gebhart/patrepeval huggingface dataset:
Two sequence- and two structure-based ML models have learned different aspects of protein biochemistry (2023)

Deep learning models are seeing increased use as methods to predict mutational effects or allowed mutations in proteins. The models commonly used for these purposes include large language models (LLMs) and 3D Convolutional Neural Networks (CNNs). These two model types have very different architectures and are commonly trained on different representations of proteins. LLMs make use of the transformer architecture and are trained purely on protein sequences whereas 3D CNNs are trained on voxelized representations of local protein structure. While comparable overall prediction accuracies have been reported for both types of models, it is not known to what extent these models make comparable specific predictions and/or generalize protein biochemistry in similar ways. Here, we perform a systematic comparison of two LLMs and two structure-based models (CNNs) and show that the different model types have distinct strengths and weaknesses. The overall prediction accuracies are largely uncorrelated between the sequence- and structure-based models. Overall, the two structure-based models are better at predicting buried aliphatic and hydrophobic residues whereas the two LLMs are better at predicting solvent-exposed polar and charged amino acids. Finally, we find that a combined model that takes the individual model predictions as input can leverage these individual model strengths and results in significantly improved overall prediction accuracy.
Elongation Factor Ts Can Act as a Steric Chaperone by Increasing the Solubility of Nucleotide Binding-Impaired Elongation Factor-Tu (2001)

Several elongation factor (EF) Tu mutants (T25A, H22Y/T25S, D80N, D138N) that have impaired nucleotide binding show decreased solubility on overexpression in the E. coli cell, an indication that they do not fold correctly. Moreover, EF-Tu[T25A] and EF-Tu[D80N] were shown to inhibit cell growth on expression, an effect attributed to their sequestration of EF-Ts [Krab, I. M., and Parmeggiani, A. (1999) J. Biol. Chem. 274, 11132--11138; Krab, I. M., and Parmeggiani, A. (1999) Biochemistry 38, 13035--13041]. We present here results showing that the co-overexpression of EF-Ts at a 1:1 ratio dramatically improves the solubility of mutant EF-Tu, although in the case of EF-Tu[D138N]--which cannot at all bind the nucleotides available in the cell--this is a slow process. Moreover, with co-overexpression of EF-Ts, the mentioned growth inhibition is relieved. We conclude that for the formation of a correct EF-Tu structure the nucleotide plays an important role as a "folding nucleus", and also that in its absence EF-Ts can act as a folding template or steric chaperone for the correct folding of EF-Tu.
Visible-light-driven Ag/Ag3PO4-based plasmonic photocatalysts: Enhanced photocatalytic performance by hybridization with graphene oxide (2012)

An efficient visible-light-driven plasmonic photocatalyst with regard to graphene oxide (GO) hybridized Ag/Ag3PO4 (Ag/Ag3PO4/GO) nanostructures has been facilely synthesized via a deposition-precipitation method. The synthesized nanostructures have been characterized by means of scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), UV-vis spectra, Fourier transform infrared spectra (FT-IR), X-ray photoelectron spectroscopy (XPS), and Raman spectra. It has been disclosed that compared with the bare Ag/Ag3PO4 nanospecies, the GO hybridized nanostructures display enhanced photocatalytic activity for the photodegradation of methyl orange pollutant under visible-light irradiation. It is suggested that the reinforced charge transfer and the suppressed recombination of electron-hole pairs in Ag/Ag3PO4/GO, the smaller size of Ag/Ag3PO4 nanospecies in Ag/Ag3PO4/GO, all of which are the consequences of the hybridization of GO, are responsible for the enhanced photocatalytic performance. The investigation might open up new opportunities to obtain highly efficient Ag3PO4-based visible-light-driven plasmonic photocatalyst for the photodegradation of organic pollutants.
Efficient table lookup algorithms for the next generation IP networks (2005)

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Highly heat conductive open‐porous aluminium fibre based parts for advanced heat transfer applications (2012)

Abstract Due to their oxygen affinity, aluminium alloys are difficult‐to‐sinter materials. Either mechanical destruction or the action of a liquid phase can be used to break oxide layers and thus achieve the desired diffusion bonds between the individual particles. In the present work, a liquid phase sintering approach is used in conjunction with high‐purity particulates and controlled processing conditions in order to obtain high‐purity, high‐porosity (up to 90 %) parts with an exclusively open porosity. Appropriate sinter conditions were determined with the help of thermodynamic calculations using the PANDAT software package. Bonding of the sintered fibre structures to tubes, sheets and other massive structures may be achieved by co‐sintering or brazing. The resulting metallic contacts allow for excellent heat transfer between the fibre structure and heat‐carrying fluids. These advantageous properties may be exploited in applications such as adsorption cooling devices or very fast phase‐change material (PCM) heat‐storage devices. The present study reports on the manufacturing of such PCM‐aluminium fibre compounds and their performance measured on a PCM storage demonstrator run in a laboratory environment.
Supervised Detection of Regulatory Motifs in DNA Sequences (2003)

Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural motifs in DNA sequences. Commonly used methods (e.g. MEME, Gibbs motif sampler) model binding sites as families of sequences described by a position weight matrix (PWM) and identify PWMs that maximize the likelihood of observed sequence data under a simple multinomial mixture model. This model assumes that the positions of the PWM correspond to independent multinomial distributions with four cell probabilities. We address supervising the search for DNA binding sites using the information derived from structural characteristics of protein-DNA interactions. We extend the simple multinomial mixture model to a constrained multinomial mixture model by incorporating constraints on the information content profiles or on specific parameters of the motif PWMs. The parameters of this extended model are estimated by maximum likelihood using a nonlinear constraint optimization method. Likelihood-based cross-validation is used to select model parameters such as motif width and constraint type. The performance of COMODE is compared with existing motif detection methods on simulated data that incorporate real motif examples from Saccharomyces cerevisiae. The proposed method is especially effective when the motif of interest appears as a weak signal in the data. Some of the transcription factor binding data of Lee et al. (2002) were also analyzed using COMODE and biologically verified sites were identified.
Pair and swap: An approach to graceful degradation for dependable chip multiprocessors (2010)

In this paper, we propose a processor-level fault tolerance technique called “Pair and Swap (P&S)” for a multi-core chip. In the P&S system, a 2n-cores-CMP (Chip Multiprocessor) which contains 2n processor cores composes n pairs. Two identical copies of a given task are executed on each pair of two processor cores and the results are compared repeatedly. If a fault is detected by a mismatch, partners of the mismatched pair are swapped with another pair and the mismatched task is re-executed from the latest checkpoint. Then, it is decided whether the fault is transient or permanent. If it is permanent, the faulty core is identified and isolated to reconfigure the entire system. P&S enables graceful degradation and tolerates both permanent and transient faults. We evaluate the performance of the proposed P&S and traditional triple module redundancy (TMR) using the Markov chains. The mean computation to failure of the P&S is about 1.4 times larger than that of dynamic TMR scheme.
The repertoire of mutational signatures in human cancer (2020)

Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic mutational signature<sup>1</sup>. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium<sup>2</sup> of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we characterized mutational signatures using 84,729,690 somatic mutations from 4,645 whole-genome and 19,184 exome sequences that encompass most types of cancer. We identified 49 single-base-substitution, 11 doublet-base-substitution, 4 clustered-base-substitution and 17 small insertion-and-deletion signatures. The substantial size of our dataset, compared with previous analyses<sup>3-15</sup>, enabled the discovery of new signatures, the separation of overlapping signatures and the decomposition of signatures into components that may represent associated-but distinct-DNA damage, repair and/or replication mechanisms. By estimating the contribution of each signature to the mutational catalogues of individual cancer genomes, we revealed associations of signatures to exogenous or endogenous exposures, as well as to defective DNA-maintenance processes. However, many signatures are of unknown cause. This analysis provides a systematic perspective on the repertoire of mutational processes that contribute to the development of human cancer.
The Strecker reaction: kinetic and equilibrium studies of cyanide addition to iminium ionsElectronic supplementary information (ESI) available: derivation of eqn. (8). See http://www.rsc.org/suppdata/ob/b4/b407853e/ (2004)

Kinetics studies are reported of the reactions of benzylidene benzylamine 4a, and of benzylidene allylamine 4b, with cyanide in aqueous buffers to give the corresponding [small alpha]-aminonitriles. The results allow the calculation of values of rate and equilibrium constants for reaction of the iminium ions formed from 4a and 4b with cyanide ions. These values are compared with those, obtained from the hydrolysis reactions, for reaction of the iminium ions with hydroxide ions and with water. Comparison with some other iminium ions reveals that those formed from 4a and 4b are relatively unreactive due to the possibilities of charge delocalisation.
Structure of the Dicyanophosphide Ion in a Crown‐Ether Sodium Salt (1979)

Comparably large positively and negatively charged structural units are present in the lattice of the 1:1:1: complex of NaP(CN) 2 , [18]crown‐6, and tetrahydrofuran: Na + /crown ether/2 THF and Na + /crown ether/2P(CN) . The P(CN) ion is planar and bent; the calculated structure is essentially confirmed by X‐ray structure analysis. P/CN interaction is slight.
Enantioselective Copper‐Catalyzed Borylative Cyclization for the Synthesis of Quinazolinones (2021)

Quinazolinones are common substructures in molecules of medicinal importance. We report an enantioselective copper-catalyzed borylative cyclization for the assembly of privileged pyrroloquinazolinone motifs. The reaction proceeds with high enantio- and diastereocontrol, and can deliver products containing quaternary stereocenters. The utility of the products is demonstrated through further manipulations.
Applications of optimization to mathematical finance (1997)

auteur qui protge cette thse.Ni la thse ni des extraits substantiels de celle-ci ne doivent tre imprims ou autrement reproduits sans son autorisation.
On the molecular basis and regulation of cellular capacitative calcium entry: Roles for Trp proteins (1996)

During the last 2 years, our laboratory has worked on the elucidation of the molecular basis of capacitative calcium entry (CCE) into cells. Specifically, we tested the hypothesis that CCE channels are formed of subunits encoded in genes related to the Drosophila trp gene. The first step in this pursuit was to search for mammalian trp genes. We found not one but six mammalian genes and cloned several of their cDNAs, some in their full length. As assayed in mammalian cells, overexpression of some mammalian Trps increases CCE, while expression of partial trp cDNAs in antisense orientation can interfere with endogenous CCE. These findings provided a firm connection between CCE and mammalian Trps. This article reviews the known forms of CCE and highlights unanswered questions in our understanding of intracellular Ca2+ homeostasis and the physiological roles of CCE.
The assessment of near vision. (1975)

There are many variables in the physiology of near vision, the end-point criteria, the types available, and the measurements made. I have suggested a hard criterion of the smallest print at the nearest distance. This controls the physiological variables and provides repeatable data for the evaluation of vision, accommodation, and binocular function.
Test-access-mechanism optimization for multi-Vdd SoCs (2015)

The use of multiple voltage levels introduces new challenges for testing Multi-V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dd</sub> SoCs. Time-Division-Multiplexing (TDM) tackles many of these challenges and offers very effective test-schedules. However, the effectiveness of TDM for minimizing test time depends on the Test-Access-Mechanism (TAM) in the SoC. Single-V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dd</sub> TAM optimization techniques consider neither the highly constrained test environment of multi-V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dd</sub> SoCs nor the benefits provided by TDM, therefore they are not suitable for multi-V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dd</sub> SoCs. In this paper, we propose the first TAM optimization technique for multi-V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dd</sub> SoCs. The proposed method exploits unique scheduling opportunities and flexibility offered by TDM, and by the means of a Branch-&-Bound approach, it quickly identifies the most effective TAM configurations. Experiments using SoCs from industry highlight the benefits of the proposed technique on multi-V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dd</sub> designs, for both single-site and multi-site test applications.
Quantitative determination of enhydrin in leaf rinse extracts and in glandular trichomes of Smallanthus sonchifolius (Asteraceae) by reversed‐phase high‐performance liquid chromatography (2005)

A simple, reliable and rapid reversed-phase HPLC-PAD procedure for the characterisation and quantitative determination of the anti-diabetic sesquiterpene lactone enhydrin (1) from Smallanthus sonchifolius (yacón) has been evaluated and validated. The approach focused on the analysis of various leaf rinse extracts, as well as the glandular trichomes of intact leaves, in which 1 was the major compound detected. The best sample preparation of a rinse extract yielded 0.67 mg/mL of 1, whilst a rapid rinse of a small piece of one dried leaf gave 0.09 mg/mL of 1; the highest concentration obtained from a glandular extract was 0.07 mg/mL. The dried leaves of S. sonchifolius were found to contain a total of 0.97% of 1.
Disentangling Factors of Variations Using Few Labels (2020)

Learning disentangled representations is considered a cornerstone problem in representation learning. Recently, Locatello et al. (2019) demonstrated that unsupervised disentanglement learning without inductive biases is theoretically impossible and that existing inductive biases and unsupervised methods do not allow to consistently learn disentangled representations. However, in many practical settings, one might have access to a limited amount of supervision, for example through manual labeling of (some) factors of variation in a few training examples. In this paper, we investigate the impact of such supervision on state-of-the-art disentanglement methods and perform a large scale study, training over 52000 models under well-defined and reproducible experimental conditions. We observe that a small number of labeled examples (0.01--0.5% of the data set), with potentially imprecise and incomplete labels, is sufficient to perform model selection on state-of-the-art unsupervised models. Further, we investigate the benefit of incorporating supervision into the training process. Overall, we empirically validate that with little and imprecise supervision it is possible to reliably learn disentangled representations.
Role of Smac/DIABLO in cancer progression (2008)

Second mitochondria-derived activator of caspase/direct inhibitor of apoptosis-binding protein with low pI (Smac/DIABLO) is a proapoptogenic mitochondrial protein that is released to the cytosol in response to diverse apoptotic stimuli, including commonly used chemotherapeutic drugs. In the cytosol, Smac/DIABLO interacts and antagonizes inhibitors of apoptosis proteins (IAPs), thus allowing the activation of caspases and apoptosis. This activity has prompted the synthesis of peptidomimetics that could potentially be used in cancer therapy. For these reasons, several authors have analyzed the expression levels of Smac/DIABLO in samples of patients from different tumors. Although dissimilar results have been found, a tissue-specific role of this protein emerges from the data. The objective of this review is to present the current knowledge of the Smac/DIABLO role in cancer and its possible use as a marker or therapeutic target for drug design.
Interpreting DNA evidence: statistical genetics for forensic scientists (1999)

Probability theory transfer evidence basic statistics population genetics statistical genetics parentage testing mixtures presenting evidence. Appendices: statistical tables solutions to exercises.
Structure Determination of a New Spirobicyclic Triterpenoid from Iris foetidissima (1990)

Abstract The novel iridal 10 has been isolated from rhizome extracts of Iris foetidissima. Its structure was established by spectroscopic methods and oxidative degradation. Final proof of the spirobicyclic nature of the compound – a new feature in the triterpenoid field – was afforded by the correlations observed in the 2D‐HMBC‐ ( 1 H‐detected multiple‐bond heteronuclear multiple‐quantum coherence) spectrum. The possible biogenesis of this unusual compound is discussed.
A mutual charge schedule information model for the vehicle-to-grid communication interface (2011)

The increasing market penetration of plug-in electric vehicles also brings along a rising number of mobility service providers. This results in various business models competing against each other for the customer's favor. As a result various smart charging approaches will be pursued. This might lead to major interoperability issues for V2G communications, if standardization bodies do not wisely address them. Hence, this work derives a generic V2G information model allowing for mutual charge schedule negotiations between EVs and grid operators. Major requirements are derived from a holistic system model and respected by the proposed design. The proposed information model allows for efficient handling of multiple tariffs for charging EVs.
Studies of the rosette inhibition test in pregnant mice: evidence of immunosuppression? (1976)

Abstract The rosette inhibition test has been utilized as a measure of immunosuppression following organ transplantation, and we have recently demonstrated that it can also be used in detecting a state of depression of lymphocyte reactivity occurring in pregnant mice. If the depression of lymphocyte reactivity provides an indication of immunosuppression, then this study has shown that, in the mouse, the spleen lymphocytes are immunosuppressed as early as 4 h after fertilization. This state persists for 13–15 days, with a return to normal 4–6 days before full term. A similar depression of normal spleen lymphocytes can be induced in vitro by incubating these lymphocytes with serum taken from pregnant mice 6 and 24 h after mating. The serum factor detected was shown to be stable when heated at 56 °C but not at 72 °C, and to be non-dialysable. It was detected in serum to a dilution of 1 in 64. Further work is being undertaken to investigate this phenomenon and to pursue the purification and identification of the pregnancy factor.
Controlled Antenna Changes at GNSS Reference Stations (2009)

Antenna changes at GNSS reference stations frequently produce discontinuities in their coordinate time series, especially in the height component. These coordinate shifts are mainly caused by changes of carrier-phase multipath effects and also, but usually to a smaller extend, by errors in the antenna phase center corrections. A monitoring method was developed and successfully tested, which requires additional GNSS observations from a local, temporary reference station. Changes of carrier-phase measurement errors due to the antenna exchange are determined and stored in L1 and L2 phase maps. The paper deals with the application of this new technique to 13 recent antenna changes in a network of permanently operating reference stations. Based on the modeling results we are able to present a detailed analysis of the effects of the antenna surroundings on discontinuities of station coordinate time series.
Parasitic Infection Among Foreign Workers: Serological Findings (2002)

We describe the results of serology for parasitic infection of 698 foreign workers. The 698 foreign workers participated included 115 Indonesians, 387 Bangladeshis, 101 Burmese, 81 Pakistanis, 6 Indians, 3 Thais, 3 Filipinoes and 2 others. Blood samples were taken from these workers and eight tests (Amoebiasis, Echinococcosis, Filariasis (bm and wb), Leishmaniasis, Malaria, Schistosomiasis and Trypanosomiasis) were performed on serum separated from the blood. Among the 698 sera tested, 38.1% were found to be positive for at least one parasitic infection. The most common antibody detected in the positive sera was antibody for amoebiasis (28.1%), followed by malaria (26.9%), echinococcosis (18.1%) and schistosomiasis (11.6%). Other tests showed a low percentage of infection with leshmaniasis (6.5%), filariasis (Brugia malayi (3%) and Wuchereria bancrofti (1%)) and trypanosomiasis (1%).
Role of Intracellular Proteases in the Antibiotic Resistance, Motility, and Biofilm Formation of Pseudomonas aeruginosa (2011)

Pseudomonas aeruginosa possesses complex regulatory networks controlling virulence and survival under adverse conditions, including antibiotic pressure, which are interconnected and share common regulatory proteins. Here, we screen a panel of 13 mutants defective in intracellular proteases and demonstrate that, in addition to the known alterations in Lon and AsrA mutants, mutation of three protease-related proteins PfpI, ClpS, and ClpP differentially affected antibiotic resistance, swarming motility, and biofilm formation.