Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast and Optimal Prediction on a Labeled Tree

We characterize, up to constant factors, the number of mistakes necessary and sufficient for sequentially predicting a given tree with binary labeled nodes. We provide an efficient algorithm achieving this number of mistakes on any tree. Tree prediction algorithms can solve the general graph prediction problem by representing the graph via one of its spanning trees. In order to cope with adversarial assignments of labels over a general graph, we advocate the use of random spanning trees, which have the additional advantage of retaining relevant spectral information of the original graph.
Chemical-shift anisotropy measurements of amide and carbonyl resonances in a microcrystalline protein with slow magic-angle spinning NMR spectroscopy.

Chemical shifts are fundamental to interpretation of NMR spectra and provide constraints for macromolecular structure determination, refinement, and validation, as well as details of active-site chemistry in enzymes. Insights into the origins of the chemical shift can be leveraged to improve chemical analysis, including conformation, bonding, and dynamics. To exploit this information fully, it is desirable to measure not only isotropic chemical shifts but also the full chemical-shift anisotropy (CSA) tensor. Until recently, most efforts to measure backbone amide and carbonyl CSAs have relied upon cross-correlated relaxation and residual anisotropic shifts in solution NMR. In solid-state NMR, analysis of sideband patterns has typically been reserved for site-specifically labeled samples or small peptides. Here we demonstrate that the Herzfeld−Berger method (Herzfeld, J.; Berger, A. E. J. Chem. Phys. 1980, 73, 6021−6030) can be applied to highly 13C,15N-enriched solid proteins, using 2D heteronuclear correl.
Immunohistochemical Localization of Plasminogen Activator Inhibitor Type 1 in Human Brain Tumors

We investigated the immunohistochemical localization of plasminogen activator inhibitor type 1 (PAI-1) in surgical specimens of 41 human intracranial tumors. Malignant tumors (7 glioblastoma multiforme, 5 anaplastic gliomas, 4 malignant meningiomas, and 9 metastatic tumors) showed consistently stronger PAI-1 immunohistoreactivity than benign or low-grade tumors (5 low-grade gliomas, 8 benign meningiomas, and 3 Schwannomas). Strong PAI-1 positivity was confined to glomeruloid-shaped proliferative vessels seen in high-grade gliomas and metastatic tumors. Blood vessels near necrotic foci and some zones of necrosis also showed strong PAI-1 positivity. PAI-1 localizes in the vascular basement membrane and perivascular connective tissue, while endothelial cells themselves show weak positivity. None of the specimens showed PAI-1 reactivity within the tumor cells per se. Localization of PAI-1 in proliferating vessels suggests that PAI-1 may be involved in angiogenesis.
Intracellular Butyryl Phosphate and Acetyl Phosphate Concentrations in Clostridium acetobutylicum and Their Implications for Solvent Formation

ABSTRACT It has been suggested (L. H. Harris, R. P. Desai, N. E. Welker, and E. T. Papoutsakis, Biotechnol. Bioeng. 67:1-11, 2000) that butyryl phosphate (BuP) is a regulator of solventogenesis in Clostridium acetobutylicum. Here, we determined BuP and acetyl phosphate (AcP) levels in fermentations of C. acetobutylicum wild type (WT), degenerate strain M5, a butyrate kinase (buk) mutant, and a phosphotransacetylase (pta) mutant. A sensitive method was developed to measure BuP and AcP in the same sample. Compared to the WT, the buk mutant had higher levels of BuP and AcP; the BuP levels were high during the early exponential phase, and there was a peak corresponding to solvent production. Consistent with this, solvent formation was initiated significantly earlier and was much stronger in the buk mutant than in all other strains. For all strains, initiation of butanol formation corresponded to a BuP peak concentration that was more than 60 to 70 pmol/g (dry weight), and higher and sustained levels corresponded to higher butanol formation fluxes. The BuP levels never exceeded 40 to 50 pmol/g (dry weight) in strain M5, which produces no solvents. The BuP profiles were bimodal, and there was a second peak midway through solventogenesis that corresponded to carboxylic acid reutilization. AcP showed a delayed single peak during late solventogenesis corresponding to acetate reutilization. As expected, in the pta mutant the AcP levels were very low, yet this strain exhibited strong butanol production. These data suggest that BuP is a regulatory molecule that may act as a phosphodonor of transcriptional factors. DNA array-based transcriptional analysis of the buk and M5 mutants demonstrated that high BuP levels corresponded to downregulation of flagellar genes and upregulation of solvent formation and stress genes.
NILC_USP: An Improved Hybrid System for Sentiment Analysis in Twitter Messages

This paper describes the NILC USP system that participated in SemEval-2014 Task 9: Sentiment Analysis in Twitter, a re-run of the SemEval 2013 task under the same name. Our system is an improved version of the system that participated in the 2013 task. This system adopts a hybrid classification process that uses three classification approaches: rule-based, lexiconbased and machine learning. We suggest a pipeline architecture that extracts the best characteristics from each classifier. In this work, we want to verify how this hybrid approach would improve with better classifiers. The improved system achieved an F-score of 65.39% in the Twitter message-level subtask for 2013 dataset (+ 9.08% of improvement) and 63.94% for 2014 dataset.
Bistability in a Gene Pool GA with Mutation

It is possible for a GA to have two stable fixed points on a single-peak fitness landscape. These can correspond to meta-stable finite populations. This phenomenon is called bistability, and is only known to happen in the presence of recombination, selection, and mutation. This paper models the bistability phenomenon using an infinite population model of a GA based on gene pool recombination. Fixed points and their stability are explicitly calculated. This is possible since the infinite population model of the gene pool GA is much more tractable than the infinite population model for the standard simple GA. For the needle-in-the-haystack fitness function, the fixed point equations reduce to a single variable polynomial equation, and stability of fixed points can be determined from the derivative of the single variable equation. We also show empirically that bistability can occur on a single-peak landscape where there is selective pressure toward the optimum at every point of the search space. ∗ This paper was written while Alden Wright was visiting the School of Computer Science, University of Birmingham, UK.
Surface Orientation from a Projected Grid

Two simple methods are given for obtaining the surface shape using a projected grid. After the camera is calibrated to the 3-D workspace, the only input date needed for the computation of surface normals are grid intersect points in a single 2-D image. The first method performs nonlinear computations based on the distortion of the lengths of the grid edges and does not require a full calibration matrix. The second method requires that a full parallel projection model of the imaging is available, which enables it to compute 3-D normals using simple linear computations. The linear method performed better overall in the experiments, but both methods produced normals within 4-8 degrees of known 3-D directions. These methods appear to be superior to methods based on shape-from-shading because the results are comparable, yet the equipment setup is simpler and the processing is not very sensitive to object reflectance. >
Opposing effects of oestradiol and progesterone on intracellular pathways and activation processes in the oxidative stress induced activation of cultured rat hepatic stellate cells

Background: Oxidative stress, including the generation of reactive oxygen species (ROS), is involved in hepatofibrogenesis. The authors’ previous studies have shown that oestradiol suppresses hepatic fibrosis in animal models and attenuates the activation of cultured rat hepatic stellate cells (HSCs), which possess oestrogen receptor subtype β and are also activated by ROS. Aims: To define the mechanisms by which female sex hormones play an antifibrogenic role in activated HSCs, the effects of oestradiol and progesterone on ROS generation processes and intracellular pathways, leading to the activation of HSCs undergoing oxidative stress, was examined. Methods: HSCs, isolated from rats, were cultured for 7 days with oestradiol or progesterone for 24 hours as pretreatment, and oxidative stress was then induced by exposure to low doses of hydrogen peroxide for another 24 hours. Results: Oestradiol inhibited ROS generation and antioxidant enzyme loss via the suppression of NADH/NADPH oxidase activity, and attenuated hydrogen peroxide induced transforming growth factor-β1 (TGF-β1) expression, HSC proliferation and transformation, and the activation of mitogen activated protein kinase (MAPK) pathways and transcription factors. Progesterone exerted a stimulatory effect through the progesterone receptor on the induction of ROS generation processes and intracellular pathways, resulting in TGF-β1 expression and HSC activation, and fibrogenic effects were inhibited by oestradiol. Conclusion: These findings show for the first time that oestradiol inhibits the activation of transcription factors by suppressing ROS generation processes and the MAPK pathways, and inactivates the downstream transcription processes involved in TGF-β1 expression and HSC activation, whereas progesterone acts in opposition to the favourable effects of oestradiol and its effects are blocked by oestradiol.
Primary treatment of leukemia relapses after allogeneic hematopoietic stem cell transplantation with reduced‐intensity conditioning second transplantation from the original donor

Acute leukemia relapsing after allogeneic hematopoietic stem cell transplantation (HSCT) has dismal outcome. Consecutive consenting patients (acute myeloid leukemia: N = 71; acute lymphoblastic leukemia: N = 37), at a median age of 37 (16–57) years, who had relapsed 7.9 (1.3–132) months post‐HSCT, were treated with three cytarabine‐based intensive regimens as reduced‐intensity conditioning (RIC), followed by infusion of mobilized HSC from the original donors. There were four treatment‐related mortalities (TRMs). Of 104 evaluable cases, 72 patients (67%) achieved complete remission (CR)/CR with incomplete hematologic recovery (CRi). The median overall survival (OS) of the entire cohort was 11.6 months. The OS of patients achieving CR/CRi after the first RIC/HSCT was 18.8 months, as compared with 3.9 months for those not (P < 0.01). For 32 patients with nonremission, 11 received a repeat RIC‐HSCT, leading to CR/CRi in three cases. Therefore, 75/108 (69%) of patients achieved CR/CRi after one or two courses of RIC‐HSCT. Among CR/CRi patients, 48 cases relapsed again after 6.1 (1.0–64.4) months. Thirty cases received a repeat RIC‐HSCT, leading to CR/CRi in 22 patients. Multivariate analyses showed a significant impact of remission duration after initial HSCT (P = 0.026) and the presence of acute graft‐versus‐host disease after RIC‐HSCT (P = 0.011) on CR/CRi. RIC‐HSCT as primary treatment for acute leukemic relapses post‐HSCT induced a high CR rate with low TRM. Optimal postremission treatment remains to be defined. Am. J. Hematol. 88:485–491, 2013. © 2013 Wiley Periodicals, Inc.
Regulation of the Voltage-gated K+ Channels KCNQ2/3 and KCNQ3/5 by Ubiquitination

The muscarine-sensitive K+ current (M-current) stabilizes the resting membrane potential in neurons, thus limiting neuronal excitability. The M-current is mediated by heteromeric channels consisting of KCNQ3 subunits in association with either KCNQ2 or KCNQ5 subunits. The role of KCNQ2/3/5 in the regulation of neuronal excitability is well established; however, little is known about the mechanisms that regulate the cell surface expression of these channels. Ubiquitination by the Nedd4/Nedd4-2 ubiquitin ligases is known to regulate a number of membrane ion channels and transporters. In this study, we investigated whether Nedd4/Nedd4-2 could regulate KCNQ2/3/5 channels. We found that the amplitude of the K+ currents mediated by KCNQ2/3 and KCNQ3/5 were reduced by Nedd4-2 (but not Nedd4) in a Xenopus oocyte expression system. Deletion experiments showed that the C-terminal region of the KCNQ3 subunit is required for the Nedd4-2-mediated regulation of the heteromeric channels. Glutathione S-transferase fusion pulldowns and co-immunoprecipitations demonstrated a direct interaction between KCNQ2/3 and Nedd4-2. Furthermore, Nedd4-2 could ubiquitinate KCNQ2/3 in transfected cells. Taken together, these data suggest that Nedd4-2 is potentially an important regulator of M-current activity in the nervous system.
Divergent Effects of Human Cytomegalovirus and Herpes Simplex Virus-1 on Cellular Metabolism

Viruses rely on the metabolic network of the host cell to provide energy and macromolecular precursors to fuel viral replication. Here we used mass spectrometry to examine the impact of two related herpesviruses, human cytomegalovirus (HCMV) and herpes simplex virus type-1 (HSV-1), on the metabolism of fibroblast and epithelial host cells. Each virus triggered strong metabolic changes that were conserved across different host cell types. The metabolic effects of the two viruses were, however, largely distinct. HCMV but not HSV-1 increased glycolytic flux. HCMV profoundly increased TCA compound levels and flow of two carbon units required for TCA cycle turning and fatty acid synthesis. HSV-1 increased anapleurotic influx to the TCA cycle through pyruvate carboxylase, feeding pyrimidine biosynthesis. Thus, these two related herpesviruses drive diverse host cells to execute distinct, virus-specific metabolic programs. Current drugs target nucleotide metabolism for treatment of both viruses. Although our results confirm that this is a robust target for HSV-1, therapeutic interventions at other points in metabolism might prove more effective for treatment of HCMV.
The effect of n‐acetyl‐cysteine on recovery of the facial nerve after crush injury

Facial nerve dysfunction can vary in severity and recovery is dependent on the character of the injury. N‐acetyl‐cysteine prevents oxidative stress and cellular damage, and its use in the setting of nerve dysfunction from crush injury has not yet been established. In this study, rats with facial nerve crush injury will be treated with n‐acetyl‐cysteine or control and functional recovery and electrophysiologic outcome will be compared.
Very fine-grained fault-tolerant routing algorithm of NoC based on buffer reuse

Fault model is the basis of research on fault-tolerant routing algorithm for Network on Chip (NoC). Since the former fine-grained fault model could not distinguish link faults from channel faults effectively, a much more fine-grained fault model is put forward, and a new fault-tolerant routing algorithm named VFFRA-BR (very fine-grained fault-tolerant routing algorithm based on buffer reuse) is proposed in this paper, to improve the utilization rate of the NoC resources. This algorithm adopts the transparent transmission mechanism based on buffer reuse (TTBR) to tolerate internal channel faults of routers. Experimental and synthesis results demonstrate that our algorithm performs better on average throughput, average latency and average hop counts of NoC while keeping a low on-chip resources overhead.
Joint symbolic dynamics for the assessment of cardiovascular and cardiorespiratory interactions

Beat-to-beat variations in heart period provide information on cardiovascular control and are closely linked to variations in arterial pressure and respiration. Joint symbolic analysis of heart period, systolic arterial pressure and respiration allows for a simple description of their shared short-term dynamics that are governed by cardiac baroreflex control and cardiorespiratory coupling. In this review, we discuss methodology and research applications. Studies suggest that analysis of joint symbolic dynamics provides a powerful tool for identifying physiological and pathophysiological changes in cardiovascular and cardiorespiratory control.
Speech synthesis in Serbian based on artificial neural networks

There are two basic groups of methods for text to speech synthesis — concatenative and parametric. Expansion of speech technology applications, made parametric methods more attractive owing to their flexibility of changing speaker and speech style. The paper describes the development of the first speech synthisizer based on deep neural networks in Serbian language by using open source Merlin toolkit. The method gave extraordinary results, as proven by subjective mark of more than 4,5 out of 5.
Accumulation and fragmentation of plastic debris in global environments

One of the most ubiquitous and long-lasting recent changes to the surface of our planet is the accumulation and fragmentation of plastics. Within just a few decades since mass production of plastic products commenced in the 1950s, plastic debris has accumulated in terrestrial environments, in the open ocean, on shorelines of even the most remote islands and in the deep sea. Annual clean-up operations, costing millions of pounds sterling, are now organized in many countries and on every continent. Here we document global plastics production and the accumulation of plastic waste. While plastics typically constitute approximately 10 per cent of discarded waste, they represent a much greater proportion of the debris accumulating on shorelines. Mega- and macro-plastics have accumulated in the highest densities in the Northern Hemisphere, adjacent to urban centres, in enclosed seas and at water convergences (fronts). We report lower densities on remote island shores, on the continental shelf seabed and the lowest densities (but still a documented presence) in the deep sea and Southern Ocean. The longevity of plastic is estimated to be hundreds to thousands of years, but is likely to be far longer in deep sea and non-surface polar environments. Plastic debris poses considerable threat by choking and starving wildlife, distributing non-native and potentially harmful organisms, absorbing toxic chemicals and degrading to micro-plastics that may subsequently be ingested. Well-established annual surveys on coasts and at sea have shown that trends in mega- and macro-plastic accumulation rates are no longer uniformly increasing: rather stable, increasing and decreasing trends have all been reported. The average size of plastic particles in the environment seems to be decreasing, and the abundance and global distribution of micro-plastic fragments have increased over the last few decades. However, the environmental consequences of such microscopic debris are still poorly understood.
Modifications of UCT and sequence-like simulations for Monte-Carlo Go

Algorithm UCB1 for multi-armed bandit problem has already been extended to algorithm UCT which works for minimax tree search. We have developed a Monte-Carlo program, MoGo, which is the first computer Go program using UCT. We explain our modification of UCT for Go application and also the sequence-like random simulation with patterns which has improved significantly the performance of MoGo. UCT combined with pruning techniques for large Go board is discussed, as well as parallelization of UCT. MoGo is now a top-level computer-Go program on 9 times 9 Go board
High-efficiency FRET-enhanced photoacoustic probes for in vivo tumor imaging

Photoacoustic imaging can provide high-resolution and high-contrast image under unprecedented depth compared with pure optical imaging techniques by making use of laser-induced ultrasound waves. Although a series of absorption-enhanced optical contrast agents for photoacoustic imaging were developed, the probe with fully conversion from absorbed light energy to acoustic energy has not been achieved so far. Here we develop a high-efficiency photoacoustic probes with fluorescence resonance energy transfer (FRET) effect for enhancement of nonradiative energy. Graphene oxide (GO) binding optical dyes (GO-dyes) were achieved to show highly fluorescence quenching and violently increased photoacoustic signal intensity. GO-dyes were constructed and testified for multi-spectral photoacoustic imaging. As a representative probe, GO-Cy7 nanoparticles were used to validate the feasibility of photoacoustic tumor molecular imaging in vivo. Our work demonstrated a new approach to construct high-efficiency FRET-enhanced multi-spectrum probes for photoacoustic molecular imaging.
Ieee Transactions on Visualization and Computer Graphics 1 Hybrid Rendering with Scheduling under Uncertainty

—As scientific data of increasing size is generated by today's simulations and measurements, utilizing dedicated server resources to process the visualization pipeline becomes necessary. In a purely server-based approach, requirements on the client-side are minimal as the client only displays results received from the server. However, the client may have a considerable amount of hardware available, which is left idle. Further, the visualization is put at the whim of possibly unreliable server and network conditions. Server load, bandwidth and latency may substantially affect the response time on the client. In this paper, we describe a hybrid method, where visualization workload is assigned to server and client. A capable client can produce images independently. The goal is to determine a workload schedule that enables a synergy between the two sides to provide rendering results to the user as fast as possible. The schedule is determined based on processing and transfer timings obtained at run-time. Our probabilistic scheduler adapts to changing conditions by shifting workload between server and client, and accounts for the performance variability in the dynamic system.
The as-1 Promoter Element Is an Oxidative Stress-Responsive Element and Salicylic Acid Activates It via Oxidative Species1

The activation sequence-1(as-1)-like element found in the promoter of some glutathione S-transferase (GST) genes, has been previously described as a salicylic acid (SA)- and auxin-responsive element. In this paper, we tested the hypothesis that the activating effect of SA on the as-1 element is mediated by oxidative species. Supporting this hypothesis, our results show that the antioxidants dimethylthiourea (DMTU) and 3-t-butyl-4-hydroxy-anizole (BHA) inhibit the SA-induced transcription of genes controlled by as-1 elements in tobacco (Nicotiana tabacum) plants [i.e. GNT35gene coding for a GST and (as-1)4 /β-glucuronidase(GUS) reporter transgene]. DMTU and BHA also inhibit SA-activated as-1-binding activity in nuclear extracts. Further support for the hypothesis that the as-1 element is activated by oxidative species comes from our result showing that light potentiates the SA-induced activation of the as-1element. Furthermore, methyl viologen, a known oxidative stress inducer in plants, also activates the as-1 element. Increasing H2O2 levels by incubation with H2O2 or with the catalase inhibitor 3-amino-1,2,5-triazole does not activate the (as-1)4 /GUS gene. On the contrary, 3-amino-1,2,5-triazole inhibits the activating effect of SA on the (as-1)4 /GUSgene. These results suggest that oxidative species other than H2O2 mediate the activation of theas-1 element by SA. Our results also suggest that even though the as-1 binding activity is stimulated by oxidative species, this is not sufficient for the transactivation of genes controlled by this element. The complex interplay between SA and reactive oxygen species in the transcriptional activation of defense genes is discussed.