gebhart/patrepeval huggingface dataset:
Using matching substructures as an optimization objective for RNA design (2017)

RNA design is a problem that has been shown to be NP-Hard. It is best described as the inverse of RNA folding. RNA folding describes the process of calculating the most likely secondary structure that a strand of nucleotides will fold into. Inversely, RNA design describes the process of designing a strand of nucleotides that will fold into a given secondary structure. The problem is made more difficult by the presence of a second objective, structural stability. Free energy is a measure of structural stability. In previous research, we have attempted to solve this problem using SIMARD (Simulated Annealing RNA Design). SIMARD employs a simulated annealing framework alongside a preselection strategy to design high-quality sequences in a reasonable amount of time. In this paper, we introduce the integration of BEAR (Brand nEw Alphabet for RNAs) to SIMARD as a way of notating secondary structures for quality evaluation. We attempt to design sequences with four different experimental configurations across two data sets. We find that representing our sequences with the BEAR grammar allows us to improve the average structural similarity of our generated sequences. We also find that SIMARD outperforms six other algorithms when running on the Eterna100 benchmark in terms of successfully designed structures.
Myocardial Contrast Echocardiography Can Be Used to Quantify Intramyocardial Blood Volume (1997)

MCE can quantify autoregulatory increases in IBV that maintain resting myocardial perfusion. These data suggest that both microvessel vasodilatation and recruitment are dual mechanisms of IBV change. MCE thus may be a clinically useful technique for the detection and quantification of coronary artery disease at rest.
A homogeneous europium cryptate-based assay for the diagnosis of mutations by time-resolved fluorescence resonance energy transfer (2001)

Oligonucleotide ligation assay (OLA) is considered to be a very useful methodology for the detection and characterization of mutations, particularly for clinical purposes. The fluorescence resonance energy transfer between a fluorescent donor and a suitable fluorophore as acceptor has been applied in the past to several scientific fields. This technique is well adapted to nucleic acid analysis such as DNA sequencing, DNA hybridization and polymerase chain reaction. We describe here a homogeneous format based on the use of a rare earth cryptate label as donor: tris-bipyridine-Eu(3+). The long-lived fluorescence of this label makes it possible to reach a high sensitivity by using a time-resolved detection mode. A non-radiative energy transfer technology, known as time-resolved amplification of cryptate emission (TRACE((R))) characterized by a temporal and spectral selectivity has been developed. The TRACE((R)) detection of characterized single nucleotide polymorphism using the OLA for allelic discrimination is proposed. We demonstrate the potentialities of this OLA-TRACE((R)) methodology through the analysis of K-ras oncogene point mutations.
On interactive secrecy over erasure networks (2012)

In this short review paper we summarize some of our recent results on interactive message secrecy for broadcast erasure channels.
Heterogeneous expression of CD5, CD10, and CD23 in Waldenstrom's macroglobulinemia (2004)

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ADAPTIVE FEEDFORWARD CONTROL FOR POSITIONING SYSTEM WITH PROGRESSIVE WAVE TYPE ULTRASONIC MOTOR (1995)

ABSTRACT This paper considers the use. of an adaptive feedforward controller for a positioning system with a progressive wave type ultrasonic motor. The parameters of the feedforward controller are adjusted by an adaptation algorithm, the objective of which is to make the feedforward controller a mathematical inverse of the motor. The error between the desired output and actual output is used as the adaptation error signal as well as the input to the nonadaptive feedback controller. After the adaptive process is completed, the input to the motor is no longer supplied by the feedback controller but by the feedforward controller. The stability of the proposed adaptive control system is analyzed and its effectiveness is tested by experiments.
Antiarrhythmic Drugs and Future Direction (2003)

Antiarrhythmic agents play an important role in the termination and suppression of both atrial and ventricular arrhythmias as primary or adjunctive therapy. The use of hybrid treatment, combining drugs with radiofrequency ablation or ICD implantation, is expected to rise as the number of patients with complex arrhythmias continues to increase (1,2). In this evolving management scenario, selection of an effective yet safe pharmacologic agent is challenging. The challenge arises from factors intrinsic to the patient, disease condition or the drug itself. These factors primarily include variability in the pathophysiologic substrate, diverse arrhythmia mechanisms, multiple clinical presentation with differing prognostic implications, along with variability in drug disposition and/or response in a highly heterogeneous patient population. Moreover, the availability of multiple therapeutic options and the narrow therapeutic index with limited ability to determine satisfactory endpoints further emphasize the need for better understanding of interactions between drug, end target, and disease condition.
Synthetic OCP heterodimers are photoactive and recapitulate the fusion of two primitive carotenoproteins in the evolution of cyanobacterial photoprotection (2017)

The orange carotenoid protein (OCP) governs photoprotection in the majority of cyanobacteria. It is structurally and functionally modular, comprised of a C-terminal regulatory domain (CTD), an N-terminal effector domain (NTD) and a ketocarotenoid; the chromophore spans the two domains in the ground state and translocates fully into the NTD upon illumination. Using both the canonical OCP1 from Fremyella diplosiphon and the presumably more primitive OCP2 paralog from the same organism, we show that an NTD-CTD heterodimer forms when the domains are expressed as separate polypeptides. The carotenoid is required for the heterodimeric association, assembling an orange complex which is stable in the dark. Both OCP1 and OCP2 heterodimers are photoactive, undergoing light-driven heterodimer dissociation, but differ in their ability to reassociate in darkness, setting the stage for bioengineering photoprotection in cyanobacteria as well as for developing new photoswitches for biotechnology. Additionally, we reveal that homodimeric CTD can bind carotenoid in the absence of NTD, and name this truncated variant the C-terminal domain-like carotenoid protein (CCP). This finding supports the hypothesis that the OCP evolved from an ancient fusion event between genes for two different carotenoid-binding proteins ancestral to the NTD and CTD. We suggest that the CCP and its homologs constitute a new family of carotenoproteins within the NTF2-like superfamily found across all kingdoms of life.
COMPARISON OF TWO AND THREE SPATIAL DIMENSIONAL SOLUTIONS OF THE WAVE EQUATION AT OCEAN-BASIN SCALES IN THE PRESENCE OF INTERNAL WAVES (2007)

Numerical solutions are given for a parabolic approximation to the acoustic wave equation at 75 Hz in two and three spatial dimensions to determine if azimuthal coupling of the field significantly affects horizontal coherence. Coupling is a small effect at 4000 km in the presence of internal gravity waves. This implies that accurate solutions are possible using computations from uncoupled vertical slices through the field. The shape of horizontal coherence is inconsistent with shapes given by two theories. Estimates of horizontal coherence at 4000 km and 25, 50, and 75 Hz are 10, 2, and 1 km respectively.
Advances in Cancer Immunotherapy (2016)

The mechanism of cancer immunotherapy is the use of immune system to treat cancer. And the Immune system is the built-in host defense mechanism which can fight against infectious agents as well as cancer. Since in 1940s, the first protective immunity against cancer was convincingly demonstrated with syn-geneic animal models, last century’s dream was to effectively prevent and cure cancers by immunological means. Individualized cancer therapy is a central goal of cancer biologists. In past years, this dream has slowly but surely become a reality. Immunotherapy is a rational means to this end—because the immune system can recognize a virtually limitless number of antigens secondary to the biology of genetic recombination in B and T lymphocytes. The Understanding of the interaction between cancer and immune system provides insights into mechanisms that can be exploited to disinhibit anti-tumor immune responses. This book covers the first-hand data in the field of cancer immunotherapy re-search, introducing the research status, the newest development, problems and outlook of cancer immunotherapy. The book is suitable for clinical practitioners and scientists; medical and medicinal students; medicinal researchers and those with an interest in cancer immunotherapy. Suggestions and opinions from read-ers are welcome.
Structural elucidation of polydopamine facilitated by ionic liquid solvation (2023)

Minimal understanding of the formation mechanism and structure of polydopamine (pDA) and its natural analogue, eumelanin, impedes the practical application of these versatile polymers and limits our knowledge of the origin of melanoma. The lack of conclusive structural evidence stems from the insolubility of these materials, which has spawned significantly diverse suggestions of pDA's structure in the literature. We discovered that pDA is soluble in certain ionic liquids. Using these ionic liquids (ILs) as solvents, we present an experimental methodology to solvate pDA, enabling us to identify pDA's chemical structure. The resolved pDA structure consists of self-assembled supramolecular aggregates that contribute to the increasing complexity of the polymer. The underlying molecular energetics of pDA solvation and a macroscopic picture of the disruption of the aggregates using IL solvents have been investigated, along with studies of the aggregation mechanism in water.
Glucocorticoid Induction of the Adipocyte Clone 5 Gene Requires High Cell Density (1991)

We have previously reported the identification of a glucocorticoid and cell-density inducible gene (clone 5) that appears to play a regulatory role in adipocyte differentiation. In the current studies we have more carefully investigated the interplay between cell growth or differentiation and the glucocorticoid responsiveness of clone 5 RNA. We find that inducibility by steroid hormone is independent of the differentiated state but surprisingly, occurs only when cells are at high cell density. In subconfluent TA1 cells clone 5 RNA is refractory to induction whereas well characterized glucocorticoid-inducible promoters such as the those from mouse mammary tumor virus and alpha-1-acid glycoprotein are induced under all conditions. These results point to the necessity of ancillary factors, absent in low density cell culture, that are required for glucocorticoid responsiveness of the clone 5 gene.
An Empirical Study of Modular Bias Mitigators and Ensembles (2022)

There are several bias mitigators that can reduce algorithmic bias in machine learning models but, unfortunately, the effect of mitigators on fairness is often not stable when measured across different data splits. A popular approach to train more stable models is ensemble learning. Ensembles, such as bagging, boosting, voting, or stacking, have been successful at making predictive performance more stable. One might therefore ask whether we can combine the advantages of bias mitigators and ensembles? To explore this question, we first need bias mitigators and ensembles to work together. We built an open-source library enabling the modular composition of 10 mitigators, 4 ensembles, and their corresponding hyperparameters. Based on this library, we empirically explored the space of combinations on 13 datasets, including datasets commonly used in fairness literature plus datasets newly curated by our library. Furthermore, we distilled the results into a guidance diagram for practitioners. We hope this paper will contribute towards improving stability in bias mitigation.
Supported iridium catalysts for the total oxidation of short chain alkanes and their mixtures: Influence of the support (2020)

Catalytic total oxidation of noxious volatile organic compounds (VOCs) is an important process to remove these compounds from the atmosphere. This is the first systematic study of the influence of the support on the activity of iridium oxide supported catalysts for the total oxidation of VOCs. Iridium catalysts supported on titania, γ-alumina, silica and zeolites have been prepared using different calcination temperatures. The activity for the total oxidation of short chain alkanes and their mixtures has been evaluated and the physicochemical properties characterized by N2 adsorption, XRD, (HR)TEM, EDX, CO-Chemisorption, TPR, XPS and Raman spectroscopy. Both the calcination temperature and the nature of the support of iridium catalysts play an important role for the catalytic performance. Silica, ZSM-5 zeolites and titania are suitable supports for IrOx, in contrast with γ-alumina. A strong influence of the Lewis acidity of the support on the turnover frequency of the iridium oxide is found. Additionally, for a given support, the calcination temperature has an effect on the catalytic activity. A possible size effect is discussed. However, the major controlling factor is the nature of the support. Therefore, our results provide a guideline towards a rational design of more active IrOx catalysts for the total oxidation of VOCs.
Reducing system dimensionality with long-range collective dipole-dipole interactions (2023)

Dimensionality plays a crucial role in long-range dipole-dipole interactions (DDIs). We demonstrate that a resonant nanophotonic structure modifies the apparent dimensionality in an interacting ensemble of emitters, as revealed by population decay dynamics. Our measurements on a dense ensemble of interacting quantum emitters in a resonant nanophotonic structure with long-range DDIs reveal an effective dimensionality reduction to $\bar{d} = 2.20 (12)$, despite the emitters being distributed in 3D. This contrasts the homogeneous environment, where the apparent dimension is $\bar{d} = 3.00$. Our work presents a promising avenue to manipulate dimensionality in an ensemble of interacting emitters.
Phase models with explicit time delays (1998)

Studying weakly connected oscillators leads to phase models. It has been proven recently that weakly connected oscillators with delayed interactions do not lead to phase models with time delays even when the delay is of the same order of magnitude as the period of oscillation. This has resulted in a fading interest in such models. We prove here that if the interaction delay between weakly connected oscillators is much longer than the period of oscillation, then the corresponding phase model does have an explicit time delay.
Quantitative immunoconfocal analysis of human myometrial gap junction connexin43 in relation to steroid hormone concentrations at term labour (1997)

The aim of this study was to quantify gap junction expression in the human myometrium in relation to progesterone and oestradiol concentrations, and to establish whether oxytocin-resistant dystocia is due to an abnormality in gap junction expression. Three groups of patients were investigated: (i) before labour (at term), (ii) normal labour and (iii) oxytocin-resistant dystocia (eight patients per group). For each patient, the concentrations of oestradiol and progesterone in maternal blood and in myometrial tissue were measured, and the number and area of immunostained connexin43 gap junctions per unit volume of tissue determined by quantitative analysis of digital images obtained by confocal microscopy. No significant difference in connexin43 gap junction content was observed between the three patient groups. When all groups were pooled, there was a significant positive correlation (P < 0.05) between the quantity of immunolabelled gap junctions and the oestradiol:progesterone ratio, but there was no significant difference in this correlation between the groups. Gap junction immunolabelling was not correlated with the progesterone or oestradiol concentration in the maternal blood or the myometrium. These data suggest that in human myometrium: (i) dystocia is not due to a reduced level of immunodetectable connexin43 gap junctions, (ii) onset of labour is not associated with a sudden increase in immunodetectable gap junction protein and (iii) gap junctions can be expressed in the presence of high progesterone concentrations.
Transplantation of Tissue-Engineered Epithelial Cell Sheets after Excimer Laser Photoablation Reduces Postoperative Corneal Haze (2006)

The transplantation of tissue-engineered epithelial cell sheets can successfully prevent the development of corneal haze after excimer laser keratectomy.
Supplementary Figure 6 from Stress Chaperone Mortalin Contributes to Epithelial-to-Mesenchymal Transition and Cancer Metastasis (2023)

&lt;p&gt;Correlation of mortalin amplification with other genes involved in human carcinogenesis. (A) Network showing correlation of mortalin amplification in Kidney Renal Clear Cell Carcinoma (RCCC, TCGA database) with other genes is shown. (B) Amplification of mortalin locus showed tight association and mutual exclusiveness with FGF1 and p53, respectively.&lt;/p&gt;
Overexpression of Manganese Superoxide Dismutase Prevents Photodynamic Therapy-Induced Porcine Esophageal Stricture (2004)

s for the 19th Annual Scientific Meeting of the International Society for Biological Therapy of Cancer, San Francisco, California, November 4-7, 2004: New Agents in Development
Antibacterial and antioxidant activity of catechin, gallic acid, and epigallocatechin-3-gallate: focus on nanoformulations (2023)

Up to one million secondary metabolites are found in plant species, some of which may have desirable therapeutic activities. Among these secondary metabolites, catechin, gallic acid, and epigallocatechin-3-gallate are natural phenolic compounds with promising antioxidant and antibacterial activity. However, these compounds have disadvantages of poor solubility, low bioavailability in physiological conditions, and side effects in patients. Therefore new strategies could rely on formulations with other synthetic and natural materials. Nanoformulations of secondary metabolites could be new efficient strategies to treat many chronic bacterial infections. Combinations and conjugates of catechin, gallic acid, and epigallocatechin-3-gallate with various antibiotics could reduce the dose of these compounds, increase their antibacterial activity, and decrease cytotoxicity against healthy cells. For instance, a smart combination of two or more secondary metabolites may improve therapeutic applications in physiological conditions. In this regard, the growth of antibiotic-resistant bacteria, specifically multidrug-resistant bacteria with overexpression of efflux pumps and expression of the penicillinase enzyme, has been inhibited significantly. According to recent investigations, this review will discuss the advances and challenges of new micro and nanoformulations of these natural products.
Quantifying the energetic cost tradeoffs of photovoltaic pumping systems for Sub-Saharan African smallholder farms (2023)

Abstract As solar technology has matured, irrigation using photovoltaic pumping systems (PVPSs) has gained popularity in developing markets as an effective means to alleviate poverty and increase food security. Yet, there remains a barrier to adoption; the upfront costs of PVPSs pose a financial burden for many low-income farmers. In a PVPS, the capital cost of the solar array contributes a large portion of upfront system costs. The solar pump is the largest energy consumer in the system, thus its efficiency directly impacts the size and cost of the solar array. There is a limited quantitative understanding of how solar pump efficiency affects the capital cost of the solar array. This study presents a technoeconomic framework to directly quantify the impact of solar pump efficiency on the cost of the solar array in a PVPS, for a range of hydraulic operating conditions. New empirical efficiency scaling laws were created by characterizing the efficiencies of 4-inch multistage centrifugal borehole pumps and induction motors. The utility of the technoeconomic framework is demonstrated through a case study comparing solar pump architectures with motors of different efficiencies. Results indicate that, despite the increased motor cost, the use of high-efficiency motors in solar pumps may lead to an overall cost reduction in a PVPS. Counter to the conventional capital cost-driven process, this work demonstrates that an efficiency-driven design process could improve low-cost, solar-powered system design. Engineers and system designers can leverage the presented framework during the design process to make informed decisions to achieve more cost-effective PVPSs.
J0330306 Estimation of Plateau Stress on Impact Test of Aluminum Foam Composite (2015)

Aluminum foam composite of aluminum alloy die casting ADC12 coated by pure aluminum A1050 was fabricated by friction stir welding (FSW) route precursor foaming method. Moreover, weight drop impact compression tests of the aluminum foam composites were carried out. We attempt to estimate the plateau stress of the aluminum foam composite based on the mean compressive stress on a maximum-porosity cross section perpendicular to the direction of compressive loading. Through the comparison of impact compression test results with the estimated results, it was expected that the plateau stress of the aluminum foam composite can be evaluated when the equivalent diameter of pores in ADC12 region is approximately equal to that of ADC12 uniform porous aluminum.