gebhart/patrepeval huggingface dataset:
Smart Detector Cell: A Scalable All-Spin Circuit for Low Power Non-Boolean Pattern Recognition (2016)

We present a new circuit for non-Boolean recognition of binary images. Employing all-spin logic (ASL) devices, logic comparators and non-Boolean decision blocks for compact and efficient computation are designed. By manipulation of fan-in number in different stages of the circuit, the structure can be extended for larger training sets or larger images. Operating based on the main similarity idea, the system is capable of constructing a mean image and compare it with a separate input image within a short decision time. Taking advantage of the nonvolatility of ASL devices, the proposed circuit is capable of hybrid memory/logic operation. Compared with the existing CMOS pattern recognition circuits, this paper achieves a smaller footprint, lower power consumption, faster decision time, and a lower operational voltage.
Parathyroid Hormone (PTH 1–34) Regulation of Rat Osteocalcin Gene Transcription (1997)

Osteocalcin (OC) is a bone-specific extracellular matrix protein expressed by mature osteoblasts during late stages of differentiation. Previous studies have shown that forskolin, an activator of adenylate cyclase, stimulated OC production. Because PTH has been shown to activate several intracellular signal transduction pathways including cAMP, inositol phosphate and intracellular calcium mobilization, we investigated whether PTH action on cAMP accumulation leads to OC promoter activation. The rat OC promoter (1095 bp) was cloned into the promoterless luciferase gene reporter vector. The transcriptional activity of the rat OC promoter was evaluated after transfection of SaOS-2, an osteosarcoma cell line, with the OC promoter followed by treatment with PTH. Maximal OC promoter activity was observed within 4-8 h after the addition of 10(-8) M PTH, whereas very little induction was seen after 24 and 48 h of treatment. The induction of OC promoter activity by PTH was concentration dependent. PTH analogs (PTH 1-84, PTH 1-34, and PTH 1-31) that stimulate intracellular cAMP accumulation, induced OC promoter activity, whereas other PTH analogs (PTH 3-34, PTH 7-34, PTH 13-34, and PTH 53-84) that do not stimulate cAMP production had no effect on OC promoter activation. Furthermore, PTH activation of the OC promoter was significantly enhanced in the presence of 3-isobutyl-1-methylxanthine (IBMX), a phosphodiesterase inhibitor. Inactivation of cAMP-dependent protein kinase A activity by either a selective protein kinase A inhibitor, H-89 (N-[2-(p-bromocinnamylamino)ethyl]-5 isoquinolinesulfonamide), or antisense oligonucleotide directed against the regulatory subunit of cAMP-dependent protein kinase A, led to a corresponding loss of OC promoter activation by PTH. 5' deletion analysis of the OC promoter demonstrated that the promoter (1095 bp) exhibited the greatest response to PTH, whereas the -198 bp construct of the OC promoter, containing only one cAMP response element and OC box, was no longer responsive. The constructs with further deletions (-120, -92, and -74) retained PTH responsiveness, but to a lesser extent. In summary, our results indicate that PTH activation of the OC promoter is a rapid event and mediated by the cAMP-dependent protein kinase A pathway. Although the novel cAMP response region overlapping the OC box is required for activation, full activation may require several cis-acting cAMP response elements or other response elements.
A New Versatile Synthesis of Xanthines with Variable Substituents in the 1-, 3-, 7- and 8-Positions (1995)

A new convenient procedure for the synthesis of a wide range of xanthines has been developed starting from 3-substituted 6-aminouracils. Nitrosation and reduction yields the corresponding 5,6-diaminouracils, which are condensed with carboxylic acids. The resulting amides can be selectively alkylated at the uracil ring nitrogen N-1 (corresponding to xanthine N-3) under mild conditions. Ring closure and, if desired, alkylation at the 7-position, yields di-, tri-, or tetrasubstituted xanthines in high yields. Sensitive substituents, such as prop-2-ynyl, can be introduced in the 1-position. Variation of the 3-substituent is considerably facilitated in comparison with the standard procedure for the preparation of xanthines.
Generative Kernels for Tree-Structured Data (2018)

This paper presents a family of methods for the design of adaptive kernels for tree-structured data that exploits the summarization properties of hidden states of hidden Markov models for trees. We introduce a compact and discriminative feature space based on the concept of hidden states multisets and we discuss different approaches to estimate such hidden state encoding. We show how it can be used to build an efficient and general tree kernel based on Jaccard similarity. Furthermore, we derive an unsupervised convolutional generative kernel using a topology induced on the Markov states by a tree topographic mapping. This paper provides an extensive empirical assessment on a variety of structured data learning tasks, comparing the predictive accuracy and computational efficiency of state-of-the-art generative, adaptive, and syntactical tree kernels. The results show that the proposed generative approach has a good tradeoff between computational complexity and predictive performance, in particular when considering the soft matching introduced by the topographic mapping.
Unlocking bandwidth for GPUs in CC-NUMA systems (2015)

Historically, GPU-based HPC applications have had a substantial memory bandwidth advantage over CPU-based workloads due to using GDDR rather than DDR memory. However, past GPUs required a restricted programming model where application data was allocated up front and explicitly copied into GPU memory before launching a GPU kernel by the programmer. Recently, GPUs have eased this requirement and now can employ on-demand software page migration between CPU and GPU memory to obviate explicit copying. In the near future, CC-NUMA GPU-CPU systems will appear where software page migration is an optional choice and hardware cache-coherence can also support the GPU accessing CPU memory directly. In this work, we describe the trade-offs and considerations in relying on hardware cache-coherence mechanisms versus using software page migration to optimize the performance of memory-intensive GPU workloads. We show that page migration decisions based on page access frequency alone are a poor solution and that a broader solution using virtual address-based program locality to enable aggressive memory prefetching combined with bandwidth balancing is required to maximize performance. We present a software runtime system requiring minimal hardware support that, on average, outperforms CC-NUMA-based accesses by 1.95 ×, performs 6% better than the legacy CPU to GPU memcpy regime by intelligently using both CPU and GPU memory bandwidth, and comes within 28% of oracular page placement, all while maintaining the relaxed memory semantics of modern GPUs.
Impact of oestradiol and inhibin A concentrations on pregnancy rate in in-vitro oocyte maturation (2000)

The purpose of the present study was to analyse the results of maturation of oocytes obtained in unstimulated normal women after a leading follicle of 10 mm diameter and an endometrium of at least 5 mm thickness were observed at ultrasound. The serum concentrations of oestradiol and inhibin A were analysed from day 3 to the day of aspiration and retrospectively evaluated. A total of 75 normal regular cycling women referred for IVF/intracytoplasmic sperm injection (ICSI) because of male factor and/or tubal disease was included (n = 87 consecutive cycles). The oocytes were aspirated transvaginally and matured for 28-36 h. ICSI was performed on all metaphase II oocytes and they were cultured to day 2 or 3 after insemination, at which time suitable embryos (maximum two) were replaced into the women. Eleven singleton pregnancies with a live fetus were obtained after transfer in 63 cycles (pregnancy rate of 13% per aspiration and 17% per transfer). Nine healthy children have been born and the remaining two pregnancies miscarried in the eighth to ninth gestational week. The serum concentrations of oestradiol on day 3 and on the day of aspiration were available in 85 cycles, and in 57 of these an increase of 100% was detected on the day of aspiration. Significantly more pregnancies were observed in these cycles compared with cycles without an increase in the concentration of oestradiol (19 versus 0% per aspiration, 24 versus 0% per transfer, P < 0.02). Further improvement in pregnancy rate was obtained if aspiration was performed after increase in inhibin A concentration (24 versus 0% per aspiration and 33 versus 0% per transfer, P < 0.02) (n = 83 cycles, where inhibin concentrations were available, and n = 42 cycles, where an increase of 80% was detected on the day of aspiration compared with day 3). Timing of aspiration may improve the developmental potential of immature oocytes.
Affinity Propagation: Clustering Data by Passing Messages (2009)

Clustering data by identifying a subset of representative examples is important for detecting patterns in data and in processing sensory signals. Such "exemplars" can be found by randomly choosing an initial subset of data points as exemplars and then iteratively refining it, but this works well only if that initial choice is close to a good solution. This thesis describes a method called "affinity propagation" that simultaneously considers all data points as potential exemplars, exchanging real-valued messages between data points until a high-quality set of exemplars and corresponding clusters gradually emerges.\n\nAffinity propagation takes as input a set of pairwise similarities between data points and finds clusters on the basis of maximizing the total similarity between data points and their exemplars. Similarity can be simply defined as negative squared Euclidean distance for compatibility with other algorithms, or it can incorporate richer domain-specific models (e.g., translation-invariant distances for comparing images). Affinity propagationâs computational and memory requirements scale linearly with the number of similarities input; for non-sparse problems where all possible similarities are computed, these requirements scale quadratically with the number of data points. Affinity propagation is demonstrated on several applications from areas such as computer vision and bioinformatics, and it typically finds better clustering solutions than other methods in less time.
cAMP-dependent Protein Kinase Regulatory Subunit Type IIβ (2004)

cAMP-dependent protein kinase (cAPK) contains a regulatory (R) subunit dimer bound to two catalytic (C) subunits. Each R monomer contains two cAMP-binding domains, designated A and B. The sequential binding of two cAMPs releases active C. We describe here the properties of RIIbeta and two mutant RIIbeta subunits, engineered by converting a conserved Arg to Lys in each cAMP-binding domain thereby yielding a protein that contains one intact, high affinity cAMP-binding site and one defective site. Structure and function were characterized by circular dichroism, steady-state fluorescence, surface plasmon resonance and holoenzyme activation assays. The Ka for RIIbeta is 610 nM, which is 10-fold greater than its Kd(cAMP) and significantly higher than for RIalpha and RIIalpha. The Arg mutant proteins demonstrate that the conserved Arg is important for both cAMP binding and organization of each domain and that binding to domain A is required for activation. The Ka of the A domain mutant protein is 21-fold greater than that of wild-type and the Kd(cAMP) is increased 7-fold, confirming that cAMP must bind to the mutated site to initiate activation. The domain B mutant Ka is 2-fold less than its Kd(cAMP), demonstrating that, unlike RIalpha, cAMP can access the A site even when the B site is empty. Removal of the B domain yields a Ka identical to the Kd(cAMP) of full-length RIIbeta, indicating that the B domain inhibits holoenzyme activation for RIIbeta. In RIalpha, removal of the B domain generates a protein that is more difficult to activate than the wild-type protein.
Milk Basic Protein (MBP) Increases Radial Bone Mineral Density in Healthy Adult Women (2002)

We studied the effects of daily intake of milk basic protein (MBP) on radial bone mineral density (BMD) in healthy adult women. Thirty-three healthy women were randomly assigned to a 6-month trial with either placebo or MBP (40 mg per day). The radial BMD of each volunteer was measured at the beginning of and at six months after the trial. The mean BMD value at the 6th month in the MBP group increased significantly at both 1/6 and 1/10 portion from the distal end of the radius, whereas that in the control group did not. The BMD gain of each volunteer in the MBP group was significantly higher than that in the placebo group. Thus a daily MBP supplementation of 40 mg in healthy adult women can significantly increase radial BMD.
Prognostic and diagnostic value of eosinopenia, C-reactive protein, procalcitonin, and circulating cell-free DNA in critically ill patients admitted with suspicion of sepsis (2014)

Our data do not support the clinical utility of cf-DNA measurement in critical care patients with SIRS. PCT is of value especially for infection identification in patients with SIRS at admission to the ICU.
MAINTENANCE HORMONAL TREATMENT IMPROVES PROGRESSION FREE SURVIVAL AFTER A FIRST LINE CHEMOTHERAPY IN PATIENTS WITH METASTATIC BREAST CANCER (2008)

The present study was conducted in patients with metastatic breast cancer. Its aim was to identify the factors which influence progression -free survival (PFS) and overall survival (OS) after the first line of chemotherapy in patients with positive tumour hormone receptor status. The patients with early disease progression during first-line chemotherapy were not included. In total, 560 patients who achieved a stable disease or a response to first-line chemotherapy were studied. The factors identified to improve the duration of PFS or OS in multivariate analysis were: number of metastatic sites (p = .01; p = .01), metastatic sites (p = .02; p = .04), Disease free interval (p = .001; p < .0001), previous hormonal therapy (p = .03; p = ns), response to first line chemotherapy (p < .0001; p = 0.0001) and an administration of maintenance hormonal therapy (p < .0001; p = .001). The major impact obtained by maintenance hormonal treatment after first-line chemotherapy in this study seems to indicate that this strategy should be recommended in patients with an ER or PgR positive tumour.
Integrative Gaming: A Framework for Sustainable Game-Based Diabetes Management (2011)

Obesity and diabetes have reached epidemic proportions in both developing and developed nations. While doctors and caregivers stress the importance of physical exercise in maintaining a healthy lifestyle, many people have difficulty subscribing to a healthy lifestyle. Virtual reality games offer a potentially exciting aid in accelerating and sustaining behavior change. However, care needs to be taken to develop sustainable models of employing games for the management of diabetes and obesity. In this article, we propose an integrative gaming paradigm designed to combine multiple activities involving physical exercises and cognitive skills through a game-based storyline. The persuasive story acts as a motivational binder that enables a user to perform multiple activities such as running, cycling, and problem solving. These activities guide a virtual character through different stages of the game. While performing the activities in the games, users wear sensors that can measure movement (accelerometers, gyrometers, magnetometers) and sense physiological measures (heart rate, pulse oximeter oxygen saturation). These measures drive the game and are stored and analyzed on a cloud computing platform. A prototype integrative gaming system is described and design considerations are discussed. The system is highly configurable and allows researchers to build games for the system with ease and drive the games with different types of activities. The capabilities of the system allow for engaging and motivating the user in the long term. Clinicians can employ the system to collect clinically relevant data in a seamless manner.
Equivalences Among Relational Expressions with the Union and Difference Operators (1980)

Queries in relational databases can be formulated in terms of relational expressions using the relational operations select, project, join, union, and difference The equivalence problem for these queries is studied with query optimization m mind It ts shown that testmg eqmvalence of relational expressions with the operators select, project, join, and union is complete m the class FIt of the polynomial-time hierarchy A nonprocedural representation for queries formulated by these expressions is proposed This method of query representation can be viewed as a generahzatlon of tableaux or conjunctive queries (which are used to represent expressions with only select, project, and join) Furthermore, this method is extended to queries formulated by relatmnal expressions that also contain the difference operator, provided that the project operator is not applied to subexpresstons with the difference operator A procedure for testing eqmvalence of these queries is given It ts shown that testmg containment of tableaux is a necessary step in testing equivalence of queries with union and difference Three important cases m which containment of tableaux can be tested m polynomial time are described, although the containment problem is shown to be NP-complete even for tableaux that correspond to expressions with only one project and several join operators
3D discrete wavelet transform architectures (2002)

Compression is a significant operation in many 3D data applications, such as magnetic resonance imaging (MRI), medical diagnosis, television, and seismic data. Employing standard 2D compression techniques do not offer efficient solutions in these applications. In this paper, a 3D discrete wavelet transform (DWT) approach is proposed for performing 3D compression. Two architectures are presented. The first architecture, called 3D-I, is a straight-forward implementation of the 3D DWT. It allows even distribution of the processing load onto 3 sets of filters, with each set doing the calculations for one dimension. The filters are easily scalable to a larger size. The control for this design is very simple, since the data are operated on in a row-column-slice fashion. The design is cascadable. Due to pipelining, all filters are utilized 100% of the time, except for the start up and wind-down times. The second proposed architecture, 3D-II, uses block inputs to reduce the amount of on-chip memory. It has a control unit to select which coefficients to pass on to the low and high pass filters. The RAM on the chip is small compared to the input size, since it depends solely on the filter sizes. The filters are parallel, since systolic filters assume that the data is fed in a non-block form such that partial calculations are done.
Application of NMR spectroscopy of chiral association complexes. 13—electron donor–acceptor complexes between racemic carbazolo[3,4‐<i>c</i>]carbazoles and an optically active acceptor (1982)

Abstract Strong electron donor–acceptor (EDA) association between carbazolo[3,4‐ c ]carbazoles and an optically active tetranitrofluorenone derivative was detected by UV–visible spectroscopy and by 1 H NMR shifts. 1 H NMR splittings at low temperatures are due to diastereomeric association complexes and, thus, prove the chirality of carbazolocarbazoles.
Gene-enzyme relationships in the proline biosynthetic pathway of Saccharomyces cerevisiae (1987)

The PRO1, PRO2, and PRO3 genes were isolated by functional complementation of pro1, pro2, and pro3 (proline-requiring) strains of Saccharomyces cerevisiae. Independent clones with overlapping inserts were isolated from S. cerevisiae genomic libraries in YEp24 (2 microns) and YCp50 (CEN) plasmids. The identity of each gene was determined by gene disruption, and Southern hybridization and genetic analyses confirmed that the bona fide genes had been cloned. Plasmids containing each gene were introduced into known bacterial proline auxotrophs, and the ability to restore proline prototrophy was assessed. Interspecies complementation demonstrated that the S. cerevisiae PRO1 gene encoded gamma-glutamyl kinase, PRO2 encoded gamma-glutamyl phosphate reductase, and PRO3 encoded delta 1-pyrroline-5-carboxylate reductase. The presence of the PRO3 gene on a high-copy-number plasmid in S. cerevisiae caused a 20-fold overproduction of delta 1-pyrroline-5-carboxylate reductase. The PRO2 gene mapped on chromosome XV tightly linked to cdc66, and the PRO3 gene was located on the right arm of chromosome V between HIS1 and the centromere.
Light Harvesting by Carotenoids Incorporated into the B850 Light-Harvesting Complex from<i>Rhodobacter</i><i>s</i><i>phaeroides</i>R-26.1:  Excited-State Relaxation, Ultrafast Triplet Formation, and Energy Transfer to Bacteriochlorophyll (2003)

Spirilloxanthin and spheroidene were reconstituted into the carotenoidless B850 light-harvesting (LH) complex from the Rhodobacter (Rb.) sphaeroides R-26.1 mutant with the aim to obtain new insights in energy transfer, triplet formation, and other relaxation phenomena in photosynthetic light harvesting. Resonance Raman measurements showed that spirilloxanthin and spheroidene are bound to the B850 complex in the same planar configuration, whereas spirilloxanthin in its native LH1 complex of Rhodospirillum (Rs.) rubrum assumes a twisted configuration. Ultrafast transient absorption measurements with excitation of the carotenoid molecules to their S2 state enabled us to identify, in both reconstituted B850 complexes, the recently found S* carotenoid singlet excited state and the direct generation of carotenoid triplet states within picoseconds through the singlet fission mechanism [Gradinaru, C. C., et al. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 2364−2369]. Global analysis has allowed us to quantify the formation yields of these states. In the B850 complex reconstituted with spheroidene, the triplet yield is 5−10%, similar to that found on the spheroidene-binding LH2 complex of Rb. sphaeroides 2.4.1 [Papagiannakis, E. et al. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 6017−6022]. The triplet state of spirilloxanthin in the B850 complex is formed with a similar low yield, in contrast to the native LH1 complex of Rs. rubrum where the triplet yield is as large as 25−30%. This illustrates that the formation of the triplet state depends on the type of complex that binds the carotenoid and not on the carotenoid itself. More specifically, the singlet fission process that underlies ultrafast triplet formation is more efficient when spirilloxanthin is bound in a distorted configuration (in Rs. rubrum) than with either spirilloxanthin or spheroidene bound in a planar configuration (in Rb. sphaeroides). The extent of geometrical deformation of the carotenoid imposed by binding to the LH complexes partly determines the carotenoid light-harvesting function by either deactivating the excited-state energy of S* by transformation into a triplet pair or allowing this energy to flow to bacteriochlorophyll. Comparison of the energy transfer properties in the spheroidene-reconstituted B850 complex, which lacks the B800 bacteriochlorophyll, with that of the LH2 complex of Rb. sphaeroides 2.4.1 suggests that, apart from a light-harvesting function, the B800 bacteriochlorophylls in LH2 may have an important role in funneling the photon energy absorbed by carotenoids toward the reaction center.