Miracle-dz/UniFAR-FTUs huggingface dataset:
MicroRNA-181a Functions as an Oncogene in Gastric Cancer by Targeting Caprin-1

MicroRNA-181a (miRNA-181a) is a multifaceted miRNA implicated in various cellular processes, particularly in cell fate determination and cellular invasion. It is frequently expressed aberrantly in human tumors and shows opposing functions in different types of cancers. In this study, we found that miRNA-181a is overexpressed in Gastric cancer (GC) tissues. Clinical and pathological analyses revealed that the expression of miRNA-181a is correlated with tumor size, lymph node metastasis, distant metastasis, and TNM stage. Kaplan-Meier analysis indicated that overexpression of miRNA-181a is associated with poor overall survival of patients with GC. Moreover, miRNA-181a is overexpressed in GC cells, and downregulation of miRNA-181a induced cell apoptosis and suppressed the proliferation, invasion, and metastasis of GC cells both in vitro and in vivo. Target prediction and luciferase reporter assay showed that caprin-1 was a direct target of miRNA-181a. Downregulation of caprin-1 expression resulted in a converse change with miRNA-181a in GC. Spearman’s correlation test confirmed that the expression of miRNA-181a expression was inversely correlated with that of caprin-1 in GC cells. Furthermore, the expression of caprin-1 increased after downregulation of miRNA-181a in the GC cells. Caprin-1 siRNA can rescue the oncogenic effect of miRNA-181a on GC cell proliferation, apoptosis, migration, and invasion. These findings suggest that miRNA-181a directly inhibits caprin-1 and promotes GC development. miRNA-181a could be a target for anticancer drug development.
The XRE Family Transcriptional Regulator SrtR in Streptococcus suis Is Involved in Oxidant Tolerance and Virulence

Streptococcus suis is a zoonotic pathogen that harbors anti-oxidative stress genes, which have been reported to be associated with virulence. Serial passage has been widely used to obtain phenotypic variant strains to investigate the functions of important genes. In the present study, S. suis serotype 9 strain DN13 was serially passaged in mice 30 times. The virulence of a single colony from passage 10 (SS9-P10) was found to increase by at least 140-fold as indicated by LD50 values, and the increased virulence was stable for single colonies from passage 20 (SS0-P20) and 30 (SS0-P30). Compared to the parental strain, the mouse-adapted strains were more tolerant to oxidative and high temperature stress. Genome-wide analysis of nucleotide variations found that reverse mutations occurred in seven genes, as indicated by BLAST analysis. Three of the reverse mutation genes or their homologs in other bacteria were reported to be virulence-associated, including ideSsuis in S. suis, a homolog of malR of Streptococcus pneumoniae, and a homolog of the prepilin peptidase-encoding gene in Legionella pneumophila. However, these genes were not involved in the stress response. Another gene, srtR (stress response transcriptional regulator), encoding an XRE family transcriptional regulator, which had an internal stop in the parental strain, was functionally restored in the adapted strains. Further analysis of DN13 and SS9-P10-background srtR-knock-out and complementing strains supported the contribution of this gene to stress tolerance in vitro and virulence in mice. srtR and its homologs are widely distributed in Gram-positive bacteria including several important human pathogens such as Enterococcus faecium and Clostridioides difficile, indicating similar functions in these bacteria. Taken together, our study identified the first member of the XRE family of transcriptional regulators that is involved in stress tolerance and virulence. It also provides insight into the mechanism of enhanced virulence after serial passage in experimental animals.
A Single-Cell Level and Connectome-Derived Computational Model of the Drosophila Brain

Computer simulations play an important role in testing hypotheses, integrating knowledge, and providing predictions of neural circuit functions. While considerable effort has been dedicated into simulating primate or rodent brains, the fruit fly (Drosophila melanogaster) is becoming a promising model animal in computational neuroscience for its small brain size, complex cognitive behavior, and abundancy of data available from genes to circuits. Moreover, several Drosophila connectome projects have generated a large number of neuronal images that account for a significant portion of the brain, making a systematic investigation of the whole brain circuit possible. Supported by FlyCircuit (http://www.flycircuit.tw), one of the largest Drosophila neuron image databases, we began a long-term project with the goal to construct a whole-brain spiking network model of the Drosophila brain. In this paper, we report the outcome of the first phase of the project. We developed the Flysim platform, which 1) identifies the polarity of each neuron arbor, 2) predicts connections between neurons, 3) translates morphology data from the database into physiology parameters for computational modeling, 4) reconstructs a brain-wide network model, which consists of 20,089 neurons and 1,044,020 synapses, and 5) performs computer simulations of the resting state. We compared the reconstructed brain network with a randomized brain network by shuffling the connections of each neuron. We found that the reconstructed brain can be easily stabilized by implementing synaptic short-term depression, while the randomized one exhibited seizure-like firing activity under the same treatment. Furthermore, the reconstructed Drosophila brain was structurally and dynamically more diverse than the randomized one and exhibited both Poisson-like and patterned firing activities. Despite being at its early stage of development, this single-cell level brain model allows us to study some of the fundamental properties of neural networks including network balance, critical behavior, long-term stability, and plasticity.
Pupillometry of Groove: Evidence for Noradrenergic Arousal in the Link Between Music and Movement

The capacity to entrain motor action to rhythmic auditory stimulation is highly developed in humans and extremely limited in our closest relatives. An important aspect of auditory-motor entrainment is that not all forms of rhythmic stimulation motivate movement to the same degree. This variation is captured by the concept of musical groove: high-groove music stimulates a strong desire for movement, whereas low-groove music does not. Here, we utilize this difference to investigate the neurophysiological basis of our capacity for auditory-motor entrainment. In a series of three experiments we examine pupillary responses to musical stimuli varying in groove. Our results show stronger pupil dilation in response to (1) high- vs. low-groove music, (2) high vs. low spectral content, and (3) syncopated vs. straight drum patterns. We additionally report evidence for consistent sex differences in music-induced pupillary responses, with males exhibiting larger differences between responses, but females exhibiting stronger responses overall. These results imply that the biological link between movement and auditory rhythms in our species is supported by the capacity of high-groove music to stimulate arousal in the central and peripheral nervous system, presumably via highly conserved noradrenergic mechanisms.
Endocrine Disrupting Chemicals Interfere With Leydig Cell Hormone Pathways During Testicular Descent in Idiopathic Cryptorchidism

Cryptorchidism, a frequent genital malformation in male newborn, remains in most cases idiopathic. On the basis of experimental, epidemiological, and clinical data, it has been included in the testicular dysgenesis syndrome and believed to be influenced, together with genetic and anatomic factors, by maternal exposure to endocrine disrupting chemicals (EDCs). Here, we analyze how EDCs may interfere with the control of testicular descent, which is regulated by two Leydig cell hormones, testosterone, and insulin like peptide 3 (INSL3).
Shared and Distinct Neural Bases of Large- and Small-Scale Spatial Ability: A Coordinate-Based Activation Likelihood Estimation Meta-Analysis

Background: Spatial ability is vital for human survival and development. However, the relationship between large-scale and small-scale spatial ability remains poorly understood. To address this issue from a novel perspective, we performed an activation likelihood estimation (ALE) meta-analysis of neuroimaging studies to determine the shared and distinct neural bases of these two forms of spatial ability. Methods: We searched Web of Science, PubMed, PsycINFO, and Google Scholar for studies regarding “spatial ability” published within the last 20 years (January 1988 through June 2018). A final total of 103 studies (Table 1) involving 2,085 participants (male = 1,116) and 2,586 foci were incorporated into the meta-analysis. Results: Large-scale spatial ability was associated with activation in the limbic lobe, posterior lobe, occipital lobe, parietal lobe, right anterior lobe, frontal lobe, and right sub-lobar area. Small-scale spatial ability was associated with activation in the parietal lobe, occipital lobe, frontal lobe, right posterior lobe, and left sub-lobar area. Furthermore, conjunction analysis revealed overlapping regions in the sub-gyrus, right superior frontal gyrus, right superior parietal lobule, right middle occipital gyrus, right superior occipital gyrus, left inferior occipital gyrus, and precuneus. The contrast analysis demonstrated that the parahippocampal gyrus, left lingual gyrus, culmen, right middle temporal gyrus, left declive, left superior occipital gyrus, and right lentiform nucleus were more strongly activated during large-scale spatial tasks. In contrast, the precuneus, right inferior frontal gyrus, right precentral gyrus, left inferior parietal lobule, left supramarginal gyrus, left superior parietal lobule, right inferior occipital gyrus, and left middle frontal gyrus were more strongly activated during small-scale spatial tasks. Our results further indicated that there is no absolute difference in the cognitive strategies associated with the two forms of spatial ability (egocentric/allocentric). Conclusion: The results of the present study verify and expand upon the theoretical model of spatial ability proposed by Hegarty et al. Our analysis revealed a shared neural basis between large- and small-scale spatial abilities, as well as specific yet independent neural bases underlying each. Based on these findings, we proposed a more comprehensive version of the behavioral model.
Biomechanical Impact of the Sclera on Corneal Deformation Response to an Air-Puff: A Finite-Element Study

Aim or Purpose: To describe the effect of varying scleral stiffness on the biomechanical deformation response of the cornea under air-puff loading via a finite-element (FE) model. Methods: A two-dimensional axisymmetric stationary FE model of the whole human eye was used to examine the effects varying scleral stiffness and intraocular pressure (IOP) on the maximum apical displacement of the cornea. The model was comprised of the cornea, sclera, vitreous, and surrounding air region. The velocity and pressure profiles of an air-puff from a dynamic Scheimpflug analyzer were replicated in the FE model, and the resultant profile was applied to deform the cornea in a multiphysics study (where the air-puff was first simulated before being applied to the corneal surface). IOP was simulated as a uniform pressure on the globe interior. The simulation results were compared to data from ex vivo scleral stiffening experiments with human donor globes. Results: The FE model predicted decreased maximum apical displacement with increased IOP and increased ratio of scleral-to-corneal Young's moduli. These predictions were in good agreement (within one standard deviation) with findings from ex vivo scleral stiffening experiments using human donor eyes. These findings demonstrate the importance of scleral material properties on the biomechanical deformation response of the cornea in air-puff induced deformation. Conclusion: The results of an air-puff induced deformation are often considered to be solely due to IOP and corneal properties. The current study showed that the stiffer the sclera, the greater will be the limitation on corneal deformation, separately from IOP. This may have important clinical implications to interpreting the response of the cornea under air-puff loading in pathologic conditions.
Color Clipping and Over-exposure Correction

Limitations of the camera or extreme contrast in scenes can lead to clipped areas in captured images. Irrespective of the cause, color clipping and over-exposure lead to loss of texture and detail, impacting the color appearance and visual quality of the image. We propose a new over-exposure and clipping correction method, which relies on the existing correlation between RGB channels of color images to recover clipped information. Using a novel region grouping approach, clipped regions are coherently treated both spatially and temporally. To reconstruct over-exposed areas where all channels are clipped we employ a brightness proﬁle reshaping scheme, which aims to preserve the appearance of highlights, while boosting local brightness. Our method is evaluated using objective metrics as well as a subjective study based on an ITU standardized protocol, showing that our correction leads to improved results compared to previous related techniques. We explore several potential applications of our method, including extending to video as well as using it as a preprocessing step prior to inverse tone mapping.
Dynamic Double Auctions: Toward First Best

We study the problem of designing dynamic double auctions for two-sided markets in which a platform intermediates the trade between one seller offering independent items to multiple buyers, repeatedly over a finite horizon, when agents have private values. Motivated by online platforms for advertising, ride-sharing, and freelancing markets, we seek to design mechanisms satisfying the following properties: no positive transfers, i.e., the platform never asks the seller to make payments nor are buyers ever paid and periodic individual rationality, i.e., every agent derives a non-negative utility from every trade opportunity. We provide mechanisms satisfying these requirements that are asymptotically efficient and budget-balanced with high probability as the number of trading opportunities grows. Moreover, we show that the average expected profit obtained by the platform under these mechanisms asymptotically approaches first best (the maximum possible welfare generated by the market). We also to extend our approach to general environments with complex, combinatorial preferences.
(1 + ε)-Approximate Incremental Matching in Constant Deterministic Amortized Time

We study the matching problem in the incremental setting, where we are given a sequence of edge insertions and aim at maintaining a near-maximum cardinality matching of the graph with small update time. We present a deterministic algorithm that, for any constant ε > 0, maintains a (1 + ε )- approximate matching with constant amortized update time per insertion.
Probabilistic Tensors and Opportunistic Boolean Matrix Multiplication

We introduce probabilistic extensions of classical deterministic measures of algebraic complexity of a tensor, such as the rank and the border rank. We show that these probabilistic extensions satisfy various natural and algorithmically serendipitous properties, such as submultiplicativity under taking of Kronecker products. Furthermore, the probabilistic extensions enable improvements over their deterministic counterparts for speciﬁc tensors of interest, starting from the tensor (cid:104) 2 , 2 , 2 (cid:105) that represents 2 × 2 matrix multiplication. While it is well known that the (deterministic) tensor rank and border rank satisfy rk (cid:104) 2 , 2 , 2 (cid:105) = 7 and rk (cid:104) 2 , 2 , 2 (cid:105) = 7 [V. Strassen, Numer. Math. 13 (1969); J. E. Hopcroft and L. R. Kerr, SIAM J. Appl. Math. 20 (1971); S. Winograd, Linear Algebra Appl. 4 (1971); J. M. Landsberg, J. AMS 19 (2006)], we show that the probabilistic tensor rank and border rank satisfy (cid:101) rk (cid:104) 2 , 2 , 2 (cid:105) ≤ 6 + 6 7 and (cid:101) rk (cid:104) 2 , 2 , 2 (cid:105) ≤ 6 + 2 3 . By submultiplicativity, this leads immediately to novel randomized algorithm designs, such as algorithms for Boolean matrix multiplication as well as detecting and estimating the number of triangles in graphs. Our algorithms are opportunistic in the sense
Modeling Handover Signaling Messages in OpenFlow-Based Mobile Software-Defined Networks

The software-defined networking (SDN) paradigm has become essential in tackling several issues and challenges in conventional networking, especially in mobile/cellular networks. In order to realize the benefits brought by SDN to mobility management, we study the effects of SDN in conjunction with OpenFlow protocol on the handover procedure. However, in this new setting, the handover still suffers from delay due to the exchange of OpenFlow signaling messages. In this paper, we focus on SDN in mobile networks and quantify the delays of handover-related OpenFlow messages in order to identify the performance measures as well as the underlying challenges. For our analysis, we provide an analytical model, using which we modeled two handover-related OpenFlow messages in such networks. To the best of our knowledge, no previous work has modeled OpenFlow messages other than Packet-in messages. In this paper, in addition to the Packet-in message, we model Port-status messages. Following our analysis, we propose a novel solution to make handover more efficient and less interruptive. Furthermore, we study our solution in an LTE architecture and compare it to an existing solution. We show that, in normal traffic conditions, our solution can decrease the handover delay as much as 20%.
Distributed Maximal Independent Set using Small Messages

Maximal Independent Set (MIS) is one of the central problems in distributed graph algorithms. The celebrated works of Luby [STOC'85] and Alon, Babai, and Itai [JALG'86] provide O(log n)-round randomized distributed MIS algorithms, which work with O(log n)-bit messages. This round complexity was improved to [MATH HERE] in a breakthrough of Barenboim, Elkin, Pettie, and Schneider [FOCS'11; JACM'16] and then to [MATH HERE] by Ghaffari [SODA'16], where Δ denotes the maximum degree. However, these improvements have one drawback: they require much larger messages, up to poly(Δ log n) bits. Indeed, the question of improving the O(log n) round complexity using small messages has remained open for three decades, for essentially all values of Δ, except for Δ = o(log n) where there are O(Δ + log* n)-round deterministic algorithms. We present a randomized distributed MIS algorithm, with O(log n)-bit messages, that achieves a round complexity of [MATH HERE]. This is the first algorithm with small messages that improves on the O(log n) round complexity of Luby and Alon et al. for a wide range of Δ, and its complexity almost matches that of the best known algorithm using unbounded message sizes. As applications of this MIS algorithm or along the way to it, we obtain improved distributed algorithms with small messages for some other well-studied problems including network decompositions, (Δ + 1)-vertex coloring, and ruling sets.
La Chinea di Papa Clemente VIII del 1598: pulitura del supporto cartaceo, tecniche di lavaggio e diagnosi ottica dei risultati

Experimental surface cleaning and washing techniques for paper artworks are discussed through the treatment of an album of prints, the Chinea of Pope Clemente VIII. The prints were disfigured by uneven darkening of the paper supports, caused by discoloring of the lining adhesive and accumulated surfaced grime. Treatment steps involved mechanical removal of surface grime; cleaning of more tenacious dirt with a water-based gel (Phytagel); detachment of the lining fabric with enzymatic compresses of amylase; washing with minimal water contact using a filtration technique, capillary action, and Igortex OL 60; deacidification; and drying. Results from reflectance spectroscopy analysis indicated that all cleaning methods employed had a positive impact on the optical properties of the prints.
Optimal Construction of Compressed Indexes for Highly Repetitive Texts

We propose algorithms that, given the input string of length n over integer alphabet of size σ, construct the Burrows-Wheeler transform (BWT), the permuted longest-common-prefix (PLCP) array, and the LZ77 parsing in O(n/ logσ n + r polylog n) time and working space, where r is the number of runs in the BWT of the input. These are the essential components of many compressed indexes such as compressed suffix tree, FM-index, and grammar and LZ77-based indexes, but also find numerous applications in sequence analysis and data compression. The value of r is a common measure of repetitiveness that is significantly smaller than n if the string is highly repetitive. Since just accessing every symbol of the string requires Ω(n/ logσ n) time, the presented algorithms are time and space optimal for inputs satisfying the assumption n/r ∈ Ω(polylog n) on the repetitiveness. For such inputs our result improves upon the currently fastest general algorithms of Belazzougui (STOC 2014) and Munro et al. (SODA 2017) which run in O(n) time and use O(n/ logσ n) working space. We also show how to use our techniques to obtain optimal solutions on highly repetitive data for other fundamental string processing problems such as: Lyndon factorization, construction of run-length compressed suffix arrays, and some classical "textbook" problems such as computing the longest substring occurring at least some fixed number of times.
Integration of Peer Instruction in Online Social Network to Enhance Higher Order Thinking Skills

<span lang="EN-US">Higher Order Thinking skills (HOTs) are important thinking skills </span><span lang="EN-GB">for <a name="_Hlk519767446"></a>lifelong learner</span><span>s</span><span lang="EN-GB">, active social responsibility and proactive employee</span><span>s</span><span lang="EN-GB"> in the 21st century</span><span lang="EN-GB">. </span><span>The</span><span lang="EN-GB"> rapid development of technology in education </span><span>has made </span><span lang="EN-GB">learning anywhere and anytime</span><span> possible</span><span lang="EN-GB">. </span><span lang="EN-US">This study was conducted to investigate </span><span>the effect of the </span><span lang="EN-US">integration of peer instruction in online social network could on students ability to answer HOTs questions. Peer instruction is one of the learning technique</span><span>s</span><span lang="EN-US"> that promote HOTs in a cooperative learning setting. </span><span>It </span><span lang="EN-US">promotes students’ participation in class and increase</span><span>s</span><span>their learning </span><span lang="EN-US">engagement. This study applied repeated measures one group pre-post test design which was carried out among 20 students (purposive sampling technique) in higher education institution. </span><span>It </span><span lang="EN-US">was carried out in 3 different sessions. Students have to answer HOTs questions in the form of multiple choices</span><span> using an</span><span lang="EN-US"> online quiz system, while peer instruction activities were carried out using and online social network app. Findings show that there is significant effect of peer instruction activities on students quiz scores and no significant difference of students peer instruction activities among the 3 learning sessions</span><span lang="EN-GB">. </span>