gebhart/patrepeval huggingface dataset:
Optimizing FPGA-based convolutional neural networks accelerator for image super-resolution (2018)

Convolutional neural networks (CNN) are widely used in various computer vision applications. Recently, there have been many studies on FPGA-based CNN accelerators to achieve high performance and power efficiency. Most of them have been on CNN-based object detection algorithms, but researches on image super-resolution have been rarely conducted. Fast super-resolution CNN (FSRCNN), well known for CNN-based super-resolution algorithm, are a combination of multiple convolutional layers and a single deconvolutional layer. Since the deconvolutional layer generates high-resolution (HR) output feature maps from low-resolution (LR) input feature maps, its execution cycles are larger than those of the convolutional layer. In this paper, we propose a novel architecture of the FPGA-based CNN accelerator with the efficient parallelization. We develop a method of transforming a deconvolutional layer into a convolutional layer (TDC), a new methodology for the deconvolutional neural networks (DCNN). There is a massive parallelization source in the deconvolutional layer where multiple outputs within the same output feature map are created with the same inputs. When this new parallelization technique is applied to the deconvolutional layer, it generates the LR output feature maps the same as the convolutional layer. Thus, the performance of the accelerator increases without any additional hardware resources because the kernel size required to generate the LR output feature maps is smaller. In addition, if there is a DSP underutilization problem in the deconvolutional layer that some of the processors are in an idle state, the proposed method solves this problem by allowing more output feature maps to be processed in parallel. Experimental results show that the proposed TDC method achieves up to 81 times higher throughput than the state-of-the-art DCNN accelerator with the same hardware resources. We also improve the speed by 7.8 times by having all layers in the hourglass-type FSRCNN to be processed in inter-layer parallelism without additional DSP usage.
Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI) (2005)

A multiplex single-nucleotide polymorphism (SNP) typing platform using 'bioluminometric assay coupled with terminator [2',3'-dideoxynucleoside triphosphates (ddNTPs)] incorporation' (named 'BATI' for short) was developed. All of the reactions are carried out in a single reaction chamber containing target DNAs, DNA polymerase, reagents necessary for converting PPi into ATP and reagents for luciferase reaction. Each of the four ddNTPs is dispensed into the reaction chamber in turn. PPi is released by a nucleotide incorporation reaction and is used to produce ATP when the ddNTP dispensed is complementary to the base in a template. The ATP is used in a luciferase reaction to release visible light. Only 1 nt is incorporated into a template at a time because ddNTPs do not have a 3' hydroxyl group. This feature greatly simplifies a sequencing spectrum. The luminescence is proportional to the amount of template incorporated. Only one peak appears in the spectrum of a homozygote sample, and two peaks at the same intensity appear for a heterozygote sample. In comparison with pyrosequencing using dNTP, the spectrum obtained by BATI is very simple, and it is very easy to determine SNPs accurately from it. As only one base is extended at a time and the extension signals are quantitative, the observed spectrum pattern is uniquely determined even for a sample containing multiplex SNPs. We have successfully used BATI to type various samples containing plural target sequence areas. The measurements can be carried out with an inexpensive and small luminometer using a photodiode array as the detector. It takes only a few minutes to determine multiplex SNPs. These results indicate that this novel multiplexed approach can significantly decrease the cost of SNP typing and increase the typing throughput with an inexpensive and small luminometer.
A Simple Design for A Force-Plate to Measure Ground Reaction Forces (1981)

ABSTRACT This paper describes an inexpensive force-plate that can measure ground reaction forces in two planes and can be built to a size or sensitivity suitable for nearly any biological application.
Resistance of small leucine-rich repeat proteoglycans to proteolytic degradation during interleukin-1-stimulated cartilage catabolism (1999)

A bovine nasal-cartilage culture system has been utilized to analyse the catabolic events occurring in response to interleukin-1β over a 14-day period. An early event following the start of interleukin-1 treatment was the release of glycosaminoglycan into the culture medium. This release was accompanied by the appearance in the tissue, and shortly thereafter also in the culture media, of a globular domain (G1)-containing aggrecan degradation product generated by the action of aggrecanase. Link protein was also released from the cartilage with a similar timeframe to that of the G1 fragment, although there was no evidence of its proteolytic degradation. By comparison with aggrecan, the small leucine-rich repeat proteoglycans decorin, biglycan and lumican showed a resistance to both proteolytic cleavage and release throughout the culture period. In contrast, fibromodulin exhibited a marked decrease in size after day 4, presumably due to proteolytic modification, but the major degradation product was retained throughout the culture period. Also in contrast with the early changes in the components of the proteoglycan aggregate, type II collagen did not display signs of extensive degradation until much later in the culture period. Collagen degradation products compatible with collagenase action first appeared in the medium by day 10 and increased thereafter. These data demonstrate that the leucine-rich repeat proteoglycans are resistant to proteolytic action during interleukin-1-stimulated cartilage catabolism, compared with aggrecan. This resistance and continued interaction with the surface of the collagen fibrils may help to stabilize the collagen fibrillar network and protect it from extensive proteolytic attack during the early phases of cartilage degeneration.
Algorithm for the determination of intrinsic optical constants of metal films: application to aluminum (1995)

Optical and electron-energy-loss data for evaporated-aluminum films have been critically analyzed and used in an iterative, self-consistent algorithm that represents a combination of the Kramers-Kronig analysis and the semiquantum-model application. The novel values of the intrinsic optical functions of aluminum have been determined in a wide spectral range from 200 µm (6.2 meV) to 0.12 nm (10 keV). These functions are in accordance with recent calculations by Lee and Chang [Phys. Rev. B 49, 2362 (1994)], with dc conductivity measurements, and are in good agreement with both peak positions and line widths obtained from electron-energy-loss experiments. The results are examined for internal consistency by inertial and f-sum rules.
Atomic Resolution of the Silicon (111)-(7×7) Surface by Atomic Force Microscopy (1995)

Achieving high resolution under ultrahigh-vacuum conditions with the force microscope can be difficult for reactive surfaces, where the interaction forces between the tip and the samples can be relatively large. A force detection scheme that makes use of a modified cantilever beam and senses the force gradient through frequency modulation is described. The reconstructed silicon (111)-(7x7) surface was imaged in a noncontact mode by force microscopy with atomic resolution (6 angstroms lateral, 0.1 angstrom vertical).
Personal Thermal Management by Metallic Nanowire-Coated Textile (2014)

Heating consumes large amount of energy and is a primary source of greenhouse gas emission. Although energy-efficient buildings are developing quickly based on improving insulation and design, a large portion of energy continues to be wasted on heating empty space and nonhuman objects. Here, we demonstrate a system of personal thermal management using metallic nanowire-embedded cloth that can reduce this waste. The metallic nanowires form a conductive network that not only is highly thermal insulating because it reflects human body infrared radiation but also allows Joule heating to complement the passive insulation. The breathability and durability of the original cloth is not sacrificed because of the nanowires' porous structure. This nanowire cloth can efficiently warm human bodies and save hundreds of watts per person as compared to traditional indoor heaters.
The influence of basic residues on the substrate specificity of protein kinase C. (1987)

The substrate specificity of protein kinase C has been examined using a series of synthetic peptide analogs of glycogen synthase, ribosomal protein S6, and the epidermal growth factor receptor. The glycogen synthase analog peptide Pro1-Leu-Ser-Arg-Thr-Leu-Ser-Val-Ala-Ala10 was phosphorylated at Ser7 with a Km of 40.3 microM. Peptide phosphorylation was strongly dependent on Arg4. When lysine was substituted for Arg4 the Km was increased approximately 20-fold. Addition of basic residues on either the NH2-terminal or COOH-terminal side of the phosphorylation site of the glycogen synthase peptide improved the kinetics of peptide phosphorylation. The analog Pro-Leu-Ser-Arg-Thr-Leu-Ser-Val-Ala-Ala-Lys-Lys was phosphorylated with a Km of 4.1 microM. Substitution of Ser7 with threonine increased the apparent Km to 151 microM. The truncated peptide Pro1-Leu-Ser-Arg-Thr-Leu-Ser-Val8 was phosphorylated with similar kinetic constants to the parent peptide, however, deletion of Val8 increased the apparent Km to 761 microM. The ribosomal peptide S6-(229-239) was phosphorylated with a Km of approximately 0.5 microM predominantly on Ser236 and is one of the most potent synthetic peptide substrates reported for a protein kinase. The apparent Km for S6 peptide phosphorylation was increased by either deletion of the NH2-terminal 3 residues Ala229-Arg-231 or by substitution of Arg238 on the COOH-terminal side of the phosphorylation site with alanine. This analog peptide, [Ala238]S6-(229-239) was phosphorylated with an approximate 6-fold reduction in Vmax and a switch in the preferred site of phosphorylation from Ser236 to Ser235. These results support the concept that basic residues on both sides of the phosphorylation site can have an important influence on the kinetics of phosphorylation and site specificity of protein kinase C.
A Phase II Study of Gemcitabine and Irinotecan in Patients With Locally Advanced or Metastatic Bladder Cancer (2012)

The results of the current study suggested that the combination of Irinogem was an effective treatment for patients with metastatic bladder cancer, with manageable toxicities. The study was closed early due to delays in accrual and loss of funding. Hence, the study lacks adequate power to make definite conclusions. Further studies in multi-institutional setting in patients with normal and compromised renal function are warranted.
The fractal geometry of proliferative diabetic retinopathy: implications for the diagnosis and the process of retinal vasculogenesis (1993)

10 retinal vessel patterns with neovascularisation at or near the optic disk (NVD) from eyes of patients with diabetic retinopathy were compared with vascular patterns from 14 normal eyes. The vascular patterns were taken from low angle fundus photographs. After digitizing, the fractal dimensions were calculated by means of the density-density correlation function method. The fractal dimension was found to be significantly higher for vessel patterns with NVD [D = 1.845 +/- 0.056 (m +/- sd)] as compared with the normal control group (D = 1.708 +/- 0.073) (p < 0.001). The fractal dimension of 1.8 appears to be a cutoff value. Higher values may indicate proliferative changes. Under these conditions the sensitivity of the method for the detection of NVD > or = Grade 3 in the Early Treatment Diabetic Retinopathy Study (ETDRS) grading system is 90%. The presence of such NVD in an eye is a "high risk characteristic" for severe visual loss, which requires panretinal laser treatment. Fractal analysis is therefore a possible new strategy for computer assisted "automated" detection and quantification of proliferative diabetic retinopathy. The fractal dimension of the new vessels suggests possible mechanisms involved in retinal vasculogenesis.
A production costing methodology for evaluation of direct load control (1991)

Direct load control (DLC) is a form of load management in which portions of the system load are under the direct operational control of the utility. Thus, the load can be modified, within limits, to match the available generating capacity, thereby minimizing events of uncontrolled load loss. It is shown that operating cost reductions produced by exogeneous models of DLC are different from those produced by dynamic models of DLC. The dynamics of DLC and an equal incremental cost scheme are described and then coupled with a Monte Carlo simulation model of the operation of thermal-based electric utilities. Various production cost measures produced by exogeneous and dynamic models of DLC are presented and discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Inflammation, But Not Telomere Length, Predicts Successful Ageing at Extreme Old Age: A Longitudinal Study of Semi-supercentenarians (2015)

To determine the most important drivers of successful ageing at extreme old age, we combined community-based prospective cohorts: Tokyo Oldest Old Survey on Total Health (TOOTH), Tokyo Centenarians Study (TCS) and Japanese Semi-Supercentenarians Study (JSS) comprising 1554 individuals including 684 centenarians and (semi-)supercentenarians, 167 pairs of centenarian offspring and spouses, and 536 community-living very old (85 to 99 years). We combined z scores from multiple biomarkers to describe haematopoiesis, inflammation, lipid and glucose metabolism, liver function, renal function, and cellular senescence domains. In Cox proportional hazard models, inflammation predicted all-cause mortality with hazard ratios (95% CI) 1.89 (1.21 to 2.95) and 1.36 (1.05 to 1.78) in the very old and (semi-)supercentenarians, respectively. In linear forward stepwise models, inflammation predicted capability (10.8% variance explained) and cognition (8(.)6% variance explained) in (semi-)supercentenarians better than chronologic age or gender. The inflammation score was also lower in centenarian offspring compared to age-matched controls with Δ (95% CI) = - 0.795 (- 1.436 to - 0.154). Centenarians and their offspring were able to maintain long telomeres, but telomere length was not a predictor of successful ageing in centenarians and semi-supercentenarians. We conclude that inflammation is an important malleable driver of ageing up to extreme old age in humans.
The Proliferative Potential of Myeloma Plasma Cells Manifest in the SCID-hu Host (1999)

The low proliferative activity of myeloma plasma cells prompted the notion that the clonotypic B cells that exist in the blood and bone marrow of all myeloma patients contain the proliferative myeloma cells (stem cell). We have exploited our severe combined immunodeficiency (SCID)-hu host system for primary myeloma to investigate whether myeloma plasma cells are capable of sustained proliferation. Purified CD38(++)CD45(-) plasma cells consistently grew and produced myeloma and its manifestations in SCID-hu hosts (8 of 9 experiments). In contrast, the plasma cell-depleted bone marrow cells from 6 patients did not grow or produce myeloma in SCID-hu hosts. Similarly, whereas plasma-cell containing blood cells from 4 patients grew and produced myeloma in hosts, neither the PC-depleted blood cells from 3 of the patients nor a blood specimen that did not contain plasma cells grew in SCID-hu hosts, regardless of their CD19-expressing cell contents. Also, in hosts injected with blood cells, although the myeloma cells were able to disseminate through the murine host system, they were only able to grow in the human bones within a human microenvironment and were not detectable in the murine blood or other organs. Interestingly, the circulating plasma cells appear to grow more avidly in the SCID-hu hosts than their bone marrow counterparts, suggesting that they represent a subpopulation of the plasma cells in the bone marrow. Although our studies clearly demonstrate the proliferative potential of myeloma plasma cells, they are suggestive, not conclusive, as to the existence of a preplasmacytic myeloma progenitor cell.
Dewetting Nucleation Centers at Soft Interfaces (2001)

We study the dewetting of a metastable liquid film, squeezed at a solid/rubber interface, induced by defects printed in the solid glass substrate. We have engraved both protruding (“Mesa”) and depression (“Vickers prints”) defects. For the Vickers prints,we find that a defect of size b dewets films of thickness e < e* = , where h0 is a microscopic “elastic length” (≈100 Å, defined by the ratio of the liquid spreading parameter S by the elastic modulus E of the soft material). The same behavior is observed for thin Mesa. However, for thick Mesa, the dewetting is limited to the defect area and does not propagate. These results agrees with a theoretical model of nucleation at soft interfaces.
The power of multimedia: combining point-to point and multi-access networks (1988)

In this paper we introduce a new network model called a muZtimedia network. It combines the point-to-point message passing network and the multiaccess channel. To benefit from the combination we design algorithms which consist of two stages: a local stage which utilizes the parallelism of the point-to-point network and a global stage which utilizes the broadcast capability of the multiaccess channel. As a reasonable approach, one wishes to balance the complexities of the two stages by obtaining an efficient partition of the network
The Calculation of Ground-Wave Field Intensity over a Finitely Conducting Spherical Earth (1941)

Equations and curves are presented which simplify the calculation of ground-wave field intensity over a finitely conducting spherical earth for transmitting and receiving antennas of arbitrary heights and polarization.
Structural Characterization of Site-Specific N-Glycosylation of Recombinant Human Factor VIII by Reversed-Phase High-Performance Liquid Chromatography−Electrospray Ionization Mass Spectrometry (1997)

The present study addresses the site occupancy and the site-specific carbohydrate microheterogeneity of N-linked oligosaccharides in recombinant human factor VIII, expressed in Chinese hamster ovary cells. The four factor VIIIa polypeptides, formed upon incubation with human thrombin, were isolated and separately subjected to proteolysis with trypsin. These tryptic digests were analyzed by reversed-phase high-performance liquid chromatography/electrospray ionization mass spectrometry. Selected ion monitoring of diagnostic carbohydrate ions was utilized to identify glycopeptide-containing chromatographic peaks. Oligomannose and complex carbohydrates were detected at the glycosylation sites of the 50 and the 73 kDa polypeptides, while all the oligosaccharides identified on the B-domain were complex-type structures. Only the 43 kDa polypeptide was found nonglycosylated. These studies established a biantennary core-fucosylated carbohydrate as the major substituent, consistent with the conclusions of the analyses on the entire N-linked carbohydrate pool (Kumar, H. P. M.; Hague, C.; Haley, T.; Starr, C. M.; Besman, M. J.; Lundblad, R.; Baker, D. Biotechnol. Appl. Biochem. 1996, 24, 207-216.). In addition, this mass spectrometric investigation revealed the presence of a complex nonfucosylated oligosaccharide not reported previously for this glycoprotein.
Cytokines in the pathogenesis of ulcerative colitis. (2011)

Ulcerative colitis is a chronic inflammatory condition of the large intestine whose etiology remains largely unknown. Its pathogenesis involves the breakdown of intestinal mucosal homeostasis due to a genetically determined miscommunication between commensal flora and the gut associated immune system. Cytokines are central components of the inflammatory pathways that take place during the active and chronic phases of ulcerative colitis. Recent research has identified several novel cytokine systems that are upregulated at the mucosa of patients with ulcerative colitis and started to unveil their functional importance for disease pathogenesis. The significance of interleukin-13 (IL-13), TNF-like cytokine 1A (TL1A), IL-33, and their receptors in ulcerative colitis is strongly supported by converging expression and functional data. These molecular systems may define subgroups of patients with uniform immunological profiles. Within these subpopulations such novel cytokine systems may serve as markers of biological activity of the disease. More importantly, they may offer unique therapeutic opportunities through the development of drugs that specifically target and neutralize well-defined inflammatory pathways.
Low-density parity-check codes based on finite geometries: a rediscovery and new results (2001)

This paper presents a geometric approach to the construction of low-density parity-check (LDPC) codes. Four classes of LDPC codes are constructed based on the lines and points of Euclidean and projective geometries over finite fields. Codes of these four classes have good minimum distances and their Tanner (1981) graphs have girth 6. Finite-geometry LDPC codes can be decoded in various ways, ranging from low to high decoding complexity and from reasonably good to very good performance. They perform very well with iterative decoding. Furthermore, they can be put in either cyclic or quasi-cyclic form. Consequently, their encoding can be achieved in linear time and implemented with simple feedback shift registers. This advantage is not shared by other LDPC codes in general and is important in practice. Finite-geometry LDPC codes can be extended and shortened in various ways to obtain other good LDPC codes. Several techniques of extension and shortening are presented. Long extended finite-geometry LDPC codes have been constructed and they achieve a performance only a few tenths of a decibel away from the Shannon theoretical limit with iterative decoding.
Generation of up-regulated allosteric variants of potato ADP-glucose pyrophosphorylase by reversion genetics (1998)

Mutagenesis of the large subunit (LS) of the potato ADP-glucose pyrophosphorylase generated an enzyme, P52L, that was insensitive to 3-phosphoglycerate (3-PGA). To identify additional residues involved in 3-PGA interaction, we subjected P52L LS DNA to a second round of mutagenesis and identified second-site revertants by their ability to restore glycogen accumulation as assessed by iodine (I2) staining. Enzymes from class I revertants with normal I2-staining had an 11- to 49-fold greater affinity for the activator 3-PGA compared with the P52L mutant and a decreased sensitivity to the inhibitor orthophosphate. Sequence analysis of these class I revertants identified a P66L mutation in R4, an E38K mutation in R20, and a G101N mutation in R10 and R32. These mutations appear to restore 3-PGA binding by counteracting the effect of the P52L mutation because introducing E38K or G101N into the wild-type LS led to enzyme variants with higher affinity for the activator 3-PGA and increased resistance to the inhibitor orthophosphate. The generation of these revertant enzymes provides additional structure-function information on the allosteric regulation of higher plant ADP-glucose pyrophosphorylases and validates a strategy for developing novel variants of the enzyme that may be useful in manipulating starch biosynthesis in higher plants.