Miracle-dz/UniFAR-FTUs huggingface dataset:
Gold nanoparticle-based miR155 antagonist macrophage delivery restores the cardiac function in ovariectomized diabetic mouse model

Diabetic cardiomyopathy is a common disease in postmenopausal women, in whom the estrogen deficiency aggravates the pathology. In this study, we have found that estrogen deficiency due to ovariectomy aggravates the inflammation in the hearts of diabetic mice, as depicted by excessive proinflammatory type 1 macrophages (M1) over anti-inflammatory type 2 macrophages (M2). Accordingly, an additional increase of reactive oxygen species, cell apoptosis, cardiac hypertrophy, and fibrosis was observed in the hearts of ovariectomized diabetic mice, in comparison with the diabetes-only group. Significantly, miR155, a potent promoter of M1 polarization, was found to be additionally enhanced in the macrophages and hearts by ovariectomy. Tail vein injection of miR155-AuNP, in which thiol-modified antago-miR155 was covalently conjugated with gold nanoparticle (AuNP), preferentially delivered the nucleic acids into the macrophages via phagocytosis. Together with the increased M2 ratio and reduced inflammation, in vivo delivery of antago-miR155 reduced cell apoptosis and restored the cardiac function. The restoration efficacy of miR155-AuNP was much better than general macrophage depletion by clodrosome. In summary, we revealed that M1/M2 imbalance contributes to the aggravated cardiomyopathy in ovariectomized diabetic mice, and therapeutically reducing miR155 in macrophages by AuNP serves as a promising strategy in improving cardiac function.
Host Cell-catalyzed S-Palmitoylation Mediates Golgi Targeting of the Legionella Ubiquitin Ligase GobX*

Background: During intracellular replication, Legionella pneumophila produces effector proteins that exploit host cell processes. Results: The effector GobX is an E3 ubiquitin ligase that targets to the Golgi where it is post-translationally modified with a palmitoyl moiety. Conclusion: Bacteria can hijack host-mediated S-palmitoylation for subcellular localization of their effectors. Significance: Pharmacological inhibition of S-palmitoylation enzymes may interfere with effector function and thus microbial virulence. The facultative intracellular pathogen Legionella pneumophila, the causative agent of Legionnaires disease, infects and replicates within human alveolar macrophages. L. pneumophila delivers almost 300 effector proteins into the besieged host cell that alter signaling cascades and create conditions that favor intracellular bacterial survival. In order for the effectors to accomplish their intracellular mission, their activity needs to be specifically directed toward the correct host cell protein or target organelle. Here, we show that the L. pneumophila effector GobX possesses E3 ubiquitin ligase activity that is mediated by a central region homologous to mammalian U-box domains. Furthermore, we demonstrate that GobX exploits host cell S-palmitoylation to specifically localize to Golgi membranes. The hydrophobic palmitate moiety is covalently attached to a cysteine residue at position 175, which is part of an amphipathic α-helix within the C-terminal region of GobX. Site-directed mutagenesis of cysteine 175 or residues on the hydrophobic face of the amphipathic helix strongly attenuated palmitoylation and Golgi localization of GobX. Together, our study provides evidence that the L. pneumophila effector GobX exploits two post-translational modification pathways of host cells, ubiquitination and S-palmitoylation.
Receptive field structure in the visual cortex: does selective stimulation induce plasticity?

Sensory areas of adult cerebral cortex can reorganize in response to long-term alterations in patterns of afferent signals. This long-term plasticity is thought to play a crucial role in recovery from injury and in some forms of learning. However, the degree to which sensory representations in primary cortical areas depend on short-term (i.e., minute to minute) stimulus variations remains unclear. A traditional view is that each neuron in the mature cortex has a fixed receptive field structure. An alternative view, with fundamentally different implications for understanding cortical function, is that each cell's receptive field is highly malleable, changing according to the recent history of the sensory environment. Consistent with the latter view, it has been reported that selective stimulation of regions surrounding the receptive field induces a dramatic short-term increase in receptive field size for neurons in the visual cortex [Pettet, M. W. & Gilbert, C. D. (1992) Proc. Natl. Acad. Sci. USA 89, 8366-8370]. In contrast, we report here that there is no change in either the size or the internal structure of the receptive field following several minutes of surround stimulation. However, for some cells, overall responsiveness increases. These results suggest that dynamic alterations of receptive field structure do not underlie short-term plasticity in the mature primary visual cortex. However, some degree of short-term adaptability could be mediated by changes in responsiveness.
Educational Question Routing in Online Student Communities

Students' performance in Massive Open Online Courses (MOOCs) is enhanced by high quality discussion forums or recently emerging educational Community Question Answering (CQA) systems. Nevertheless, only a small number of students answer questions asked by their peers. This results in instructor overload, and many unanswered questions. To increase students' participation, we present an approach for recommendation of new questions to students who are likely to provide answers. Existing approaches to such question routing proposed for non-educational CQA systems tend to rely on a few experts, what is not applicable in educational domain where it is important to involve all kinds of students. In tackling this novel educational question routing problem, our method (1) goes beyond previous question-answering data as it incorporates additional non-QA data from the course (to improve prediction accuracy and to involve more of the student community) and (2) applies constraints on users' workload (to prevent user overloading). We use an ensemble classifier for predicting students' willingness to answer a question, as well as students' expertise for answering. We conducted an online evaluation of the proposed method using an A/B experiment in our CQA system deployed in edX MOOC. The proposed method outperformed a baseline method (non-educational question routing enhanced with workload restriction) by improving recommendation accuracy, keeping more community members active, and increasing an average number of their contributions.
Impacts of Surface Water Diversions for Marijuana Cultivation on Aquatic Habitat in Four Northwestern California Watersheds

Marijuana (Cannabis sativa L.) cultivation has proliferated in northwestern California since at least the mid-1990s. The environmental impacts associated with marijuana cultivation appear substantial, yet have been difficult to quantify, in part because cultivation is clandestine and often occurs on private property. To evaluate the impacts of water diversions at a watershed scale, we interpreted high-resolution aerial imagery to estimate the number of marijuana plants being cultivated in four watersheds in northwestern California, USA. Low-altitude aircraft flights and search warrants executed with law enforcement at cultivation sites in the region helped to validate assumptions used in aerial imagery interpretation. We estimated the water demand of marijuana irrigation and the potential effects water diversions could have on stream flow in the study watersheds. Our results indicate that water demand for marijuana cultivation has the potential to divert substantial portions of streamflow in the study watersheds, with an estimated flow reduction of up to 23% of the annual seven-day low flow in the least impacted of the study watersheds. Estimates from the other study watersheds indicate that water demand for marijuana cultivation exceeds streamflow during the low-flow period. In the most impacted study watersheds, diminished streamflow is likely to have lethal or sub-lethal effects on state-and federally-listed salmon and steelhead trout and to cause further decline of sensitive amphibian species.
NICAD: Accurate Detection of Near-Miss Intentional Clones Using Flexible Pretty-Printing and Code Normalization

This paper examines the effectiveness of a new language- specific parser-based but lightweight clone detection approach. Exploiting a novel application of a source transformation system, the method accurately finds near-miss clones using an efficient text line comparison technique. The transformation system assists the method in three ways. First, using agile parsing it provides user-specified flexible pretty- printing to remove noise, standardize formatting and break program statements into parts such that potential changes can be detected as simple linewise text differences. Second, it provides efficient flexible extraction of potential clones to be compared using island grammars and agile parsing to select granularities and enumerate potential clones. Third, using transformation rules it provides flexible code normalization to allow for local editing differences between similar code segments and filtering out of uninteresting parts of potential clones. In this paper we introduce the theory and practice of the framework and demonstrate its use in finding function clones in C code. Early experiments indicate that the method is capable of finding near-miss clones with high precision and recall, and with reasonable performance.
On the minimum latency transmission scheduling in wireless networks with power control under SINR constraints

In order to alleviate interference and contention in a wireless network, we may exploit the existence of multiple orthogonal channels or time slots, thus achieving a substantial improvement in performance. In this paper, we study a joint transmission scheduling and power control problem that arises in wireless networks. The goal is to assign channels (or time slots) and transmitting powers to communication links such that all communication requests are processed correctly, specified quality‐of‐service requirements are met, and the number of required time slots is minimised. First, we formulate the problem as a mixed‐integer linear programming. Then, we show that the problem considered is non‐deterministic polynomial‐time hard, and subsequently, we propose non‐trivial bounding techniques to solve it. Optimisation methods are also discussed, including a column generation approach, specifically designed to find bounds for the transmission scheduling problem. Moreover, we develop optimisation techniques in which the bounding techniques are integrated in order to derive the optimal solution to the problem faster. We close with an extensive computational study, which shows that despite the complexity of the problem, the proposed methodology scales to problems of non‐trivial size. Our algorithms can therefore be used for static wireless networks where propagation conditions are almost constant and a centralised agent is available (e.g. cellular networks where the base station can act as a centralised agent or wireless mesh networks), and they can also serve as a benchmark for the performance evaluation of heuristic, approximation or distributed algorithms that aim to find near‐optimal solutions without information about the whole network. Copyright © 2013 John Wiley & Sons, Ltd.
Quick Affective Judgments: Validation of a Method for Primed Product Comparisons

A method for primed product comparisons was developed, based on the methodological considerations of emotional appraisal process and affective mental contents. The method was implemented as a computer tool, which was utilised in two experiments (N = 18 for both). Ten adjectives served as primes, and five drinking glass pictures as stimuli. Participants' task was to choose a preference between two glasses, given the priming adjective. The results validate the method by providing test-retest reliability measures and showing convergence with questionnaires. Further, different evaluation times between the primes and the stimuli reveal the existence of different mental processes associated with various aspects of product experience, as predicted by appraisal theory. The results have various implications for experience research and development in HCI, as they demonstrate how the method can be used for product evaluation and the analysis of the mental processes, which users use to evaluate the products.
Effects of mold geometries and imprinted polymer resist thickness on ultrasonic nanoimprint lithography

This paper investigated the effects of imprinted resist thickness and mold geometries on the polymer flow and the temperature distribution of ultrasonic nanoimprint lithography (U-NIL) through numerical simulations and experiments. In simulations, the velocity fields in the imprinting stage and the temperature distributions in ultrasonic vibrations are performed under variations of convexity width, cavity width and thickness of the imprinted polymer resist. The study of the velocity field, including the lateral and vertical velocity, is significant because the velocity field can directly describe the mode of the polymer deformation, which is the key role to determine the mechanism of nanoimprint forming. Though the velocity field is crucial for the polymer deformation, it is often ignored and is rarely found in the literature. In ultrasonic vibrations, the temperature distribution of U-NIL is different from that of the thermal NIL and deserves to be investigated. Moreover, the combined effects of the imprinting stage and ultrasonic vibrations in the U-NIL process are discussed. Furthermore, experiments were conducted to verify the results performed by the numerical simulations. In this work, the simulations and experiments provide a deep understanding of polymer flow affected by the velocity field and temperature distribution during U-NIL, which should be well applied to a thermal NIL.
Confirmation of deadlock potentials detected by runtime analysis

This paper presents a framework for confirming deadlock potentials detected by runtime analysis of a single run of a multi-threaded program. The multi-threaded program under examination is instrumented to emit lock and unlock events. When the instrumented program is executed, a trace is generated consisting of the lock and unlock operations performed during that specific run. A lock graph is constructed which can reveal deadlock potentials in the form of cycles. The effectiveness of this analysis is caused by the fact that successful non-deadlocking runs yield as good, and normally better, information as deadlocking runs. Each cycle is then used to construct an observer that can detect the occurrence of the corresponding real deadlock, should it occur during subsequent test runs; and a controller, which, when composed with the program, determines the optimal scheduling strategy that will maximize the probability for the corresponding real deadlock to occur. The framework is formalized in terms of transition systems and is implemented in Java.
The distributed denial of service attacks (DDoS) prevention mechanisms on application layer

As DDOS attacks interrupt internet services, DDOS tools confirm the effectiveness of the current attack. DDOS attack and countermeasures continue to increase in number and complexity. In this paper, we explore the scope of the DDoS flooding attack problem and attempts to combat it. A contemporary escalation of application layer distributed denial of service attacks on the web services has quickly transferred the focus of the research community from conventional network based denial of service. As a result, new genres of attacks were explored like HTTP GET Flood, HTTP POST Flood, Slowloris, R-U-Dead-Yet (RUDY), DNS etc. Also after a brief introduction to DDOS attacks, we discuss the characteristics of newly proposed application layer distributed denial of service attacks and embellish their impact on modern web services.
Resist performance in soft x-ray projection lithography

An important issue for resists used in soft x-ray projection lithography (SXPL) is high absorption. Absorption coefficients of both organic and inorganic formulations range from 2 - 6 micrometers -1, requiring the use of very thin (50 - 100 nm) layers to avoid excessive absorption and resulting pattern sidewall degradation. Such thin films are typically used as the imaging layer in a bi- or tri-level processing scheme to achieve the required pattern depth. In this work, we report experimental and theoretical studies of imaging performance in the resists PMMA and SAL 601 at an SXPL exposure wavelength of 13.9 nm. Absorption coefficients ((alpha) ) have been measured for, and SXPL images recorded in both of these resists. A Mo/Si multilayer-coated Schwarzschild objective having known aberrations and illuminated by a laser plasma soft x-ray source has been used to produce images. Calculated aberrated aerial images are used in conjunction with the measured values of (alpha) to model the expected resist profiles and these are compared to experiment. Imaging performance as a function of resist absorption and estimates of resist exposure latitude are also discussed.
The Max-Min High-Order Dynamic Bayesian Network for Learning Gene Regulatory Networks with Time-Delayed Regulations

Accurately reconstructing gene regulatory network (GRN) from gene expression data is a challenging task in systems biology. Although some progresses have been made, the performance of GRN reconstruction still has much room for improvement. Because many regulatory events are asynchronous, learning gene interactions with multiple time delays is an effective way to improve the accuracy of GRN reconstruction. Here, we propose a new approach, called Max-Min high-order dynamic Bayesian network (MMHO-DBN) by extending the Max-Min hill-climbing Bayesian network technique originally devised for learning a Bayesian network's structure from static data. Our MMHO-DBN can explicitly model the time lags between regulators and targets in an efficient manner. It first uses constraint-based ideas to limit the space of potential structures, and then applies search-and-score ideas to search for an optimal HO-DBN structure. The performance of MMHO-DBN to GRN reconstruction was evaluated using both synthetic and real gene expression time-series data. Results show that MMHO-DBN is more accurate than current time-delayed GRN learning methods, and has an intermediate computing performance. Furthermore, it is able to learn long time-delayed relationships between genes. We applied sensitivity analysis on our model to study the performance variation along different parameter settings. The result provides hints on the setting of parameters of MMHO-DBN.
HIV testing.

Alabama Rape, sodomy, sexual misconduct , sexual torture, sexual abuse or any other crime in which the victim was compelled to engage in sexual activity by force or threat of force, and i t appears f rom the nature of the charge that the t ransmission of body fluids f rom one person to another may have been involved. Testing of a d e f e n d a n t charged with the cr ime of rape, sodomy, sexual misconduct , sexual tor ture, sexual abuse or any other cr ime in which the victim was compel led to engage in sexual activity by force or threat of force is available upon the reques t of the victim or the paren t o r guardian of a minor victim. Testing is required for al l persons sen tenced to conf inement or imprisonment in any city or county jail, or state correct ional facility for 30 or more consecut ive days, regardless of what offense they may have committed. Upon the request of the vict im or the parent or guardian of a minor victim, the district at torney is required to file a motion with the court for an order requir ing the defendant to submit to a tes t for any sexually t ransmit ted disease. The court shall then determine i f there is probable cause to believe that: the crime of rape, sodomy, sexual misconduct , sexual torture, sexual abuse or any other crime in which the victim was compel led to engage in sexual activity by force or threat of force was commit ted; and the t ransmiss ion of body fluids was involved. All persons sentenced to conf inement or imprisonment in any city or county jail, or state correct ional facility for 30 or more consecutive days are tested for those sexually t ransmi t ted d iseases designated by the State Board of Health upon entering the facility, regardless of what offense they may have commit ted .
Noncontact photoacoustic tomography imaging using a low-coherence interferometer with rapid detection of phase modulation

A photoacoustic tomography imaging system using a low-coherence interferometer with rapid detection of phase modulation was designed, fabricated, and tested for biologic imaging. A noncontact probing technique was applied to improve the practicability of the system. The technique is experimentally verified by the image of a simulated tissue sample and the blood vessels within a mouse ear flap (pinna) in vivo. The system’s axial and lateral resolutions are evaluated at 45 and ~15 μm, respectively. The system’s imaging depth is 1mm in a special phantom. The results show that the system has the feasibility to be used as a photoacoustic tomography imaging method, and it may provide a kind of possibility of noncontact real-time PAT.
The Human UTY Gene Encodes a Novel HLA-B8-Restricted H-Y Antigen1

The mammalian Y chromosome encodes male-specific minor histocompatibility (H-Y) Ags that are recognized by female T cells in an MHC-restricted manner. Two human H-Y epitopes presented by HLA-A2 and HLA-B7, respectively, have been identified previously and both are derived from the SMCY gene. We previously isolated CD8+ CTL clones that recognized a male-specific minor histocompatibility Ag presented by HLA-B8. In contrast to the SMCY-encoded H-Y epitopes, the B8/H-Y Ag was not presented by fibroblasts from male donors, suggesting that it was encoded by a novel gene. We now report that the HLA-B8-restricted H-Y epitope is defined by the octameric peptide LPHNHTDL corresponding to aa residues 566–573 of the human UTY protein. Transcription of the UTY gene is detected in a wide range of human tissues, but presentation of the UTY-derived H-Y epitope to CTL by cultured human cells shows significant cell-type specificity. Identification of this CTL-defined H-Y epitope should facilitate analysis of its contribution to graft/host interactions following sex-mismatched organ and bone marrow transplantation.
Quantification of CD4+ T Cell Alloreactivity and Its Control by Regulatory T Cells Using Time‐Lapse Microscopy and Immune Synapse Detection

Assays designed to select transplant recipients for immunosuppression withdrawal have met with limited success, perhaps because they measure events downstream of T cell–alloantigen interactions. Using in vitro time‐lapse microscopy in a mouse transplant model, we investigated whether transplant outcome would result in changes in the proportion of CD4+ T cells forming prolonged interactions with donor dendritic cells. By blocking CD4–MHC class II and CD28–B7 interactions, we defined immunologically relevant interactions as those ≥500 s. Using this threshold, T cell–dendritic cell (T‐DC) interactions were examined in rejection, tolerance and T cell control mediated by regulatory T cells. The frequency of T‐DC contacts ≥500 s increased with T cells from mice during acute rejection and decreased with T cells from mice rendered unresponsive to alloantigen. Regulatory T cells reduced prolonged T‐DC contacts. Importantly, this effect was replicated with human polyclonally expanded naturally occurring regulatory T cells, which we have previously shown can control rejection of human tissues in humanized mouse models. Finally, in a proof‐of‐concept translational context, we were able to visualize differential allogeneic immune synapse formation in polyclonal CD4+ T cells using high‐throughput imaging flow cytometry.