gebhart/patrepeval huggingface dataset:
Efficient protocol for qubit initialization with a tunable environment (2016)

We propose an efficient qubit initialization protocol based on a dissipative environment that can be dynamically adjusted. Here the qubit is coupled to a thermal bath through a tunable harmonic oscillator. On-demand initialization is achieved by sweeping the oscillator rapidly into resonance with the qubit. This resonant coupling with the engineered environment induces fast relaxation to the ground state of the system, and a consecutive rapid sweep back to off resonance guarantees weak excess dissipation during quantum computations. We solve the corresponding quantum dynamics using a Markovian master equation for the reduced density operator of the qubit-bath system. This allows us to optimize the parameters and the initialization protocol for the qubit. Our analytical calculations show that the ground-state occupation of our system is well protected during the fast sweeps of the environmental coupling and, consequently, we obtain an estimate for the duration of our protocol by solving the transition rates between the low-energy eigenstates with the Jacobian diagonalization method. Our results suggest that the current experimental state of the art for the initialization speed of superconducting qubits at a given fidelity can be considerably improved.
All-optical 3R regeneration and NRZ to RZ conversion Based on InP Related Semiconductor Optical Devices (2006)

We report an experimental demonstration of all-optical 3R regeneration with a format conversion from NRZ-to-RZ. It shows a good performance using a Mach-Zehnder interferometer wavelength converter and a self-pulsating multi-section laser diode with DFB reflector
New Esters of 4-Amino-5-chloro-2-methoxybenzoic Acid as Potent Agonists and Antagonists for 5-HT4Receptors (1997)

A number of benzoates derived from 4-amino-5-chloro-2-methoxybenzoic acid and substituted 1-piperidineethanol were synthesized and found to be potent 5-HT4 receptor agonists in the electrically-stimulated myenteric plexus and longitudinal muscle of the guinea pig ileum and the rat esophagus muscle. Monosubstitution of the piperidine ring with Me, OH, NH-Ac, or CONH2 groups gave compounds equipotent to 7a (ML 10302), a 5-HT4 receptor agonist previously reported to have nanomolar affinity. 7a,k were as potent as serotonin (5-HT) but had maximal responses which were only 60-80% of that of 5-HT, suggesting a partial agonist profile for these compounds. Binding assays were performed with [3H]GR 113808 in the rat striatum, and several of these compounds were found to have nanomolar affinity for 5-HT4 receptors (7a, Ki = 1.07 +/- 0.5 nM; 7k, Ki = 1.0 +/- 0.3 nM). The introduction of two methyl groups on the piperidine ring brought about a dramatic change in the pharmacological profile of 2-[(cis- and trans-3,5-dimethylpiperidinyl)ethyl]-4-amino-5-chloro-2- methoxybenzoate, 7g,h. 7g (Ki = 0.26 +/- 0.06 nM) inhibited the relaxant action of 5-HT in the rat esophagus muscle with a pA2 value of 8.6. The advantage of the ester function was demonstrated by comparing the activity of several such compounds at 5-HT4 receptors with those of the corresponding amidic derivatives. This difference was less marked when the basic moiety was sterically constrained as in the quinuclidine and tropane moieties. Structural analyses of 7a,g were performed by determining their X-ray crystal structures and by molecular modeling (SYBYL). A relatively limited number of minimum energy conformers was found for both compounds. They were characterized by the cis folded conformation of the ethyl chain and by the orientation of the lone pair of the nitrogen atom pointing out of the molecule as seen in conformationally-constrained benzamides such as zacopride and renzapride. A hypothetical model for the 5-HT4 receptor with two sites for the binding of agonist and antagonist molecules was proposed.
Semantic Issues of OCL: Past, Present, and Future (2024)

We report on the results of a long-term project to formalize the semantics of OCL 2.0 in Higher-order Logic (HOL). The ultimate goal of the project is to provide a formalized, machine-checked semantic basis for a theorem proving environment for OCL (as an example for an object-oriented specification formalism) which is as faithful as possible to the original informal semantics. We report on various (minor) inconsistencies of the OCL semantics, discuss the more recent attempt to align the OCL semantics with UML 2.0 and suggest several extensions which make, in our view, OCL semantics more fit for future extensions towards program verifications and specification refinement.
Specific binding of eukaryotic initiation factor 2 to satellite tobacco necrosis virus RNA at a 5′-terminal sequence comprising the ribosome binding site (1981)

The mRNA-binding property of eukaryotic initiation factor 2 (eIF-2) was examined by studying its interaction with satellite tobacco necrosis virus (STNV) RNA carrying a (32)P-labeled 5' end. The RNA molecules bound by limiting amounts of eIF-2 were isolated and digested with pancreatic and T1 RNases. Digestion patterns showed that the labeled STNV RNA preparation offered to eIF-2 was heterogeneous, containing more than 30 different 5' ends; by contrast, the RNA selected by eIF-2 possessed predominantly one 5' end, pApGpUp..., the 5'-terminal sequence of intact STNV RNA. Binding analysis of individual 5'-terminal fragments generated from isolated, intact, STNV RNA by partial digestion with T1 RNase showed that eIF-2 does not bind detectably to the 32-nucleotide fragment ending with the initiation codon AUG or to shorter ones, but it does bind the 44-nucleotide fragment that contains the ribosome binding site. In addition to the structural features localized at the 5' end of STNV RNA, eIF-2 appears to recognize a conformation found only in larger molecules, because intact RNA and large 5-'-terminal fragments are bound preferentially over smaller ones. However, binding of short 5'-terminal STNV RNA fragments to eIF-2 is specific, as judged by competition with STNV and ribosomal RNA. Finally, binding of eIF-2 to intact STNV RNA leads to a conformational change in the RNA that greatly facilitates cleavage by T1 and P1 RNases at sites in the vicinity of the initiation region. These results show that eIF-2 interacts specifically with the 5'-terminal region of STNV RNA that contains the ribosome binding site and causes local unfolding of the RNA structure.
XAIR: A Framework of Explainable AI in Augmented Reality (2023)

Explainable AI (XAI) has established itself as an important component of AI-driven interactive systems. With Augmented Reality (AR) becoming more integrated in daily lives, the role of XAI also becomes essential in AR because end-users will frequently interact with intelligent services. However, it is unclear how to design effective XAI experiences for AR. We propose XAIR, a design framework that addresses when, what, and how to provide explanations of AI output in AR. The framework was based on a multi-disciplinary literature review of XAI and HCI research, a large-scale survey probing 500+ end-users’ preferences for AR-based explanations, and three workshops with 12 experts collecting their insights about XAI design in AR. XAIR’s utility and effectiveness was verified via a study with 10 designers and another study with 12 end-users. XAIR can provide guidelines for designers, inspiring them to identify new design opportunities and achieve effective XAI designs in AR.
Pectenotoxin-2 induces G1 arrest of the cell cycle in synovial fibroblasts of patients with rheumatoid arthritis (2011)

Rheumatoid arthritis (RA), a chronic inflammatory disease, is characterized by hyperplasia of the synovial fibroblasts, due in part to increased cell growth. This study investigated the mechanisms underlying the anti-proliferative action of pectenotoxin-2 (PTX-2), isolated from marine sponges, in synovial fibroblasts obtained from RA patients. PTX-2 concentration-dependently inhibited the growth of synovial fibroblasts, arresting them in the G1 phase of their cell cycle. The G1 arrest was correlated with down-regulation of cyclin D1 and cyclin-dependent kinase (Cdk) 6, with a concomitant up-regulation of the tumor suppressor, p53, and the Cdk inhibitor, p21 (WAF1/CIP1). Following PTX-2 treatment of synovial fibroblasts, an increased binding of p21 with Cdk2 and Cdk6 was paralleled by a significant decrease in retinoblastoma protein (pRB) phosphorylation and in the protein levels of E2F transcription factors. Thus, PTX-2 might help identify new therapeutic agents against RA-mediated hyperplasia of synovial fibroblasts.
Injectable Polymer–Nanoparticle Hydrogels for Local Immune Cell Recruitment (2019)

The ability to engineer immune function has transformed modern medicine, highlighted by the success of vaccinations and recent efforts in cancer immunotherapy. Further directions in programming the immune system focus on the design of immunomodulatory biomaterials that can recruit, engage with, and program immune cells locally in vivo. Here, we synthesized shear-thinning and self-healing polymer-nanoparticle (PNP) hydrogels as a tunable and injectable biomaterial platform for local dendritic cell (DC) recruitment. PNP gels were formed from two populations of poly(ethylene glycol)-<i>block</i>-polylactide (PEG-<i>b</i>-PLA) NPs with the same diameter but different PEG brush length (2 or 5 kDa). PEG-<i>b</i>-PLA NPs with the longer PEG brush exhibited improved gel formation following self-assembly and faster recovery after shear-thinning. In all cases, model protein therapeutics were released via Fickian diffusion in vitro, and minor differences in the release rate between the gel formulations were observed. PNP hydrogels were loaded with the DC cytokine CCL21 and injected subcutaneously in a murine model. CCL21-loaded PNP hydrogels recruited DCs preferentially to the site of injection in vivo relative to non-CCL21-loaded hydrogels. Thus, PNP hydrogels comprise a simple and tunable platform biomaterial for in vivo immunomodulation following minimally invasive subcutaneous injection.
Validating Seed Data Samples for Synthetic Identities – Methodology and Uniqueness Metrics (2020)

This work explores the identity attribute of synthetic face samples derived from Generative Adversarial Networks. The goal is to determine if individual samples are unique in terms of identity, firstly with respect to the seed dataset that trains the GAN model and secondly with respect to other synthetic face samples. Two approaches are introduced to enable the comparative analysis of large sets of synthetic face samples. The first of these uses ROC curves to determine identity uniqueness using a number of large publicly available datasets of real facial samples to provide reference ROCs as a baseline. The second approach uses a thresholding technique utilizing again large publicly available datasets as a reference. For this approach, new metrics are introduced, and a technique is provided to remove the most connected data samples within a large synthetic dataset. The remaining synthetic samples can be considered as unique as data samples gathered from different real individuals. Several StyleGAN models are used to create the synthetic datasets, and variations in key model parameters are explored. It is concluded that the resulting synthetic data samples exhibit excellent uniqueness when compared with the original training dataset, but significantly less uniqueness when comparisons are made within the synthetic dataset. Nevertheless, it is possible to remove the most highly connected synthetic data samples. Thus, in some cases, up to 92% of the data samples in a 20k synthetic dataset can be shown to exhibit similar uniqueness to data samples taken from real public datasets.
Abstract 239: Nitric Oxide Suppresses the Angiogeneic Potential of Mesenchymal Stem Cells (2012)

Introduction: Mesenchymal stem cells (MSCs) participate in blood vessel formation which is crucial for tissue regeneration. However, the mechanism involved in regulating MSC angiogenesis remains elusive. We examined the role of Nitric Oxide (NO) in this process by comparing angiogenesis by MSCs derived from wild type mice and mice lacking S-nitrosoglutathione reductase (GSNOR-/-), an enzyme that increases intracellular GSNO and enhances endogenous S-nitrosylation (a ubiquitous redox-related modification of cysteine thiol by NO) Hypothesis: Nitric oxide signaling pathways are mediated via small molecular thiols that regulate MSC angiogenesis. Method: Bone marrow-derived MSCs were isolated from wild type and GSNOR-/- mice and grown for 7 days in endothelial growth media followed by 24h in Matrigel (in vitro angiogenesis assay) in the presence of either vehicle, 15µM L-NAME (a nitric oxide synthase (NOS) inhibitor) or 500µM SNAP (a nitric oxide donor). Human (h)MSCs were similarly treated with vehicle, 15µM L-NAME and 100µM SNAP. MSC NO production and NOS expression were assessed. Results: Both types of MSCs exhibited similar levels of NO production and NOS expression, however, in the Matrigel Assay, MSCs from GSNOR-/- mice formed fewer (29.9±12.0 vs.. 50.0±15.4, p&lt;0.001) and shorter (62.8 ± 34.6 µm vs. 105.9±57.0 µm, p&lt;0.001) tubes than MSCs derived from wild type mice. L-NAME treatment normalized GSNOR-/- tube number (49.9 ± 14.8, p&lt;0.001) and length (82.8±42.5 µm, p&lt;0.001). Treatment of wild type MSCs with SNAP impaired tube formation (15.6±9.0, p&lt;0.001) and length (57.1±24.9 µm, p&lt;0.001). Similarly, hMSCs treated with SNAP exhibited impaired tube formation, both in number (25.0±4.9 vs. 49.2±8.1, p&lt;0.001) and length (81±29.1 vs. 128.0±52.5 µm, p&lt;0.001) compared to vehicle treated MSCs. L-NAME had no effect on hMSCs . Conclusion: These findings are consistent with a paradoxical negative influence of NO/GSNO on vascular formation by MSCs and reveal a novel mechanism whereby NO/GSNO inhibits MSC dependent angiogenesis. These findings have implications for disease states characterized by excessive or dysregulated angiogenesis; moreover NO deficient environments may trigger MSC mediated angiogenesis.
Immune Responses to Chemically Modified Bacterial α-Amylase (1974)

A heavy conjugate (D31-BαA) of bacterial α-amylase [EC 3.2.1.1] (BαA) with diazotized 4-aminoquinoline 1-oxide (4AQO) was prepared. After removal of the cross-reacting materials in the product with an immunoadsorbent of mouse anti-BαA antibody, D38-BαA was obtained. The reactivity of D38-BαA with anti-BαA antibody was tested by inhibition of passive hemagglutination (PHA) with BαA-coated erythrocytes and the enzymatic procedure. Inhibition of PHA was detected by BαA at 3×10−9 M and by D38-BαA at 2×10−5M. The decrease in the neutralizing activity of anti-BαA antibody against BαA by a 4.08×10−5M solution of D38-BαA corresponded to that obtained with a 5.1×120−8M solution of N-bromosuccinimide-treated BαA (NBS-BαA), which completely lost its enzymatic activity without alteration in its antigenic properties. It was confirmed that there was little cross-reactivity between native BαA and D38-BαA. Antisera against D38-BαA contained anti-hapten antibody, but no detectable anti-BαA antibody. However, priming with the same antigen induced the immunological memory of BαA, since enhanced anti-BαA antibody response was observed in these mice primed with D38-BαA. The specificity of enhancement by priming with the modified antigen was demonstrated by the lack of effect on the immune response to Taka-amylase A (TAA). The degree of enhancement induced by various doses of D38-BαA was similar to that observed with 1 μg of native BαA. These results appear to be in good agreement with the general observation that recognition of antigens at the T cell level is less specific than that at the level of B cells.
Synergistic and antagonistic effects in flame retardancy of an intumescent epoxy resin (2011)

Phosphorus‐based products are able to strongly reduce the flammability of epoxy resins. In order to further improve their fire behavior, combinations of a conventional flame retardant (ammonium polyphosphate [APP]) and two other particles have been investigated. The partial substitution of APP by carbon nanotubes reveals an antagonism between these two compounds in terms of heat release rate measured by mass‐loss calorimetry. On the contrary, the combination with octamethyl polyhedral oligomeric silsesquioxane leads to a huge synergistic effect. These effects are mainly attributed to the char structures. Furthermore, the two systems were studied by thermogravimetric analysis, and they exhibit modifications of the degradation temperatures. The existence of different stabilization effects was also revealed. Copyright © 2011 John Wiley &amp; Sons, Ltd.
Microwave-to-optical transduction with erbium ions coupled to planar photonic and superconducting resonators (2023)

Optical quantum networks can connect distant quantum processors to enable secure quantum communication and distributed quantum computing. Superconducting qubits are a leading technology for quantum information processing but cannot couple to long-distance optical networks without an efficient, coherent, and low noise interface between microwave and optical photons. Here, we demonstrate a microwave-to-optical transducer using an ensemble of erbium ions that is simultaneously coupled to a superconducting microwave resonator and a nanophotonic optical resonator. The coherent atomic transitions of the ions mediate the frequency conversion from microwave photons to optical photons and using photon counting we observed device conversion efficiency approaching 10<sup>-7</sup>. With pulsed operation at a low duty cycle, the device maintained a spin temperature below 100 mK and microwave resonator heating of less than 0.15 quanta.
Plasma sodium concentration and sodium excretion in the anaesthetized dog. (1976)

1. The effect of acute alterations of plasma sodium concentration (PNa) on renal sodium excretion (UNaV) was investigated by three types of experiments on anaesthetized dogs: (a) A local increase in PNa at one kidney was produced by infusion of hypertonic saline directly into its artery while systemic levels of PNa were stabilized by haemodialysis. (b) Systemic levels of PNa were lowered by exchange transfusion of blood for an equal volume of salt‐free dextran‐in‐dextrose solution. The results were contrasted with those observed after similar exchanges, but using dextran‐in‐saline solution. (c) The level of PNa was altered by varying the sodium concentration of a saline solution infused at a fixed rate either intravenously or into one renal artery. 2. All three types of experiment suggest a dependence of UNaV on PNa Analysis demonstrated that this relationship was not due to contemporary changes in: packed cell volume; plasma solids concentration; plasma potassium concentration; blood pressure or plasma hydrogen ion concentration. The distribution of these variables did not change with PNa except for plasma hydrogen ion concentration. Moreover, the relationship persisted when data were selected to exclude clearance periods in which the value for any variable had shifted past the group mean obtained before PNa was altered. 3. The fall in UNaV at low levels of PNa could be attributed to a fall in glomerular filtration rate (GFR), but the progressive rise in UNaV seen as PNa exceeded 150 m‐mole 1(‐1) occurred despite a fall in GFR and no apparent change in the mean filtered load of sodium. These results suggest that the increased sodium excretion accompanying raised levels of PNa is due to reduced tubular re‐absorption of sodium.
A Novel Admixture-Based Pharmacogenetic Approach to Refine Warfarin Dosing in Caribbean Hispanics (2016)

ClinicalTrials.gov NCT01318057.
Role of Dimerization in the Catalytic Properties of the Escherichia coli Disulfide Isomerase DsbC (2009)

The bacterial protein-disulfide isomerase DsbC is a homodimeric V-shaped enzyme that consists of a dimerization domain, two alpha-helical linkers, and two opposing thioredoxin fold catalytic domains. The functional significance of the two catalytic domains of DsbC is not well understood yet. We have engineered heterodimer-like DsbC derivatives covalently linked via (Gly(3)-Ser) flexible linkers. We either inactivated one of the catalytic sites (CGYC), or entirely removed one of the catalytic domains while maintaining the putative binding area intact. Variants having a single active catalytic site display significant levels of isomerase activity. Furthermore, mDsbC[H45D]-dim[D53H], a DsbC variant lacking an entire catalytic domain but with an intact dimerization domain, also showed isomerase activity, albeit at lower levels. In addition, the absence of the catalytic domain allowed this protein to catalyze in vivo oxidation. Our results reveal that two catalytic domains in DsbC are not essential for disulfide bond isomerization and that a determining feature in isomerization is the availability of a substrate binding domain.
Phase II Clinical Trial to Evaluate the Efficacy of Transanal Endoscopic Total Mesorectal Excision for Rectal Cancer (2018)

Transanal endoscopic total mesorectal excision showed acceptable results based on perioperative and short-term oncologic outcomes. Further investigations are necessary to show the benefits and long-term outcomes of this procedure. See Video Abstract at http://links.lww.com/DCR/A563.
Design insights for a mobile based sensor application framework (2015)

Modern day smart phones are powerful connected sensory and computation nodes for crowd-sensing, urban-sensing and personal-sensing applications. We have developed an Internet of Things (IoT) platform that can seamlessly handle data from the wide variety of sensors available on mobile phones. It can store and run aggregated analysis on the data in real-time. However, mobile phones themselves are a very heterogeneous set of devices. Each phone comes with a different array of sensors with varying sensitivity and control functions. Also, there are multiple development environments and programming languages. A final problem is seamless prototyping of applications offline and then seamless partitioning of the algorithm between phone and the cloud. In this paper we present early design elements of a framework aimed at addressing these issues.
Therapeutic quality control of oral anticoagulant therapy comparing the short‐acting acenocoumarol and the long‐acting phenprocoumon (2002)

To investigate whether the different pharmacokinetics of acenocoumarol (t(1/2) = 11 h) and phenprocoumon (t(1/2) = 140 h) result in a different quality of anticoagulation, we studied patients from the Leiden anticoagulation clinic treated between 1998 and 1999 for more than 16 weeks. Two hundred and twenty-eight pairs were closely matched for indication for oral anticoagulant therapy (OAT), age, sex and date of start of treatment. Four hundred and fifty six patients with 7245 International Normalized Ratio (INR) checks yielded 230 patient-years. Quality of OAT calculated over the whole treatment period was higher with phenprocoumon as expressed by the number of INR checks in the therapeutic range (phenprocoumon: 42.7%, acenocoumarol: 36.5%, difference: 6.1%, CI(95) of the difference: 3.0-9.3%) and by time in range (phenprocoumon: 46.6%, acenocoumarol: 41.6%, difference: 5.0%, CI(95) of the difference: 1.3-8.6%). After the initial 6 weeks of OAT, the differences became more pronounced (difference: 6.1%, CI(95): 1.8-10.4%). The incidence of severe bleeding complications was similar (phenprocoumon: 0.04/patient/year vs acenocoumarol: 0.03/patient/year) with a slight excess of minor bleeds with phenprocoumon (0.19/patient/year vs 0.06/patient/year). We conclude that phenprocoumon leads to a better quality of OAT than acenocoumarol. As there is no difference in major bleeding complications and only a small difference in minor bleeding complications, phenprocoumon is preferable to acenocoumarol for prolonged OAT.