gebhart/patrepeval huggingface dataset:
Exploring functional variant discovery in non-coding regions with SInBaD (2012)

The thousand genomes project and many similar ongoing large-scale sequencing efforts require new methods to predict functional variants in both coding and non-coding regions in order to understand phenotype and genotype relationships. We report the design of a new model SInBaD (Sequence-Information-Based-Decision-model) which relies on nucleotide conservation information to evaluate any annotated human variant in all known exons, introns, splice junctions and promoter regions. SInBaD builds separate mathematical models for promoters, exons and introns, using the human disease mutations annotated in human gene mutation database as the training dataset for functional variants. The ten-fold cross validation shows high prediction accuracy. Validations on test datasets, demonstrate that variants predicted as functional have a significantly higher occurrence in cancer patients. We also applied our model to variants found in four different individual human genomes to identify a set of functional variants, which might be of interest for further studies. Scores for any possible variants for all annotated genes are available under http://tingchenlab.cmb.usc.edu/sinbad/. SInBaD supports the current standard format of genotyping, the variant call files (VCF 4.0), making it easy to integrate it into any existing next-generation sequencing pipeline. The accuracy of SNP detection poses the only limitation to the use of SInBaD.
Cooperative catalysis with binary Lewis acid–Lewis base system for the coupling of carbon disulfide and epoxides (2012)

The cycloaddition of epoxides with carbon disulfide proceeds effectively by using a binary catalyst system of tetradentate Schiff‐base aluminum complexes (designated as salenAlX) as Lewis acid in connection with a nucleophilic co‐catalyst, such as quaternary ammonium salt. The steric factor of the substituent groups on the aromatic rings of salenAlX and the anion of quaternary ammonium salt all have significant effects on the activity of the binary catalyst system, as well as the selectivities of the resultant cyclic products. The effects of temperature, time and the molar ratio of reactants were also investigated in detail with regard to propylene oxide with carbon disulfide, and a plausible mechanism was proposed. Copyright © 2012 John Wiley & Sons, Ltd.
Superconducting narrow band pass filters for advanced multiplexers (2002)

X-band microstrip filters with a 50-MHz-wide passband that provide 1.3-dB insertion loss at 77 K using copper ground planes have been built. Recent advances in double side coating of lanthanum aluminate substrates with YBa/sub 2/Cu/sub 3/O/sub 7- delta / will lower this figure to 0.6 dB. Circuit designs were evaluated for intermodulation distortion effects. An improvement over previous designs has increased the third-order output intercept point to +29 dBm. Methods of nondestructive dielectric and conductor loss testing were used to evaluate materials throughout the filter development.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
On Meaning in<i>Nutcracker</i> (1984)

Nutcracker has earned for itself such a secure place in repertoires and in the hearts of audiences that the problems it faced in its first production, and the criticisms it generated then, have dimmed to the point of being matters of specialist concern. They are a practical concern for the producer who would mount the work on the basis of the libretto published in 1892, for that libretto, as we shall observe, is flawed. The original collaborators, for reasons that are now unclear, nevertheless proceeded without amending it. Perhaps Ivan Vsevolozhsky, who had a hand in choosing the subject matter of the ballet and who drew its costume designs, was under pressure to produce something new in his other capacity as Director of Imperial Theatres. One can likewise only speculate why Marius Petipa, 73 years old at the time, withdrew from the production. Perhaps he was in fact ill, as he claimed; perhaps the realization of the libretto's flaws made illness prudent. But the most inexplicable question is why the fastidious Tchaikovsky continued work, for soon after beginning to compose he found the prospect of completing the ballet so vexing as to complain bitterly to Vsevolozhsky, and beg for respite. Tchaikovsky owed no small debt to Vsevolozhsky for advancing his career, it is true, but the demands of art took precedence even over his solicitous attitude toward the Director, and Vsevolozhsky knew this. Tchaikovsky, moreover, would not be expected to maintain appearances when dealing with such an important issue, as Petipa might have been, working day to day in the theatre. What made the composer continue? Certainty is beyond reach in establishing a definitive answer to this question. A number of conjectures, however, each by itself tentative but persuasive in concert with the others, may explain why Tchaikovsky stayed his course. The purpose here is to put forward that explanation, in the hope that the early history of Nutcracker will no longer be a concern of specialists alone, but will enhance the appreciation of this work for all lovers of ballet.
"Implementation of unimodal to multimodal biometrie feature level fusion of combining face iris and ear in multi-modal biometric system" (2017)

In this paper is on combining the features face ear and iris to single modal to multimodal combine of the obtain better accuracy improvement as compared to the privies system. The paper discusses a new research area to introduce ear as the feature for multimodal biometric our system is to implement a multimodal an multialgorithmic biometric system combining Ear iris and Face recognition. We have developed the secure facial features based authentication system Multi modal biometric system is one of the major areas of study identified with large applications in recognition system. Single modal-biometric systems have to challenge with a variety of problems such as intra-class variations, noisy data, non-universality and unacceptable error rates. Some of these limitations can be solved with multi modal Biometric systems. In this paper we are going implement a multi modal biometric system combining the feature of face iris and ear modalities to obtain better accuracy as compared to the privies based system.
Rollover risk prediction of heavy vehicle in interaction with infrastructure (2007)

This paper presents a concept of a warning system to prevent rollover of heavy vehicles. The system consists of several sensors which measure the heavy vehicle dynamics. Initially, these dynamics states are observed using observers, and then, knowing the infrastructure characteristics, the risk of rollover is predicted and assessed using the lateral acceleration of the vehicle, the height of the centre of gravity, and the Load Transfer Ratio (LTR). This coefficient is calculated using the estimated load on each wheel.
In vitro biosynthesis of bacterial peptidoglycan using d-Cys-containing precursors: fluorescent detection of transglycosylation and transpeptidation (2009)

Peptidoglycan precursors containing D-Cys at position 4 were polymerised to form a synthetic peptidoglycan layer, which could be fluorescently labelled, providing a new method to monitor peptidoglycan transglycosylation and transpeptidation.
Selective Down-Regulation of Glioma-Associated Oncogene 2 Inhibits the Proliferation of Hepatocellular Carcinoma Cells (2007)

The sonic hedgehog (Shh) pathway contributes to the initiation and progression of tumors with various origins when aberrantly activated. In this study, we investigated if the Shh pathway is important for the proliferation of hepatocellular carcinoma (HCC) cells and also began to identify which components of the pathway play a pivotal role in the biology of HCC. Expression levels of components in the pathway were measured, and glioma-associated oncogene (Gli) 2 levels were found to be considerably higher in human HCC lines compared with normal liver. Gli2 levels were also higher in tumor tissue from HCC patients compared with normal liver. Antisense oligonucleotides (ASO) were used to specifically down-regulate Gli2, and this led to decreased proliferation of various HCC cell lines. However, inhibition of Gli1 and Gli3 with ASOs did not decrease proliferation in most HCC cell lines and inhibitors targeting the upstream components of the pathway, including smoothened (Smo), displayed antiproliferative effects in only a subset of HCC cell lines. Moreover, in cancer cells harboring Smo mutations or unresponsive to the Smo inhibitor 3-keto-N-aminoethylaminoethylcaproyldihydrocinnamoyl cyclopamine, the Gli2 ASO was still able to inhibit proliferation. The importance of Gli2 in HCC proliferation was further confirmed by the changes in expression levels of genes, such as Bcl-2, c-Myc, and p27, following suppression of Gli2 expression. Taken together, these results suggest that, among the Gli transcription factors, Gli2 plays a predominant role in the proliferation of HCC cells and the suppression of Gli2 expression may provide a useful therapeutic option for the treatment of HCC.
Development of novel tunable light scattering coating materials for fiber optic diffusers in photodynamic cancer therapy (2009)

Abstract To homogenize light emitted from fiber optic diffusers for photodynamic therapy (PDT), novel coating materials with tunable properties were designed. A class VI medical grade UV‐curable acrylic resin for biomedical applications was used for the polymer matrix, and titanium dioxide (TiO 2 ) was added to the resin as a scattering agent. UV‐curability of coatings containing TiO 2 was significantly influenced by the grade and surface treatment of the TiO 2 studied. Despite using a free‐radical system without inert gas protection, all samples demonstrated considerable thermal postcuring. A novel TiO 2 surface treatment methodology was developed based on unsaturated alkoxyorganosilanes combined with unsaturated carboxylic acids for compatibilizing TiO 2 for use in the resin material studied. By adjusting the concentration of the surface‐modifying agent, the scattering efficiency and UV curability can be controlled by decreasing the effective particle size and enhancing the dispersibility of the powder filler within the resin. This modification will enable fine‐tuning of the effective size of TiO 2 particles to the wavelength of laser light to be scattered to maximize scattering efficiency in photodynamic cancer therapy and possibly also in other forms of cancer treatment (interstitial laser hyperthermia or interstitial laser photocoagulation). © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
Influence of acetyl-L-carnitine infusion on haemodynamic parameters and survival of circulatory-shock patients. (1991)

The clinical use of acetyl carnitine in circulatory shock has its theoretical basis in the ability of this molecule to restore enzyme activity inhibited by hypoxia, acting as an acetyl donor. Moreover the action of carnitine on an injured myocardium encouraged us to examine the clinical effect of this drug during heart failure. A double-blind clinical study was performed in ten Italian intensive care units on 115 patients with septic, cardiac of traumatic shock, by using acetyl-L-carnitine infusion for 12 hours, with a previous single bolus intravenously. The results showed a good response to the drug in terms of blood oxygenation during the course of sepsis and heart failure. The heart rate as well as right atrial pressure decreased significantly in patients with cardiogenic shock. In septic patients systolic and mean arterial pressures increased also. The present data suggests the use of acetyl-L-carnitine as an adjuvant to the commonly used therapy in hypoxic conditions.
Computer-assisted prediction, classification, and delimitation of protein binding sites in nucleic acids (1993)

We present a method to determine the location and extent of protein binding regions in nucleic acids by computer-assisted analysis of sequence data. The program ConsIndex establishes a library of consensus descriptions based on sequence sets containing known regulatory elements. These defined consensus descriptions are used by the program ConsInspector to predict binding sites in new sequences. We show the programs to correctly determine the significant regions involved in transcriptional control of seven sequence elements. The internal profile of relative variability of individual nucleotide positions within these regions paralleled experimental profiles of biological significance. Consensus descriptions are determined by employing an anchored alignment scheme, the results of which are then evaluated by a novel method which is superior to cluster algorithms. The alignment procedure is able to include several closely related sequences without biasing the consensus description. Moreover, the algorithm detects additional elements on the basis of a moderate distance correlation and is capable of discriminating between real binding sites and false positive matches. The software is well suited to cope with the frequent phenomenon of optional elements present in a subset of functionally similar sequences, while taking maximal advantage of the existing sequence data base. Since it requires only a minimum of seven sequences for a single element, it is applicable to a wide range of binding sites.
Highly Efficient TiO2 Film Photocatalyst. Degradation of Gaseous Acetaldehyde (1994)

Abstract A glass-supported pure anatase film with an extremely high photocatalytic activity has been prepared. Photocatalytic properties of the film were investigated by measuring the degradation of gaseous acetaldehyde under relatively strong (black fluorescent light) and weak (white fluorescent light) UV light irradiations. It was found that the photocatalytic efficiency was higher than that of Degussa P25, one of the most efficient commercial TiO2 powders.
Methional, a cellular metabolite, induces apoptosis preferentially in G2/M-Synchronized BAF3 murine lymphoid cells (1998)

We have previously shown that methional, derived from 4-methylthio-2-oxobutanoate, is a cellular mediator of apoptosis in BAF3 b0 murine lymphoid cells, which are dependent on IL3 for their growth in culture. When cells synchronized in S phase by double thymidine block were treated with methional immediately after thymidine withdrawal, methional was unable to induce DNA-strand breaks, whereas it inhibited the progression of cells from S to G2/M phases. This inhibition of cell cycle progression was associated with a 53% decrease in DNA synthesis. In contrast, when BAF3 b0 cells were synchronized in G2/M phase using SK&F 96365, and treated with methional immediately after drug removal, methional induced DNA-strand breaks in 49% of cells in 4 h, compared to 12% in controls. As contact time increased from 4 to 8 h, DNA-strand breaks increased to 94% in methional-treated cells compared to 11% in controls. These observations on G2/M-synchronized cells are different from those seen in BAF3b0 cells in G1 phase, 3 h after their release from the G2/M block, in that there was no decrease in size of the G1 population even after an additional 4 h incubation in the presence of methional. These results, taken together, provide a rational basis for using combinations of methional and G2/M blockers as inducers of DNA-strand breaks and apoptosis in murine lymphoid cells.
A Novel Method for Assessing Insulin Dose Adjustments by Patients with Diabetes (2007)

Background: Insulin treated diabetic patients often do not adjust their insulin doses. We developed a method to provide a quantitative and qualitative assessment of this behavior. Methods: Fourteen patients provided logbook pages of their self-monitoring of blood glucose (SMBG) data and insulin doses. We compared the actual decisions of patients in real-life to what they would decide on the same SMBG, as an a posteriori exercise. We also compared these decisions and those proposed by 6 diabetologists on the same sets of data to the recommendations made by HumaLink, an automated insulin dosage system. Results: 1) Patients in real-life modified their insulin doses least often. However, given a chance to make these decisions a posteriori, they modified their insulin doses more often. HumaLink proposed changes even more often, and diabetologists were the most aggressive in changing insulin doses. 2) The decisions proposed by the patients in real-life or a posteriori and by the diabetologists were compared to the recommendations made by HumaLink, using a decisions analysis grid (DAG). For these three groups, full disagreement with HumaLink (patient or physician increases while HumaLink decreases and the opposite) was observed for less than 5% of the cases. 3) By comparison to HumaLink, patient decisions seemed guided by the desire to avoid hypoglycemia. By contrast, decisions by diabetologists seemed often to be guided by the desire to avoid hyperglycemia. Conclusion: These methods provide an objective evaluation of insulin dose adjustments by patients with diabetes and may be useful to assess the effectiveness of educational programs.
Quercetin glycosides in Psidium guajava L. leaves and determination of a spasmolytic principle. (1994)

The traditional herbal remedy from Psidium guajava leaves has been medically proposed in Mexico as effective treatment of acute diarrhea. A methanolic leaf extract was subjected to a bioassay-guided isolation of spasmolytic constituents. Six fractions were separated on a polyvinylpolypyrrolidine (PVPP) column using a water methanol-gradient. The fraction containing flavonols inhibited peristalsis of guinea pig ileum in vitro. A trace of quercetin aglycone together with five glycosides was isolated from this active fraction and identified as quercetin 3-O-alpha-L-arabinoside (guajavarin); quercetin 3-O-beta-D-glucoside (isoquercetin); quercetin 3-O-beta-D-galactoside (hyperin); quercetin 3-O-beta-L-rhamnoside (quercitrin) and quercetin 3-O-gentobioside. Biological activity of each pure compound was studied in the same bioassay. Obtained results suggest that the spasmolytic activity of the Psidium guajava leaf remedy is mainly due to the aglycone quercetin, present in the leaf and in the extract mainly in the form of five flavonols, and whose effect is produced when these products are hydrolyzed by gastrointestinal fluid.
Emergence of protein fold families through rational design (2005)

Diverse proteins with similar structures are grouped into families of homologs and analogs, if their sequence similarity is higher or lower, respectively, than 20%-30%.It was suggested that protein homologs and analogs originate from a common ancestor and diverge in their distinct evolutionary time scales, emerging as a consequence of the physical properties of the protein sequence space.Although a number of studies have determined key signatures of protein family organization, the sequence-structure factors that differentiate the two evolution-related protein families remain unknown.Here, we stipulate that subtle structural changes, which appear due to accumulating mutations in the homologous families, lead to distinct packing of the protein core and, thus, novel compositions of core residues.The latter process leads to the formation of distinct families of homologs.We propose that such differentiation results in the formation of analogous families.To test our postulate, we developed a molecular modeling and design toolkit, Medusa, to computationally design protein sequences that correspond to the same fold family.We find that analogous proteins emerge when a backbone structure deviates only 1-2 A ˚root-mean-square deviation from the original structure.For close homologs, core residues are highly conserved.However, when the overall sequence similarity drops to ;25%-30%, the composition of core residues starts to diverge, thereby forming novel families of protein homologs.This direct observation of the formation of protein homologs within a specific fold family supports our hypothesis.The conservation of amino acids in designed sequences recapitulates that of the naturally occurring sequences, thereby validating our computational design methodology.
Measurement of relative state-to-state rate constants for the reaction D+H2(<i>v</i>, <i>j</i>)→HD(<i>v</i>′, <i>j</i>′)+H (1992)

We have measured state-to-state integral rate constants for the reaction D+H2(v,j) →HD(v′=0,1,2;j′)+H, in which the H2 reagent was either in the ground state, H2(v=0,j), or prepared in the first excited vibrational state, H2(v=1, j=1), by stimulated Raman pumping. Translationally hot D atoms were produced via UV photolysis of DI, generating two center-of-mass collision energies corresponding to the two I atom spin–orbit states. Resonance-enhanced multiphoton ionization and time-of-flight mass spectrometry were employed to detect the nascent HD product in a quantum-state-specific manner. Two experimental geometries were used: (1) a probe-laser-induced geometry, in which the same laser both initiated the reaction, by photolysis of DI, and detected the HD and (2) an independent-photolysis-source geometry, in which photolysis of DI was carried out by an independent laser. We find that vibrational excitation of the H2 reagent results in substantial HD rotational excitation for each product vibrational state, a shift in the vibrational product state distribution such that the rates for the reaction D+H2(v=1, j=1) into HD(v′=0) and HD(v′=1) are comparable, and somewhat surprisingly, almost no change in the total rate into HD(v′=0,1,2;j′). The experimental results are consistent with a model in which internal energy is conserved, i.e., internal energy of the reagents appears as internal energy of the products, while relative translational energy of the reagents appears primarily as translation of the products. Good to excellent agreement is found between the experiment and recent quantum-mechanical scattering calculations of Neuhauser, Judson, and Kouri. Minor discrepancies persist, however, between theory and experiment for some product rotational distributions.
Some Active Derivatives of Penicillin (1969)

The antibacterial activities of a number of amide derivatives of penicillin against both penicillin-sensitive and penicillin-resistant cultures were determined. Several of them were found to possess significant inhibitory activity against certain gram-positive bacteria. The amides, although resistant to the destructive action of beta-lactamase, did not protect G in competitive experiments. One derivative, the O-benzylhydroxamide of penicillin G, was active against six or eight penicillin-resistant strains of Staphylococcus aureus (minimal inhibitory concentration, 0.2 mug/ml or less), but was found to have only a minimal in vivo activity against mouse Streptococcus infections.
Switched control of bilinear converters via pseudolinearization (1989)

A method is proposed for designing regulating feedback control laws in bilinear networks such as the boost and the buck-boost DC-DC power supplies. A pseudolinearization approach is taken to the average pulsewidth modulated controlled model with physically meaningful local state coordinate transformations. For such transformations, the perturbed average model is independent of the operating point and exhibits a linear structure in Brunovsky's canonical form. The feedback regulation scheme is thus considerably simplified from the conceptual viewpoint.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>