Miracle-dz/UniFAR-FTUs huggingface dataset:
Sp1 and Sp3 Are Oxidative Stress-Inducible, Antideath Transcription Factors in Cortical Neurons

Neuronal cell death in response to oxidative stress may reflect the failure of endogenous adaptive mechanisms. However, the transcriptional activators induced by oxidative stress in neurons that trigger adaptive genetic responses have yet to be fully elucidated. We report that basal DNA binding of the zinc finger transcription factors Sp1 and Sp3 is unexpectedly low in cortical neurons in vitro and is significantly induced by glutathione depletion-induced or hydrogen peroxide-induced oxidative stress in these cells. The increases in Sp1/Sp3 DNA binding reflect, in part, increased levels of Sp1 and Sp3 protein in the nuclei of cortical neurons. Similar induction of Sp1 and Sp3 protein is also observed in neurons in vivo in a chemical or a genetic model of Huntington's disease, two rodent models in which neuronal loss has been attributed to oxidative stress. Sustained high-level expression of full-length Sp1 or full-length Sp3, but not the Sp1 zinc finger DNA-binding domain alone, prevents death in response to oxidative stress, DNA damage, or both. Taken together, these results establish Sp1 and Sp3 as oxidative stress-induced transcription factors in cortical neurons that positively regulate neuronal survival.
Event-driven manufacturing: Unified management of primitive and complex events for manufacturing monitoring and control

Events are an integral part of todays manufacturing supervision and control software. However, state-of-the-art event management systems only cover selected levels of the automation pyramid, thus limiting the possibilities for holistic event-driven manufacturing monitoring and control. We propose a unified management of events across all levels of the automation pyramid. Thereby we utilize primitive and complex/composite events, i.e. logical or temporal combinations of primitive events to enable realtime shop floor control. We provide a comprehensive description of the overall architecture and the components necessary for a unified event management system based on the Publish/Subscribe paradigm. We detail the opportunities and challenges in applying the concept of complex event processing to the domain of manufacturing.
Forecasting plug-in electric vehicles load profile using artificial neural networks

Plug-in electric vehicles (PEVs) are becoming very popular these days and consequently, their load management will be a challenging issue for the network operators in the future. This paper proposes an artificial intelligence approach based on neural networks to forecast daily load profile of individual and fleets of randomly plugged-in PEVs, as well as the upstream distribution transformer loading. An artificial neural network (ANN) model will be developed to forecast daily arrival time (Ta) and daily travel distance (Dtr) of individual PEV using historical data collected for each vehicle in the past two years. The predicted parameters are then will be used to forecast transformer loading with PEV charging activities. The results of this paper will be very beneficial to coordination and charge/discharge management of PEVs as well as demand load management, network planning and operation proposes. Detailed simulations are presented to investigate the feasibility and accuracy of the proposed forecasting strategy.
Wrinkle meshes

We present a simple and fast method to add wrinkles to dynamic meshes such as simulated cloth or the skin of an animated character. To get the desired surface details, we attach a higher resolution wrinkle mesh to the coarse base mesh allowing the wrinkle vertices to deviate from their attachment positions within a limited range. The shape of the wrinkle mesh is determined by a static solver which runs in parallel to the motion of the base mesh. Our method can be used to automatically enhance a purely animated skin mesh with wrinkles which would be a tedious task to do by hand. The fact that the tessellation of the wrinkle mesh can be chosen independently of the structure of the base mesh can be used to control the look of the wrinkles. The locations of wrinkle formation can be defined by painting the maximum distance the wrinkle mesh is allowed to deviate from the base mesh. The second important application of wrinkle meshes is to add detail to simulated meshes such as cloth. Our method allows one to reduce the resolution of the simulation mesh without losing interesting surface detail. This speeds up the simulation, collision detection and handling and it reduces stretchiness. We show the efficiency and visual quality of the approach in a real-time setting.
Predicting visible differences in high dynamic range images: model and its calibration

New imaging and rendering systems commonly use physically accurate lighting information in the form of high-dynamic range (HDR) images and video. HDR images contain actual colorimetric or physical values, which can span 14 orders of magnitude, instead of 8-bit renderings, found in standard images. The additional precision and quality retained in HDR visual data is necessary to display images on advanced HDR display devices, capable of showing contrast of 50,000:1, as compared to the contrast of 700:1 for LCD displays. With the development of high-dynamic range visual techniques comes a need for an automatic visual quality assessment of the resulting images. In this paper we propose several modifications to the Visual Difference Predicator (VDP). The modifications improve the prediction of perceivable differences in the full visible range of luminance and under the adaptation conditions corresponding to real scene observation. The proposed metric takes into account the aspects of high contrast vision, like scattering of the light in the optics (OTF), nonlinear response to light for the full range of luminance, and local adaptation. To calibrate our HDR VDP we perform experiments using an advanced HDR display, capable of displaying the range of luminance that is close to that found in real scenes.
COP-coated vesicles are involved in the mitotic fragmentation of Golgi stacks in a cell-free system

Rat liver Golgi stacks fragmented when incubated with mitotic but not interphase cytosol in a process dependent on time, temperature, energy (added in the form of ATP) and cdc2 kinase. The cross-sectional length of Golgi stacks fell in the presence of mitotic cytosol by approximately 50% over 30 min without a corresponding decrease in the number of cisternae in the stack. The loss of membrane from stacked and single cisternae occurred with a half-time of approximately 20 min, and was matched by the appearance of both small (50-100 nm in diameter) and large (100-200 nm in diameter) vesicular profiles. Small vesicular profiles constituted more than 50% of the total membrane after 60 min of incubation and they were shown to be vesicles or very short tubules by serial sectioning. In the presence of GTP gamma S all of the small vesicles were COP-coated and both the extent and the rate at which they formed were sufficient to account for the production of small vesicles during mitotic incubation. The involvement of the COP-mediated budding mechanism was confirmed by immunodepletion of one of the subunits of COP coats (the coatomer) from mitotic cytosol. Vesicles were no longer formed but highly fenestrated networks appeared, an effect reversed by the readdition of purified coatomer. Together these experiments provide strong support for our hypothesis that the observed vesiculation of the Golgi apparatus during mitosis in animal cells is caused by continued budding of COP-coated transport vesicles but an inhibition of their fusion with their target membranes.
Stationary Phase-Specific Virulence Factor Overproduction by a lasR Mutant of Pseudomonas aeruginosa

Secreted virulence factors of the human pathogen Pseudomonas aeruginosa are often under quorum sensing control. Cells lacking the quorum-sensing regulator LasR show reduced virulence factor production under typical laboratory conditions and are hypo-virulent in short-term animal infection models, yet lasR mutants are frequently associated with long-term infection in cystic fibrosis patients. Here, I show that in stationary-phase or slow-growth conditions, lasR cells continuously and strongly produce the important virulence factor pyocyanin while wild-type cells do not. Pyocyanin overproduction by lasR cells is permitted by loss of repression by RsaL, a LasR-dependent negative regulator. lasR cells also contribute pyocyanin in mixed cultures, even under “cheating” conditions where they depend on their wild-type neighbors for nutrients. Finally, some clinical P. aeruginosa isolates with lasR mutations can overproduce pyocyanin in the laboratory. These results imply that slow-growing clinical populations of lasR cells in chronic infections may contribute to virulence by producing pyocyanin under conditions where lasR + cells do not.
Representation Discovery for Kernel-Based Reinforcement Learning

Recent years have seen increased interest in non-parametric reinforcement learning. There are now practical kernel-based algorithms for approximating value functions; however, kernel regression requires that the underlying function being approximated be smooth on its domain. Few problems of interest satisfy this requirement in their natural representation. In this paper we define value-consistent pseudometric (VCPM), the distance function corresponding to a transformation of the domain into a space where the target function is maximally smooth and thus well-approximated by kernel regression. We then present DKBRL, an iterative batch RL algorithm interleaving steps of Kernel-Based Reinforcement Learning and distance metric adjustment. We evaluate its performance on Acrobot and PinBall, continuous-space reinforcement learning domains with discontinuous value functions.
High-level synthesis for DSP applications using heterogeneous functional units

This paper addresses high level synthesis for realtime digital signal processing (DSP) architectures using heterogeneous functional units (FUs). For such special purpose architecture synthesis, an important problem is how to assign a proper FV type to each operation of a DSP application and generate a schedule in such a way that all requirements can be met and the total cost can be minimized. In the paper, we propose a two-phase approach to solve this problem. In the first phase, we propose an algorithm to assign proper FU types to applications such that the total cost can be minimized while the timing constraint is satisfied. In the second phase, based on the assignments obtained in the first phase, we propose a minimum resource scheduling algorithm to generate a schedule and a feasible configuration that uses as little resource as possible. The experimental results show that our approach can generate high-performance assignments and schedules with great reduction on total cost compared with the previous work.
Control flow analysis in scheme

Traditional flow analysis techniques, such as the ones typically employed by optimizing Fortran compilers, do not work for Scheme-like languages. This paper presents a flow analysis technique — control flow analysis — which is applicable to Scheme-like languages. As a demonstration application, the information gathered by control flow analysis is used to perform a traditional flow analysis problem, induction variable elimination. Extensions and limitations are discussed. The techniques presented in this paper are backed up by working code. They are applicable not only to Scheme, but also to related languages, such as Common Lisp and ML.
Cytotoxicity and DNA damage in the neutrophils of patients with sickle cell anaemia treated with hydroxyurea

Hydroxyurea (HU) is the most important advance in the treatment of sickle cell anaemia (SCA) for preventing complications and improving quality of life for patients. However, some aspects of treatment with HU remain unclear, including their effect on and potential toxicity to other blood cells such as neutrophils. This study used the measurement of Lactate Dehydrogenase (LDH) and Methyl ThiazolTetrazolium (MTT) and the comet assay to investigate the cytotoxicity and damage index (DI) of the DNA in the neutrophils of patients with SCA using HU.In the LDH and MTT assays, a cytoprotective effect was observed in the group of patients treated, as well as an absence of toxicity. When compared to patients without the treatment, the SS group (n=20, 13 women and 07 men, aged 18-69 years), and the group of healthy individuals (AA) used as a control group (n=52, 28 women and 24 men, aged 19-60 years), The SSHU group (n=21, 11 women and 10 men, aged 19-63 years) showed a significant reduction (p 20 months), demonstrating that despite the cytoprotective effects in terms of cell viability, the use of HU can induce DNA damage in neutrophils.
Flocking Behaviour: Agent-Based Simulation and Hierarchical Leadership

We have studied how leaders emerge in a group as a consequence of interactions among its members. We propose that leaders can emerge as a consequence of a self-organized process based on local rules of dyadic interactions among individuals. Flocks are an example of self-organized behaviour in a group and properties similar to those observed in flocks might also explain some of the dynamics and organization of human groups. We developed an agent-based model that generated flocks in a virtual world and implemented it in a multi-agent simulation computer program that computed indices at each time step of the simulation to quantify the degree to which a group moved in a coordinated way (index of flocking behaviour) and the degree to which specific individuals led the group (index of hierarchical leadership). We ran several series of simulations in order to test our model and determine how these indices behaved under specific agent and world conditions. We identified the agent, world property, and model parameters that made stable, compact flocks emerge, and explored possible environmental properties that predicted the probability of becoming a leader.
Golgi Structure Correlates with Transitional Endoplasmic Reticulum Organization in Pichia pastoris and Saccharomyces cerevisiae

Golgi stacks are often located near sites of “transitional ER” (tER), where COPII transport vesicles are produced. This juxtaposition may indicate that Golgi cisternae form at tER sites. To explore this idea, we examined two budding yeasts: Pichia pastoris, which has coherent Golgi stacks, and Saccharomyces cerevisiae, which has a dispersed Golgi. tER structures in the two yeasts were visualized using fusions between green fluorescent protein and COPII coat proteins. We also determined the localization of Sec12p, an ER membrane protein that initiates the COPII vesicle assembly pathway. In P. pastoris, Golgi stacks are adjacent to discrete tER sites that contain COPII coat proteins as well as Sec12p. This arrangement of the tER-Golgi system is independent of microtubules. In S. cerevisiae, COPII vesicles appear to be present throughout the cytoplasm and Sec12p is distributed throughout the ER, indicating that COPII vesicles bud from the entire ER network. We propose that P. pastoris has discrete tER sites and therefore generates coherent Golgi stacks, whereas S. cerevisiae has a delocalized tER and therefore generates a dispersed Golgi. These findings open the way for a molecular genetic analysis of tER sites.
RNase Activity of Polynucleotide Phosphorylase Is Critical at Low Temperature in Escherichia coli and Is Complemented by RNase II

ABSTRACT In Escherichia coli, the cold shock response is exerted upon a temperature change from 37°C to 15°C and is characterized by induction of several cold shock proteins, including polynucleotide phosphorylase (PNPase), during acclimation phase. In E. coli, PNPase is essential for growth at low temperatures; however, its exact role in this essential function has not been fully elucidated. PNPase is a 3′-to-5′ exoribonuclease and promotes the processive degradation of RNA. Our screening of an E. coli genomic library for an in vivo counterpart of PNPase that can compensate for its absence at low temperature revealed only one protein, another 3′-to-5′ exonuclease, RNase II. Here we show that the RNase PH domains 1 and 2 of PNPase are important for its cold shock function, suggesting that the RNase activity of PNPase is critical for its essential function at low temperature. We also show that its polymerization activity is dispensable in its cold shock function. Interestingly, the third 3′-to-5′ processing exoribonuclease, RNase R of E. coli, which is cold inducible, cannot complement the cold shock function of PNPase. We further show that this difference is due to the different targets of these enzymes and stabilization of some of the PNPase-sensitive mRNAs, like fis, in the Δpnp cells has consequences, such as accumulation of ribosomal subunits in the Δpnp cells, which may play a role in the cold sensitivity of this strain.
Long-distance connections in the Copper Age: New evidence from the Alpine Iceman’s copper axe

25 years after the discovery in the Ötztal Italian Alps, the 5,300-year-old mummy keeps providing key information on human biological and medical conditions, aspects of everyday life and societal organization in the Copper Age. The hand axe found with the body of the Alpine Iceman is one of the rare copper objects that is firmly dated to the early Copper Age because of the radiocarbon dating of the axe wooden shaft. Here we report the measurement of the lead isotope ratios of the copper blade. The results unambiguously indicate that the source of the metal is the ore-rich area of Southern Tuscany, despite ample evidence that Alpine copper ore sources were known and exploited at the time. The experimental results are discussed within the framework of all the available coeval archaeometallurgical data in Central-Southern Europe: they show that the Alps were a neat cultural barrier separating distinct metal circuits. The direct evidence of raw metal or object movement between Central Italy and the Alps is surprising and provides a new perspective on long-distance relocation of goods and relationships between the early Copper Age cultures in the area. The result is in line with the recent investigations re-evaluating the timing and extent of copper production in Central Italy in the 4th millennium BC.
Inverse procedural modeling of facade layouts

In this paper, we address the following research problem: How can we generate a meaningful split grammar that explains a given facade layout? To evaluate if a grammar is meaningful, we propose a cost function based on the description length and minimize this cost using an approximate dynamic programming framework. Our evaluation indicates that our framework extracts meaningful split grammars that are competitive with those of expert users, while some users and all competing automatic solutions are less successful.
Gesture interaction algorithm based on navigation information

Selection and manipulation are one of the fundamental aspects of gesture interaction. Selection is the precondition of gesture interaction. Collision detection is a key step in the gesture operation, which determines the reality and immersion of gesture interaction. However, the current related approach lack of a unified interaction model, thus it is difficult to fundamentally improve the user experience. In this paper, it is the application of navigation information to guide the object selection and collision detection. This paper obtains the navigation information of object selection and collision detection by cognitive information including the historical data of 3D hand, the hand and the object state information and the relative relationship between the hand and object, and uses the navigation information to guide the operator to carry out the next step operation. The main innovation is the establishment of a unified interaction model which is based cognitive information, and the correlation algorithm is proposed and implemented. The experimental results show that, the algorithm described in this paper not only reduce the time cost of object selection and collision detection, but also enhance the user's sense of immersion and allow users to operate more comfortable and enjoyable.
Essays on Information and Conflict

This dissertation explores the relationship between informational asymmetries and costly conflict in the international system. While it is well-known that information asymmetries may cause conflict, little research explores the origins of such asymmetries. This dissertation explores the role of intelligence, diplomacy, and military strategy in revealing information. I show that, under broad conditions, states will often fail to disclose information about themselves and fail to gather information about their opponents. In consequence, the ability to gather information does not undermine the link between uncertainty and war.
Results of treatment with hyper-CVAD, a dose-intensive regimen, in adult acute lymphocytic leukemia.

PURPOSE To evaluate the efficacy and toxicity of Hyper-CVAD (fractionated cyclophosphamide, vincristine, doxorubicin, and dexamethasone), a dose-intensive regimen, in adult acute lymphocytic leukemia (ALL). PATIENTS AND METHODS Adults with newly diagnosed ALL referred since 1992 were entered onto the study; treatment was initiated in 204 patients between 1992 and January 1998. No exclusions were made because of older age, poor performance status, organ dysfunction, or active infection. Median age was 39.5 years; 37% were at least 50 years old. Mature B-cell disease (Burkitt type) was present in 9%, T-cell disease in 17%. Leukocytosis of more than 30 x 10(9)/L was found in 26%, Philadelphia chromosome-positive disease in 16% (20% of patients with assessable metaphases), CNS leukemia at the time of diagnosis in 7%, and a mediastinal mass in 7%. Treatment consisted of four cycles of Hyper-CVAD alternating with four cycles of high-dose methotrexate (MTX) and cytarabine therapy, together with intrathecal CNS prophylaxis and supportive care with antibiotic prophylaxis and granulocyte colony-stimulating factor therapy. Maintenance in patients with nonmature B-cell ALL included 2 years of treatment with mercaptopurine, MTX, vincristine, and prednisone (POMP). RESULTS Overall, 185 patients (91%) achieved complete remission (CR) and 12 (6%) died during induction therapy. Estimated 5-year survival and 5-year CR rates were 39% and 38%, respectively. The incidence of CNS relapse was low (4%). Compared with 222 patients treated with vincristine, doxorubicin, and dexamethasone (VAD) regimens, our patients had a better CR rate (91% v 75%, P <.01) and CR rate after one course (74% v 55%, P <.01) and better survival (P <.01), and a smaller percentage had more than 5% day 14 blasts (34% v 48%, P =.01). Previous prognostic models remained predictive for outcome with Hyper-CVAD therapy. CONCLUSION Hyper-CVAD therapy is superior to our previous regimens and should be compared with established regimens in adult ALL.
Test Generation for Designs with On-Chip Clock Generators

High performance designs often use the on-chip device PLLs for accurate test clock generation during testing. The on-chip clock generator is designed in a programmable way to facilitate the test generation process and it in turn creates additional constraints for the automatic test pattern generation (ATPG) tool. This paper describes an efficient and effective method to take the hardware restrictions originated from the on-chip clock generators into account in order to avoid generating clock sequences that cannot be produced by hardware. Experimental results on industrial designs show test pattern reduction and/or ATPG run time reduction when compared with the test generation method that enumerates valid clock sequences explicitly and restricts the test generation within enumerated test sequences.