Miracle-dz/UniFAR-FTUs huggingface dataset:
pbsacct: A Workload Analysis System for PBS-Based HPC Systems

The PBS family of resource management systems have historically not included workload analysis tools, and the currently available third-party workload analysis packages have often not had a way to identify the applications being run through the batch environment. This paper introduces the pbsacct system, which solves the application identification problem by storing job scripts with accounting information and allowing the development of site-specific heuristics to map job script patterns to applications. The system consists of a database, data ingestion tools, and command-line and web-based user interfaces. The paper will discuss the pbsacct system and deployments at two sites, the National Institute for Computational Sciences and the Ohio Supercomputer Center. Workload analyses for systems at each site are also discussed.
Discovery of X-ray pulsations in the Be/X-ray binary IGR J21343+4738

We report on the discovery of X-ray pulsations in the Be/X-ray binary IGR J21343+4738 during an XMM-Newton observation. We obtained a barycentric corrected pulse period of 320.35+-0.06 seconds. The pulse profile displays a peak at low energy that flattens at high energy. The pulse fraction is 45+-3$% and independent of energy within the statistical uncertainties. The 0.2-12 keV spectrum is well fit by a two component model consisting of a blackbody with kT=0.11+-0.01 keV and a power law with photon index Gamma=1.02+-0.07. Both components are affected by photoelectric absorption with a equivalent hydrogen column density NH=(1.08+-0.15)x 10^{22} cm^{-2} The observed unabsorbed flux is 1.4x10^{-11} erg cm^{-2} s^{-1} in the 0.2-12 keV energy band. Despite the fact that the Be star's circumstellar disc has almost vanished, accretion continues to be the main source of high energy radiation. We argue that the observed X-ray luminosity (LX~10^{35} erg s^{-1}) may result from accretion via a low-velocity equatorial wind from the optical companion.
Fast model predictive control of 3-DOF helicopter

In order to solve the problem that model predictive control, MPC, is difficult to apply to the large scale system or fast dynamic system, in this paper, we describe a new fast online optimization predictive control method. This method is to exploit the structure of the QPs that arise in MPC, reorder the appropriate variable and use the advanced interior-point to improve the control performance and achieve the rapid control objective. At the same time, we apply the method to the 3-DOF helicopter, and make a comparison between the fast MPC and the traditional MPC. The advantage of the fast MPC are concluded.
Highly Scalable Parallel Algorithms for Sparse Matrix Factorization

In this paper, we describe scalable parallel algorithms for symmetric sparse matrix factorization, analyze their performance and scalability, and present experimental results for up to 1,024 processors on a Gray T3D parallel computer. Through our analysis and experimental results, we demonstrate that our algorithms substantially improve the state of the art in parallel direct solution of sparse linear systems-both in terms of scalability and overall performance. It is a well known fact that dense matrix factorization scales well and can be implemented efficiently on parallel computers. In this paper, we present the first algorithms to factor a wide class of sparse matrices (including those arising from two- and three-dimensional finite element problems) that are asymptotically as scalable as dense matrix factorization algorithms on a variety of parallel architectures. Our algorithms incur less communication overhead and are more scalable than any previously known parallel formulation of sparse matrix factorization. Although, in this paper, we discuss Cholesky factorization of symmetric positive definite matrices, the algorithms can be adapted for solving sparse linear least squares problems and for Gaussian elimination of diagonally dominant matrices that are almost symmetric in structure. An implementation of one of our sparse Cholesky factorization algorithms delivers up to 20 GFlops on a Gray T3D for medium-size structural engineering and linear programming problems. To the best of our knowledge, this is the highest performance ever obtained for sparse Cholesky factorization on any supercomputer.
A Server Based ASR Approach to Automated Cryptanalysis of Two Time Pads in Case of Speech

Keystream reuse in stream ciphers in case of textual data has been the focus of cryptanalysis for quite some time. The first ever use of hidden Markov models based speech recognition approach to cryptanalysis of encrypted digitized speech signals in a keystream reuse situation was presented by us in [1]. In this paper, we extend the idea presented in [1] and show the applicability of different speech recognition architectures in mobile environment to automatically recover the digitized speech signals encrypted under the same keystream. The server based automatic speech recognition (ASR) approach and its associated architectures are adapted to make them applicable in our attack. The two main implementation architectures of network speech recognition (NSR) from the acoustic front-end point of view are compared with respect to automated cryptanalysis of the two time pads of stream ciphered digitized speech. The simulation experiments performed on conventional speech recognition tools are presented for both the NSR architectures.
Pulseshaping in UWB Systems Using Semidefinite Programming with Non-Constant Upper Bounds

A critical obstacle for ultra wideband (UWB) communications is conformity to restrictions set on the allowed interference with other wireless devices. Using trains of N amplitude modulated basic pulses gives an FIR filter like design when disregarding the power spectral density (PSD) of the basic pulse. These leads to implementation losses and should be avoided. We quantify these losses and introduce an FIR filter design using semidefinite programming which can incorporate the basic pulse PSD by introducing non-constant upper bounds in the design. This leads to optimal designs and increases available signal power at no extra implementation complexity, just by choosing more optimal filter coefficients
Detection of human feature in abandoned object with modern security alert system using Android Application

Abandoned object detection is used to identify the unattended, strange object for a specific time period. Abandoned object detection plays a vital role in the places where there is high security alerts e.g. terrorist hits. Human feature Detection is done to differentiate between humans from arbitrary objects. It is implemented for the real time situation and capturing of live streaming videos. In previous methodologies only security alarms were used to alert the user. But proposed system checks whether the detected abandoned object is human being or static object like bag. The image of abandoned object is sent to the security guard through E-Mail and Android Application. This system is divided into three parts as follows: 1. Abandoned Object Detection 2. Human feature Detection 3. Security Alert System.
Biomedical Cancer Imaging Analysis

Image analysis for cancer imaging is becoming increasingly integrated into clinical workflow. As imaging technology is becoming more and more sophisticated, providing volumetric, multi-modality and dynamic acquisitions, the large amount of spatiotemporal data available poses increasingly challenging problems for the radiologists, oncologists, and other clinicians involved in cancer treatment, calling for automated, robust and accurate image analysis solutions. One aspect of interpreting such data correctly is the problem of patient motion, due to different scanning systems, patient movements, or respiratory motion. Over the past five years, the Biomedical Image Analysis lab at Oxford has developed a range of image analysis tools for multi-modal and dynamic image motion correction, in particular for lung cancer and colorectal cancer. A summary of these efforts is given here, and future research challenges are identified.
A Support Tool for Tagset Mapping

Many different tagsets are used in existing corpora; these tagsets vary according to the objectives of specific projects (which may be as far apart as robust parsing vs. spelling correction). In many situations, however, one would like to have uniform access to the linguistic information encoded in corpus annotations without having to know the classification schemes in detail. This paper describes a tool which maps unstructured morphosyntactic tags to a constraint-based, typed, configurable specification language, a ``standard tagset''. The mapping relies on a manually written set of mapping rules, which is automatically checked for consistency. In certain cases, unsharp mappings are unavoidable, and noise, i.e. groups of word forms {\sl not} conforming to the specification, will appear in the output of the mapping. The system automatically detects such noise and informs the user about it. The tool has been tested with rules for the UPenn tagset \cite{up} and the SUSANNE tagset \cite{garside}, in the framework of the EAGLES\footnote{LRE project EAGLES, cf. \cite{eagles}. } validation phase for standardised tagsets for European languages.
ConSIT: a conditioned program slicer

Conditioned slicing is a powerful generalisation of static and dynamic slicing which has applications to many problems in software maintenance and evolution, including reuse, reengineering and program comprehension. However there has been relatively little work on the implementation of conditioned slicing. Algorithms for implementing conditioned slicing necessarily involve reasoning about the values of program predicates in certain sets of states derived from the conditioned slicing criterion, making implementation particularly demanding. The paper introduces ConSIT, a conditioned slicing system which is based upon conventional static slicing, symbolic execution and theorem proving. ConSIT is the first fully automated implementation of conditioned slicing. An implementation of ConSIT is available for experimentation at http://www.mcs. gold.ac. uk//spl tilde/mas01sd/consit.html.
A Polynomial Regularity Lemma for Semialgebraic Hypergraphs and Its Applications in Geometry and Property Testing

Fox, Gromov, Lafforgue, Naor, and Pach proved a regularity lemma for semi-algebraic $k$-uniform hypergraphs of bounded complexity, showing that for each $\epsilon>0$ the vertex set can be equitably partitioned into a bounded number of parts (in terms of $\epsilon$ and the complexity) so that all but an $\epsilon$-fraction of the $k$-tuples of parts are homogeneous. We prove that the number of parts can be taken to be polynomial in $1/\epsilon$. Our improved regularity lemma can be applied to geometric problems and to the following general question on property testing: is it possible to decide, with query complexity polynomial in the reciprocal of the approximation parameter, whether a hypergraph has a given hereditary property? We give an affirmative answer for testing typical hereditary properties for semi-algebraic hypergraphs of bounded complexity.
Periodic and Static Strain Investigations with Borehole Strainmeters and GPS

Yellowstone Lake, located within the greater Yellowstone Caldera, is an important part of the overall Yellowstone volcanic system, moderating and interacting with the hydrothermal system and the subsurface magmatic system. A curious feature evident in nearly a decade of shear strain surrounding Lake Yellowstone, direct lake level, wind and barometric pressure measurements, is a persistent seiche. During 2009-2018, seiches are routinely recorded with periods of 11.5, 13.4, 50.4 and 76 minutes with amplitudes ranging from 2 cm to 15 cm. Unexpectedly seiches are present even when the lake is covered by a thick sheet of ice (~ 1m). Hence common mechanisms for exciting or sustaining a seiche cannot apply: wind, barometric pressure gradients, landslide impulses and/or teleseismic shaking. We deduce that the seiche is excited and maintained by hydrothermal systems venting beneath the floor of the lake. Two methods to drive the seiche are proposed: aperiodic eruptions (i.e. underwater geysers) and the periodic "puffing" which is commonly associated with geothermal wells and ocean bottom hydrothermal systems. We propose that the high-Q of the system that quantifies its persistence following impulsive starts, is sustained by positive feedback between pressure changes associated with the seiche and the multi-phase hydrothermal system below or at the floor of the lake.
Rhinocetin, a Venom-derived Integrin-specific Antagonist Inhibits Collagen-induced Platelet and Endothelial Cell Functions

Background: Snaclecs affect the hemostasis of snakebite victims upon envenomation. Results: Rhinocetin, a novel snaclec, inhibits integrin α2β1-dependent functions of human platelets and endothelial cells. Conclusion: The actions of rhinocetin are consistent with hemorrhagic symptoms upon envenomation. Significance: Due to its inhibitory actions on integrin α2β1, rhinocetin may have potential diagnostic and therapeutic values. Snaclecs are small non-enzymatic proteins present in viper venoms reported to modulate hemostasis of victims through effects on platelets, vascular endothelial, and smooth muscle cells. In this study, we have isolated and functionally characterized a snaclec that we named “rhinocetin” from the venom of West African gaboon viper, Bitis gabonica rhinoceros. Rhinocetin was shown to comprise α and β chains with the molecular masses of 13.5 and 13 kDa, respectively. Sequence and immunoblot analysis of rhinocetin confirmed this to be a novel snaclec. Rhinocetin inhibited collagen-stimulated activation of human platelets in a dose-dependent manner but displayed no inhibitory effects on glycoprotein VI (collagen receptor) selective agonist, CRP-XL-, ADP-, or thrombin-induced platelet activation. Rhinocetin antagonized the binding of monoclonal antibodies against the α2 subunit of integrin α2β1 to platelets and coimmunoprecipitation analysis confirmed integrin α2β1 as a target for this venom protein. Rhinocetin inhibited a range of collagen-induced platelet functions such as fibrinogen binding, calcium mobilization, granule secretion, aggregation, and thrombus formation. It also inhibited integrin α2β1-dependent functions of human endothelial cells. Together, our data suggest rhinocetin to be a modulator of integrin α2β1 function and thus may provide valuable insights into the role of this integrin in physiological and pathophysiological scenarios, including hemostasis, thrombosis, and envenomation.
Just a piece of paper? The effect of marriage on health

There is extensive evidence that married people are, on average, healthier than their unmarried counterparts. It is unclear how much this positive correlation can be explained by the selection of healthier people into marriage. In this paper, I estimate the effect of marriage relative to cohabitation on health and disability. I control for selection into marriage by instrumenting marital status using state and time variation in marriage tax penalties. After controlling for selection, low education men benefit from marriage whilst all other men are no better off if married. For women with more than high school education, marriage increases the probability of reporting a health problem.
Effects of Insect Viruses and Pesticides on Glutathione S-Transferase Activity and Gene Expression in Bombyx mori

ABSTRACT Glutathione S-transferase (GST) is a gene family generally associated with detoxification and plays an important role in detoxifying exogenous compounds. The silkworm Bombyx mori is an important economic animal for silk production. However, it is liable to infection by a number of viruses and chemical agents that can contaminate its food and growing environment. Here we conducted a comparative study of strain- and tissue-specific expressions of GST in the silkworm under infections by Bombyx mori nuclear polyhedrosis virus (BmNPV) and Bombyx mori densonucleosis virus (BmDNV) and under the stress of pesticides (insecticide and herbicide). BmDNV induced an increase of GST at 24 h and a decrease at 48 and 72 h in the midgut of the DNV-susceptible strain and a decrease at 24 h and increase at 48 and 72 h in the midgut of the DNV-tolerant strain. BmDNV induced a significant increase of GST from 24 to 72 h in the fat body of both DNV-susceptible and DNV-tolerant strains. In contrast, BmNPV induced a significant decrease of GST in both the fat body and midgut of the NPV-susceptible strain and induced increase of GST from 24 to 48 h in the midgut and at 72 h in the fat body of the NPV-tolerant strain. All of these results suggest that BmGST activity varies with the strain, tissue, feeding behavior, and developmental stage of the silkworm. On treating silkworm larvae with pesticides (insecticide and herbicide), expression of the BmGSTS2 gene increased noticeably in the midgut and reached a peak at 6 to 12 h. The mRNA level of BmGSTS2 in the midgut increased during administration of the chemicals, suggesting that the induction of BmGSTS2 is part of the defense mechanism against exogenous chemicals.
Graphics processing unit based direct simulation Monte Carlo

The direct simulation Monte Carlo (DSMC) is a computational method for fluid mechanics simulation in the regime of rarefied gas flow. It is a numerical solution of the Boltzmann equation based on an individual particle basis. Accurate simulations typically require particle numbers in the range of hundreds of thousands to millions. Such large simulations require an inordinate amount of time for processing using serial computing on central processing units (CPUs). In this paper we investigate data-parallel techniques on graphics processing units (GPUs) to execute very large scale DSMC simulations. We have designed and implemented Bird’s method on a three-dimensional simulation domain that includes complex geometry interactions. We also have tested and verified the statistical and theoretical accuracy of our implementation. Our results show substantial performance improvements (nearly two orders of magnitude) over Bird’s serial implementation without loss of accuracy.
The File System Belongs in the Kernel

This paper argues that a shared, distributed name space and I/O interface should be implemented inside the operating system kernel. The grounding for the argument is a comparison between the Sprite network operating system and the Mach microkernel. Sprite optimizes the common case of file and device access, both local and remote, by providing a kernel-level implementation. Sprite also allows for user-level extensibility by letting a user-level process implement the naming and I/O interfaces of the file system. Mach, in contrast, provide general interprocess communication and does not define a file system protocol in the kernel. [Published in the Proceedings of the 2nd USENIX Mach Symposium, Nov 20-22, 1991, pages 233250]
pH-Dependant Antifungal Activity of Valproic Acid against the Human Fungal Pathogen Candida albicans

Current antifungal drugs suffer from limitations including toxicity, the emergence of resistance and decreased efficacy at low pH that are typical of human vaginal surfaces. Here, we have shown that the antipsychotic drug valproic acid (VPA) exhibited a strong antifungal activity against both sensitive and resistant Candida albicans in pH condition similar to that encountered in vagina. VPA exerted a strong anti-biofilm activity and attenuated damage of vaginal epithelial cells caused by C. albicans. We also showed that VPA synergizes with the allylamine antifungal, Terbinafine. We undertook a chemogenetic screen to delineate biological processes that underlies VPA-sensitivity in C. albicans and found that vacuole-related genes were required to tolerate VPA. Confocal fluorescence live-cell imaging revealed that VPA alters vacuole integrity and support a model where alteration of vacuoles contributes to the antifungal activity. Taken together, this study suggests that VPA could be used as an effective antifungal against vulvovaginal candidiasis.
A Market Framework for Eliciting Private Data

We propose a mechanism for purchasing information from a sequence of participants. The participants may simply hold data points they wish to sell, or may have more sophisticated information; either way, they are incentivized to participate as long as they believe their data points are representative or their information will improve the mechanism's future prediction on a test set. The mechanism, which draws on the principles of prediction markets, has a bounded budget and minimizes generalization error for Bregman divergence loss functions. We then show how to modify this mechanism to preserve the privacy of participants' information: At any given time, the current prices and predictions of the mechanism reveal almost no information about any one participant, yet in total over all participants, information is accurately aggregated.
An agenda for meeting the special needs of multiple birth families.

Over 80,000 multiple birth babies are born each year in the U.S. Their families must cope with a constellation of complex physical and psychosocial challenges, which jeopardizes their health and functioning. The demands of twin pregnancy and the parenting of twins, triplets, quadruplets, quintuplets or more puts these families at disproportionately high risk for infant mortality, birth defects, child abuse, substance abuse, financial problems and marital problems. Health and social service resources must be developed to alleviate the stresses associated with multiple birth and to empower parents to cope well. Guidelines for policies, parent education, professional training and service delivery developed for the California Department of Health Service, Maternal and Child Health Branch, are here offered for the consideration of policy makers and public health planners.
Integration of the radiative transfer equation for polarized light: The exponential solution

The radiative transfer equation (RTE) for polarized light accepts a convenient exponential solution when the absorption matrix commutes with its integral. We characterize some of the matrix depth variations which are compatible with the commutation condition. Eventually the vector solution may be diagonalized and one may obtain four independent scalar solutions with four optical depths, complex in general. When the commutation condition is not satisfied, one must resort to a determination of an appropriate evolution operator, which is shown to be well determined mathematically, but whose explicit form is, in general, not easy to apply in a numerical code. However, we propose here an approach to solve a general case not satisfying the commutation condition.
Raisins, Sultanas, and Currants: Lexical Classification and Abstraction Via Context Priming

In this paper we discuss the results of experiments which use a context, essentially an ordered set of lexical items, as the seed from which to build a network representing statistically important relationships among lexical items in some corpus. A metric is then applied to the nodes in the network in order to discover those pairs of items related by high indices of similarity. The goal of this research is to instantiate a class of items corresponding to each item in the priming context. We believe that this instantiation process is ultimately a special case of abstraction over the entire network; in this abstraction, similar nodes are collapsed into metanodes which may then function as if they were single lexical items.