gebhart/patrepeval huggingface dataset:
22 Predicting RNA Secondary Structure (2006)

In the “RNA World” hypothesis, RNA is the molecule responsible for both catalysis and transmission of genetic information. In various ways, RNA still performs these functions. To function as more than an information carrier, RNA must fold into specific three-dimensional shapes. Determining the canonical base-pairing, i.e., secondary structure, of RNA is the cornerstone for predicting three-dimensional structure (Turner et al. 1988; Chapter 23) because helices in RNA are usually stronger than the tertiary interactions that connect elements of secondary structure (Crothers et al. 1974; Banerjee et al. 1993; Jaeger et al. 1993; Laing and Draper 1994; Tinoco and Bustamante 1999). The folding of RNA may be determined by kinetics or thermodynamics or both. The observations that many known RNAs can be renatured outside the cell and that the secondary structures of domains of less than 500 nucleotides can be predicted with about 73% accuracy from known thermodynamics (Mathews et al. 1999a, 2004a) suggest that their functional folds are largely determined by thermodynamics. Thus, thermodynamics can be a useful tool for interpreting in vitro experiments of RNA evolution and providing insight into the early stages of natural selection. Folding of an RNA chain is a unimolecular reaction:(1)U⇌F   K=[F]/[U]=e-ΔGo/RT Here, K is the equilibrium constant giving the ratio of concentrations for folded, F, and unfolded, U, species at equilibrium; Δ G ° is the standard free-energy difference between F and U; R is the gas constant, 1.987 cal K −1 mole −1 ; and T is the temperature in kelvins. The challenge of predicting secondary...
Ovarian Function in Superoxide Dismutase 1 and 2 Knockout Mice (1998)

Copper/zinc superoxide dismutase (SOD1) and manganese superoxide dismutase (SOD2) are the two major intracellular enzymes which inactivate superoxide radicals. SOD1 is present in both cytoplasmic and nuclear compartments whereas SOD2 is localized to mitochondria. Both enzymes are expressed in multiple tissues as well as ovaries of several species including humans and rodents. Dominant mutations in SOD1 are associated with amyotrophic lateral sclerosis. We have previously demonstrated that SOD2-deficient mice die within three weeks of birth due to oxidative mitochondrial injury in central nervous system neurons and cardiac myocytes. In this report, we demonstrate that female homozygous mutant mice lacking SOD1 can survive to the adult stage but are subfertile. Whereas breeding of 5 SOD1 heterozygote females produced an average of 1.0 litter/month with 8.6 offspring/litter (n = 31 litters), only 11 of 16 SOD1 homozygote mice over a 2-6 month period became pregnant averaging 0.23 litters/month with an average litter size of 2.7 (n = 21 litters). Histological analysis of the ovaries from SOD1-deficient mice often reveals many primary and small antral follicles but few corpora lutea. In addition, ovaries from postnatal SOD2-deficient mice, transplanted to the bursa of wild-type hosts, show all stages of folliculogenesis including corpora lutea and can give rise to viable offspring. These studies support an important role of SOD1 in female reproductive function and suggest that SOD2 is not essential for ovarian function.
Effect of Ion Distribution on Conductivity of Block Copolymer Electrolytes (2009)

Energy-filtered transmission electron microscopy (EFTEM) was used to determine the distribution of lithium ions in solid polymer electrolytes for lithium batteries. The electrolytes of interest are mixtures of bis(trifluoromethane)sulfonimide lithium salt and symmetric poly(styrene-block-ethylene oxide) copolymers (SEO). In contrast to current solid and liquid electrolytes, the conductivity of SEO/salt mixtures increases with increasing molecular weight of the copolymers. EFTEM results show that the salt is increasingly localized in the middle of the poly(ethylene oxide) (PEO) lamellae as the molecular weight of the copolymers is increased. Calculations of the inhomogeneous local stress field in block copolymer microdomains, modeled using self-consistent field theory, provide a quantitative explanation for this observation. These stresses, which increase with increasing molecular weight, interfere with the ability of PEO chains to coordinate with lithium cations near the walls of the PEO channels where ion mobility is expected to be low.
Measurement and modeling of scintillation intensity to estimate turbulence parameters in an Earth-space path (1984)

The theoretical and experimental aspects of the analysis of amplitude scintillations as a possible practical remote-sensing tool of atmospheric turbulence parameters with special emphasis on earth-space paths are explored. Theoretical studies and experimentation reveal that the scintillation variance when complemented with spectral analysis and suitable modeling of the path leads to realistic values of the parameters. A layered turbulent structure has been studied in particular, the strategy of data analysis is given in detail, and the limitations due to the cross-path wind profile are discussed.
Porphyromonas gingivalis lipopolysaccharide lipid A heterogeneity: differential activities of tetra- and penta-acylated lipid A structures on E-selectin expression and TLR4 recognition (2006)

Porphyromonas gingivalis is a gram-negative bacterium strongly associated with periodontitis, a chronic inflammatory disease of the tissue surrounding the tooth root surface. Lipopolysaccharide (LPS) obtained from P. gingivalis is unusual in that it has been shown to display an unusual amount of lipid A heterogeneity containing both tetra- and penta-acylated lipid A structures. In this report, it is shown that penta-acylated lipid A structures facilitate E-selectin expression whereas tetra-acylated lipid A structures do not. Furthermore, it is shown that tetra-acylated lipid A structures are potent antagonists for E-selectin expression. Both tetra- and penta-acylated lipid A structures interact with TLR4 although experiments utilizing human, mouse and human/mouse chimeric TLR4 proteins demonstrated that they interact differentially with the TLR4 signalling complexes. The presence of two different structural types of lipid A in P. gingivalis LPS, with opposing effects on the E-selectin response suggests that this organism is able to modulate innate host responses by alterations in the relative amount of these lipid A structures.
From Microporous Regular Frameworks to Mesoporous Materials with Ultrahigh Surface Area: Dynamic Reorganization of Porous Polymer Networks (2008)

High surface area organic materials featuring both micro- and mesopores were synthesized under ionothermal conditions via the formation of polyaryltriazine networks. While the polytrimerization of nitriles in zinc chloride at 400 degrees C produces microporous polymers, higher reaction temperatures induce the formation of additional spherical mesopores with a narrow dispersity. The nitrogen-rich carbonaceous polymer materials thus obtained present surface areas and porosities up to 3300 m(2) g(-1) and 2.4 cm(3) g(-1), respectively. The key point of this synthesis relies on the occurrence of several high temperature polymerization reactions, where irreversible carbonization reactions coupled with the reversible trimerization of nitriles allow the reorganization of the dynamic triazine network. The ZnCl2 molten salt fulfills the requirement of a high temperature solvent, but is also required as catalyst. Thus, this dynamic polymerization system provides not only highly micro- and mesoporous materials, but also allows controlling the pore structure in amorphous organic materials.
Transcutaneous Intrafold Injection for Unilateral Vocal Fold Paralysis: Functional Results (1990)

This paper presents the technique of transcutaneous intrafold silicone injection and the functional results of 44 procedures in 42 patients. The injection is given under local anesthesia with the patient in a supine position. The needle is inserted through the cricothyroid space. The location of the needle as well as the effect of injection is monitored by means of a fiberscope connected to a television camera and screen. The preoperative and postoperative vocal function was multidimensionally evaluated with the use of a test battery consisting of the maximum phonation time (MPT), mean airflow rate (MFRc), fundamental frequency (F0) range and sound pressure level (SPL) range of phonation, pitch perturbation quotient (PPQ), amplitude perturbation quotient (APQ), and normalized noise energy (NNEa). In the majority of the patients, MPT, F0 range, and SPL range increased and MFRc, PPQ, APQ, and NNEa decreased postoperatively. In the overall evaluation based on the test values of these parameters, the result was excellent for 16 procedures, good for 16, fair for 7, and poor for 5. The most frequent cause of failure was an insufficient amount injected.
Identification of heme-binding proteins in the cell membranes of Vibrio anguillarum (1996)

Two strains of Vibrio anguillarum belonging to O1 and O2 serotypes were examined for their ability to bind hemin and hemoglobin. Whole cells as well as membrane extracts from both strains could clearly bind hemin and hemoglobin constitutively. Hemoglobin binding was completely inhibited by a 100-fold excess of unlabelled hemoglobin and also by hemin, suggesting the existence of specific receptors for heme groups in the cell membranes. Several hemin-binding and hemoglobin-binding bands with similar molecular sizes were detected in polyacrylamide gels as well as in Western blots. Only two of these protein bands in both strains were iron-regulated while the others were independent of the cell iron status. We conclude that both serotypes of V. anguillarum possess heme-binding abilities by means of membrane proteins.
Avoidance of Manual Labeling in Robotic Autonomous Navigation Through Multi-Sensory Semi-Supervised Learning (2017)

Imitation learning holds the promise to address challenging robotic tasks such as autonomous navigation. It however requires a human supervisor to oversee the training process and send correct control commands to robots without feedback, which is always prone to error and expensive. To minimize human involvement and avoid manual labeling of data in the robotic autonomous navigation with imitation learning, this paper proposes a novel semi-supervised imitation learning solution based on a multi-sensory design. This solution includes a suboptimal sensor policy based on sensor fusion to automatically label states encountered by a robot to avoid human supervision during training. In addition, a recording policy is developed to throttle the adversarial affect of learning too much from the suboptimal sensor policy. This solution allows the robot to learn a navigation policy in a self-supervised manner. With extensive experiments in indoor environments, this solution can achieve near human performance in most of the tasks and even surpasses human performance in case of unexpected events such as hardware failures or human operation errors. To best of our knowledge, this is the first work that synthesizes sensor fusion and imitation learning to enable robotic autonomous navigation in the real world without human supervision.
High impedance fault detection for industrial power systems (2003)

The authors describe the characteristics of high-impedance faults and the most effective techniques for detecting them. The benefits of high-impedance fault detection for industrial power systems are identified. It is shown that the most effective high-impedance-fault detection system incorporates several algorithms and monitors a number of parameters to ensure sensitivity and correct operation. Operating the detector in an alarm mode improves safety and fault location with minimal effect on service continuity. A valuable use for such a detector would be the identification of incipient faults, so that critical loads can be switched to another source before the fault becomes bolted and requires the circuit to be cleared. Using a detector in this way could save substantial down-time costs for critical processes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The glycosylation of human synovial lubricin: implications for its role in inflammation (2010)

Acidic proteins were isolated from synovial fluid from two osteoarthritic and two rheumatoid arthritic patients and identified by MS. It was found that the most abundant protein in all of the samples was the mucin-like protein lubricin. Further characterization of lubricin from the different patients by LC (liquid chromatography)-MS of released oligosaccharides showed that the core 1 O-linked oligosaccharides NeuAc alpha2-3Gal beta1-3GalNAc and NeuAc alpha2-3Gal beta1-3(NeuAc alpha2-6)GalNAc were the dominating structures on lubricin. The latter was found to be more prevalent in the rheumatoid arthritis samples, indicating that sialylation is up-regulated as part of the inflammatory response. In addition to these dominating structures, core 2 structures were also found in low amounts, where the largest was the disialylated hexasaccharide corresponding to the sequence NeuAc alpha2-3Ga lbeta1-3(NeuAc alpha2-3Gal beta1-3/4GlcNAc beta1-6)GalNAc. It was also found that a small proportion of the core 2 oligosaccharides carried sulfate. The ability of lubricin to present complex glycosylation reflecting the state of the joint tissue makes lubricin a candidate as a carrier of inflammatory oligosaccharide epitopes. In particular, it was shown that lubricin from inflamed arthritic tissue was recognized by the antibody MECA-79 and thus carried the sulfated epitope proposed to be part of the L-selectin ligand that is responsible for recruitment of leucocytes to inflammatory sites.
The Rapalogue, CCI-779, Improves Salivary Gland Function following Radiation (2014)

The standard of care for head and neck cancer typically includes surgical resection of the tumor followed by targeted head and neck radiation. However depending on tumor location and stage, some cases may not require surgical resection while others may be treated with chemoradiation. Unfortunately, these radiation treatments cause chronic negative side effects for patients. These side effects are associated with damage to surrounding normal salivary gland tissue and include xerostomia, changes in taste and malnutrition. The underlying mechanisms of chronic radiation-induced salivary gland dysfunction are unknown, however, in rodent models persistently elevated proliferation is correlated with reduced stimulated salivary flow. The rapalogue, CCI-779, has been used in other cell systems to induce autophagy and reduce proliferation, therefore the aim of this study was to determine if CCI-779 could be utilized to ameliorate chronic radiation-induced salivary gland dysfunction. Four to six week old Atg5f/f; Aqp5-Cre, Atg5+/+; Aqp5-Cre and FVB mice were treated with targeted head and neck radiation. FVB mice were treated with CCI-779, chloroquine, or DMSO post-radiation. Stimulated salivary flow rates were determined and parotid and submandibular salivary gland tissues were collected for analyses. Mice with a defect in autophagy, via a conditional knockout of Atg5 in the salivary glands, display increased compensatory proliferation in the acinar cell compartment and hypertrophy at 24-72 hours following radiation. FVB mice treated with post-therapy CCI-779 have significant improvements in salivary gland physiology as determined by stimulated salivary flow rates, proliferation indices and amylase production and secretion. Consequently, post-radiation use of CCI-779 allows for improvement of salivary gland function and reestablishment of glandular homeostasis. As CCI-779 is already FDA approved for other uses, it could have a secondary use to alleviate the chronic side effects in head and neck cancer patients who have completed anti-tumor therapy.
Query estimation by adaptive sampling (2003)

The ability to provide accurate and efficient result estimations of user queries is very important for the query optimizer in database systems. In this paper, we show that the traditional estimation techniques with data reduction points of view do not produce satisfiable estimation results if the query patterns are dynamically changing. We further show that to reduce query estimation error, instead of accurately capturing the data distribution, it is more effective to capture the user query patterns. In this paper, we propose query estimation techniques that can adapt to user query patterns for more accurate estimates of the size of selection or range queries over databases.
Alphavirus Vectors: Applications for DNA Vaccine Production and Gene Expression (2000)

Replication-deficient alphavirus vectors have been developed for efficient high-level transgene expression. The broad host range of alphaviruses has allowed infection of a wide variety of mammalian cell lines and primary cultures. Particularly, G protein-coupled receptors have been expressed at high levels and subjected to binding and functional studies. Expression in suspension cultures has greatly facilitated production of large quantities of recombinant proteins for structural studies. Injection of recombinant alphavirus vectors into rodent brain resulted in local reporter gene expression. Highly neuron-specific expression was obtained in hippocampal slice cultures in vivo. Additionally, preliminary studies in animal models suggest that alphavirus vectors can be attractive candidates for gene therapy applications. Traditionally alphavirus vectors, either attenuated strains or replication-deficient particles, have been used to elicit efficient immune responses in animals. Recently, the application of alphaviruses has been extended to naked nucleic acids. Injection of DNA as well as RNA vectors has demonstrated efficient antigen production. In many cases, protection against lethal challenges has been obtained after immunization with alphavirus particles or nucleic acid vectors. Alphavirus vectors can therefore be considered as potentially promising vectors for vaccine production.
The properties of solutions of copper salts in pyridine and quinoline (1960)

M. Parris and R. J. P. Williams, Discuss. Faraday Soc., 1960, 29, 240 DOI: 10.1039/DF9602900240
Virion and soluble antigens of japanese encephalitis virus (1975)

Japanese encephalitis virions contain a 58 X 10-3-molecular-weight envelope glycoprotein antigen that can be solubilized with sodium lauryl sulfate and separated from other virion structural polypeptides and viral ribonucleic acid by gel filtration chromatography. The 58 X 10-3-molecular-weight envelope protein is the major antigen responsible for cross-reactivity of the virion in complement fixation tests with other closely related arboviruses. A naturally occurring soluble complement-fixing antigen is found in Japanese encephalitis mouse brain preparations after removal of particulate antigens. After partial purification by gel filtration and isoelectric focusing, the 53 X 10-3-molecular weight soluble complement-fixing antigen is more type specific than the Japanese encephalitis envelope antigen in complement fixation tests. Further, the Japanese encephalitis soluble complement-fixing antigen is stable to treatment with sodium lauryl sulfate and 2-mercaptoethanol, whereas virion complement-fixing antigens are unstable after this treatment.
Purification and characterization of furin, a Kex2-like processing endoprotease, produced in Chinese hamster ovary cells. (1992)

Furin, a mammalian homolog of the yeast Kex2 protease, is associated with Golgi membranes and is involved in cleavage of precursor proteins at sites marked by the Arg-X-Lys/Arg-Arg (RXK/RR) motif. We have recently shown that a furin mutant lacking the transmembrane domain can be secreted from cDNA-transfected cells with proteolytic activity for the fluorogenic peptide t-butoxycarbonyl-Arg-Val-Arg-Arg-4-methylcoumarin-7- amide. In this study, we purified and characterized the recombinant furin from the conditioned medium of these cells. Furin was purified as a mixture of 83- and 81-kDa forms and a 96-kDa form. The differences in molecular mass were not due to differences in molecular mass were not due to differences in glycosylation. Moreover, all forms had the same NH2-terminal sequence beginning at the residue after the Arg-Ala-Lys-Arg sequence. These data suggest that the three different forms may be produced by differential COOH-terminal processing of a furin molecule and that mature furin may be autocatalytically produced. Both enzyme preparations showed a pH optimum at 7.0, required Ca2+ for the activity, and showed essentially the same inhibitor profile. These properties resembled those of the Kex2 protease. Both preparations efficiently cleaved fluorogenic peptides with an RXK/RR sequence and moderately cleaved a peptide with an RXXR sequence, but did not cleave dibasic peptides. The sequence requirements determined in vitro were compatible with those determined by expression studies in cultured cells. These data unequivocally demonstrate that furin is an endogenous cellular protease responsible for cleavage of precursor proteins mainly at RXK/RR sites.
Transcranial magnetic stimulation: studying the brain--behaviour relationship by induction of ‘virtual lesions’ (1999)

Transcranial magnetic stimulation (TMS) provides a non-invasive method of induction of a focal current in the brain and transient modulation of the function of the targeted cortex. Despite limited understanding about focality and mechanisms of action, TMS provides a unique opportunity of studying brain-behaviour relations in normal humans. TMS can enhance the results of other neuroimaging techniques by establishing the causal link between brain activity and task performance, and by exploring functional brain connectivity.
China Incorporated: The First Corporation Law of the People's Republic of China (1995)

Effective since 1994, the first national corporation law of the People's Republic of China ("PRC" or "China") pursues a distinctive mission: to meld the organizational structure of Western capitalist business into a political and economic regime that maintains socialist principles and goals. The Eighth National People's Congress adopted the Corporation Law ("Law") in 1993, plainly modeling it on American and other Western corporation codes. The Law, however, should not be expected to produce business entities comparable to American corporations in the near future.
The Specificity of Nitroxyl Chemistry Is Unique Among Nitrogen Oxides in Biological Systems (2011)

The importance of nitric oxide in mammalian physiology has been known for nearly 30 years. Similar attention for other nitrogen oxides such as nitroxyl (HNO) has been more recent. While there has been speculation as to the biosynthesis of HNO, its pharmacological benefits have been demonstrated in several pathophysiological settings such as cardiovascular disorders, cancer, and alcoholism. The chemical biology of HNO has been identified as related to, but unique from, that of its redox congener nitric oxide. A summary of these findings as well as a discussion of possible endogenous sources of HNO is presented in this review.