gebhart/patrepeval huggingface dataset:
Layout Optimization for Quantum Circuits with Linear Nearest Neighbor Architectures (2016)

This paper is concerned with the physical design of quantum logic circuits. More precisely, it addresses the problem of minimizing the number of required qubit reorderings (achieved by inserting explicit SWAP gates) when mapping a quantum circuit into a linear nearest neighbor quantum archi-tecture. First, an interaction graph that captures the interaction distances among various qubits in the quantum circuit is constructed. The interaction graph is utilized to partition the quantum circuit into a set of subcircuits such that the number of required qubit reoderings within each subcircuit is provably no more than a given threshold. Next, a Minimum Linear Arrangement problem for each subcircuit is formulated and solved to achieve the minimum number of internal qubit reorderings and determine the subcircuit input and output qubit orderings. Finally, a bubble sort algorithm is repeatedly employed to minimize the number of qubit reorderings that are required between the consecutive subcircuits. Experiments done on various quantum Fourier transform circuits as well as various reversible logic circuits demonstrate the effectiveness of the proposed approach.
Evaluation of radiation dose to organs during kilovoltage cone‐beam computed tomography using Monte Carlo simulation (2014)

Image-guided techniques for radiation therapy have improved the precision of radiation delivery by sparing normal tissues. Cone-beam computed tomography (CBCT) has emerged as a key technique for patient positioning and target localization in radiotherapy. Here, we investigated the imaging radiation dose delivered to radiosensitive organs of a patient during CBCT scan. The 4D extended cardiac-torso (XCAT) phantom and Geant4 Application for Tomographic Emission (GATE) Monte Carlo (MC) simulation tool were used for the study. A computed tomography dose index (CTDI) standard polymethyl methacrylate (PMMA) phantom was used to validate the MC-based dosimetric evaluation. We implemented an MC model of a clinical on-board imager integrated with the Trilogy accelerator. The MC model's accuracy was validated by comparing its weighted CTDI (CTDIw) values with those of previous studies, which revealed good agreement. We calculated the absorbed doses of various human organs at different treatment sites such as the head-and-neck, chest, abdomen, and pelvis regions, in both standard CBCT scan mode (125 kVp, 80 mA, and 25 ms) and low-dose scan mode (125 kVp, 40 mA, and 10 ms). In the former mode, the average absorbed doses of the organs in the head and neck and chest regions ranged 4.09-8.28 cGy, whereas those of the organs in the abdomen and pelvis regions were 4.30-7.48 cGy. In the latter mode, the absorbed doses of the organs in the head and neck and chest regions ranged 1.61-1.89 cGy, whereas those of the organs in the abdomen and pelvis region ranged between 0.79-1.85 cGy. The reduction in the radiation dose in the low-dose mode compared to the standard mode was about 20%, which is in good agreement with previous reports. We opine that the findings of this study would significantly facilitate decisions regarding the administration of extra imaging doses to radiosensitive organs.
Evaluating Diversity in Classical Planning (2014)

Applications that require alternative plans challenge the single solution, single quality metric assumptions upon which many classical planners are designed and evaluated. To evaluate the distinctness of alternative plans (i.e., plan sets), researchers have created diversity metrics that often measure the set difference between the actions of plans. Many approaches for generating plan sets embed the same diversity metric in a weighted evaluation function to guide the search mechanism, thus confounding the search process with its evaluation. We discover that two diversity metrics fail to distinguish similar plans from each other or to identify plans with extraneous actions, so we introduce two new diversity metrics, \emph{uniqueness} and \emph{overlap}, to capture these cases. We then examine the tradeoffs of producing diverse plans while we control for plan length and metric interaction and confirm that metric interaction can significantly impact search performance. We show that planners searching for plan sets must consider a third metric, \emph{parsimony}, that prefers shorter plans while maximizing diversity.We evaluate three existing approaches for generating diverse plans and two new algorithms that are designed to explicitly manage diversity and interaction between the diversity and quality metrics. Our findings synthesize and extend recent results in plan diversity.
Supervised Learning by Training on Aggregate Outputs (2007)

Supervised learning is a classic data mining problem where one wishes to be be able to predict an output value associated with a particular input vector. We present a new twist on this classic problem where, instead of having the training set contain an individual output value for each input vector, the output values in the training set are only given in aggregate over a number of input vectors. This new problem arose from a particular need in learning on mass spectrometry data, but could easily apply to situations when data has been aggregated in order to maintain privacy. We provide a formal description of this new problem for both classification and regression. We then examine how k-nearest neighbor, neural networks, and support vector machines can be adapted for this problem.
Two-Dimensional Quantum Key Distribution (QKD) Protocol for Increased Key Rate Fiber-Based Quantum Communications (2017)

We experimentally prove a novel two-dimensional QKD scheme, relying on differential phasetime shifting (DPTS) of strongly attenuated weak coherent pulses. We demonstrate QKD transmission up to 170 km standard fiber, and even include a classical channel up to 90 km.
THE ROLE OF PERPENDICULAR RECORDING IN THE FUTURE OF HARD DISK STORAGE (1997)

20 years of enthusiastic development have been insufficient to make perpendicular recording successful in the HDD marketplace. An examination is made of the attributes that make it unattractive at current areal densities. Those attributes are reexamined in the light of the coming superparamagnetic limit for storage media. A challenge is issued to the supporters of perpendicular recording, that they perform a technology demonstration under a particular set of rules for success. This is considered essential if perpendicular recording is to be seriously considered as a candidate to replace longitudinal recording within the next ten years.
Automatic acquisition of hyponyms from large text corpora (1992)

We describe a method for the automatic acquisition of the hyponymy lexical relation from unrestricted text. Two goals motivate the approach: (i) avoidance of the need for pre-encoded knowledge and (ii) applicability across a wide range of text. We identify a set of lexico-syntactic patterns that are easily recognizable, that occur frequently and across text genre boundaries, and that indisputably indicate the lexical relation of interest. We describe a method for discovering these patterns and suggest that other lexical relations will also be acquirable in this way. A subset of the acquisition algorithm is implemented and the results are used to augment and critique the structure of a large hand-built thesaurus. Extensions and applications to areas such as information retrieval are suggested.
Molecular regulation of hematopoietic cytokines: Implications and indications for clinical use in pediatric oncology (1992)

Proliferation and differentiation of hematopoietic progenitor cells are regulated by a network of stimulatory and inhibitory cytokines. An understanding of the molecular mechanisms of growth control may provide a physiologic basis for the innovative therapy of bone marrow disorders. Among various accessory cells, bone marrow T lymphocytes are capable of stimulating, as well as inhibiting, hematopoietic progenitor cells. We have now elucidated molecular mechanisms regulating the differential expression of T cell genes encoding for the stimulatory and inhibitory hematopoietic programs. Stimulation of hematopoiesis requires granulocyte-macrophage colony stimulating factor (GM-CSF), whereas inhibition requires interferon-gamma (IF gamma). Both cytokines can be induced by interleukin-2 (IL2). The T cell IL2 receptor consists of a 75 kD chain (p75) mainly expressed on a subset of resting T cells and a 55 kD chain (p55) which is strongly expressed upon T cell activation. P55 and p75 associate on activated T cells to form a dimeric receptor molecule exhibiting high affinity for IL2. The p75 monomer has an intermediate affinity for IL2. Expression of p55 in the context of the high affinity IL2 receptor constitutes a requirement for T cell IFg release. In contrast, p75 alone is capable of mediating the production of GM-CSF. Thus, T cells may be capable of selective production of cytokines with specific effects in hematopoietic growth control. Utilizing a human peripheral blood leukocyte genomic library, we identified various clones containing the entire GM-CSF gene, including coding and regulatory regions. Cloning of the GM-CSF gene allowed clinical studies utilizing recombinant DNA-derived GM-CSF. Chemotherapy-induced neutropenia contributes to both complications of cytotoxic therapy as well as increased relapse incidence of underlying disease. In a prospective randomized study, we have demonstrated that GM-CSF abrogates neutropenia following aplasiogenic chemotherapy in children and adolescents with solid tumors, and that GM-CSF may reduce the duration of infectious episodes after cytotoxic therapy. Next, we escalated the cumulative doses of cytotoxic therapy in an ablative regimen followed by hematopoietic stem cell transplantation to treat patients with poor prognosis pediatric tumors. Morbidity of this highly toxic ablative regimen depends on the duration of myeloid aplasia. Median duration of aplasia following hyper-VAMP was 13 days with CM-CSF and 29 days without GM-CSF. In addition, we have employed p55 blocking monoclonal antibody for prevention of graft vs. host disease in bone marrow transplantation. The understanding of specific molecular mechanisms of hematopoietic immuno-regulation can thus be utilized to provide novel approaches to the treatment of bone marrow failure and cancer.
ASP Chemical Flooding Without the Need for Soft Water (2008)

Abstract Alkaline-surfactant-polymer (ASP) flooding using conventional alkali requires soft water. However, soft water is not always available, and softening hard brines may be very costly or infeasible in many cases depending on the location, the brine composition and other factors. For instance, conventional ASP uses sodium carbonate to reduce the adsorption of the surfactant and generate soap in-situ by reacting with acidic crude oils; however, calcium carbonate precipitates unless the brine is soft. A form of borax known as metaborate has been found to sequester divalent cations such as Ca++ and prevent precipitation. This approach has been combined with the screening and selection of surfactant formulations that will perform well with brines with high salinity and hardness. We demonstrate this approach in this paper by combining high performance, low cost surfactants with co-surfactants that increase salinity and hardness tolerance with metaborate. Chemical formulations containing surfactants and alkali in hard brine were screened for performance and tolerance using microemulsion phase behavior experiments and crude at reservoir temperature. A formulation was found that with an optimum salinity of 120,000 ppm TDS (with 6600 ppm divalent cations) that performed well in core floods with high oil recovery and almost zero final chemical flood residual oil saturation. Additionally, chemical formulations containing sodium metaborate and hard brine gave nearly 100% oil recovery, with no indication of precipitate formation. Metaborate chemistry was incorporated into the mechanistic UTCHEM simulator and the simulator was then used to model the core floods. Overall, novel ASP with metaborate performed comparable to conventional ASP using sodium carbonate in soft water, demonstrating advancements in ASP adaptation to hard, saline reservoirs without the need for soft brine, which increases the number of oil reservoirs that are candidates for enhanced oil recovery using ASP flooding.
LEAFY COTYLEDON 2 activation is sufficient to trigger the accumulation of oil and seed specific mRNAs in Arabidopsis leaves (2005)

LEAFY COTYLEDON 2 (LEC2) is a key regulator of seed maturation in Arabidopsis. To unravel some of its complex pleiotropic functions, analyses were performed with transgenic plants expressing an inducible LEC2:GR protein. The chimeric protein is functional and can complement lec2 mutation. Interestingly, the induction of LEC2 leads to the accumulation of storage oil in leaves. In addition, short-term induction and use of translation inhibitors allowed to demonstrate that LEC2 can directly trigger the accumulation of seed specific mRNAs. Consistent with these results, the expression of three other major seed regulators namely, LEC1, FUS3, and ABI3 were also induced by LEC2 activation.
Decoupled Direct Memory Access: Isolating CPU and IO Traffic by Leveraging a Dual-Data-Port DRAM (2015)

Memory channel contention is a critical performance bottleneck in modern systems that have highly parallelized processing units operating on large data sets. The memory channel is contended not only by requests from different user applications (CPU access) but also by system requests for peripheral data (IO access), usually controlled by Direct Memory Access (DMA) engines. Our goal, in this work, is to improve system performance byeliminating memory channel contention between CPU accesses and IO accesses. To this end, we propose a hardware-software cooperative data transfer mechanism, Decoupled DMA (DDMA) that provides a specialized low-cost memory channel for IO accesses. In our DDMA design, main memoryhas two independent data channels, of which one is connected to the processor (CPU channel) and the other to the IO devices (IO channel), enabling CPU and IO accesses to be served on different channels. Systemsoftware or the compiler identifies which requests should be handled on the IO channel and communicates this to the DDMA engine, which then initiates the transfers on the IO channel. By doing so, our proposal increasesthe effective memory channel bandwidth, thereby either accelerating data transfers between system components, or providing opportunities to employ IO performance enhancement techniques (e.g., aggressive IO prefetching)without interfering with CPU accessesWe demonstrate the effectiveness of our DDMA framework in two scenarios: (i) CPU-GPU communication and (ii) in-memory communication (bulk datacopy/initialization within the main memory). By effectively decoupling accesses for CPU-GPU communication and in-memory communication from CPU accesses, our DDMA-based design achieves significant performanceimprovement across a wide variety of system configurations (e.g., 20% average performance improvement on a typical 2-channel 2-rank memory system).
Fibroblasts and macrophages cooperate to create a pro-tumorigenic and immune resistant environment via activation of TGF-β/IL-6 pathway in neuroblastoma (2022)

Tumor-associated macrophages (TAM) and cancer-associated fibroblasts (CAF) and their precursor mesenchymal stromal cells (MSC) are often detected together in tumors, but how they cooperate is not well understood. Here, we show that TAM and CAF are the most abundant nonmalignant cells and are present together in untreated human neuroblastoma (NB) tumors that are also poorly infiltrated with T and natural killer (NK) cells. We then show that MSC and CAF-MSC harvested from NB tumors protected human monocytes (MN) from spontaneous apoptosis in an interleukin (IL)-6 dependent mechanism. The interactions of MN and MSC with NB cells resulted in a significant induction or increase in the expression of several pro-tumorigenic cytokines/chemokines (TGF-β1, MCP-1, IL-6, IL-8, and IL-4) but not of anti-tumorigenic cytokines (TNF-α, IL-12) by MN or MSC, while also inducing cytokine expression in quiescent NB cells. We then identified a TGF-β1/IL-6 pathway where TGF-β1 stimulated the expression of IL-6 in NB cells and MSC, promoting TAM survival. Evidence for the contribution of TAM and MSC to the activation of this pathway was then provided in xenotransplanted NB tumors and patients with primary tumors by demonstrating a direct correlation between the presence of CAF and p-SMAD2 and p-STAT3. The data highlight a new mechanism of interaction between TAM and CAF supporting their pro-tumorigenic function in cancer.
Nonsense and temperature-sensitive mutations in PEX13 are the cause of complementation group H of peroxisome biogenesis disorders (1999)

Peroxisome biogenesis disorders, including Zellweger syndrome (ZS), neonatal adrenoleukodystrophy (NALD) and infantile Refsum disease, are lethal hereditary diseases caused by abnormalities in peroxisomal assembly. To date, 12 genotypes have been identified. We now have evidence that the complete human cDNA encoding Pex13p, an SH3 protein of a docking factor for the peroxisome targeting signal 1 receptor (Pex5p), rescues peroxisomal matrix protein import and its assembly in fibroblasts from PBD patients of complementation group H. In addition, we detected mutations on the human PEX13 cDNA in two patients of group H. A severe phenotype of a ZS patient (H-02) was homozygous for a nonsense mutation, W234ter, which results in the loss of not only the SH3 domain but also the putative transmembrane domain of Pex13p. A more mildly affected NALD patient (H-01), whose fibroblasts showed the temperature-sensitive (TS) phenotype, was homozygous for a missense mutation in the SH3 domain of Pex13p, I326T. This mutant PEX13 cDNA expression in a PEX13-defective CHO mutant showed I326T to be a TS mutation and thus suggested that Pex13p with the I326T mutation in the SH3 domain is stable at 30 degrees C but is somewhat unstable at 37 degrees C.
Interferometric synthetic aperture microscopy implementation on a floating point multi-core digital signal processer (2013)

The transition of optical coherence tomography (OCT) technology from the lab environment towards the more challenging clinical and point-of-care settings is continuing at a rapid pace. On one hand this translation opens new opportunities and avenues for growth, while on the other hand it also presents a new set of challenges and constraints under which OCT systems have to operate. OCT systems in the clinical environment are not only required to be user friendly and easy to operate, but should also be portable, have a smaller form factor coupled with low cost and reduced power consumption. Digital signal processors (DSP) are in a unique position to satisfy the computational requirements for OCT at a much lower cost and power consumption compared to the existing platforms such as CPU and graphics processing units (GPUs). In this work, we describe the implementation of optical coherence tomography (OCT) and interferometric synthetic aperture microscopy (ISAM) processing on a floating point multi-core DSP (C6678, Texas Instruments). ISAM is a computationally intensive data processing technique that is based on the re-sampling of the Fourier space of the data to yield spatially invariant transverse resolution in OCT. Preliminary results indicate that 2DISAM processing at 70,000 A-lines/sec and OCT at 180,000 A-lines/sec can be achieved with the current implementation using available DSP hardware.
An Enhanced Structure-from-Motion Paradigm Based on the Absolute Dual Quadric and Images of Circular Points (2013)

This work aims at introducing a new unified Structure from Motion (SfM) paradigm in which images of circular point-pairs can be combined with images of natural points. An imaged circular point-pair encodes the 2D Euclidean structure of a world plane and can easily be derived from the image of a planar shape, especially those including circles. A classical SfM method generally runs two steps: first a projective factorization of all matched image points (into projective cameras and points) and second a camera self calibration that updates the obtained world from projective to Euclidean. This work shows how to introduce images of circular points in these two SfM steps while its key contribution is to provide the theoretical foundations for combining "classical" linear self-calibration constraints with additional ones derived from such images. We show that the two proposed SfM steps clearly contribute to better results than the classical approach. We validate our contributions on synthetic and real images.
Hydrogen Evolution Catalyzed by Aluminum‐Bridged Cobalt Diglyoximate Complexes (Eur. J. Inorg. Chem. 22‐23/2013) (2013)

The cover picture shows the core of the crystal structure of an aluminium-bridged cobalt diglyoximate catalyst for hydrogen evolution. The redox chemistry of such species is dependent on the number of aluminum centers and the nature of the ancillary ligand coordinated to aluminum. Characterization of several cobalt diglyoximato complexes connected by one or two aluminum bridges and their electrocatalytic behavior for proton reduction are discussed in the article by T. Agapie et al. on p. 3840 ff. For more on the story behind the cover research, see the Cover Profile. The front cover picture shows the core of the crystal structure of an aluminium-bridged cobalt diglyoximate catalyst for hydrogen evolution. The redox chemistry of such species is dependent on the number of aluminum centers and the nature of the ancillary ligand coordinated to aluminum. Characterization of several cobalt diglyoximato complexes connected by one or two aluminum bridges and their electrocatalytic behavior for proton reduction are discussed in the article by T. Agapie et al. on p. 3840 ff. For more on the story behind the cover research, see the Cover Profile.
Evaluating data distribution and drift vulnerabilities of machine learning algorithms in secure and adversarial environments (2014)

Machine learning is continuing to gain popularity due to its ability to solve problems that are difficult to model using conventional computer programming logic. Much of the current and past work has focused on algorithm development, data processing, and optimization. Lately, a subset of research has emerged which explores issues related to security. This research is gaining traction as systems employing these methods are being applied to both secure and adversarial environments. One of machine learning’s biggest benefits, its data-driven versus logic-driven approach, is also a weakness if the data on which the models rely are corrupted. Adversaries could maliciously influence systems which address drift and data distribution changes using re-training and online learning. Our work is focused on exploring the resilience of various machine learning algorithms to these data-driven attacks. In this paper, we present our initial findings using Monte Carlo simulations, and statistical analysis, to explore the maximal achievable shift to a classification model, as well as the required amount of control over the data.
A multicenter study evaluating three methods for counting residual WBCs in WBC‐reduced blood components: Nageotte hemocytometry, flow cytometry, and microfluorometry (2000)

Automated methods for counting residual donor WBCs in WBC-reduced cellular components offer advantages of improved precision and greater accuracy than are seen with the Nageotte hemocytometer method. Automated methods are less labor-intensive but more costly than microscopic methods. Preparation and shipping methods will need further refinement for samples to be counted more than 24 hours after sample collection.