EM sets, the resulting diagram provides insight into the behavior of the spectral unmixing under a varying amount of endmembers (EMs). Furthermore, we utilize condition-residuum-diagrams to realize an EM reduction algorithm that starts with an initially extracted, over-complete EM set. An over-complete EM set commonly exhibits a good unmixing result, i.e. a lower reconstruction residuum, but due to its partial redundancy, the unmixing gets numerically unstable, i.e. the unmixed abundances values are less reliable. Our greedy reduction scheme improves the EM set by reducing the condition number, i.e. enhancing the set's stability, while keeping the reconstruction error as low as possible. The resulting set sequence gives hint to the optimal EM set and its size. We demonstrate the benefit of our condition-residuum-diagram and reduction scheme on well-studied datasets with known reference EM set sizes for several well-known EE algorithms.
Population genetics of the main population of brown bears in southwest Asia

Genetic studies of the Eurasian brown bear (Ursus arctos) have so far focused on populations from Europe and North America, although the largest distribution area of brown bears is in Asia. In this study, we reveal population genetic parameters for the brown bear population inhabiting the Grand Kaçkar Mountains (GKM) in the north east of Turkey, western Lesser Caucasus. Using both hair (N = 147) and tissue samples (N = 7) collected between 2008 and 2014, we found substantial levels of genetic variation (10 microsatellite loci). Bear samples (hair) taken from rubbing trees worked better for genotyping than those from power poles, regardless of the year collected. Genotyping also revealed that bears moved between habitat patches, despite ongoing massive habitat alterations and the creation of large water reservoirs. This population has the potential to serve as a genetic reserve for future reintroductions in the Middle East. Due to the importance of the GKM population for on-going and future conservation actions, the impacts of habitat alterations in the region ought to be minimized; e.g., by establishing green bridges or corridors over reservoirs and major roads to maintain habitat connectivity and gene flow among populations in the Lesser Caucasus.
Function matters: a review of terminological differences in applied and basic clicker training research

In clicker training, animal trainers pair a small device (a “clicker”) with a reward when teaching or maintaining responding. Animal trainers often assume clicker training is a “science-based” way to train animals. But, the few studies that have compared clicker training to a control have not provided evidence that adding a clicker is beneficial to training. This may be because research on clicker training has studied only one of several potential functions of the clicker stimulus that have been discussed by animal trainers. A systematic approach to researching the function of the clicker in clicker training would benefit from collaboration between applied and basic researchers. However, this will require that terminological differences between animal trainers and basic researchers are reconciled. This paper reviews the few studies that have compared clicker training to a control group and then discusses how trainers and basic researchers use the same terminology in functionally different ways—suggesting the empirical support for mechanisms underlying clicker training is less robust than previously assumed. These differences highlight many opportunities to answer basic and applied research questions relative to clicker training methods. Advancements in clicker training methods will benefit animal trainers who have been using clicker training for decades as well as applied practitioners who have extended clicker training to humans in educational and clinical settings.
Intraosseous pressure during loading and with vascular occlusion in an animal model

Objectives We studied subchondral intraosseous pressure (IOP) in an animal model during loading, and with vascular occlusion. We explored bone compartmentalization by saline injection. Materials and Methods Needles were placed in the femoral condyle and proximal tibia of five anaesthetized rabbits and connected to pressure recorders. The limb was loaded with and without proximal vascular occlusion. An additional subject had simultaneous triple recordings at the femoral head, femoral condyle and proximal tibia. In a further subject, saline injections at three sites were carried out in turn. Results Loading alone caused a rise in subchondral IOP from 11.7 mmHg (sd 7.1) to 17.9 mmHg (sd 8.1; p < 0.0002). During arterial occlusion, IOP fell to 5.3 mmHg (sd 4.1), then with loading there was a small rise to 7.6 mmHg (sd 4.5; p < 0.002). During venous occlusion, IOP rose to 20.2 mmHg (sd 5.8), and with loading there was a further rise to 26.3 mmHg (sd 6.3; p < 0.003). The effects were present at three different sites along the limb simultaneously. Saline injections showed pressure transmitted throughout the length of the femur but not across the knee joint. Conclusion This is the first study to report changes in IOP in vivo during loading and with combinations of vascular occlusion and loading. Intraosseous pressure is not a constant. It is reduced during proximal arterial occlusion and increased with proximal venous occlusion. Whatever the perfusion state, in vivo load is transferred partly by hydraulic pressure. We propose that joints act as hydraulic pressure barriers. An understanding of subchondral physiology may be important in understanding osteoarthritis and other bone diseases. Cite this article: M. Beverly, S. Mellon, J. A. Kennedy, D. W. Murray. Intraosseous pressure during loading and with vascular occlusion in an animal model. Bone Joint Res 2018;7:511–516. DOI: 10.1302/2046-3758.78. BJR-2017-0343.R2.
Active-Alert Hypnosis: History, Research, and Applications

After a brief review of the history of the idea of an activity-increasing hypnotic induction procedure with eyes open and pedaling a bicycle ergometer, the features of active-alert hypnotic induction are summarized. Results of research conducted on healthy volunteers revealed the behavioral, experiential, physiological, and interactional characteristics of the induced altered state of consciousness (ASC), showing both similarities and differences between traditional and active-alert hypnosis. A short description of the application of the method is followed by two brief case studies.
ERβ-mediated induction of cystatins results in suppression of TGFβ signaling and inhibition of triple-negative breast cancer metastasis

Significance Triple-negative breast cancer (TNBC) is the most aggressive form of breast cancer and patients exhibit high rates of recurrence and mortality in part due to lack of treatment options beyond standard-of-care chemotherapy regimens. In the subset of TNBCs that express estrogen receptor beta (ERβ), ligand-mediated activation of ERβ elicits potent anticancer effects. We report here the elucidation of the ERβ cistrome and transcriptome in TNBC and identify a mechanism whereby ERβ induces cystatin gene expression resulting in inhibition of canonical TGFβ signaling and a blockade of metastatic phenotypes. These findings suggest that ERβ-targeted therapies represent a treatment option for the subset of women with ERβ-expressing TNBC. Triple-negative breast cancer (TNBC) accounts for a disproportionately high number of deaths due to a lack of targeted therapies and an increased likelihood of distant recurrence. Estrogen receptor beta (ERβ), a well-characterized tumor suppressor, is expressed in 30% of TNBCs, and its expression is associated with improved patient outcomes. We demonstrate that therapeutic activation of ERβ elicits potent anticancer effects in TNBC through the induction of a family of secreted proteins known as the cystatins, which function to inhibit canonical TGFβ signaling and suppress metastatic phenotypes both in vitro and in vivo. These data reveal the involvement of cystatins in suppressing breast cancer progression and highlight the value of ERβ-targeted therapies for the treatment of TNBC patients.
Self-citation is the hallmark of productive authors, of any gender

It was recently reported that men self-cite >50% more often than women across a wide variety of disciplines in the bibliographic database JSTOR. Here, we replicate this finding in a sample of 1.6 million papers from Author-ity, a version of PubMed with computationally disambiguated author names. More importantly, we show that the gender effect largely disappears when accounting for prior publication count in a multidimensional statistical model. Gender has the weakest effect on the probability of self-citation among an extensive set of features tested, including byline position, affiliation, ethnicity, collaboration size, time lag, subject-matter novelty, reference/citation counts, publication type, language, and venue. We find that self-citation is the hallmark of productive authors, of any gender, who cite their novel journal publications early and in similar venues, and more often cross citation-barriers such as language and indexing. As a result, papers by authors with short, disrupted, or diverse careers miss out on the initial boost in visibility gained from self-citations. Our data further suggest that this disproportionately affects women because of attrition and not because of disciplinary under-specialization.
Modelling and temporal evaluation of networked control systems using timed automata with guards and (max,+) algebra

ABSTRACT In this paper, we have proposed a new approach to evaluate the response time of Networked Control Systems (NCS) working under client/server protocol. For this, we have used two tools of discrete event systems: Timed Automata with Guards (TAGs) and (max,+) algebra. A preliminary result is to define a formal representation to describe the behaviour for TAGs with multiple clocks in (max,+) algebra and to deduce some performance indicators of these asynchronous models. The second contribution consists of modelling the NCS with TAGs and determining the upper bounds of the response time by an analytical formula. Finally, we have shown the agreement between experimental measures of the response time found in the literature and the theoretical predictions of our formulas.
Exercise of Varying Durations: No Acute Effects on Cognitive Performance in Adolescents

Participation in structured physical activity is assumed to have a positive effect on cognitive and academic performance. A single bout of moderate to vigorous exercise has been found to have a small acute positive effect on the cognitive performance of children and adolescents. However, the dose-response effects of exercise duration are largely unknown. Therefore, the current study examined the acute effects of moderate-to-vigorous exercise with a duration of either 10, 20, or 30 min on selective attention and working memory performance of young adolescents. One hundred and nineteen adolescents (11–14 years old) participated in a randomized, controlled crossover study. Adolescents were assigned to one of the three exercise durations, each paired with a sedentary control session of the same duration. Cognitive performance was measured before and immediately after the exercise and control condition. The Attention Network Test and n-back task were used to measure selective attention and working memory, respectively. There were no significant exercise effects on selective attention (i.e., alerting, orienting, or executive control) or working memory performance measured immediately after the exercise bouts. Furthermore, there were no differential effects of exercise duration. In sum, acute exercise bouts with a duration of 10, 20, or 30 min did not improve, but neither deteriorate cognitive performance of young adolescents compared to a sedentary control condition.
Extraction, purification, and structure characterization of polysaccharides from Crassostrea rivularis

Abstract Crude polysaccharide was prepared from Crassostrea rivularis by 30% (w/v) potassium hydroxide solution at 90°C for 120 min. Three fractions (OG1, OG2, and OG3) were purified by DEAE‐52 cellulose and Sepharose 2B gel column chromatography. The chemical structures were determined using gas chromatography (GC), high‐performance gel permeation chromatography (HPGPC), Fourier‐transform infrared (FT‐IR) spectroscopy, and 1H and 13C nuclear magnetic resonance (NMR) spectroscopy. The results indicated that OG1 was composed of rhamnose and little mannose (8.71%), the ratio of Rha: Gal: Xyl: Fuc in OG3 were 14:5.5:3:1. And their average molecular weights (Mw) were about 1.66 × 106 and 2.33 × 106 Da, respectively. OG2 was composed only of glucose (98.23%), which means it was glycogen. OG2 was consisted mainly of →4)‐ α‐D‐Glc‐(1→, with the branch chain every 6.5 glucose residues on average, which is →4,6)‐α‐D‐Glc‐(1→ and trace amount of α‐D‐Glc‐(1→ branched units. The Mw was 2.27 × 106 Da. It provides the bases for the bioactivity research.
Stochastic Second-order Methods for Non-convex Optimization with Inexact Hessian and Gradient

Trust region and cubic regularization methods have demonstrated good performance in small scale non-convex optimization, showing the ability to escape from saddle points. Each iteration of these methods involves computation of gradient, Hessian and function value in order to obtain the search direction and adjust the radius or cubic regularization parameter. However, exactly computing those quantities are too expensive in large-scale problems such as training deep networks. In this paper, we study a family of stochastic trust region and cubic regularization methods when gradient, Hessian and function values are computed inexactly, and show the iteration complexity to achieve $\epsilon$-approximate second-order optimality is in the same order with previous work for which gradient and function values are computed exactly. The mild conditions on inexactness can be achieved in finite-sum minimization using random sampling. We show the algorithm performs well on training convolutional neural networks compared with previous second-order methods.