gebhart/patrepeval huggingface dataset:
Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching (2005)

The proliferation of online text, such as found on the World Wide Web and in online databases, motivates the need for space-efficient text indexing methods that support fast string searching. We model this scenario as follows: Consider a text T consisting of n symbols drawn from a fixed alphabet $\Sigma$. The text T can be represented in $n \lg |\Sigma|$ bits by encoding each symbol with $\lg |\Sigma|$ bits. The goal is to support fast online queries for searching any string pattern P of m symbols, with T being fully scanned only once, namely, when the index is created at preprocessing time. The text indexing schemes published in the literature are greedy in terms of space usage: they require $\Omega(n \lg n)$ additional bits of space in the worst case. For example, in the standard unit cost RAM, suffix trees and suffix arrays need $\Omega(n)$ memory words, each of $\Omega(\lg n)$ bits. These indexes are larger than the text itself by a multiplicative factor of $\Omega(\smash{\lg_{|\Sigma|} n})$, which is significant when $\Sigma$ is of constant size, such as in \textsc{ascii} or \textsc{unicode}. On the other hand, these indexes support fast searching, either in $O(m \lg |\Sigma|)$ time or in $O(m +\lg n)$ time, plus an output-sensitive cost $O(\mathit{occ})$ for listing the $\mathit{occ}$ pattern occurrences. We present a new text index that is based upon compressed representations of suffix arrays and suffix trees. It achieves a fast $\smash{O(m /\lg_{|\Sigma|} n + \lg_{|\Sigma|}^\epsilon n)}$ search time in the worst case, for any constant $0 < \epsilon \leq 1$, using at most $\smash{\bigl(\epsilon^{-1} + O(1)\bigr) \, n \lg |\Sigma|}$ bits of storage. Our result thus presents for the first time an efficient index whose size is provably linear in the size of the text in the worst case, and for many scenarios, the space is actually sublinear in practice. As a concrete example, the compressed suffix array for a typical 100 MB \textsc{ascii} file can require 30--40 MB or less, while the raw suffix array requires 500 MB. Our theoretical bounds improve \emph{both} time and space of previous indexing schemes. Listing the pattern occurrences introduces a sublogarithmic slowdown factor in the output-sensitive cost, giving $O(\mathit{occ} \, \smash{\lg_{|\Sigma|}^\epsilon n})$ time as a result. When the patterns are sufficiently long, we can use auxiliary data structures in $O(n \lg |\Sigma|)$ bits to obtain a total search bound of $O(m /\lg_{|\Sigma|} n + \mathit{occ})$ time, which is optimal.
A role for ion homeostasis in yeast ionic liquid tolerance (2022)

The model yeast <i>Saccharomyces cerevisiae</i> is being developed as a biocatalyst for the conversion of renewable lignocellulosic biomass into biofuels. The ionic liquid 1-ethyl-3-methylimidazolium chloride (EMIMCl) solubilizes lignocellulose for deconstruction into fermentable sugars, but it inhibits yeast fermentation. EMIMCl tolerance is mediated by the efflux pump Sge1p and uncharacterized protein Ilt1p. Through genetic investigation, we found that disruption of ion homeostasis through mutations in genes encoding the Trk1p potassium transporter and its protein kinase regulators, Sat4p and Hal5p, causes EMIMCl sensitivity. These results suggest that maintenance of ion homeostasis is important for tolerance to EMIMCl.
Manufacturing Over Many Scales: High Fidelity Macroscale Coverage of Nanoporous Metal Arrays via Lift‐Off‐Free Nanofabrication (2014)

A low-cost, high-throughput, lift-off-free nanolithographic method is developed for creating hexagonal arrays of sub-30-nm-sized pores on a metal film, achieving uniform coverage over an entire wafer of 10 cm in diameter. Spherical nanodomains of poly(methyl methacrylate) are demonstrated to be well-controlled and self-aligned within a polystyrene matrix layer on a metal thin film without any intermediary coating. After removal of PMMA, the porous PS thin film acts as an etch mask for defining nanoscale pores in the metal underlayer by Ar ion beam milling, resulting in wafer-scale patterning with great fidelity. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Energy-Efficient Device Discovery in D2D Cellular Networks for Public Safety Scenario (2019)

Energy-efficient device discovery is vital in public-safety systems. We investigate the problem of maximizing the number of discovered users under the major constraint of overlay interference, which occurs in device-to-device (D2D) communications, from users simultaneously accessing the resources. To solve this problem, we propose a D2D discovery maximization (D2D-DM) iterative algorithm, which provides the capability to switch the discovery mode from half-duplex to in-band full-duplex, when signal-to-interference-noise ratio falls below a predefined threshold. Moreover, the open-loop power control scheme is adopted for power-limited users. Simulation results demonstrate that the proposed D2D-DM scheme significantly enhances the number of discovered users as compared to conventional static resource allocation and the random backoff schemes.
Thirty Days in 2020 and How They Future-Proofed a University (2023)

The COVID-19 pandemic was a catalyst for change in myriad ways. While nearly all the societal changes were negative, the crisis also brought about positive adaptations in response to this crisis. National Louis University's (NLU's) initial response to the crisis, beginning in February 2020 and through subsequent decisive actions, kept the university vibrant throughout the pandemic. Perhaps more importantly, these actions created a foundation for long-term institutional success. The steps included technological enhancements and intentional activities focused on ensuring that institutional personnel would remain connected to each other and to the students that NLU serves. Many of these changes are now a permanent part of the institution as the world moves past the COVID-19 era. Utilizing NLU as an exemplar, recommendations will be given designed to help college and university leadership evolve in this new hybrid reality. Ultimately, the institutions that can effectively adapt to this hybrid existence will be the ones most capable of continued success in an uncertain future.
Promoter DNA-methylation in the TH-MYCN neuroblastoma mouse model (2014)

High-resolution genome-sequencing efforts have discovered a wealth of mutations in genes encoding epigenetic regulators, providing evidence for their predominant role in cancer development. In a previous study, we identified prognostic methylation biomarkers in neuroblastoma using genome-wide promoter methylation analysis. However, therapeutic targeting of the neuroblastoma epigenome remains poorly explored. Therefore, as a prelude to testing of novel epigenetic drugs, we performed MBD-based genome-wide methylation sequencing to establish the methylation pattern in a series of seven tumors from a MYCN-driven neuroblastoma mouse model. Seven hundred nineteen promoters, representing 516 unique genes, are commonly methylated in all seven mouse tumors. This list of methylated genes mainly consists of protein coding genes and pseudogenes, but also contains long noncoding RNAs, microRNAs and small nucleolar RNAs, of which long noncoding RNAs and microRNAs rank amongst the most extensively methylated genes (on the basis of peak height). Interestingly, the protocadherin alpha and beta clusters, which are methylated in virtually every human neuroblastoma tumor, are fully methylated in all seven mouse tumors, supporting the notion that this model can be applied to study DNA methylation in neuroblastoma. Finally, initial cross-species methylation analysis, suggest several cancer-associated genes as interesting hyper-methylated candidate genes for further study. Together, these data show that the TH-MYCN mouse model is valuable in the study of neuroblastoma epigenetics, and provide the rationale for testing of novel epigenetic drugs.
Editorial: In this issue (2015)

In this issue, we are hosting several reviews on topics of broad interests, such as therapeutic or prophylactic antibodies, and the role of autophagy in autoimmunity.
Toward a theory of the general-anesthetic-induced phase transition of the cerebral cortex. I. A thermodynamics analogy (2001)

In a recent paper the authors developed a stochastic model for the response of the cerebral cortex to a general anesthetic agent. The model predicted that there would be an anesthetic-induced phase change at the point of transition into unconsciousness, manifested as a divergence in the electroencephalogram spectral power, and a change in spectral energy distribution from being relatively broadband in the conscious state to being strongly biased towards much lower frequencies in the unconscious state. Both predictions have been verified in recent clinical measurements. In the present paper we extend the model by calculating the equilibrium distribution function for the cortex, allowing us to establish a correspondence between the cortical phase transition and the more familiar thermodynamic phase transitions. This correspondence is achieved by first identifying a cortical free energy function, then by postulating that there exists an inverse relationship between an anesthetic effect and a quantity we define as cortical excitability, which plays a role analogous to temperature in thermodynamic phase transitions. We follow standard thermodynamic theory to compute a cortical entropy and a cortical "heat capacity," and we investigate how these will vary with anesthetic concentration. The significant result is the prediction that the entropy will decrease discontinuously at the moment of induction into unconsciousness, concomitant with a release of "latent heat" which should manifest as a divergence in the analogous heat capacity. There is clear clinical evidence of heat capacity divergence in historical anesthetic-effect measurements performed in 1977 by Stullken et al. [Anesthesiology 46, 28 (1977)]. The discontinuous step change in cortical entropy suggests that the cortical phase transition is analogous to a first-order thermodynamic transition in which the comatose-quiescent state is strongly ordered, while the active cortical state is relatively disordered.
Towards Promoting Backup-Sharing in Survivable Virtual Network Design (2016)

In a virtualized infrastructure where multiple virtual networks (or tenants) are running atop the same physical network (e.g., a data center network), a single facility node (e.g., a server) failure can bring down multiple virtual machines, disconnecting their corresponding services and leading to millions of dollars in penalty cost. To overcome losses, tenants or virtual networks can be augmented with a dedicated set of backup nodes and links provisioned with enough backup resources to assume any single facility node failure. This approach is commonly referred to as Survivable Virtual Network (SVN) design. The achievable reliability guarantee of the resultant SVN could come at the expense of lowering the substrate network utilization efficiency, and subsequently its admissibility, since the provisioned backup resources are reserved and remain idle until failures occur. Backup-sharing can replace the dedicated survivability scheme to circumvent the inconvenience of idle resources and reduce the footprints of backup resources. Indeed the problem of SVN design with backup-sharing has recurred multiple times in the literature. In most of the existing work, designing an SVN is bounded to a fixed number of backup nodes; further backup-sharing is only explored and optimized during the embedding phase. This renders the existing redesign techniques agnostic to the backup resource sharing in the substrate network, and highly dependent on the efficiency of the adopted mapping approach. In this paper, we diverge from this dogmatic approach, and introduce ProRed, a novel prognostic redesign technique that promotes the backup resource sharing at the virtual network level, prior to the embedding phase. Our numerical results prove that this redesign technique achieves lower-cost mapping solutions and greatly enhances the achievable backup sharing, boosting the overall network's admissibility.
Cancer immunology: the search for specificity. (1982)

The major focus of cancer immunology has shifted away from arguments about the validity of the immunosurveillance theory of cancer to the more basic question of tumor-specific antigens. Despite vast effort aimed at demonstrations of such antigens, their existence in the generality of cancer remains unproved. Serological analysis of 3 tumor types, mouse leukemia and sarcoma and human malignant melanoma, has received the most attention, and a rudimentary classification of the surface antigens expressed by these tumors has begun to emerge. The prime candidates for antigens that can be considered tumor specific are the few instances of Class 1 antigens that have now been serologically defined on mouse and human tumors. These antigens show an absolute restriction to individual tumors and are not demonstrable on any other normal or malignant cell type. Biochemical and genetic characterizations of Class 1 antigens represent an essential next step in an evaluation of the significance of these antigens. The surprising features of the thymus leukemia (TL) antigens of the mouse provide insight into the genetic origin of another key class of tumor antigens, i.e., those with characteristic properties of both differentiation and tumor-specific antigens. In normal mice, TL antigens are restricted to cells in the thymus, and strains differ with regard to expression versus nonexpression of TL antigens. Genetic information for TL is universal in mice, however, as leukemias that develop in mice normally lacking TL are found to express TL. What is clear from the past two decades of research in cancer immunology is that a far more detailed knowledge of surface antigens of tumor cells will be necessary before we can begin to assess the possibility of immunological control of cancer.
Self-Assembly of Multidomain Peptides: Sequence Variation Allows Control over Cross-Linking and Viscoelasticity (2009)

An important goal in supramolecular chemistry is to achieve controlled self-assembly of molecules into well-defined nanostructures and the subsequent control over macroscopic properties resulting from the formation of a nanostructured material. Particularly important to our lab is control over viscoelasticity and bioactivity. Recently we described a multidomain peptide motif that can self-assemble into nanofibers 2 x 6 x 120 nm. In this work we describe how sequence variations in this general motif can be used to create nanofibrous gels that have storage moduli, which range over 2 orders of magnitude and can undergo shear thinning and shear recovery while at the modest concentration of 1% by weight. Gel formation is controlled by addition of oppositely charged multivalent ions such as phosphate and magnesium and can be carried out at physiological pH. We also demonstrate how maximum strength can be obtained via covalent capture of the nanofibers through disulfide bond formation. Together these hydrogel properties are ideally suited as injectable materials for drug and cell delivery.
Vehicle-to-Vehicle Front-to-Side Crash Compatibility Analysis Using a CAE Based Methodology (2007)

Fundamental physics and numerous field studies have clearly shown a higher fatality risk for occupants in smaller and lighter vehicles when colliding with the heavier one, especially when the struck vehicle is a passenger car and the striking vehicle is a light trucks and vans (LTV) or an sport utility vehicle (SUV). The consensus is that the significant parameters influencing compatibility in front-to-side crashes are geometric interaction, vehicle stiffness, and vehicle mass. The effect of each individual design parameter, however, is not clearly understood. A finite element (FE) model-based design of experiments (DOE) methodology focused on evaluating the effects of a few striking vehicle design variables on dummy responses of the struck vehicle in front-to-side impact was developed. This study utilized a deterministic approach including optimally spaced Latin hypercube sampling which allowed analytical prediction equations for dummy responses to be generated from twenty-one simulation runs. Selected response variables were the dummy injury measures Thoracic Trauma Index (TTI) and pelvis acceleration. Several multi-dimensional response surfaces were constructed based on the simulation results and found to be well correlated (R²=0.83 and R²=0.94 for TTI and pelvis acceleration, respectively). Results indicate that lower front-end structures in vehicle-to-vehicle front-to-side collisions have the greatest effect on reducing (struck vehicle driver) TTI than other design variables. This was found to contrast the pelvic acceleration results, which tended to increase with lower front structure height of the striking vehicle. The stiffness and mass showed moderate significance on the TTI with less mass effect than stiffness. The mass showed no significant effect on the pelvis acceleration.
Pediatric Type 1 Diabetes: Mechanisms and Impact of Technologies on Comorbidities and Life Expectancy (2023)

Type 1 diabetes (T1D) is one of the most common chronic diseases in childhood, with a progressively increasing incidence. T1D management requires lifelong insulin treatment and ongoing health care support. The main goal of treatment is to maintain blood glucose levels as close to the physiological range as possible, particularly to avoid blood glucose fluctuations, which have been linked to morbidity and mortality in patients with T1D. Indeed, the guidelines of the International Society for Pediatric and Adolescent Diabetes (ISPAD) recommend a glycated hemoglobin (HbA1c) level < 53 mmol/mol (<7.0%) for young people with T1D to avoid comorbidities. Moreover, diabetic disease strongly influences the quality of life of young patients who must undergo continuous monitoring of glycemic values and the administration of subcutaneous insulin. In recent decades, the development of automated insulin delivery (AID) systems improved the metabolic control and the quality of life of T1D patients. Continuous subcutaneous insulin infusion (CSII) combined with continuous glucose monitoring (CGM) devices connected to smartphones represent a good therapeutic option, especially in young children. In this literature review, we revised the mechanisms of the currently available technologies for T1D in pediatric age and explored their effect on short- and long-term diabetes-related comorbidities, quality of life, and life expectation.
Effects of Self Irradiation from 238Pu on Candidate Ceramics for Plutonium Immobilization (2003)

In this document, we describe the results of radiation damage testing and characterization for specimens that were resintered to re-establish crystallinity. The phases in these specimens have become amorphous from radiation induced damage over the 8 months since sintering.
Lithium Insertion in an Oriented Nanoporous Oxide with a Tunnel Structure: Ti2Nb2O9 (2008)

The electrochemical study of the empty tunnel structure Ti2Nb2O9 shows that it can intercalate lithium reversibly, through a solid−solution process, leading to the phase Li4Ti2Nb2O9. The high-resolution electron microscopy study of this phase shows that Ti2Nb2O9 exhibits an exceptional nanoporosity, involving the formation of aligned holes throughout the whole microcrystal, which may favor, together with the presence of tunnels, the diffusion of lithium during the insertion. The reversible capacity of this phase, of 125 mAh/g at 1.57 V vs Li/Li+, after 30 cycles, shows its great reversibility.
One-pot synthesis of Schiff base compounds via photocatalytic reaction in the coupled system of aromatic alcohols and nitrobenzene using CdIn2S4 photocatalyst (2018)

The use of solar energy to drive organic reactions under mild conditions provides a sustainable pathway for green synthesis and has been one of the primary goals pursued by scientists. In this research, the cadmium indium sulfide (CdIn2S4) photocatalyst was prepared using a simple solvothermal method and was thoroughly characterized using X-ray powder diffraction, UV-visible absorption spectra, nitrogen adsorption-desorption isotherms, scanning electron microscopy, transmission electron microscopy and X-ray spectroscopy measurements. The photocatalytic performance of the CdIn2S4 photocatalyst was evaluated using photocatalytic synthesis of Schiff base compounds in a coupled system of aromatic alcohols and nitrobenzene under visible light irradiation. The yield of N-benzylideneaniline reached up to 32% in the coupled system of benzyl alcohol and nitrobenzene under visible light illumination for 8 h. Furthermore, the changes for the amounts of aromatic aldehydes and AL as intermediate products during the photocatalytic process were also investigated. Using isotopic tracing, a possible reaction mechanism for the photocatalytic synthesis of N-benzylideneaniline and the redox reactions in the coupled system of benzyl alcohol and nitrobenzene was proposed. It is hoped that this strategy can provide an effective pathway for the traditional organic synthesis and transformation using photocatalytic technology under mild conditions.
Predicting Queueing Delays (1999)

This paper investigates the possibility of predicting each customer's waiting time in queue before starting service in a multiserver service system with the first-come first-served service discipline, such as a telephone call center. A predicted waiting-time distribution or an appropriate summary statistic such as the mean or the 90th percentile may be communicated to the customer upon arrival and possibly thereafter in order to improve customer satisfaction. The predicted waiting-time distribution may also be used by the service provider to better manage the service system, e.g., to help decide when to add additional service agents. The possibility of making reliable predictions is enhanced by exploiting information about system state, including the number of customers in the system ahead of the current customer. Additional information beyond the number of customers in the system may be obtained by classifying customers and the service agents to which they are assigned. For nonexponential service times, the elapsed service times of customers in service can often be used to advantage to compute conditional-remaining-service-time distributions. Approximations are proposed to convert the distributions of remaining service times into the distribution of the desired customer waiting time. The analysis reveals the advantage from exploiting additional information.