gebhart/patrepeval huggingface dataset:
A generative modeling approach for benchmarking and training shallow quantum circuits (2019)

Abstract Hybrid quantum-classical algorithms provide ways to use noisy intermediate-scale quantum computers for practical applications. Expanding the portfolio of such techniques, we propose a quantum circuit learning algorithm that can be used to assist the characterization of quantum devices and to train shallow circuits for generative tasks. The procedure leverages quantum hardware capabilities to its fullest extent by using native gates and their qubit connectivity. We demonstrate that our approach can learn an optimal preparation of the Greenberger-Horne-Zeilinger states, also known as “cat states”. We further demonstrate that our approach can efficiently prepare approximate representations of coherent thermal states, wave functions that encode Boltzmann probabilities in their amplitudes. Finally, complementing proposals to characterize the power or usefulness of near-term quantum devices, such as IBM’s quantum volume, we provide a new hardware-independent metric called the qBAS score. It is based on the performance yield in a specific sampling task on one of the canonical machine learning data sets known as Bars and Stripes. We show how entanglement is a key ingredient in encoding the patterns of this data set; an ideal benchmark for testing hardware starting at four qubits and up. We provide experimental results and evaluation of this metric to probe the trade off between several architectural circuit designs and circuit depths on an ion-trap quantum computer.
The influence of fibrin polymerization and platelet-mediated contractile forces on citrated whole blood thromboelastography profile (2006)

Thromboelastography analysis providing a global assessment of coagulation is gaining new interest in clinical practice. MinimalTF triggered whole blood thromboelastography provides a valuable tool for studying the kinetics of clot formation (expressed by the parameters R, K and alpha-angle) and the physical characteristics of the clot, such as its firmness and the elastic modulus shear (expressed by the parameters maximal amplitude MA and G). We studied the influence of fibrin polymerization and platelet functional status on each parameter of thromboelastographic trace obtained by minimalTF activation inWB by employing increasing concentrations of a fibrin polymerization inhibitors (the tetrapeptide Gly-Pro-Arg-Pro-OH.AcOH; Pefabloc-FG) and an inhibitor of actin polymerization (Cytochalasin D). Pefabloc-FG at concentrations higher than 5 mg/ml prolonged the R and K times and decreased the alpha-angle in a concentration-dependent manner but it did not modify MA and G parameters. At the concentration of 5 mg/ml, Pefabloc-FG completely inhibited clot formation. Cytochalasin D had no effect on R time but decreased the alpha-angle, MA and G parameters by reaching a plateau at the concentration of 5 microM. The effect of cytochalasin D was more pronounced on MA and G than on the alpha-angle. A combination of both Pefabloc-FG (0.5 mg/ml) and cytochalasin D (50 microM) significantly decreased alpha-angle compared to control as well as their single effect. However, G value was dramatically reduced in the presence of cytochalasin D exposure, without any additional effect when both inhibitors were combined. This study confirms the importance of fibrin polymerisation on the kinetics of thrombus formation and demonstrates the close association between the quality of the thrombus and the functional status of platelets. Normal platelet contractile forces are of major importance for the maximum amplitude of TEG which is related to the strength and elastic modulus of the thrombus.
Voltammetry on Microfluidic Chip Platforms (2000)

Microfluidic chip devices are shown to be attractive platforms for performing microscale voltammetric analysis and for integrating voltammetric procedures with on-chip chemical reactions and fluid manipulations. Linear-sweep, square-wave, and adsorptive-stripping voltammograms are recorded while electrokinetically "pumping" the sample through the microchannels. The adaptation of voltammetric techniques to microfluidic chip operation requires an assessment of the effect of relevant experimental variables, particularly the high voltage used for driving the electroosmotic flow, upon the background current, potential window, and size or potential of the voltammetric signal. The exact potential window of the chip detector is dependent upon the driving voltage. Manipulation of the electroosmotic flow opens the door to hydrodynamic modulation (stopped-flow) and reversed-flow operations. The modulated analyte velocity permits compensation of the microchip voltammetric background. Reversal of the driving voltage polarity offers extended residence times in the detector compartment. Rapid square-wave voltammetry/flow injection operation allows a detection limit of 2 x 10(-12) mol (i.e., 2 pmol) of 2,4,6-trinitrotoluene (TNT) in connection with 47 nL of injected sample. The ability of integrating chemical reactions with voltammetric detection is demonstrated for adsorptive stripping measurements of trace nickel using the nickel-dimethylglyoxime model system. The voltammetric response is characterized using catechol, hydrazine, TNT, and nickel as test species. The ability to perform on-chip voltammertic protocols in advantageous over nanovial voltammetric operations that lack a liquid-handling capability. Coupling the versatility of microfluidic chips with the rich information content of voltammetry thus opens an array of future opportunities.
The in vitro biological effect of nerve growth factor is inhibited by synthetic peptides. (1990)

Nerve growth factor (NGF)1 is a neurotrophic polypeptide that acts via specific receptors to promote the survival and growth of neurons. To delineate the NGF domain(s) responsible for eliciting biological activity, we synthesized small peptides corresponding to three regions in NGF that are hydrophilic and highly conserved. Several peptides from mouse NGF region 26-40 inhibited the neurite-promoting effect of NGF on sensory neurons in vitro. Inhibition was sequence-specific and could be overcome by increasing the concentration of NGF. Moreover, peptide actions were specific for NGF-mediated events in that they failed to block the neurotrophic activity of ciliary neuronotrophic factor (CNTF) or phorbol 12-myristate 13-acetate (PMA). In spite of the inhibition of NGF activity, peptides did not affect the binding of radiolabeled NGF. These studies define one region of NGF that may be required for neurotrophic activity.
Comparison of vitamin D and 25-hydroxyvitamin D absorption in the rat (1982)

We have studied the intestinal absorption of physiological amounts of vitamin D and 25-hydroxyvitamin D [25(OH)D3] in vivo from jejunal sacs in rats with thoracic and bile duct cannulas. Under all test conditions, absorption of 25(OH)D was greater than absorption of vitamin D. The majority of absorbed vitamin D and 25(OH)D was transported from the intestine in portal blood rather than lymph. When the luminal fluid contained 2.5 mM oleic acid and monoolein, the presence of taurocholate did not affect total intestinal absorption of vitamin D or 25(OH)D but increased recovery of vitamin in lymph. When luminal fat content was increased to 10 mM oleic acid and monoolein, total absorption of both vitamin D and 25(OH)D was enhanced by taurocholate. No significant metabolism of vitamin D or 25(OH)D occurred during absorption and transport in lymph. Fifty-three percent of lymph vitamin D was found in the chylomicron fraction, compared with only 13% of 25(OH)D. Inhibition of chylomicron synthesis by cycloheximide decreased vitamin D absorption by 46% but diminished 25(OH)D absorption by only 30%. These differences in behavior of vitamin D and 25(OH)D during absorption may explain the superior absorption of 25(OH)D in patients with malabsorption.
Adeno-associated virus serotype 2 induces cell-mediated immune responses directed against multiple epitopes of the capsid protein VP1 (2009)

Adeno-associated virus serotype 2 (AAV-2) has been developed as a gene therapy vector. Antibody and cell-mediated immune responses to AAV-2 or AAV-2-transfected cells may confound the therapeutic use of such vectors in clinical practice. In one of the most detailed examinations of AAV-2 immunity in humans to date, cell-mediated and humoral immune responses to AAV-2 were characterized from a panel of healthy blood donors. The extent of AAV-2-specific antibody in humans was determined by examination of circulating AAV-2-specific total IgG levels in plasma from 45 normal donors. Forty-one donors were seropositive and responses were dominated by IgG1 and IgG2 subclasses. Conversely, AAV-2-specific IgG3 levels were consistently low in all donors. Cell-mediated immune recall responses were detectable in nearly half the population studied. In vitro restimulation with AAV-2 of peripheral blood mononuclear cell cultures from 16 donors elicited gamma interferon (IFN-gamma) (ten donors), interleukin-10 (IL-10) (eight donors) and interleukin-13 (IL-13) (four donors) responses. Using a series of overlapping peptides derived from the sequence of the VP1 viral capsid protein, a total of 59 candidate T-cell epitopes were identified. Human leukocyte antigen characterization of donors revealed that the population studied included diverse haplotypes, but that at least 17 epitopes were recognized by multiple donors and could be regarded as immunodominant. These data indicate that robust immunological memory to AAV-2 is established. The diversity of sequences recognized suggests that attempts to modify the AAV-2 capsid, as a strategy to avoid confounding immunity, will not be feasible.
Strategic internal covalent cross-linking of TNF produces a stable TNF trimer with improved TNFR2 signaling (2015)

Stable TNF trimers, created by internal covalent cross-linking, show improved signaling. The high structural homology within the TNF superfamily provides an opportunity to extend internal cross-linking to other TNF superfamily proteins to produce active trimers with improved stability and receptor signaling, and with potential applications for cancer, autoimmunity, infections, and transplantation.
Orally bioavailable small-molecule inhibitor of transcription factor Stat3 regresses human breast and lung cancer xenografts (2012)

Computer-aided lead optimization derives a unique, orally bioavailable inhibitor of the signal transducer and activator of transcription (Stat)3 Src homology 2 domain. BP-1-102 binds Stat3 with an affinity (K(D)) of 504 nM, blocks Stat3-phospho-tyrosine (pTyr) peptide interactions and Stat3 activation at 4-6.8 μM, and selectively inhibits growth, survival, migration, and invasion of Stat3-dependent tumor cells. BP-1-102-mediated inhibition of aberrantly active Stat3 in tumor cells suppresses the expression of c-Myc, Cyclin D1, Bcl-xL, Survivin, VEGF, and Krüppel-like factor 8, which is identified as a Stat3 target gene that promotes Stat3-mediated breast tumor cell migration and invasion. Treatment of breast cancer cells with BP-1-102 further blocks Stat3-NF-κB cross-talk, the release of granulocyte colony-stimulating factor, soluble intercellular adhesion molecule 1, macrophage migration-inhibitory factor/glycosylation-inhibiting factor, interleukin 1 receptor antagonist, and serine protease inhibitor protein 1, and the phosphorylation of focal adhesion kinase and paxillin, while enhancing E-cadherin expression. Intravenous or oral gavage delivery of BP-1-102 furnishes micromolar or microgram levels in tumor tissues and inhibits growth of human breast and lung tumor xenografts.
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood (2003)

The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximum- likelihood principle, which clearly satisfies these requirements. The core of this method is a simple hill-climbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distance-based method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximum-likelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant plastids, thus reaching a speed of the same order as some popular distance-based and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/.
TanDEM-X: A Satellite Formation for High-Resolution SAR Interferometry (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> TanDEM-X (TerraSAR-X add-on for Digital Elevation Measurements) is an innovative spaceborne radar interferometer that is based on two TerraSAR-X radar satellites flying in close formation. The primary objective of the TanDEM-X mission is the generation of a consistent global digital elevation model (DEM) with an unprecedented accuracy, which is equaling or surpassing the HRTI-3 specification. Beyond that, TanDEM-X provides a highly reconfigurable platform for the demonstration of new radar imaging techniques and applications. This paper gives a detailed overview of the TanDEM-X mission concept which is based on the systematic combination of several innovative technologies. The key elements are the bistatic data acquisition employing an innovative phase synchronization link, a novel satellite formation flying concept allowing for the collection of bistatic data with short along-track baselines, as well as the use of new interferometric modes for system verification and DEM calibration. The interferometric performance is analyzed in detail, taking into account the peculiarities of the bistatic operation. Based on this analysis, an optimized DEM data acquisition plan is derived which employs the combination of multiple data takes with different baselines. Finally, a collection of instructive examples illustrates the capabilities of TanDEM-X for the development and demonstration of new remote sensing applications. </para>
Wavelength swept ASE source (2009)

We present a novel wavelength swept light source for Optical Coherence Tomography (OCT). Arbitrary sweep rates up to 2x170kHz are achieved by phase-shifted control of two optical bandpass-filters to compensate light propagation effects.
Animal Models of Cardiovascular Diseases (2011)

Cardiovascular diseases are the first leading cause of death and morbidity in developed countries. The use of animal models have contributed to increase our knowledge, providing new approaches focused to improve the diagnostic and the treatment of these pathologies. Several models have been developed to address cardiovascular complications, including atherothrombotic and cardiac diseases, and the same pathology have been successfully recreated in different species, including small and big animal models of disease. However, genetic and environmental factors play a significant role in cardiovascular pathophysiology, making difficult to match a particular disease, with a single experimental model. Therefore, no exclusive method perfectly recreates the human complication, and depending on the model, additional considerations of cost, infrastructure, and the requirement for specialized personnel, should also have in mind. Considering all these facts, and depending on the budgets available, models should be selected that best reproduce the disease being investigated. Here we will describe models of atherothrombotic diseases, including expanding and occlusive animal models, as well as models of heart failure. Given the wide range of models available, today it is possible to devise the best strategy, which may help us to find more efficient and reliable solutions against human cardiovascular diseases.
Cancer and Bone* (1998)

I. Introduction II. Normal Calcium and Bone Homeostasis A. Bone remodeling B. Calcium homeostasis C. Defenses against hyper- and hypocalcemia III. Humoral Mechanisms by Which Solid Tumors Affect the Skeleton A. Hypercalcemia B. Oncogenic osteomalacia C. Tumor lysis syndrome IV. Local Mechanisms by Which Tumors Affect the Skeleton A. Clinical manifestations B. Pathophysiology of the metastatic process to bone C. Local tumor syndromes in bone D. Therapy of tumor in bone
Autogenous replacement of the meniscus cartilage: Analysis of results and mechanisms of failure (1995)

Autogenous replantation of meniscal cartilage (resection of 80% of the meniscus cartilage followed by immediate replantation) was performed in 14 dogs as a control arm of a meniscal replacement study. The purpose was to assess the ability of the excised tissue to heal to the intact rim and function as a meniscus cartilage. This procedure is an idealized model of allografting meniscus cartilage in that the tissue is fresh, autogenous, and perfectly sized. If this procedure did not succeed, it seemed likely to the authors that allografting meniscal cartilage would have diminished chances for success. Evaluation of these replant failures led us to speculate that the causes and mechanisms might include slow or incomplete revascularization, inadequate mechanical fixation or stabilization, and, perhaps, some type of rejection phenomenon not examined or confirmed in the present study. We believe these mechanisms will be particularly deleterious for allografted meniscal cartilages and recommend further extensive evaluation of meniscal allografts before wide clinical use.
HeLa Cell R-Deoxyribonucleic Acid Polymerases (1974)

Abstract R-DNA polymerase activity in HeLa cells is found in both the nuclear and cytoplasmic compartments. Extensive purification of the enzyme activity in the cytoplasm shows it to be separable into two distinct activities, I and II. Comparable purification of the nuclear R-DNA polymerase yields one main enzymatic activity which is apparently similar to cytoplasmic R-DNA polymerase II. R-DNA polymerase I copies poly(A) templates but not poly(C), poly(I), or poly(U) homopolymers, whereas Form II of the enzyme can copy all of the homopolymers. The two forms of the enzyme show different inhibition patterns in the presence of salt or ethanol. Both R-DNA polymerases are 110,000 daltons as measured by sedimentation studies and show Km values for deoxynucleoside triphosphates (approximately 5 x 10-7 m) that are one order of magnitude or more lower than the Km values of the DNA dependent-DNA polymerases of HeLa cells. Neither HeLa cell R-DNA polymerase I nor II is inhibited by antisera prepared against the reverse transcriptase obtained from either the Mason-Pfizer monkey virus, the Woolly monkey virus, or the Rauscher murine leukemia virus.
A single-chain insulin-like growth factor I/insulin hybrid binds with high affinity to the insulin receptor (1995)

1. To investigate the structure/function relationship of the interaction between ligand and receptor in the insulin-like growth factor I (IGF-I) and insulin receptor systems we have prepared and characterized a single-chain insulin/IGF-I hybrid. The single-chain hybrid consists of the insulin molecule combined with the C domain of IGF-I. The single-chain hybrid was found to bind with high affinity to both truncated soluble insulin receptors and membrane-bound holoreceptors. The affinity for interacting with the soluble truncated insulin receptors was 55-94% relative to insulin, and affinity for membrane-bound insulin receptors was 113% of that of insulin. Furthermore we found that the affinity of the single-chain hybrid molecule for IGF-I receptors was 19-28% relative to IGF-I. 2. The affinity of the single-chain hybrid for chimeric insulin/IGF-I receptors exceeded that of either natural ligand. This indicates that coordinately changing domains of the receptors and the ligands can induce higher affinity of ligand for receptor, supporting the idea that these receptors have a common ligand-binding site [Kjeldsen, Andersen, Wiberg, Rasmussen, Schäffer, Balschmidt, Møller and Møller (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 4404-4408]. 3. In contrast with what was generally assumed about the ligand structure required for binding to the insulin receptor we demonstrate the first single-chain insulin analogue that can bind with high affinity to the insulin receptor.
Multiple Calcium Channels and Neuronal Function (1987)

Recent investigations have demonstrated that neurons have a number of different types of calcium channels, each with their own unique properties and pharmacology. These calcium channels may be important in the control of different aspects of nerve activity. Some of the possibilities can now be discussed.
HIV-1 Conserved-Element Vaccines: Relationship between Sequence Conservation and Replicative Capacity (2013)

To overcome the problem of HIV-1 variability, candidate vaccine antigens have been designed to be composed of conserved elements of the HIV-1 proteome. Such candidate vaccines could be improved with a better understanding of both HIV-1 evolutionary constraints and the fitness cost of specific mutations. We evaluated the in vitro fitness cost of 23 mutations engineered in the HIV-1 subtype B Gag-p24 Center-of-Tree (COT) protein through fitness competition assays. While some mutations at conserved sites exacted a high fitness cost, as expected under the assumption that the most conserved residue confers the highest fitness, there was no overall strong relationship between sequence conservation and replicative capacity. By comparing sites that have evolved since the beginning of the epidemic to those that have remain unchanged, we found that sites that have evolved over time were more likely to correspond to HLA-associated sites and that their mutation had limited fitness costs. Our data showed no transcendent link between high conservation and high fitness cost, indicating that merely focusing on conserved segments of HIV-1 would not be sufficient for a successful vaccine strategy. Nonetheless, a subset of sites exacted a high fitness cost upon mutation--these sites have been under selective pressure to change since the beginning of the epidemic but have proved virtually nonmutable and could constitute preferred targets for vaccine design.