gebhart/patrepeval huggingface dataset:
Measuring and modeling on-chip interconnect power on real hardware (2016)

On-chip data movement is a major source of power consumption in modern processors, and future technology nodes will exacerbate this problem. Properly understanding the power that applications expend moving data is vital for inventing mitigation strategies. Previous studies combined data movement energy, which is required to move information across the chip, with data access energy, which is used to read or write onchip memories. This combination can hide the severity of the problem, as memories and interconnects will scale differently to future technology nodes. Thus, increasing the fidelity of our energy measurements is of paramount concern. We propose to use physical data movement distance as a mechanism for separating movement energy from access energy. We then use this mechanism to design microbenchmarks to ascertain data movement energy on a real modern processor. Using these microbenchmarks, we study the following parameters that affect interconnect power: (i) distance, (ii) interconnect bandwidth, (iii) toggle rate, and (iv) voltage and frequency. We conduct our study on an AMD GPU built in 28nm technology and validate our results against industrial estimates for energy/bit/millimeter. We then construct an empirical model based on our characterization and use it to evaluate the interconnect power of 22 real-world applications. We show that up to 14% of the dynamic power in some applications can be consumed by the interconnect and present a range of mitigation strategies.
Group velocity dispersion measurements of microstructured fibers (2001)

Summary form only given. There has been great recent interest in microstructured fibers that consist of a regular arrangement of holes stretched along silica or air core. These fibers can guide light either by opening a photonic bandgap or, in the case of silica core, by total internal reflection. Microstructure fibers have unique dispersion properties that can be engineered by their structural parameters. It is important to have reliable theoretical model for successful design of fibers with desired properties. We measured GVD in three types of microstructured fibers and compared the data with the results from theoretical simulation made with MIT Photonic-Band package.
Volume rendering algorithms for three-dimensional ultrasound imaging: Image quality and real-time performance analysis (2009)

One of the key additions to clinical ultrasound (US) systems during the last decade has been the incorporation of three-dimensional (3D) imaging as a native mode. These systems provide interactive volume rendering and display of 3D data. However, interactive volume rendering is challenging due to the large amount of data I/O and computation required. Many rendering techniques have been developed ranging from fast algorithms with lower image quality to sophisticated algorithms with better image quality, e.g., shear-warp, shear-image-order, pre-integration and direct ray casting. In this paper, we discuss pros and cons of each of these rendering algorithms in terms of algorithm complexity and image quality. We also discuss a new rendering algorithm that we have proposed: pre-integrated shear-image-order (PISIO). PISIO algorithm overcomes the image-quality limitations of other fast algorithms and provides a fine balance between computation and image quality. To demonstrate the interactive performance of these algorithms, we implemented them on a programmable multicore processor, i.e., IBM Cell processor. We present the results in this paper.
BALB/c Mice Show Impaired Hepatic Tolerogenic Response Following AAV Gene Transfer to the Liver (2010)

Following adeno-associated virus (AAV) gene transfer to the liver, both C57BL/6 and BALB/c mice show long-term expression of nonself transgene antigens along with the absence of a transgene-specific immune response. However, in this study, we report that despite the equal ability to induce T-cell tolerance to vector-encoded antigens, the underlying mechanisms are entirely different in these two strains. We have previously shown that in C57BL/6 mice, cytotoxic T lymphocyte (CTL) responses to systemic AAV-delivered antigens are suppressed by combined actions of hepatic regulatory T cells (Tregs), Kupffer cells, and hepatic suppressive cytokines. In stark contrast, our present findings reveal that such tolerogenic response is not induced in the liver of BALB/c mice systemically administered with AAV. As a result, these mice fail to suppress a transgene-specific CTL response induced by a strong immunogenic challenge and express dramatically reduced levels of AAV-encoded antigen. Interestingly, there was active B-cell tolerance to the transgene antigen, which was mediated by splenic Tregs. We conclude that lack of tolerance induction in the liver renders BALB/c mice susceptible to CTL-mediated clearance of transduced hepatocytes.
Per-organ assessment of subject-induced susceptibility distortion for MR-only male pelvis treatment planning (2018)

Our work suggests that subject-induced susceptibility distortions caused by bladder/rectal conditions are generally small and subject-dependent. Local changes may be non-negligible within the CTV, thus proper management of filling status is warranted. Future work evaluating the impact of multiple models to accommodate for extreme status changes may be advantageous.
Bubble Forming Films for Spatial Selective Cell Killing (2021)

Abstract Photodynamic and photothermal cell killing at the surface of tissues finds applications in medicine. However, a lack of control over heat dissipation following a treatment with light might damage surrounding tissues. A new strategy to kill cells at the surface of tissues is reported. Polymeric films are designed in which iron oxide nanoparticles are embedded as photosensitizers. Irradiation of the films with pulsed laser light generates water vapor bubbles at the surface of the films. It is found that “bubble‐films” can kill cells in close proximity to the films due to mechanical forces which arise when the bubbles collapse. Local irradiation of bubble‐films allows for spatial selective single cell killing. As nanosurgery becomes attractive in ophthalmology to remove superficial tumors, bubble‐films are applied on the cornea and it is found that irradiation of the bubble‐films allows spatial and selective killing of corneal cells. As i) the photosensitizer is embedded in the films, which reduces its uptake by cells and spreading into tissues and ii) the bubble‐films can be removed from the tissue after laser treatment, while iii) a low laser fluence is sufficient to generate vapor bubbles, it is foreseen that bubble‐films might become promising for safe resection of superficial tumors.
L-Leucyl-L-Leucine Methyl Ester (LLME) Treated Non-Myeloablative Allogeneic Hematopoietic Stem Cell Transplantation (HSCT) for Patients With Hematological Malignancies (2011)

GVHD remains an obstacle for allogeneic HSCT. While T cell depletion of donor grafts results in much lower incidences of GVHD, rejection and poor immune recovery are often associated with this approach. To address these issues, we developed a transplant approach using LLME to test the hypothesis that the selected depletion of T cells containing cytotoxic effector granules would result in less significant GVHD while at the same time preserving GVT effects and infectious immunity. LLME preferentially kills cytotoxic effector granule bearing lymphocytes including most NK and CD8 T cells with relative sparing of CD4 T cells. Fourteen patients, with a median age of 57 years with high risk disease were transplanted from related or unrelated donors after a conditioning regimen of flu/cyclo/ara-C. Prior to the infusion of the donor inoculum, we performed CD34 selection using the Isolex® system to separate the graft into CD34+ and CD34- fractions. The CD34- fraction was then treated with LLME to selectively deplete the cytotoxic effector granule containing subsets, thus avoiding stem cell exposure to LLME. Patients received the CD34 selected stem cell product (median CD34 dose 4.13 x 106/kg). This HSC product contained 5 x 104 untreated CD3 cells/kg in the initial 6 patients treated, but due to significant GVHD, the final 8 patients received 2.5 x 104 untreated CD3 cells/kg. One day later, the LLME treated CD34- fraction (median CD3 dose 8.74 x106 /kg) was infused. One patient died shortly after the stem cell infusion from infectious complications. All 13 evaluable patients engrafted WBC by day 14. Two patients experienced late rejection. One of these patients is still alive 3 years later with evidence of recurrent disease and the other patient eventually died of relapsed disease. Of the remaining 11 patients, 3 patients developed grade III-IV GVHD and 1 patient developed cGVHD. All 4 of these patients died of GVHD related causes. Three patients died of complications from relapsed disease and 1 additional patient died of infectious complications. Four patients are alive at a minimum of 3 years post transplant. Two of these patients have relapsed disease, 1 patient is disease free with 100% donor chimerism and one patient is disease free with a persistence of 5% host cells. This study shows that LLME can be used to treat lymphocytes without affecting initial engraftment, but relapse and GVHD remain significant barriers in this high risk population.
Clinical implementation of model-based dose planning for indoor daylight photodynamic therapy of skin (Conference Presentation) (2020)

In recent years much work has been done to show treatment efficacy using daylight as the activation mechanism of PpIX-based PDT for non-melanoma skin cancers and pre-cancerous actinic keratosis. Many previous studies assume sufficient fluence is delivered during a 2-3 hour period, but fail to consider shifts in the UV spectral composition throughout the day and transient weather conditions. Using a model-based approach we have developed a dose planning application to provide clinicians with information regarding minimum necessary treatment times. Clinical photobleaching data comparing indoor daylight and conventional red-light PDT have been collected to test the viability of this model.
A Distributed Control System Framework for Automotive Powertrain Control with OSEK Standard and CAN Network (1999)

&lt;div class="htmlview paragraph"&gt;This paper presents a distributed control system framework for next-generation automotive control systems, in which various control units are connected with CAN bus. The framework is a software platform that performs communication between control units and invocation of application programs. The framework includes necessary functions for data transmission to meet end-to-end timing constraints in distributed control systems. Application programmers don't have to write any communication procedure but focus on developing application programs with appropriate API (Application Program Interface). The framework is based on driving force management and also OSEK, which is a standard real-time operating system (OSEK-OS) and a communication protocol (CAN) for automotive control. We are now applying our prototype framework to an adaptive cruise control system in our experimental vehicle.&lt;/div&gt;
Effect of Ta2O5 Matrix Additions on the Microstructure and Mechanical Properties of SiC Fiber-Reinforced Lithia-Alumina-Silica Composites (2008)

Additions of 0 to 9 mol% Ta2O5 to a lithia-alumina-silica glass-ceramic matrix Nicalon SiC reinforced composite increased the elastic modulus and ultimate strength of the composite. The additive fostered spherulitic growth of β-spodumene solid solution crystals which concentrated Ta2O5, at the boundaries of the spherulites and adjacent to the fiber-matrix carbon-rich interphases. These regions reacted with the interphases as well as soluble carbon monoxide gas to convert them to TaC. The improvement in mechanical properties is attributed to TaC particulate reinforcement, and suggests a simple glass-ceramic route to the fabrication of particulate-reinforced ceramic matrix composites.
Total synthesis, isolation, surfactant properties, and biological evaluation of ananatosides and related macrodilactone-containing rhamnolipids (2021)

Rhamnolipids are a specific class of microbial surfactants, which hold great biotechnological and therapeutic potential. However, their exploitation at the industrial level is hampered because they are mainly produced by the opportunistic pathogen <i>Pseudomonas aeruginosa</i>. The non-human pathogenic bacterium <i>Pantoea ananatis</i> is an alternative producer of rhamnolipid-like metabolites containing glucose instead of rhamnose residues. Herein, we present the isolation, structural characterization, and total synthesis of ananatoside A, a 15-membered macrodilactone-containing glucolipid, and ananatoside B, its open-chain congener, from organic extracts of <i>P. ananatis</i>. Ananatoside A was synthesized through three alternative pathways involving either an intramolecular glycosylation, a chemical macrolactonization or a direct enzymatic transformation from ananatoside B. A series of diasteroisomerically pure (1→2), (1→3), and (1→4)-macrolactonized rhamnolipids were also synthesized through intramolecular glycosylation and their anomeric configurations as well as ring conformations were solved using molecular modeling in tandem with NMR studies. We show that ananatoside B is a more potent surfactant than its macrolide counterpart. We present evidence that macrolactonization of rhamnolipids enhances their cytotoxic and hemolytic potential, pointing towards a mechanism involving the formation of pores into the lipidic cell membrane. Lastly, we demonstrate that ananatoside A and ananatoside B as well as synthetic macrolactonized rhamnolipids can be perceived by the plant immune system, and that this sensing is more pronounced for a macrolide featuring a rhamnose moiety in its native <sup>1</sup> <i>C</i> <sub>4</sub> conformation. Altogether our results suggest that macrolactonization of glycolipids can dramatically interfere with their surfactant properties and biological activity.
Heuristic evaluations for accessibility decisions: a systematic literature review (2023)

There are more and more people who are using technology on a daily basis to communicate and access information, including the elderly and people with disabilities. Assistive technologies, also called technical aids, are accessibility and inclusion resources that provide a greater degree of autonomy and assistance for people who have some degree of difficulty in using resources in their contact with real and virtual environments. The aim of this study is to investigate the perceptions about the heuristic assessment of accessibility in software by undertaking a systematic review of the literature that covers the last 5 years. This started off with a total of 8548 published papers that are indexed in the Scopus and Web of Science databases. Twelve relevant research questions were drawn up that were answered in accordance with the results found in the final set of articles. Two groups of keywords were created to assist in the search for papers and a filtering process was applied to the results of the searches. The research shows, by means of figures and tables, evidence about the growth of scientific papers in the area. The lead authors and journals that publish on evaluating the accessibility of software are listed, as are answers to the questions about which evaluative models, heuristics, metrics, limitations, assistive technologies and target audiences are most cited in published papers. This study also analyzes the co-citation of the references and couples bibliographic sources. The research showed evidence that there is no general consensus on the use of a single model to assess accessibility, but that the W3C WCAG guidelines are the sources most used to reference heuristics and metrics in studies of this type. It was also noticed that most studies do not focus on assistive technologies, but are widely used to support decisions on websites.
Temperature dependence of x-ray absorption spectra in the ferromagnetic Heusler alloysMn2VAlandCo2FeAl (2010)

We investigate the temperature dependence of the spin-resolved unoccupied density of states (DOS) in ferromagnetic ${\text{Co}}_{2}\text{FeAl}$ and ferrimagnetic ${\text{Mn}}_{2}\text{VAl}$ epitaxial films on MgO(100) using x-ray magnetic circular dichroism. We observe an unexpected strong temperature dependence of the DOS beyond the change expected from the Fermi distribution function. An increase in spectral weight is observed for majority states below the Fermi energy in the case of ${\text{Mn}}_{2}\text{VAl}$ and for minority states above the Fermi energy in the case of ${\text{Co}}_{2}\text{FeAl}$. Reduced atomic order near the interface suppresses the unexpected temperature dependence of the DOS for ${\text{Mn}}_{2}\text{VAl}$.
Detection of a human chromosomal translocation t(8;9) in a baby with multiple malformations using two‐color fluorescence in situ hybridization (1994)

A human chromosomal translocation t(8;9) was detected using two‐color fluorescence in situ hybridization with probes capable of staining the entire lengths of each of these chromosomes. The chromosome 8 probe was labeled with biotin and detected with Texas red, while the chromosome 9 probe was labeled with AAF and detected with FITC . In normal metaphase spreads, two metaphases from the proband, two red, one green and one part red and part green derivative chromosome were seen. The bicolor chromosome corresponded to translocation of a chromosome 8 segment to the distal part of the q region of one chromosome 9, as originally indicated by banding analysis. In interphase nuclei of the proband, four domains with bright fluorescence were recognized in many nuclei. Two were red, one was green, and the fourth had portions of both colors, indicating the presence of the translocation.
<title>Optical Clock Distribution To Silicon Chips</title> (1986)

Timing constraints for state-of-the-art very large scale integrated circuits (VLSI) in silicon are rapidly approaching communication limits available with layered two-dimensional metal and polysilicon wiring approaches. For such communication-limited systems, reliable clock distribution is a key concern. The range of finite differences in signal delays over clock wires of various lengths for large chips creates a timing skew that is significant when compared to the switching time of transistors in the circuit. The high bandwidth and three-dimensionality of imaging optical systems suggest that optical clock distribution systems have the potential to overcome the timing barriers presented by planar wiring. Clock signals can be holographically mapped to detector sites within small functional cells on a chip surface. Within each functional cell, the clock is distributed via surface wires with negligible delays, reducing skew effects to the variation in reaction times of the photodetectors on the chip. Experiments simulating the response of optical clock detection circuits in standard 4 micron CMOS technology have been performed.
Coupled pre‐mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli (2011)

Transcriptional responses to extracellular stimuli involve tuning the rates of transcript production and degradation. Here, we show that the time-dependent profiles of these rates can be inferred from simultaneous measurements of precursor mRNA (pre-mRNA) and mature mRNA profiles. Transcriptome-wide measurements demonstrate that genes with similar mRNA profiles often exhibit marked differences in the amplitude and onset of their production rate. The latter is characterized by a large dynamic range, with a group of genes exhibiting an unexpectedly strong transient production overshoot, thereby accelerating their induction and, when combined with time-dependent degradation, shaping transient responses with precise timing and amplitude.
A flexible micromachined optical sensor for simultaneous measurement of pressure and shear force distribution on foot (2003)

Lower limb complications associated with diabetes include the development of plantar ulcers that can lead to infection and subsequent amputation. While it is known from force plate analyses that there are medial/lateral and anterior/posterior shear components of the ground reaction force, there is little known about the actual distribution of this force during daily activities, nor about the role that shear plays in causing plantar ulceration. Furthermore, one critical reason why these data have not been obtained previously is the lack of a validated, widely used, commercially available shear sensor, in part because of the various technical issues associated with shear measurement. Here we have developed novel means of tranducing plantar shear and pressure stress via a new microfabricated optical system. The pressure/shear sensor consists of an array of optical waveguides lying in perpendicular rows and columns separated by elastomeric pads. A map of pressure and shear stress is constructed based on observed macro bending through the intensity attenuation from the physical deformation of two adjacent perpendicular optical waveguides. The uniqueness of the sensor is in its batch fabrication process, which involves injection molding and embossing techniques with Polydimethylsiloxane (PDMS) as the optical medium. Here we present the preliminary results of the prototype. The sensor has been shown to have low noise and responds linearly to applied loads. The smallest detectable force on each sensor element based on the current setup is ~0.1 N. The smallest area we have resolved in our mesh sensor is currently 950x950&mu;m<sup>2</sup>
On the Use of Composite Charges to Determine Insensitive Explosive Material Properties at the Laboratory Scale (2010)

Abstract Laboratory‐scale air‐blast experiments an gram‐range composite explosive charges are presented. The composite charges consist of a spherical booster charge surrounded by a concentric, spherical “candidate material” shell charge. By way of composite charge explosive characterization, the candidate explosive material is able to be characterized through the “removal” of the known booster effects. Using peak shock wave pressures, a method is developed to remove the booster effects from the composite charge’s signature to yield the sole effects of the candidate explosive material, permitting its characterization. Air‐blast explosive tests are conducted using digital high‐speed shadowgraph visualization to measure the resulting shock wave radial position as a function of time. Booster and composite charge data are converted to Mach number versus shock wave radius profiles and subsequently to peak shock wave pressure versus shock wave radius profiles for characterization of the shell material. Explosives tested include: PETN, RDX, HMX, and Alliant Bullseye® SP.
In Situ HRSTEM Observation of the Synthesis of Nanostructured LiFePO (2010)

Abstract not Available.