Miracle-dz/UniFAR-FTUs huggingface dataset:
Response of Anaerobic Ammonium-Oxidizing Bacteria to Hydroxylamine

ABSTRACT Anaerobic ammonium oxidation is a recent addition to the microbial nitrogen cycle, and its metabolic pathway, including the production and conversion of its intermediate hydrazine, is not well understood. Therefore, the effect of hydroxylamine addition on the hydrazine metabolism of anaerobic ammonium-oxidizing (anammox) bacteria was studied both experimentally and by mathematical modeling. It was observed that hydroxylamine was disproportionated biologically in the absence of nitrite into dinitrogen gas and ammonium. Little hydrazine accumulated during this process; however, rapid hydrazine production was observed when nearly all hydroxylamine was consumed. A mechanistic model is proposed in which hydrazine is suggested to be continuously produced from ammonium and hydroxylamine (possibly via nitric oxide) and subsequently oxidized to N2. The electron acceptor for hydrazine oxidation is hydroxylamine, which is reduced to ammonium. A decrease in the hydroxylamine reduction rate, therefore, leads to a decrease in the hydrazine oxidation rate, resulting in the observed hydrazine accumulation. The proposed mechanism was verified by a mathematical model which could explain and predict most of the experimental data.
The pipeline of facial animation fast forward: the NMA example

In the domain of computer graphic, to achieve facial animation looks like real human performance without any bias is always the holy grail of related research academy and industry[Ma 2008]. Next Media Animation (NMA) as the Asia's leading animation studio is famous for applying the fast production pipeline to generate news animation and cartoon episodes. We has developed a unique pipeline, following the scenario to assemble models from our own data base with mocap data to render out news story for worldwide broadcasting in two hours. However, for the high-end quality, to develop a practical and fast pipeline for merging facial animation into NMA current news pipeline without any additional time request has become an issue of our Media Lab R&D team.
Improved salt and subsalt model with common offset RTM tomography: A case history in deepwater, Gulf of Mexico

We focus on extracting new value to previously acquired orthogonal WAZ surveys in the Mississippi Canyon area where some of the largest and still active deep water discoveries reside. Some analyses estimate that many large subsalt/presalt fields can still be discovered. In this study, the subsalt images which are critical to exploration are enhanced by applying new processing methodologies. The key technologies that have contributed to improved images are: 1) Common Offset RTM (COR) gathers for dirty salt and subsalt velocity tomography update 2) Dual-Directional Image Stack (DDIS) with target image-based sum weighting to improve poorly illuminated subsalt areas.
Privacy-Preserving Whole Genome Sequence Processing through Proxy-Aided ORAM

Widespread use and low prices of genomic sequencing bring us into the area of personalized medicine and biostatistics of large cohorts. As the processed genomic data is highly sensitive, Privacy-Enhancing Technologies for genomic data need to be developed. In this work, we present a novel and flexible mechanism for the private processing of whole genomic sequences which is flexible enough to support any query. The basic underlying idea is to store DNA in several small encrypted blocks, use ORAM mechanisms to access the desired blocks in an oblivious manner, and finally run secure two-party protocols to privately compute the desired functionality on the retrieved encrypted blocks. Our construction keeps all sensitive information hidden and reveals only the end result to the legitimate party. Our main technical contribution is the design of a new ORAM that allows for access rights delegation while not requiring the data owner to be online to reshuffle the database. We validate the practicability of our approach through experimental studies.
Robbing the bandit: less regret in online geometric optimization against an adaptive adversary

We consider "online bandit geometric optimization," a problem of iterated decision making in a largely unknown and constantly changing environment. The goal is to minimize "regret," defined as the difference between the actual loss of an online decision-making procedure and that of the best single decision in hindsight. "Geometric optimization" refers to a generalization of the well-known multi-armed bandit problem, in which the decision space is some bounded subset of Rd, the adversary is restricted to linear loss functions, and regret bounds should depend on the dimensionality d, rather than the total number of possible decisions. "Bandit" refers to the setting in which the algorithm is only told its loss on each round, rather than the entire loss function.McMahan and Blum [10] presented the best known algorithm in this setting, and proved that its expected additive regret is O(poly(d)T3/4). We simplify and improve their analysis of this algorithm to obtain regret O(poly(d)T2/3). We also prove that, for a large class of full-information online optimization problems, the optimal regret against an adaptive adversary is the same as against a non-adaptive adversary.
Hardware Acceleration of Bayesian Neural Networks Using RAM Based Linear Feedback Gaussian Random Number Generators

Bayesian neural networks (BNNs) have been proposed to address the problem of model uncertainty in training. By introducing weights associated with conditioned probability distributions, BNN is capable to resolve overfitting issues commonly seen in conventional neural networks. Frequent usage of Gaussian random variables requires a properly optimized Gaussian Random Number Generator (GRNG). The high hardware cost of conventional GRNG makes the hardware realization of BNN challenging. In this paper, a new hardware acceleration architecture for variational inference in BNNs is proposed to facilitate the applicability of BNN in larger-scale applications. In addition, the proposed implementation introduced the RAM based Linear Feedback based GRNG (RLF-GRNG) for effective weight sampling in BNNs. The RAM based Linear Feedback method can effectively utilize RAM resources for parallel Gaussian random number generation while requiring limited and sharable control logic. Implementation on an Altera Cyclone V FPGA suggests that the RLF-GRNG utilizes much less RAM resources compared to other GRNG methods. Experiments results show that the proposed hardware implementation of a BNN can still attain similar accuracy compared to software implementation.
A Branch-Price-and-Cut Algorithm for Packing Cuts in Undirected Graphs

The cut packing problem in an undirected graph is to find a largest cardinality collection of pairwise edge-disjoint cuts. We provide the first experimental study of this NP-hard problem that is interesting from a pure theorist’s viewpoint as well as from the standpoint of scientific applications (e.g., in bioinformatics and network reliability). So far it could not be solved exactly. We propose a branch-price-and-cut algorithm to optimally solve instances from various graph classes, random and from the literature, with up to several hundred vertices. In particular, we investigate how complexity results match computational experience and how combinatorial properties help improve the algorithm’s performance.
An initial exploration of the factors influencing retrieval of Web images in Greek queries

A number of queries are submitted to the image searching mechanisms of Google, Yahoo and MSN and their results are analyzed. The analysis shows that queries which are in different forms (e.g. upper case and lower case) but have exactly the same content retrieve different images. The paper also presents a tool which takes as input a user query and based on knowledge of the linguistic characteristics of Greek produces different forms of this query. It then submits the new queries to Google and merges the recalled images.
Partitioning of Hypercubes by Resolution of Combinatorial Designs

A method for the partitioning of multiprocessors with a static interconnection network in hypercube topology is presented. It is based on the view of a static interconnection network as a combinatorial design. Our mere interest is to show that by means of a transformation, well-established methods of combinatorial design theory can be used to manage tasks emerging from parallel processing, rather than to give a highly efficient hardware-related partitioning technique.
Resonant Cyclotron Scattering in Magnetars’ Emission

We present a systematic fit of a model of resonant cyclotron scattering (RCS) to the X-ray data of 10 magnetars, including canonical and transient anomalous X-ray pulsars (AXPs) and soft gamma repeaters (SGRs). In this scenario, nonthermal magnetar spectra in the soft X-rays (i.e., below ~10 keV) result from resonant cyclotron scattering of the thermal surface emission by hot magnetospheric plasma. We find that this model can successfully account for the soft X-ray emission of magnetars, while using the same number of free parameters as in the commonly used empirical blackbody plus power-law model. However, while the RCS model can alone reproduce the soft X-ray spectra of AXPs, the much harder spectra of SGRs below 10 keV require the addition of a power-law component (the latter being the same component responsible for their hard X-ray emission). Although this model in its present form does not explain the hard X-ray emission (i.e., above ~20 keV) of a few of these sources, we took this further component into account in our modeling not to overlook its contribution in the ~4-10 keV band. We find that the entire class of sources is characterized by magnetospheric plasma with a density which, at resonant radius, is about 3 orders of magnitude higher than the Goldreich-Julian electron density. The inferred values of the intervening hydrogen column densities are also in better agreement with more recent estimates. Although the treatment of the magnetospheric scattering used here is only approximated, its successful application to all magnetars shows that the RCS model is capable of catching the main features of the spectra observed below ~10 keV.
Vertical partitioning of CO2 production within a temperate forest soil

The major driving factors of soil CO2 production - substrate supply, temperature, and water content - vary vertically within the soil profile, with the greatest temporal variations of these factors usually near the soil surface. Several studies have demonstrated that wetting and drying of the organic horizon contributes to temporal variation in summertime soil CO2 efflux in forests, but this contribution is difficult to quantify. The objectives of this study were to partition CO2 production vertically in a mixed hardwood stand of the Harvard Forest, Massachusetts, USA, and then to use that partitioning to evaluate how the relative contributions of CO2 production by genetic soil horizon vary seasonally and interannually. We measured surface CO2 efflux and vertical soil profiles of CO2 concentration, temperature, water content, and soil physical characteristics. These data were applied to a model of effective diffusivity to estimate CO2 flux at the top of each genetic soil horizon and the production within each horizon. A sensitivity analysis revealed sources of uncertainty when applying a diffusivity model to a rocky soil with large spatial heterogeneity, especially estimates of bulk density and volumetric water content and matching measurements of profiles and surface fluxes. We conservatively estimate that the O horizon contributed 40-48% of the total annual soil CO2 efflux. Although the temperature sensitivity of CO2 production varied across soil horizons, the partitioning of CO2 production by horizon did not improve the overall prediction of surface CO2 effluxes based on temperature functions. However, vertical partitioning revealed that water content covaried with CO2 production only in the O horizon. Large interannual variations in estimates of O horizon CO2 production indicate that this layer could be an important transient interannual source or sink of ecosystem C. © 2006 Blackwell Publishing Ltd.
SAILS: static analysis of information leakage with sample

In this paper, we introduce Sails, a new tool that combines Sample, a generic static analyzer, and a sophisticated domain for leakage analysis. This tool does not require to modify the original language, since it works with mainstream languages like Java, and it does not require any manual annotation. Sails can combine the information leakage analysis with different heap abstractions, inferring information leakage over programs dealing with complex data structures. We applied Sails to the analysis of the SecuriBench-micro suite. The experimental results show the effectiveness of our approach.
Dissertation Proposal: Evolving Robust Software

Over the past fifty years software developers have been selecting, reusing and modifying efficient and robust software development tools, code and design patterns. This history of development, through a process mirroring natural selection, results in some surprisingly biological features of software which this proposed work will investigate and exploit. The dual goals of this investigation are increased understanding of existing software, and new tools for software development and maintenance. I will focus on properties that are exhibited by evolved complex systems and arise through natural selection and adaptation to survival in the world. Some properties, such as the amenability to random evolutionary processes and robustness to variability in constituent parts, will be shown to be applicable to engineered software systems.
Digoxin Use and Subsequent Clinical Outcomes in Patients With Atrial Fibrillation With or Without Heart Failure in the ENGAGE AF‐TIMI 48 Trial

Background Digoxin is widely used in patients with atrial fibrillation despite the lack of randomized controlled trials. Observational studies report conflicting results regarding its association with mortality, perhaps because of residual confounding by the presence of heart failure (HF). Methods and Results In the ENGAGE AF‐TIMI 48 (Effective Anticoagulation With Factor Xa Next Generation in Atrial Fibrillation‐Thrombolysis in Myocardial Infarction 48) trial, clinical outcomes of patients with atrial fibrillation with and without HF were examined by baseline digoxin use during a median follow‐up of 2.8 years. HF was defined at baseline as prior or current clinical stage C or D HF. Of 21 105 patients enrolled, 6327 (30%) were treated with digoxin at baseline. Among patients without HF (n=8981), digoxin use (20%) was independently associated with sudden cardiac death (adjusted hazard ratio, 1.51; 95% CI, 1.10–2.08), with no significant interaction by age, sex, left ventricular ejection fraction, renal function, or concomitant medications (P>0.05 for each). Consistent results were observed using propensity matching (adjusted hazard ratio for sudden cardiac death, 1.90; 95% CI, 1.36–2.65). Among patients with HF (n=12 124), digoxin use (37%) was associated with an increase in all‐cause death, cardiovascular death, sudden cardiac death, and death caused by HF/cardiogenic shock (P<0.01 for each), but not with noncardiovascular death, stroke/systemic embolism, or myocardial infarction. Conclusions In this observational analysis of patients with atrial fibrillation without investigator‐reported HF, digoxin use was significantly associated with sudden cardiac death. While residual confounding cannot be excluded, the association between digoxin use and worse clinical outcomes highlights the need to examine digoxin use, particularly when prescribed to control heart rate in patients with atrial fibrillation in a randomized trial. Clinical Trial Registration URL: http://www.clinicaltrials. gov. Unique identifier: NCT00781391.
The influence of land-use change and landscape dynamics on the climate system: relevance to climate-change policy beyond the radiative effect of greenhouse gases

Our paper documents that land-use change impacts regional and global climate through the surface-energy budget, as well as through the carbon cycle. The surface-energy budget effects may be more important than the carbon-cycle effects. However, land-use impacts on climate cannot be adequately quantified with the usual metric of ‘global warming potential’. A new metric is needed to quantify the human disturbance of the Earth's surface-energy budget. This ‘regional climate change potential’ could offer a new metric for developing a more inclusive climate protocol. This concept would also implicitly provide a mechanism to monitor potential local-scale environmental changes that could influence biodiversity.
Respiration amplitude analysis for REM and NREM sleep classification

In previous work, single-night polysomnography recordings (PSG) of respiratory effort and electrocardiogram (ECG) signals combined with actigraphy were used to classify sleep and wake states. In this study, we aim at classifying rapid-eye-movement (REM) and non-REM (NREM) sleep states. Besides the existing features used for sleep and wake classification, we propose a set of new features based on respiration amplitude. This choice is motivated by the observation that the breathing pattern has a more regular amplitude during NREM sleep than during REM sleep. Experiments were conducted with a data set of 14 healthy subjects using a linear discriminant (LD) classifier. Leave-one-subject-out cross-validations show that adding the new features into the existing feature set results in an increase in Cohen's Kappa coefficient to a value of κ = 0.59 (overall accuracy of 87.6%) compared to that obtained without using these features (κ of 0.54 and overall accuracy of 86.4%). In addition, we compared the results to those reported in some other studies with different features and signal modalities.
Peristaltic gel pump driven by chemical energy

Stimuli-responsive polymer gels have been applied to soft actuators. Especially, electroactive polymers are said to be promising materials as advanced soft actuators. Its mechanical motion is controlled by the external stimuli such as a change in solvent composition, pH, temperature and electric field etc. On the other hand, living organisms exhibit an autonomous motion driven by the chemical energy. In this study, we report a novel gel pump that can move spontaneously without external driving stimuli. The gel pump converts the chemical energy of the oscillatory reaction into the mechanical energy inside the gel. Although the gel is completely composed of synthetic polymer, it shows autonomous motion as if it is alive.
Utility Guided Pattern Mining

JAGANNATH , SANDHYA . Utility Guided Pattern Mining (Under the direction of Dr. Jon Doyle). This work is an initial exploration of the use of the decision-theoretic concept of utility to guide pattern mining. We present the use of utility functions as against thresholds and constraints as the mechanism to express user preferences and formulate several pattern mining problems that use utility functions. Utility guided pattern mining provides the twin benefits of capturing user preferences precisely using utility functions and of expressing user focus by choosing an appropriate utility guided pattern mining problem. It addresses the drawbacks of threshold guided pattern mining, the specification of threshold and the assumption of a fixed level of interest. We examine the problem of mining patterns with the best utility values in detail. We examine monotonicity properties of utility functions and the composition of utility functions from sub-utility functions as mechanisms to prune the search space. We also present a top-down approach for generating projected databases from FP-Trees, which is an order of magnitude faster than methods proposed in the literature. UTILITY GUIDED PATTERN MINING BY SANDHYA JAGANNATH A THESIS SUBMITTED TO THE GRADUATE FACULTY OF NORTH CAROLINA STATE UNIVERSITY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE DEPARTMENT OF COMPUTER SCIENCE RALEIGH NOVEMBER 2003
A dynamic Web agent for verifying the security and integrity of a Web site's contents

To harness safe operation of Web-based systems in Web environments, we propose an SSPA (Server-based SHA-1 Page-digest Algorithm) to verify the integrity of Web contents before the server issues an HTTP response to a user request. In addition to standard security measures, our Java implementation of the SSPA, which is called the Dynamic Security Surveillance Agent (DSSA), provides further security in terms of content integrity to Web-based systems. Its function is to prevent the display of Web contents that have been altered through the malicious acts of attackers and intruders on client machines. This is to protect the reputation of organisations from cyber-attacks and to ensure the safe operation of Web systems by dynamically monitoring the integrity of a Web site's content on demand. We discuss our findings in terms of the applicability and practicality of the proposed system. We also discuss its time metrics, specifically in relation to its computational overhead at the Web server, as well as the overall latency from the clients' point of view, using different Internet access methods. The SSPA, our DSSA implementation, some experimental results and related work are all discussed.
Functional anatomy of macaque striate cortex. III. Color

Using spatially diffuse stimuli (or sinusoidal gratings of very low spatial frequency), levels of 14C-2-deoxy-d-glucose (DG) uptake produced by color-varying stimuli are much greater than those produced by luminance-varying stimuli in macaque striate cortex. Such a difference in DG results is consistent with previous psychophysical and electrophysiological results from man and monkey. In DG experiments with color-varying gratings of low and middle spatial frequencies, or with spatially diffuse color variations, DG uptake was highest in the cytochrome oxidase blobs, as was also seen with low-spatial-frequency luminance gratings. High-spatial-frequency, color-varying uptake patterns were shifted to cover both blob and interblob regions in a manner similar to that of the patterns obtained with middle-spatial- frequency luminance stimuli. However, in no instance did chromatic gratings produce uptake restricted to the interblob regions, as with the pattern seen with the highest-spatial-frequency luminance gratings. Thus, DG uptake is relatively higher in the interblob regions when comparing luminance with color-varying gratings that are otherwise similar. It was also possible to show DG evidence for receptive-field double-opponency in the upper-layer blobs, but color sensitivity in layer 4Cb appears single-opponent. The DG results suggest that color sensitivity is also high in the lower-layer (layers 5 + 6) blobs, and that many layer 5 receptive fields are double-opponent. Striate layers 4Ca and 4B-appeared color-insensitive in a wide variety of DG tests; this supports the idea of a color-insensitive stream running from the magnocellular LGN layers through striate layers 4Ca and 4B to extrastriate areas MT and V3. There was also a major effect due to wavelength: long and short wavelengths produced much more uptake than did middle wavelengths, even when all colors were equated for luminance and saturation. No variation with eccentricity was seen in cortical color sensitivity, at least between 0 degrees and 10 degrees.