gebhart/patrepeval huggingface dataset:
GCM-SIV: Full Nonce Misuse-Resistant Authenticated Encryption at Under One Cycle per Byte. (2015)

Authenticated encryption schemes guarantee both privacy and integrity, and have become the default level of encryption in modern protocols. One of the most popular authenticated encryption schemes today is AES-GCM due to its impressive speed. The current CAESAR competition is considering new modes for authenticated encryption that will improve on existing methods. One property of importance that is being considered more today – due to multiple real-life cases of faulty sources of randomness – is that repeating nonces and IVs can have disastrous effects on security. A (full) nonce misuse-resistant authenticated encryption scheme has the property that if the same nonce is used to encrypt the same message twice, then the same ciphertext is obtained and so the fact that the same message was encrypted is detected. Otherwise, full security is obtained – even if the same nonce is used for different messages. In this paper, we present a new fully nonce misuse-resistant authenticated encryption scheme that is based on carefully combining the GCM building blocks into the SIV paradigm of Rogaway and Shrimpton. We provide a full proof of security of our scheme, and an optimized implementation using the AES-NI and PCLMULQDQ instruction sets. We compare our performance to the highly optimized OpenSSL 1.0.2 implementation of GCM and show that our nonce misuse-resistant scheme is only 14% slower on Haswell architecture and 19% slower on Broadwell architecture. On Broadwell, GCM-SIV encryption takes only 0.92 cycles per byte, and GCM-SIV decryption is exactly the same as GCM decryption taking only 0.77 cycles per byte. In addition, we compare to other optimized authenticated-encryption implementations carried out by Bogdanov et al., and conclude that our mode is very competitive. Beyond being very fast, our new mode of operation uses the same building blocks as GCM and so existing hardware and software can be utilized to easily deploy GCM-SIV. We conclude that GCM-SIV is a viable alternative to GCM, providing full nonce misuse-resistance at little cost.
MP16-14 CLINICAL IMPLICATION OF METASTASECTOMY IN METACHRONOUS METASTATIC RENAL CELL CARCINOMA IN THE ERA OF TARGETED THERAPY (2017)

INTRODUCTION AND OBJECTIVES: To assess the clinical implication of complete and incomplete metastasectomy in the patients having metachronous metastatic RCC (mRCC).
Models, abstractions, and architectures (2015)

Bridging disparate realms of physical and cyber system components requires models and methods that enable rapid evaluation of design alternatives in cyber-physical systems (CPS). The diverse intellectual traditions of physical and mathematical sciences makes this task exceptionally hard. This paper seeks to explore potential solutions by examining specific examples of CPS applications in automobiles and smart buildings. Both smart buildings and automobiles are complex systems with embedded knowledge across several domains. We present our experiences with development of CPS applications to illustrate the challenges that arise when expertise across domains is integrated into the system, and show that creation of models, abstractions, and architectures that address these challenges are key to next generation CPS applications.
Advances in immune-based therapies of renal cell carcinoma (2004)

Renal cell carcinoma (RCC) is the most prevalent malignancy within the kidney, and over 40% of patients with RCC will die from their disease. Approximately a third of patients present with metastatic disease and a third of patients undergoing nephrectomy for clinically localized RCC will develop metastases. Metastatic RCC poses a therapeutic challenge due to its resistance to conventional modes of therapy such as chemotherapy and radiation therapy. While it is clear that strides have been made against metastatic RCC, the overall objective response rates of interleukin-2- and interferon-alpha-based immunotherapy remain at approximately 20%. Despite advances in biologic- and immune-based therapies, long-term survival for patients with metastatic RCC remains modest. Furthermore, the toxicity profile of these cytokine regimens is significant. Advances in the understanding of the nature of tumor antigens and their optimal presentation, and in the regulatory mechanisms that govern the immune system, have provided multiple novel immunotherapy intervention strategies with increased specificity and potentially fewer side effects. Such strategies are currently being tested in clinical trials.
Automated and on-demand provisioning of virtual machines for database applications (2007)

Utility computing delivers compute and storage resources to applications as an 'on-demand utility', much like electricity, from a distributed collection of computing resources. There is great interest in running database applications on utility resources (e.g., Oracle's Grid initiative) due to reduced infrastructure and management costs, higher resource utilization, and the ability to handle sudden load surges. Virtual Machine (VM) technology offers powerful mechanisms to manage a utility resource infrastructure. However, provisioning VMs for applications to meet system performance goals, e.g., to meet service level agreements (SLAs), is an open problem. We are building two systems at Duke - Shirako and NIMO - that collectively address this problem.
Scaling vertical-cavity surface-emitting laser reliability for petascale systems (2006)

We evaluate vertical-cavity surface-emitting lasers (VCSELs) reliability for next-generation high-productivity computers wherein several hundreds of terabits of bandwidth are envisioned. VCSEL failure rates are modeled, and an empirical relationship for VCSEL scaling versus bit rate and aperture is presented to explore the reliability of VCSEL-based links. The effects of VSCEL sparing, water cooling, and redundancy at the system level are analyzed.
Hypoxia Inhibits Cavin-1 and Cavin-2 Expression and Down-Regulates Caveolae in Adipocytes (2014)

During obesity, a hypoxic state develops within the adipose tissue, resulting in insulin resistance. To understand the underlying mechanism, we analyzed the involvement of caveolae because they play a crucial role in the activation of insulin receptors. In the present study, we demonstrate that in 3T3-L1 adipocytes, hypoxia induces the disappearance of caveolae and inhibits the expression of Cavin-1 and Cavin-2, two proteins necessary for the formation of caveolae. In mice, hypoxia induced by the ligature of the spermatic artery results in the decrease of cavin-1 and cavin-2 expression in the epididymal adipose tissue. Down-regulation of the expression of cavins in response to hypoxia is dependent on hypoxia-inducible factor-1. Indeed, the inhibition of hypoxia-inducible factor-1 restores the expression of cavins and caveolae formation. Expression of cavins regulates insulin signaling because the silencing of cavin-1 and cavin-2 impairs insulin signaling pathway. In human, cavin-1 and cavin-2 are decreased in the sc adipose tissue of obese diabetic patients compared with lean subjects. Moreover, the expression of cavin-2 correlates negatively with the homeostatic model assessment index of insulin resistance and glycated hemoglobin level. In conclusion, we propose a new mechanism in which hypoxia inhibits cavin-1 and cavin-2 expression, resulting in the disappearance of caveolae. This leads to the inhibition of insulin signaling and the establishment of insulin resistance.
The imaging properties of gradient index optical fibres (2004)

The optical properties of gradient index optical fibre are described as the basis for an undergraduate experiment. Its imaging ability is demonstrated by results obtained by two of the authors during their final year undergraduate research projects.
Spatially Resolved Heterogeneous Electrocatalyst Degradation in Polymer Electrolyte Fuel Cells Subjected to Accelerated Aging Conditions (2022)

This work quantifies in-plane spatial heterogeneity (polymer electrolyte fuel cell cathode inlet vs outlet) in Pt particle size growth and distribution as a function of nitrogen (N 2 ) flow rate during a square-wave accelerated stress test (AST). The average Pt particle sizes for membrane electrode assemblies (MEAs) subjected to N 2 flow rates ranging from 4–16 sccm cm −2 are in the range 9–10.5 nm at the end-of-life (EOL) with similar electrochemically active surface area (ECSA) loss (∼65%). However, Pt particle size at EOL exhibits spatial heterogeneity: greater Pt particle size growth occurs near the flow field outlet than the inlet. The spatial heterogeneity for a fully-humidified N 2 flow is believed to originate from non-uniform humidification (outlet is more humidified than the inlet) across the cell for a co-flow arrangement. A first-order rate model for ECSA loss predicts linear increase of the rate constant with N 2 flow rate. The polarization losses of the aged MEAs over a wide range of operating conditions increase with N 2 flow rate. From the results of this work, for holistically assessing durability of Pt catalysts in fuel cells at high humidity conditions, it is recommended to include purge gas flow rate as a stressor during an AST.
ROI-based SNR scalable JPEG2000 image transcoding (2005)

This paper presents a quality scalable Region-of-Interest (ROI) transcoding technique for JPEG2000 image transmission over narrowband networks. The proposed scheme employs a structure analysis of the bitstream, packet extraction and reorganization, as well as a prioritization of ROIs and background with desired qualities. Since the proposed scheme does not involve any re-encoding operation, either for the wavelet coefficients or for the packet header, it has very low complexity. This paper studies the output picture quality of various transcoder configurations, discusses the bandwidth savings achieved by the scheme and also presents a complexity evaluation. Experimental results show that significant bandwidth reduction for image transmission is achieved and image quality for monitoring surveillance video is maintained with a very minimal amount of complexity in the transcoder.
Synthesis and Conformation of Multi‐Vicinal Fluoroalkane Diastereoisomers (2007)

Doing the twist: Differences in behavior between isomers of straight-chain alkanes bearing four vicinal fluorine atoms are revealed by conformational analyses (X-ray diffraction, NMR spectroscopy). For example, computational studies show that the all-syn vicinal fluoroalkane (see picture, C gray, F green, H white) adopts a helical conformation, while the anti-syn-anti isomer prefers to be linear. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z701988_s.pdf or from the author. 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.
Proceedings of the 2011 ACM SIGPLAN Workshop on Memory Systems Performance and Correctness (2011)

We are pleased to present the proceedings of the 2011 Workshop on Memory Systems Performance and Correctness (MSPC 2011). Continuing the previous five successful workshops, MSPC 2011 provides a forum for publishing and discussing the implications of the changes to both memory performance and correctness on various multi- and many-core systems---from supercomputers to servers to mobile devices---and the related software and hardware innovations. It fosters collaboration among researchers in a range of fields including compilers, memory management, programming languages, architecture, operating systems, performance evaluation, and workload characterization.

Among 30 submissions we received, 25 were complete, which consist of 21 position papers and 4 position abstracts. Each paper received three reviews from the program committee. Through online discussions from April 21 to 28, the program committee selected the 10 position papers and 2 position abstracts in these proceedings. The final program contains papers covering a broad range of topics related with the new challenges in memory systems performance and correctness. In addition to the papers, we are fortunate to include a keynote talk (joint with ISMM) from Onur Mutlu on memory systems in the many-core era.
DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells (2010)

The initiative significantly improves our understanding of DC biology and regulatory networks. Developing a systems biology approach for immune system holds the promise of translating knowledge on the immune system into more successful immunotherapy strategies.
Original Article Bilateral peripheral neural activity observed in vivo following unilateral nerve injury (2013)

Manganese-enhanced magnetic resonance imaging (MRI) is a surrogate method to measure calcium content in nervous system since manganese physiologically follows calcium. Manganese is detectable in MRI and therefore visualizes structures and cell populations that actively regulate calcium. Since calcium is actively recruited for the transmission of action potentials, our purpose is to validate manganese-enhanced MRI for detection of changes in lumbar nerves related to nociception. A neuropathic pain model was created by chronic constrictive injury of the left sciatic nerve of Sprague-Dawley rats. Behavioral measurements, using von Frey's tests, confirmed the presence of significant allodynia in the left hind limb of animals in the injured group. T1-weighted fast spin echo images were obtained of the lumbar cord and plexus of animals with injured left sciatic nerve and uninjured animals (control) scanned in a 7 Tesla magnet after intraperitoneal manganese chloride administration four weeks after sur- gery. Lumbar nerve roots and sciatic nerves in the injured group show increased normalized manganese-enhanced MRI signal, representing manganese enhancement, compared to the control group. In conclusion, animals with neuropathic pain in the left hind limb show increased manganese uptake in not only the injured sciatic nerve but also in the contralateral uninjured sciatic nerve on manganese-enhanced MRI in vivo. Although poorly understood, this finding corroborates ex vivo finding of bilateral nociceptive-related molecular changes in the nervous system of unilateral pain models.
Electrochromic nanocomposite films (2013)

The present invention provides an electrochromic nanocomposite film. In an exemplary embodiment, the electrochromic nanocomposite film, includes (1) a solid matrix of oxide based material and (2) transparent conducting oxide (TCO) nanostructures embedded in the matrix. In a further embodiment, the electrochromic nanocomposite film farther includes a substrate upon which the matrix is deposited. The present invention also provides a method of prepg. an electrochromic nanocomposite film.
Brain biopsy sampling by using prospective stereotaxis and a trajectory guide (2001)

In combination with prospective stereotaxis, the trajectory guide provided a safe and accurate way to perform brain biopsy procedures.
Highly Sensitive 3-Tesla Real Inversion Recovery MRI Detects Leptomeningeal Contrast Enhancement in Chronic Active Multiple Sclerosis (2023)

Real-IR a promising tool to detect, characterize, and understand the significance of LME in MS. The association between PRL and LME highlights a possible role of the leptomeninges in sustaining chronic inflammation.
Short and standard stem prostheses are both viable options for minimally invasive total hip arthroplasty. (2011)

Minimally invasive total hip arthroplasty (MIS THA) has recently increased in popularity. Concurrently, newly developed short femoral components are being used. These short components may make insertion during MIS approaches easier and preserve more bone than traditional femoral stems, while providing a more anatomic stress distribution in the proximal femur. Our purpose was to review the literature concerning MIS THA, to determine if using short stems over standard femoral components is beneficial and if surgical approach affects the ability to use any type of stem. Successful clinical survivorship and functional outcomes have been reported with both short and standard length femoral implant types for all MIS approaches. Therefore, the type of implant should be chosen based on other factors, such as diagnosis, bone type and condition, patient age, and surgeon preference.
Bicriteria Data Compression (2019)

Since the seminal work by Shannon, theoreticians have focused on designing compressors targeted at minimizing the output size without sacrificing much of the compression/decompression efficiency. On the other hand, software engineers have deployed several heuristics to implement compressors aimed at trading compressed space versus compression/decompression efficiency in order to match their application needs. In this paper we fill this gap by introducing the bicriteria data-compression problem that seeks to determine the shortest compressed file that can be decompressed in a given time bound. Then, inspired by modern data-storage applications, we instantiate the problem onto the family of Lempel--Ziv-based compressors (such as Snappy and LZ4) and solve it by combining in a novel and efficient way optimization techniques, string-matching data structures, and shortest path algorithms over properly (bi-)weighted graphs derived from the data-compression problem at hand. An extensive set of experiments complements our theoretical achievements by showing that the proposed algorithmic solution is very competitive with respect to state-of-the-art highly engineered compressors.
The cis -regulatory dynamics of embryonic development at single cell resolution (2017)

ABSTRACT Single cell measurements of gene expression are providing new insights into lineage commitment, yet the regulatory changes underlying individual cell trajectories remain elusive. Here, we profiled chromatin accessibility in over 20,000 single nuclei across multiple stages of Drosophila embryogenesis. Our data reveal heterogeneity in the regulatory landscape prior to gastrulation that reflects anatomical position, a feature that aligns with future cell fate. During mid embryogenesis, tissue granularity emerges such that cell types can be inferred by their chromatin accessibility, while maintaining a signature of their germ layer of origin. We identify over 30,000 distal elements with tissue-specific accessibility. Using transgenic embryos, we tested the germ layer specificity of a subset of predicted enhancers, achieving near-perfect accuracy. Overall, these data demonstrate the power of shotgun single cell profiling of embryos to resolve dynamic changes in open chromatin during development, and to uncover the cis -regulatory programs of germ layers and cell types.
<title>Optimal transform coefficient selection for images</title> (1996)

An algorithm for methodically deriving rate-distortion points for transform coefficient selection schemes for images is presented. The idea is to iteratively generate a set of convex hulls from which a composite operational rate- distortion curve is derived. Although this approach can be used to generate optimal interior rate-distortion points, the complexity is high. A fast suboptimal approach is then proposed which is based upon a modified version of threshold selection. In the modified threshold selection algorithm, each transform block operates on a point along a non-convex rate-distortion curve which is generated from rank ordering of coefficients in the block. Simulations of this fast algorithm using finely quantized DCT coefficients from an image with separate coding of amplitudes and runlengths show that very good rate-distortion performance can be obtained. These simulations also suggest that the modified threshold selection curve tends to lie within the first few convex hulls generated from the composite shell method. The modified threshold selection algorithm provides a fast way for achieving good rate-distortion performance in transform coding systems.
APEnet+ project status (2012)

We present an update of the status of the APEnet+ project, which is a custom 3D Torus interconnect system for GPU-accelerated computing clusters. The network host adapter hosts an FPGA-based programmable Network Processor, with one PCIe x8 Gen2 host link, on-board routing & switching logic, and up to six bidirectional off-board links each running up to 34 Gbps. A simple RDMA protocol and an experimental direct network-to-GPU interface bring a significant latency reduction for inter-node data transfers, even in those cases where one or more GPUs are involved. A justification for APEnet+ design choices on LQCD algorithms and some preliminary performance results for node-to-node synthetic communication tests and a will be shown, together with an overview of ongoing developments.
Size‐Tunable Photothermal Germanium Nanocrystals (2017)

Abstract Germanium nanocrystals (ncGe) have not received as much attention as silicon nanocrystals (ncSi). However, Ge has demonstrated superiority over Si nanomaterials in some applications. Examples include, high charge–discharge rate lithium‐ion batteries, [1] small band‐gap opto‐electronic devices, [2] and photo‐therapeutics. [3] When stabilized in an oxide matrix (ncGe/GeO x ), its high charge‐retention has enabled non‐volatile memories. [4] It has also found utility as a high‐capacity anode material for Li‐ion batteries with impressive stability. [5] Herein, we report an organic‐free synthesis of size‐controlled ncGe in a GeO x matrix as well as freestanding ncGe, via the thermal disproportionation of GeO prepared from thermally induced dehydration of Ge(OH) 2 . The photothermal effect of ncGe, quantified by Raman spectroscopy, is found to be size dependent and superior to ncSi. This advance suggests applications of ncGe in photothermal therapy, desalination, and catalysis.
Chromium Catalysts Supported by a Nonspectator NPN Ligand: Isolation of Single‐Component Chromium Polymerization Catalysts (2008)

Schaltbare katalytische Aktivität – von einer nichtselektiven Ethylenoligomerisierung zur Trimerisierung und sogar Polymerisation – zeigt der Chromkomplex 1, abhängig von der aktivierenden Alkylaluminiumverbindung. AlMe3 oder iBu2AlCl ergeben hoch aktive Einkomponenten-Polymerisationskatalysatoren (siehe Schema; R=Me, PE=Polyethylen), deren Aktivität durch zusätzliche Alkylaluminiumverbindung verändert oder inhibiert werden kann.
Undersmoothed Kernel Entropy Estimators (2008)

We develop a ldquoplug-inrdquo kernel estimator for the differential entropy that is consistent even if the kernel width tends to zero as quickly as 1/ <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> , where <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> is the number of independent and identically distributed (i.i.d.) samples. Thus, accurate density estimates are not required for accurate kernel entropy estimates; in fact, it is a good idea when estimating entropy to sacrifice some accuracy in the quality of the corresponding density estimate.
Temporal evolution of self-phase modulation dynamics in a semiconductor optical amplifier under multiwavelength pulse amplification (2005)

The temporal evolution of self-phase modulation dynamics in a semiconductor optical amplifier is studied for the amplification of multiwavelength pulses using pump-probe techniques. Two photon absorption and four wave mixing effects are observed as well.