gebhart/patrepeval huggingface dataset:
Accelerating Graph Analytics by Co-Optimizing Storage and Access on an FPGA-HMC Platform (2018)

Graph analytics, which explores the relationships among interconnected entities, is becoming increasingly important due to its broad applicability, from machine learning to social sciences. However, due to the irregular data access patterns in graph computations, one major challenge for graph processing systems is performance. The algorithms, softwares, and hardwares that have been tailored for mainstream parallel applications are generally not effective for massive, sparse graphs from the real-world problems, due to their complex and irregular structures. To address the performance issues in large-scale graph analytics, we leverage the exceptional random access performance of the emerging Hybrid Memory Cube (HMC) combined with the flexibility and efficiency of modern FPGAs. In particular, we develop a collaborative software/hardware technique to perform a level-synchronized Breadth First Search (BFS) on a FPGA-HMC platform. From the software perspective, we develop an architecture-aware graph clustering algorithm that exploits the FPGA-HMC platform»s capability to improve data locality and memory access efficiency. From the hardware perspective, we further improve the FPGA-HMC graph processor architecture by designing a memory request merging unit to take advantage of the increased data locality resulting from graph clustering. We evaluate the performance of our BFS implementation using the AC-510 development kit from Micron and achieve $2.8 \times$ average performance improvement compared to the latest FPGA-HMC based graph processing system over a set of benchmarks from a wide range of applications.
Requirement of PFKFB4 in anchorage independent growth and tumorigenesis (2007)

A88 Transformed cells need abundant glucose relative to normal cells in order to satisfy their increased anabolic and energetic needs. Fructose 2,6 bisphosphate (F2,6BP) is a potent allosteric activator of 6-phosphofructo-1-kinase (PFK-1), the rate-limiting step in glycolysis. In previous studies, we have found that F2,6BP is required for increased glucose flux into anabolic pathways and is necessary for the anchorage-independent growth of neoplastic cells. The steady state concentration of F2,6BP depends on a family of bifunctional 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatases encoded by four genes (PFKFB1-4). Although the expression of the PFKFB3 isozyme has been observed to be increased in cancer cells and to be required for ras transformation, a methodical examination of the expression of all four isozyme mRNAs has not been previously performed. We examined the relative expression of the PFKFB1-4 mRNA species in 40 human tumor tissue samples using multiplex RT-PCR and surprisingly observed that the testes isozyme (PFKFB4) mRNA levels were increased in 85% of the samples relative to matched adjacent normal tissues. To further explore the requirement of PFKFB4 in transformed cells, we used small interfering RNA (siRNA) species to knock down PFKFB4 in a mammalian cancer cell line (A549 lung adenocarcinoma) and found a 50% reduction in PFKFB4 protein expression (by Western blot), decreased F2,6BP levels (~45% less than in control cells) and, in addition, a diminished capacity for anchorage independent growth in soft agar (oligofectamine control 110 ± 7colonies, siR1 23± 3 and siR2 17± 4 colonies (n=3), 15 days of culture). When siRNA treated A549 cells were injected subcutaneously into athymic mice, the PFKFB4 siRNA treated tumors were significantly smaller than control siRNA tumors (tumor volumes: PFKFB4 siR2 154± 50 mm3vs. lamin 496±98 mm3, 21 days of growth). In conclusion, our data indicate that PFKFB4 is necessary for tumorigenicity as demonstrated by soft agar colony formation and tumor growth in vivo and support its further investigation as a possible new target for the development of anti-neoplastic therapies.
Integrated front-end for on line continuous calibration of Rogowski coil current transducer (2014)

The Rogowski coil is a traditional current-to-voltage transducer. To use it for high-accuracy measurement of low frequency AC current, it is necessary to have a very precise sensor geometry and very specific conditions, such as a stable temperature and a centered primary conductor in order to minimize errors. Conversely, it is also possible to compensate for these errors by using a sensor calibration. This paper presents a new continuous calibration system for Rogowski coil current transducer (RCCT). It features a reference conductor added close to the primary conductor and a calibration circuit which has been integrated in CMOS technology. First experimental results obtained with a homemade RCCT show that we drastically improve the immunity of the sensor to the primary conductor position with an error below ±2 % when the calibration is active against −8% to +4% without calibration. Limitations of the method are also discussed.
Human Neural Stem Cells Overexpressing Choline Acetyltransferase Restore Cognitive Function of Kainic Acid-Induced Learning and Memory Deficit Animals (2011)

Alzheimer disease (AD) is a progressive neurodegenerative disease, which is characterized by loss of memory and cognitive function. In AD patients dysfunction of the cholinergic system is the main cause of cognitive disorders, and decreased activity of choline acetyltransferase (ChAT), an enzyme responsible for acetylcholine (ACh) synthesis, is observed. In the present study we investigated if brain transplantation of human neural stem cells (NSCs) genetically modified to encode ChAT gene improves cognitive function of kainic acid (KA)-induced learning deficit rats. Intrahippocampal injection of KA to hippocampal CA3 region caused severe neuronal loss, resulting in profound learning and memory deficit. F3.ChAT human NSCs transplanted intracerebroventricularly improved fully the learning and memory function of KA-induced learning deficit animals, in parallel with the elevation of ACh levels in cerebrospinal fluid. F3.ChAT human NSCs migrated to the KA-induced injury site (CA3) and differentiated into neurons and astrocytes. The present study demonstrates that human NSCs expressing ChAT have lesion-tropic property and improve cognitive function of learning deficit model rats with hippocampal injury by increasing ACh level.
Designing flocked energy-absorbing material layers into sport and military helmet pads (2021)

A systematic study is reported on applying flocked energy-absorbing materials (FEAM) to designing sport and military helmet pad structures. An executed parametric study shows that the impact force absorbing (IFA) properties of FEAM elements are optimized when using (a) higher denier flock fiber (60 to 100 denier) and (b) longer flock fibers (3 to 4 mm length) at higher flock densities. Continuing work focuses on the importance of IFA/areal density ratios in helmet pad functional design. It is found that foam materials like vinyl-nitrile and ethylene vinyl acetate (EVA) inherently exhibit higher IFA/areal density (IFA/AD) ratios than FEAM material structures. With this finding, a new strategy for developing sport and military helmet pads was devised involving the combination of foam and FEAM layer elements. Here, the meritorious properties of foam materials (light weight and excellent IFA properties) and the excellent IFA and breathability (wearer comfort, sweat and heat management) properties of FEAM could be favorably encompassed. A plan was conceived and implemented whereby combination foam/FEAM test pads having high amounts of the high IFA/AD ratio VN-600 or EVA foam layer component were impact tested. By gradually introducing the more comfortable, breathable, body-heat managing FEAM layers into the helmet pad structure, some “trade-off” helmet pad configurations were designed and evaluated. Experiments showed that helmet pad designs having not more than 40% to 50% FEAM content should produce adequate IFA/AD ratio “trade-off” property helmet pad configurations.
Time Course of Recovery of Juvenile Skeletal Muscle After Botulinum Toxin A Injection (2004)

Ma J, Elsaidi GA, Smith TL, Walker FO, Tan KH, Martin E, Koman LA, Paterson Smith B: Time course of recovery of juvenile skeletal muscle after botulinum toxin A injection: An animal model study. Am J Phys Med Rehabil 2004;83:774–780. Objective: To study the effects of neuromuscular blockade using botulinum toxin A on juvenile muscles at a dosage of 6 units/kg body weight in a rat model. Design: A total of 34 male Sprague-Dawley rats (1-mo old) were used. A small incision was made along the posterior aspect of the left hind leg with the exposure of the gastrocnemius. Botulinum toxin A was injected at a dosage of 6 units/kg body weight in the medial and lateral heads of the muscle. An equivalent volume of saline were injected into the right gastrocnemius (control). Motor evoked action potentials, muscle force generation, and muscle mass and neuromuscular junction morphometry were analyzed at different time intervals up to 1 yr after toxin injection. Results: During the 1–2 wks after botulinum toxin A injection, muscle mass, electrophysiologic variables, and muscle force generation were significantly reduced but returned to nearly normal at 6 mos postinjection. In the study group, neuromuscular junction gutter depth became significantly shallower 2 mos after injection, then normalized at 1 yr. There was a nonsignificant trend toward larger neuromuscular junctions from the gastrocnemius injected with botulinum toxin A. Conclusion: Our findings provide scientific evidence to support the clinical situation in which the interinjection interval of 3–6 mos of botulinum toxin A at a similar dosage is used.
Identification and Evaluation of New Primer Sets for the Detection of Lentivirus Proviral DNA (1992)

We have developed sets of degenerate oligonucleotides designed to detect pol gene sequences from any member of the lentivirus subfamily when used as primers in amplification techniques such as the polymerase chain reaction (PCR). This pan-lentivirus-specific primer set (PLSPS) consists of primers, LV1, LV2, and LV3, based on conserved regions common to lentiviruses only. Our protocol is based on primary amplification with LV1 and LV2 followed by secondary amplification with a nested primer set based on the YM/VDD motif found in all reverse transcriptases (or "DDMY," in the opposite direction), and LV3, a block of lentivirus homology nested just downstream of LV1. PLSPS-PCR analysis of DNA from cells infected with HIV-1, HIV-2, SIVmac239, BIV, visna, EIAV, CAEV, OPPV, or FIV resulted in the amplification of appropriately sized products. Sequence analysis of the LV1/2 products, cloned into pBluescript (pBS), indicated that at least 20% (most often, > 80%) contained the predicted lentivirus pol sequence. Greater than 95% of the LV3/DDMY products contained the expected lentiviral sequences. Using the PLSPS, lentivirus pol sequences could typically be detected at levels of one copy in 2 x 10(6) cells after secondary amplification. No specific lentiviral PCR products were detected in DNA from uninfected human or mouse monocytes, feline or bovine leukocytes, mouse, rat or human fibroblast cell lines, chicken embryo fibroblasts, Tahr lung cells, or cell lines infected with the following retroviruses which are not lentiviruses: Rous sarcoma virus, Moloney leukemia virus or Kirsten sarcoma virus, mouse mammary tumor virus, human T-cell lymphotropic virus I, and feline leukemia virus.(ABSTRACT TRUNCATED AT 250 WORDS)
AgInS<sub>2</sub>quantum dots for the detection of trinitrotoluene (2016)

AgInS<sub>2</sub> (AIS) quantum dots (QDs) were synthesized via a thermal decomposition reaction with dodecylamine as the ligand to help stabilize the QDs. This reaction procedure is relatively easy to implement, scalable to large batches (up to hundreds of milligrams of QDs are produced), and a convenient method for the synthesis of chalcogenide QDs. Metal powders of AgNO<sub>3</sub> and In(NO<sub>3</sub>)<sub>3</sub>, were used as the metal precursors while diethyldithiocarbamate was used as the sulfur source. The AIS QDs were characterized via transmission electron microscopy, atomic force microscopy, and energy dispersive x-ray spectroscopy. As an application for these less toxic nanomaterials, we demonstrate the selective detection of Trinitrotoluene (TNT) at concentrations as low as 6 micromolar (μM) and without the functionalization of a ligand that is specifically designed to interact with TNT molecules. We also demonstrate a simple approach to patterning the AIS QDs onto filter paper, for the detection of TNT molecules by eye. Collectively, the ease of the synthesis of the less toxic AIS QDs, and the ability to detect TNT molecules by eye suggest an attractive route to highly sensitive and portable substrates for environmental monitoring, chemical warfare agent detection, and other applications.
Nanovalved Adsorbents for CH<sub>4</sub> Storage (2016)

A novel concept of utilizing nanoporous coatings as effective nanovalves on microporous adsorbents was developed for high capacity natural gas storage at low storage pressure. The work reported here for the first time presents the concept of nanovalved adsorbents capable of sealing high pressure CH4 inside the adsorbents and storing it at low pressure. Traditional natural gas storage tanks are thick and heavy, which makes them expensive to manufacture and highly energy-consuming to carry around. Our design uses unique adsorbent pellets with nanoscale pores surrounded by a coating that functions as a valve to help manage the pressure of the gas and facilitate more efficient storage and transportation. We expect this new concept will result in a lighter, more affordable product with increased storage capacity. The nanovalved adsorbent concept demonstrated here can be potentially extended for the storage of other important gas molecules targeted for diverse relevant functional applications.
Strained-Silicon on Silicon and Strained-Silicon on Silicon-Germanium on Silicon by Relaxed Buffer Bonding (2006)

We report the creation of two novel complementary metal oxide semiconductor (CMOS)-compatible platforms: strained-silicon on silicon (SSOS) and strained-silicon on silicon-germanium on silicon (SGOS). SSOS substrate has an epitaxially defined, strained-silicon layer directly on silicon wafer without an intermediate SiGe or oxide layer. SSOS is a homochemical heterojunction, i.e., a heterojunction defined by strain state only and not by an accompanying compositional change. SGOS has an epitaxially defined SiGe layer between the strained-silicon channel and the Si substrate, which may prove necessary to prevent excessive off-state leakage in metal oxide semiconductor (MOS) devices due to overlap of source-drain contacts and the interfacial misfit array
Wavefront Sensorless Adaptive Optics Imaging in the Living Eye (2013)

Wavefront sensorless adaptive optics imaging was performed in human eyes using a stochastic parallel gradient descent algorithm in an adaptive optics scanning laser ophthalmoscope. Image quality was similar for wavefront sensorless and wavefront sensor-based control.
One-Step Isolation of Lactoferrin Using Immobilized Monoclonal Antibodies (1987)

Immunoaffinity columns made with monoclonal antibodies to either human or bovine lactoferrins were prepared to isolate human lactoferrin or bovine lactoferrin from milks by a single chromatographic step. Recoveries of human lactoferrin and bovine lactoferrin were 98 and 97%, respectively. The human lactoferrin recovered from defatted human colostrum was 98% pure with 93% iron-binding capacity. Amount of recovered bovine lactoferrin, as well as purity and iron-binding capacity, varied widely depending on the source of bovine milks and pretreatments (particularly pasteurization temperature). The best source to isolate bovine lactoferrin was raw skim milk yielding a protein 97% pure and with a 99% iron-binding capacity. Thus, immunoaffinity chromatography provides an effective one-pass isolation of highly pure human or bovine lactoferrin with reasonable recovery and iron-binding capacity.
TU-EE-A3-05: Current Challenges in DICOM GSDF Calibration For Medical Displays (2006)

Purpose: Over the last few years liquid crystal displays have replaced the traditional light box in medical imaging. When display systems are used for primary diagnosis they need to comply with the DICOM GSDF standard. Previous work already demonstrated that limited grayscale depth and viewing angle dependency of LCD results into lower calibration accuracy. As original contribution this paper investigates the impact of spatial noise and non-uniformities on calibration accuracy. Additionally we will also quantify the relative importance of each of those three shortcomings of medical LCDs. Method and Materials: To study the effect of non-uniformity and spatial noise on DICOM GSDF compliance, we compare the observed transfer curve after calibration with the target DICOM GSDF curve and this for multiple locations across the display. The display used is a 5 Mega Pixel monochrome medical LCD display. We also analyze the typical GSDF compliance metrics dL/L and JNDs/step and compare these plots for the other effects of viewing angle dependency and grayscale depth. Results: Current calibration practice is to characterize the native transfer curve of the display at only one position (often the centre). However there is significant variation in native transfer curve across the display surface and therefore calibration will only be accurate at the position where the characterization took place. On other display positions the average target luminance distortion compared to GSDF ranges from a few JNDs to over 20 JNDs. A technique of spatial noise-reduction can solve this problem. We also observe that spatial-noise is much more important than viewing angle and grayscale depth for typical usage. Conclusion: This paper has demonstrated that non-uniformities and spatial noise can result into poor calibration accuracy. Also a possible solution to the problem has been described. Conflict of Interest: Research sponsored by Barco Medical Imaging Systems.
A closed-form integral model of spiral inductor using the Kramers-Kronig relations (2005)

In this letter, a closed-form integral model is presented for the rectangular micromachined spiral inductor. The Kramers-Kronig relations provide an elegant theory to describe the inductor behavior without having complicated geometric analysis. Simulation and measurement results validate that the model can provide satisfactory prediction to the inductance of on-chip freely-suspended spiral inductors. Meanwhile, unlike conventional Greenhouse-based formulations, the self-resonant frequency of inductor can be predicted using the integral model.
Development of a sensitive serodiagnostic assay for human Lyme disease based on immunodominant epitopes of an in vivo expressed microbial surface antigen (45.19) (2010)

Abstract Lyme disease (LD) is a common bacterial infection transmitted by the ticks belonging to Ixodes scapularis complex. The diagnosis of LD is complicated by several factors, including unnoticed exposure and variation in patient presentation. Serology is currently the primary laboratory means of diagnosis in suspected LD cases, and the development of new diagnostics is an important goal of LD research. Central to this effort is the identification and characterization of new immunodominant antigens to serve as serodiagnostic markers. Borrelia burgdorferi, the causative agent of LD, encodes BBK07, an outer membrane lipoprotein thought to be an important antigen expressed during infection. We show that BBK07 gene expression is selectively induced during mammalian infection when compared to B. burgdorferi grown in vitro or in ticks. We show that BBK07 is surface-exposed on the bacterium, and that an antibody response to BBK07 is detectable throughout the murine infection. We use recombinant BBK07 protein to dissect the early (IgM) and late (IgG) immune response over the course of infection. A synthetic overlapping peptide library of BBK07 was used to identify the most immunogenic epitopes of the antigen using a human LD serum panel. We used a combination of immunodominant peptides to develop a specific and sensitive assay for the diagnosis of LD. These data suggest possible development of a BBK07 peptide-based serodiagnostic kit for the detection of human LD.
Radiofrequency pulse design in parallel transmission under strict temperature constraints (2013)

Although further confidence in the thermal models is needed, this study shows that RF pulse design under strict temperature constraints is within reach, allowing better RF pulse performance and faster acquisitions at ultra-high fields at the cost of higher sequence complexity.
SSTP: A scalable and secure transport protocol for smart grid data collection (2011)

Emerging smart grid networks are expected to have massive amounts of data continuously generated from various measuring devices (intelligent sensors, advanced meters, electric vehicle charging stations) which are embedded in the power grid. Data generated from these measuring devices must be delivered securely and reliably to utility control centers for wide-area monitoring and control and to estimate the overall grid status in a timely and precise manner. The collected data is also used for incentivizing consumer participation for improving power stability. Transport protocol requirements for such periodic grid measurement data are characterized as lifetime-lived, secure, and reliable delivery of short flows (usually less than 1.5 KB) over utility-Wide Area Networks (WANs). However, our survey shows that there is no well-known transport protocol that can support the above characteristics in a scalable and light-weight manner. Motivated by this, we design a scalable and secure transport protocol, SSTP, exploiting the notion of a “State-token” which is issued with each server message and which is subsequently attached to corresponding client message delivered to the server. Compared with existing well-known transport and security schemes, SSTP enables scalable server deployments as servers do not keep state (for security and communication) per client and thus computation/memory overheads are significantly reduced.
Desarrollo biotecnológico de un nuevo bioinsecticida basado en el nucleopoliedrovirus simple de Helicoverpa armigera (HearSNPV) (2016)

El taladro del tomate, Helicoverpa armigera (Hubner) (Lepidoptera; Noctuidae), es una especie polifaga que causa perdidas economicas en una gran variedad de cultivos en todo el mundo (TAY y col., 2013). En Epana, los danos mas importantes los produce en el cultivo del tomate (TORRES-VILA y col.,2003). Para el control de esta especie se utilizan, en la mayoria de las situaciones, de forma sistematica y casi exclusiva insecticidas quimicos de sintesis. Sin embargo, el control quimico origina importantes problemas para el medio ambiente y para la salud publica. Por ello, desde la Union Europea se ha legislado para promover la utilizacion de alternativas no quimicas (Directiva 2009/128/CE) entre las que se incluyen los insecticidas de origen microbiano. Los bioinsecticidas que utilizan los baculovirus como ingrediente activo han demostrado ser un eficaz agente de control biologico para muchas especies de lepidopteros que causan plagas incluida Helicoverpa armigera (MOSCARDI y col.,2011)