Miracle-dz/UniFAR-FTUs huggingface dataset:
A role of autophagy in PTP4A3-driven cancer progression

Autophagy, a “self-eating” cellular process, has dual roles in promoting and suppressing tumor growth, depending on cellular context. PTP4A3/PRL-3, a plasma membrane and endosomal phosphatase, promotes multiple oncogenic processes including cell proliferation, invasion, and cancer metastasis. In this study, we demonstrate that PTP4A3 accumulates in autophagosomes upon inhibition of autophagic degradation. Expression of PTP4A3 enhances PIK3C3-BECN1-dependent autophagosome formation and accelerates LC3-I to LC3-II conversion in an ATG5-dependent manner. PTP4A3 overexpression also enhances the degradation of SQSTM1, a key autophagy substrate. These functions of PTP4A3 are dependent on its catalytic activity and prenylation-dependent membrane association. These results suggest that PTP4A3 functions to promote canonical autophagy flux. Unexpectedly, following autophagy activation, PTP4A3 serves as a novel autophagic substrate, thereby establishing a negative feedback-loop that may be required to fine-tune autophagy activity. Functionally, PTP4A3 utilizes the autophagy pathway to promote cell growth, concomitant with the activation of AKT. Clinically, from the largest ovarian cancer data set (GSE 9899, n = 285) available in GEO, high levels of expression of both PTP4A3 and autophagy genes significantly predict poor prognosis of ovarian cancer patients. These studies reveal a critical role of autophagy in PTP4A3-driven cancer progression, suggesting that autophagy could be a potential Achilles heel to block PTP4A3-mediated tumor progression in stratified patients with high expression of both PTP4A3 and autophagy genes.
A Probabilistic Lifestyle-Based Trajectory Model for Social Strength Inference from Human Trajectory Data

With the pervasiveness of location-based social networks, it becomes increasingly important to consider the social characteristics of locations shared among persons. Several studies have been proposed to infer social strength by using trajectory similarity. However, these studies have two major shortcomings. First, they rely on the explicit co-occurrence of check-in locations. In this situation, a user pair of two friends who seldom share common locations or a user pair of two strangers who heavily share common visited locations will receive an unreliable estimation of the real social strength between them. Second, these studies do not consider how the overall trajectory patterns of users change with the varying of living styles. In this article, we propose a probabilistic generative model to mine latent lifestyle-related patterns from human trajectory data for inferring social strength. It can automatically learn functionality topics consisting of locations with similar service functions and transition probabilities over the set of functionality topics. Furthermore, a lifestyle is modeled as a unique transition probability matrix over the set of functionality topics. A user has a preference distribution over the set of lifestyles, and he or she is able to select over multiple lifestyles to adapt to different living contexts. The learned lifestyle-related patterns are subsequently used as features in a supervised learner for both strength estimation and link prediction. We conduct extensive experiments to evaluate the performance of the proposed method on two real-world datasets. The experimental results demonstrate the effectiveness of our proposed method.
Defect formation and critical dynamics in the early Universe

We study the nonequilibrium dynamics leading to the formation of topological defects in a symmetry-breaking phase transition of a quantum scalar field with \lambda\Phi^4 self-interaction in a spatially flat, radiation-dominated Friedmann-Robertson-Walker Universe. The quantum field is initially in a finite-temperature symmetry-restored state and the phase transition develops as the Universe expands and cools. We present a first-principles, microscopic approach in which the nonperturbative, nonequilibrium dynamics of the quantum field is derived from the two-loop, two-particle-irreducible closed-time-path effective action. We numerically solve the dynamical equations for the two-point function and we identify signatures of topological defects in the infrared portion of the momentum-space power spectrum. We find that the density of topological defects formed after the phase transition scales as a power law with the expansion rate of the Universe. We calculate the equilibrium critical exponents of the correlation length and relaxation time for this model and show that the power law exponent of the defect density, for both overdamped and underdamped evolution, is in good agreement with the "freeze-out" scenario of Zurek. We introduce an analytic dynamical model, valid near the critical point, that exhibits the same power law scaling of the defect density with the quench rate. By incorporating the realistic quench of the expanding Universe, our approach illuminates the dynamical mechanisms important for topological defect formation. The observed power law scaling of the defect density with the quench rate, observered here in a quantum field theory context, provides evidence for the "freeze-out" scenario in three spatial dimensions.
Acellular allogeneic nerve grafting combined with bone marrow mesenchymal stem cell transplantation for the repair of long-segment sciatic nerve defects: biomechanics and validation of mathematical models

We hypothesized that a chemically extracted acellular allogeneic nerve graft used in combination with bone marrow mesenchymal stem cell transplantation would be an effective treatment for long-segment sciatic nerve defects. To test this, we established rabbit models of 30 mm sciatic nerve defects, and treated them using either an autograft or a chemically decellularized allogeneic nerve graft with or without simultaneous transplantation of bone marrow mesenchymal stem cells. We compared the tensile properties, electrophysiological function and morphology of the damaged nerve in each group. Sciatic nerves repaired by the allogeneic nerve graft combined with stem cell transplantation showed better recovery than those repaired by the acellular allogeneic nerve graft alone, and produced similar results to those observed with the autograft. These findings confirm that a chemically extracted acellular allogeneic nerve graft combined with transplantation of bone marrow mesenchymal stem cells is an effective method of repairing long-segment sciatic nerve defects.
Lattice determination of the critical point of QCD at finite T and μ

Based on universal arguments it is believed that there is a critical point (E) in QCD on the temperature (T) versus chemical potential (μ) plane, which is of extreme importance for heavy-ion experiments. Using finite size scaling and a recently proposed lattice method to study QCD at finite μ we determine the location of E in QCD with nf = 2+1 dynamical staggered quarks with semi-realistic masses on Lt = 4 lattices. Our result is TE = 160±3.5 MeV and μE = 725±35 MeV. For the critical temperature at μ = 0 we obtained Tc = 172±3 MeV.
Cluster-formation in the Rosette molecular cloud at the junctions of filaments

For many years feedback processes generated by OB-stars in molecular clouds, including expanding ionization fronts, stellar winds, or UV-radiation, have been proposed to trigger subsequent star formation. However, hydrodynamic models including radiation and gravity show that UV-illumination has little or no impact on the global dynamical evolution of the cloud. The Rosette molecular cloud, irradiated by the NGC2244 cluster, is a template region for triggered star-formation, and we investigated its spatial and density structure by applying a curvelet analysis, a filament-tracing algorithm (DisPerSE), and probability density functions (PDFs) on Herschel column density maps, obtained within the HOBYS key program. The analysis reveals not only the filamentary structure of the cloud but also that all known infrared clusters except one lie at junctions of filaments, as predicted by turbulence simulations. The PDFs of sub-regions in the cloud show systematic differences. The two UV-exposed regions have a double-peaked PDF we interprete as caused by shock compression. The deviations of the PDF from the log-normal shape typically associated with low- and high-mass star-forming regions at Av~3-4m and 8-10m, respectively, are found here within the very same cloud. This shows that there is no fundamental difference in the density structure of low- and high-mass star-forming regions. We conclude that star-formation in Rosette - and probably in high-mass star-forming clouds in general - is not globally triggered by the impact of UV-radiation. Moreover, star formation takes place in filaments that arose from the primordial turbulent structure built up during the formation of the cloud. Clusters form at filament mergers, but star formation can be locally induced in the direct interaction zone between an expanding HII--region and the molecular cloud.
On the Evidence Based Peer-to-peer Resource Management in Distributed Computing Systems 1

In this paper we propose an accountability management framework for resource sharing in peer-to-peer (P2P) distributed computing systems. On the basis of a generalized e-coin paradigm, we developed the management framework based on the distribution of resource credit/policy, exchange of service and service evidences, and accountability management. A tree topology is assumed for the distribution of resource credit and policies, so that P2P parties can have an absolute reference of the credential of principals, and make the system scalable. Common resource management operations involving splitting, merging and the propagation of system attributes (such as the ownership of the resources) are bound to the resource credit to become resource evidence after the services are rendered. We propose three e-coin binding techniques for those resource delegation scenarios, so that the credit policy (distributed by the credential authority), the resource attribute (sent from the provider) and the resource order (acknowledged from the consumer) can be cryptographically tied with the warrant, the response and the challenge respectively in the e-coin for the generation of the anonymous evidence on the delegation events.
Climate adaptation in the Anthropocene: Constructing and contesting urban risk regimes

The Anthropocene heralds a new era of heightened and unknown risks, particularly regarding the impacts of climate change. This article explores the initial phase of organizing for climate adaptation in Boston, Massachusetts, examining how multiple actors, including business, government, and community organization, are interacting as they attempt to comprehend, assess, and act on this issue. To understand this process of organizing, we develop the concept of ‘risk regime’ as a contingently stabilized system with governance, economic, and discursive dimensions. We draw from theories of risk, organizational resilience, and urban regimes and value regimes to develop the ‘risk regime’ framework, which provides a nuanced view of contestation, collaboration, and accommodation among actors with differential interests, knowledge, and influence on the process. We suggest how the character, evolution, and stabilization of the regime is influenced by competing imaginaries regarding, for example, the nature and manageability of risk, the need for radical change, and the role of markets versus regulations in addressing tensions between economic and sustainability goals. We demonstrate that the regime for adaptation has grown out of the organizational and discursive infrastructure for addressing climate mitigation, or carbon control, but that the unique character of adaptation presents different, and perhaps more difficult challenges.
Deep Ensemble Detection of Congestive Heart Failure Using Short-Term RR Intervals

Heart rate variability (HRV) is an effective predictor of congestive heart failure (CHF). However, important challenges exist regarding the effective temporal feature extraction and efficient classification using high-dimensional HRV representations. To solve these challenges, an ensemble method for CHF detection using short-term HRV data and deep neural networks was proposed. In this paper, five open-source databases, the BIDMC CHF database (BIDMC-CHF), CHF RR interval database (CHF-RR), MIT-BIH normal sinus rhythm (NSR) database, fantasia database (FD), and NSR RR interval database (NSR-RR), were used. Additionally, three RR segment length types (N = 500, 1000, and 2000) were used to evaluate the proposed method. First, we extracted the expert features of RR intervals (RRIs) and then built a long short-term memory-convolutional neural network-based network to extract deep-learning (DL) features automatically. Finally, an ensemble classifier was used for CHF detection using the above features. With blindfold validation (three CHF subjects and three normal subjects), the proposed method achieved 99.85%, 99.41%, and 99.17% accuracy on N = 500, 1000, and 2000 length RRIs, respectively, using the BIDMC-CHF, NSR, and FD databases. With blindfold validation (six CHF subjects and six normal subjects), the proposed method achieved 83.84%, 87.54%, and 85.71% accuracy on N = 500, 1000, and 2000 length RRIs, respectively, using the NSR-RR and CHF-RR ndatabases. Based on feature ranking, the significant effectiveness provided by the DL features has been proven. The results have shown that the deep ensemble method can achieve reliable CHF detection using short-term heart rate signals and enable CHF detection through intelligent hardware.
Methods for Presenting Braille Characters on a Mobile Device with a Touchscreen and Tactile Feedback

Three novel interaction methods were designed for reading six-dot Braille characters from the touchscreen of a mobile device. A prototype device with a piezoelectric actuator embedded under the touchscreen was used to create tactile feedback. The three interaction methods, scan, sweep, and rhythm, enabled users to read Braille characters one at a time either by exploring the characters dot by dot or by sensing a rhythmic pattern presented on the screen. The methods were tested with five blind Braille readers as a proof of concept. The results of the first experiment showed that all three methods can be used to convey information as the participants could accurately (91-97 percent) recognize individual characters. In the second experiment the presentation rate of the most efficient and preferred method, the rhythm, was varied. A mean recognition accuracy of 70 percent was found when the speed of presenting a single character was nearly doubled from the first experiment. The results showed that temporal tactile feedback and Braille coding can be used to transmit single-character information while further studies are still needed to evaluate the presentation of serial information, i.e., multiple Braille characters.
How to Use Garbling for Privacy Preserving Electronic Surveillance Services

Various applications following the Internet of Things (IoT) paradigm have become a part of our everyday lives. Therefore, designing mechanisms for security, trust and privacy for this context is important. As one example, applications related to electronic surveillance and monitoring have serious issues related to privacy. Research is needed on how to design privacy preserving surveillance system consisting of networked devices. One way to implement privacy preserving electronic surveillance is to use tools for multiparty computations. In this paper, we present an innovative way of using garbling, a powerful cryptographic primitive for secure multiparty computation, to achieve privacy preserving electronic surveillance. We illustrate the power of garbling in a context of a typical surveillance scenario. We discuss the di erent security measures related to garbling as well as e ciency of garbling schemes. Furthermore, we suggest further scenarios in which garbling can be used to achieve privacy preservation.
Levels, Distribution, and Health Risks of Polycyclic Aromatic Hydrocarbons in Four Freshwater Edible Fish Species from the Beijing Market

We first estimated the content of polycyclic aromatic hydrocarbons (PAHs) in the brain, liver, bladder, roe, and muscle of four species of edible freshwater fish from the Beijing market. The distribution characteristics of PAHs in these tissues and organs were analyzed to determine their health risks to humans. The results showed that the residual levels of wet weight and lipid-normalized weight ∑PAHs in various tissues of these fish ranged from 0.51 ng·g−1 to 28.78 ng·g−1 and from 93.62 ng·g−1 to 8203.43 ng·g−1, respectively. The wet weight contents of ∑PAHs were relatively higher in the brain and lower in the liver and muscle. But the differences were not significant. And the differences of lipid-normalized weight PAHs were significant, which in the bighead carp were found significantly the highest, followed in crucian carp, and the lowest in grass carp and carp. The contents of ∑PAHs were the highest in the liver and the lowest in the brain. In the tissues with a higher lipid content, higher residual levels of PAHs were found. The carcinogenic risks for humans from residual ∑PAHs in the various fish tissues were far below 10−5.
A case study in using massively parallel simulation for extreme-scale torus network codesign

A high-bandwidth, low-latency interconnect will be a critical component of future exascale systems. The torus network topology, which uses multidimensional network links to improve path diversity and exploit locality between nodes, is a potential candidate for exascale interconnects. The communication behavior of large-scale scientific applications running on future exascale networks is particularly important and analytical/algorithmic models alone cannot deduce it. Therefore, before building systems, it is important to explore the design space and performance of candidate exascale interconnects by using simulation. We improve upon previous work in this area and present a methodology for modeling and simulating a high-fidelity, validated, and scalable torus network topology at a packet-chunk level detail using the Rensselaer Optimistic Simulation System (ROSS). We execute various configurations of a 1.3 million node torus network model in order to examine the effect of torus dimensionality on network performance with relevant HPC traffic patterns. To the best of our knowledge, these are the largest torus network simulations that are carried out at such a detailed fidelity. In terms of simulation performance, a 1.3 million node, 9-D torus network model is shown to process a simulated exascale-class workload of nearest-neighbor traffic with 100 million message injections per second per node using 65,536 Blue Gene/Q cores in a simulation run-time of only 25 seconds. We also demonstrate that massive-scale simulations are a critical tool in exascale system design since small-scale torus simulations are not always indicative of the network behavior at an exascale size. The take-away message from this case study is that massively parallel simulation is a key enabler for effective extreme-scale network codesign.
EVALUATION OF TOLERABILITY AND EFFICACY OF GLUCOSAMINE WITH CHONDROITIN IN THE TREATMENT OF KNEE OSTEOARTHRITIS - A DOUBLE BLIND MULTICENTRE RANDOMIZED PROSPECTIVE COMPARATIVE STUDY

There are few comparative studies conducted with glucosamine (GlcN1 (glucosamine sulfate with potassium chloride), GlcN2 (glucosamine sulfate plus chondroitin sulfate) along with ChoN3 (chondroitin sulfate alone)) in the treatment of knee osteoarthritis. In this study the treated groups were studied for alleviation of pain and joint stiffness with correlation of measurement of urinary pyridinium cross links such as pyridinoline (Pyr) and deoxypyridinoline (Dpyr). Hence, this study was eventually planned to evaluate the efficacy, safety and tolerability of glucosamine with chondroitin sulfate treated groups. Urinary pyridinium crosslinks such as Pyr and Dpyr measurement are used to monitor the clinical status as well as bone turnover of OA patients. These two collagen crosslinks measured in urine, which provides information both on the pathogenesis of OA as well as the rate of bone turnover. The results of this study suggest that GlcN2 and ChoN3 can relieve pain, improving functional ability and joint mobility so as to enhance the quality of life for osteoarthritis patients.
COMP-Angiopoietin1 Potentiates the Effects of Bone Morphogenic Protein-2 on Ischemic Necrosis of the Femoral Head in Rats

Angiogenesis is considered essential for proper bone regeneration. The purpose of this investigation was to determine if a combined therapy of bone morphogenetic protein-2 (BMP-2) and cartilage oligomeric matrix protein angiopoietin-1 (COMP-Ang1) can potentiate the therapeutic effect of BMP-2 in a rat model of ischemic necrosis of the femoral head (INFH). INFH was surgically induced in the femoral head of rats, and the animals were divided into the following groups: 1) a sham-operated group (sham group), 2) a bovine serum albumin-injected group (BSA group), 3) a BMP-2-injected group (BMP-2 group), and 4) a COMP-Ang1 and BMP-2-injected group (COMP-Ang1 + BMP-2 group) (n = 20/group). Radiologic, histologic, and histomorphometric assessments were performed to assess femoral head morphology, vascular density, and bone resorption activity. Western blots and immunohistochemical staining were performed to evaluate production of BMP-related signaling proteins in C3H10T1/2 cells and tissues. Real-time RT-PCR was performed to investigate expression of the target integrin gene, and the effect of integrin on C3H10T1/2 cells was determined using a cell adhesion assay. Radiographs obtained six weeks after injection revealed better preservation of the architecture of the femoral head in the COMP-Ang1 + BMP-2 group compared with the BSA and BMP-2 groups. Histological findings indicated increased trabecular bone and vascularity and decreased osteoclast bone resorption activity in the COMP-Ang1 + BMP-2 group compared with those in the BSA and BMP-2 groups. The combination of COMP-Ang1 and BMP-2 increased phosphorylation of Smad1/3/5, p38, and Akt. Increased integrin α3 and β1 mRNA expression in the COMP-Ang1 + BMP-2 group promoted cell adhesion. These results suggest that COMP-Ang1 preserved the necrotic femoral head through the potentiation of BMP-2 signaling pathways and angiogenesis. Combination treatment with COMP-Ang1 and BMP-2 may be a clinically useful therapeutic application in INFH.