gebhart/patrepeval huggingface dataset:
“Cell-Free Synthetic Biology”: Synthetic Biology Meets Cell-Free Protein Synthesis (2019)

Since Nirenberg and Matthaei used cell-free protein synthesis (CFPS) to elucidate the genetic code in the early 1960s [1], the technology has been developed over the course of decades and applied to studying both fundamental and applied biology [2]. Cell-free synthetic biology integrating CFPS with synthetic biology has received attention as a powerful and rapid approach to characterize and engineer natural biological systems. The open nature of cell-free (or in vitro) biological platforms compared to in vivo systems brings an unprecedented level of control and freedom in design [3]. This versatile engineering toolkit has been used for debugging biological networks, constructing artificial cells, screening protein libraries, prototyping genetic circuits, developing biosensors, producing metabolites, and synthesizing complex proteins including antibodies, toxic proteins, membrane proteins, and novel proteins containing nonstandard (unnatural) amino acids. The <i>Methods and Protocols</i> "Cell-Free Synthetic Biology" Special Issue consists of a series of reviews, protocols, benchmarks, and research articles describing the current development and applications of cell-free synthetic biology in diverse areas. [...].
Tailored TCOs (2011)

The metal-like electrical conductivity in combination with a high visual transmittance is the characteristic property that opens up a broad spectrum of applications to transparent conductive oxides (TCOs). To fulfill the manifold requirements in each individual case, especially the optical properties of TCOs have to be adapted. The transmittance in the near infrared spectral range can be tailored by a modification of the carrier concentration &Nu; and mobility &mu;. The theoretical description for this behavior is based on the well-known Drude theory. Highly conductive indium tin oxide films (ITO) have been prepared by pulsed DC magnetron sputtering. However, due to its excellent electrical properties, the plasma resonance of free carriers occurs near the visual spectral range which results in a very low transmittance in the NIR. In contrast, ITO films with a NIR transmittance of ca. 80% have been prepared by plasma ion assisted evaporation. The combination of high transmittance and low resistivity of &rho;=7.4x10<sup>-6</sup>&Omega; was achieved by a decrease of the carrier concentration and a simultaneous enhancement of the electron mobility &mu;. Secondary, the transmittance of aluminum doped zinc oxide films (AZO) in the UV spectral range could be adapted by changing the doping concentration &Nu;. This is a direct consequence of the Burstein-Moss shift that leads to a band gap widening dependent on &Nu;. However, the comparison of the experimental data with theory has shown that the contrary effect of band gap narrowing is not negligible, too.
Patterns of Regional Cerebral Blood Flow Associated With Low Hemoglobin in the Baltimore Longitudinal Study of Aging (2012)

In nondemented individuals, lower hemoglobin is associated with elevated relative CBF in specific cortical areas but reduced CBF in other areas. Whether this association between anemia and CBF in the absence of chronic diseases and in a normal physiologic range is related to clinical endpoints warrants further study.
Optimization of High Temperature SiC Volumetric Solar Absorber (2014)

Focusing on radiative properties (absorption and scattering coefficient, scattering phase-function) of silicon carbide foams, several predictive models are compared to spectral transmittance and reflectance measurements (bi-directional and directional- hemispherical) in the aim of determining new correlations based on ceramic foam characteristics (struts/pores size and porosity). A mono-dimensional modeling is developed to solve Navier-stokes equations (conservation of mass and momentum) and energy equations (coupled heat transfers) inside the absorber. Several radiative models are tested to approximate the radiative transfer equation end compute the radiative source term (Rosseland, P-1 model, and two-flux approximation). Numerical simulations are compared to reference results obtained with Monte-Carlo algorithm using net-exchange formulation.
Equivalence checking using cuts and heaps (1997)

This paper presents a verification technique which isspecifically targeted to formally comparing large combinational circuits with some structural similarities. The approach combines the application of BDDs withcircuit graph hashing, automatic insertion of multiple cut frontiers, and a controlled elimination of false negative verification results caused by the cuts. Twoideas fundamentally distinguish the presented technique from previous approaches. First, originating from the cut frontiers, multiple BDDs are computedfor the internal nets of the circuit, and second, theBDD propagation is prioritized by size and discontinued once a given limit is exceeded.
Allele-specific expression assays using Solexa (2009)

We present a new method with the capacity to measure ASE for large numbers of assays using as little as one lane of a Solexa flowcell. This will be a valuable technique for molecular and population genetic studies, as well as for verification of genome-wide data sets.
PERFORMANCES OF A NEW GENERATION OF METAL OXIDE GAS SENSOR BASED ON NANOSTRUCTURED-SnO 2 AND ON HIGH OPERATING TEMPERATURE MICROHOTPLATE (2009)

International audience
An Improved Technique for the Internal Mammary Artery Coronary Bypass Graft Procedure (1988)

An improved technique for internal mammary artery graft preparation is described. Following cautery dissection of the internal mammary artery (IMA) pedicle, the pedicle investing fascia is incised to the adventitial level along a single plane. This incision allows the tissue around the internal mammary artery to fall away and severs the muscular constrictions that often surround the internal mammary artery. Balloon calibration is performed to identify remaining constrictions and to relieve internal mammary artery spasm. A shear force limiting gauge insures that the exerted balloon force remains below the level demonstrated to cause intimal damage during electron microscopic studies. This technique allows full internal mammary artery distention without the devascularizing effects of full skeletonization. Distention of the distal internal mammary artery provides an enlarged hood to facilitate suture placement. Elongation of the internal mammary artery during balloon calibration aids in the performance of sequential grafts. This technique has been applied to 793 patients over the past five years. Postcalibration flow rates increased 3- to 18-fold over precalibration flow rates. Two early occlusions occurred during this series, one due to endothelial strippage prior to the development and use of the shear force limiting gauge. Follow-up showed 93.3% of patients to be asymptomatic. This combination of fascial incision and balloon calibration appears to offer safe technical and functional improvements to the performance of the internal mammary artery graft.
Characterization of Cover-Plate Bolted Steel Joints with Full-Field Measurements (2015)

The combination of cover-plate bolted joints commonly used in steel structures allows the transfer of various internal loads such as bending, shear or axial forces. The mechanical behavior of these joints is complex because it depends on both the contact evolution due to load transfer between bolts and holes, and the elastoplastic response of the constitutive material of the plates. The interaction between the holes in the plates is also of great importance regarding the various configurations of joint and hole positions. The different failure modes such as net section fracture, gross section plastic yielding, shear out and bearing, are difficult to predict because they combine local compression under bolt and shear at loaded end distance of the plate. Many studies analyze the behavior of cover-plate joints by combining finite element approaches and/or experiments, but for obvious practical or economic reasons, only limited numbers of strain gages are employed to estimate the strain distribution in the components of the joints. Here the grid method is used to analyze in details the strain distribution on the plates with various configurations of bolts and holes positions. This approach enables us to observe the strain fields in the plate around the bolts during both the elastic and plastic phases of the material response. The obtained results help understanding the evolution of the failure zones regarding mainly the bearing mode. They can also be used as a reference to calibrate sophisticated finite element models.
Automated Algorithm Selection: Survey and Perspectives (2018)

It has long been observed that for practically any computational problem that has been intensely studied, different instances are best solved using different algorithms. This is particularly pronounced for computationally hard problems, where in most cases, no single algorithm defines the state of the art; instead, there is a set of algorithms with complementary strengths. This performance complementarity can be exploited in various ways, one of which is based on the idea of selecting, from a set of given algorithms, for each problem instance to be solved the one expected to perform best. The task of automatically selecting an algorithm from a given set is known as the per-instance algorithm selection problem and has been intensely studied over the past 15 years, leading to major improvements in the state of the art in solving a growing number of discrete combinatorial problems, including propositional satisfiability and AI planning. Per-instance algorithm selection also shows much promise for boosting performance in solving continuous and mixed discrete/continuous optimisation problems. This survey provides an overview of research in automated algorithm selection, ranging from early and seminal works to recent and promising application areas. Different from earlier work, it covers applications to discrete and continuous problems, and discusses algorithm selection in context with conceptually related approaches, such as algorithm configuration, scheduling, or portfolio selection. Since informative and cheaply computable problem instance features provide the basis for effective per-instance algorithm selection systems, we also provide an overview of such features for discrete and continuous problems. Finally, we provide perspectives on future work in the area and discuss a number of open research challenges.
Automatic Emotion-Based Music Classification for Supporting Intelligent IoT Applications (2019)

With the arrival of the fourth industrial revolution, new technologies that integrate emotional intelligence into existing IoT applications are being studied. Of these technologies, emotional analysis research for providing various music services has received increasing attention in recent years. In this paper, we propose an emotion-based automatic music classification method to classify music with high accuracy according to the emotional range of people. In particular, when the new (unlearned) songs are added to a music-related IoT application, it is necessary to build mechanisms to classify them automatically based on the emotion of humans. This point is one of the practical issues for developing the applications. A survey for collecting emotional data is conducted based on the emotional model. In addition, music features are derived by discussing with the working group in a small and medium-sized enterprise. Emotion classification is carried out using multiple regression analysis and support vector machine. The experimental results show that the proposed method identifies most of induced emotions felt by music listeners and accordingly classifies music successfully. In addition, comparative analysis is performed with different classification algorithms, such as random forest, deep neural network and K-nearest neighbor, as well as support vector machine.
Effects of Induced Hypertension on Intracranial Pressure and Flow Velocities of the Middle Cerebral Arteries in Patients With Large Hemispheric Stroke (2002)

In patients with large hemispheric stroke without an acute ICP crisis, induced hypertension enhances cerebral perfusion pressure and augments the V(m)MCA(s), more so on the affected side. The ICP slightly increases; however, this is probably not clinically significant.
Immunological and Virological Investigationson Owl Monkeys Infected with Herpesvirus saimiri (1974)

The association between the induction of antibodies to early antigens (EA) with the detection of virusinfected peripheral blood lymphocytes, and the possible correlation of these factors with the response of lymphocytes to different mitogens was investigated in owl monkeys infected with Herpesvirus saimiri (HVS). There was a positive correlation between the production of antibodies to EA and the quantitative recovery of virus from peripheral blood lymphocytes. The loss of responsiveness of lymphocytes from leukemic owl monkeys to T-cell mitogens paralleled these two parameters suggesting that virus genome-carrying lymphocytes are functionally altered.
Poly(A) polymerase I of Escherichia coli: characterization of the catalytic domain, an RNA binding site and regions for the interaction with proteins involved in mRNA degradation (1999)

Poly(A) polymerase I (PAP I) of Escherichia coli is a member of the nucleotidyltransferase (Ntr) superfamily that includes the eukaryotic PAPs and all the known tRNA CCA-adding enzymes. Five highly conserved aspartic acids in the putative catalytic site of PAP I were changed to either alanine or proline, demonstrating their importance for polymerase activity. A glycine that is absolutely conserved in all Ntrs was also changed yielding a novel mutant protein in which ATP was wastefully hydrolysed in a primer-independent reaction. This is the first work to characterize the catalytic site of a eubacterial PAP and, despite the conservation of certain sequences, we predict that the overall architecture of the eukaryotic and eubacterial active sites is likely to be different. Binding sites for RNase E, a component of the RNA degradosome, and RNA were mapped by North-western and Far-western blotting using truncated forms of PAP I. Additional protein-protein interactions were detected between PAP I and CsdA, RhlE and SrmB, suggesting an unexpected connection between PAP I and these E. coli DEAD box RNA helicases. These results show that the functional organization of PAP I is similar to the eukaryotic PAPs with an N-terminal catalytic domain, a C-terminal RNA binding domain and sites for the interaction with other protein factors.
Inter-kernel Reuse-aware Thread Block Scheduling (2020)

As GPUs have become more programmable, their performance and energy benefits have made them increasingly popular. However, while GPU compute units continue to improve in performance, on-chip memories lag behind and data accesses are becoming increasingly expensive in performance and energy. Emerging GPU coherence protocols can mitigate this bottleneck by exploiting data reuse in GPU caches across kernel boundaries. Unfortunately, current GPU thread block schedulers are typically not designed to expose such reuse. This article proposes new hardware thread block schedulers that optimize inter-kernel reuse while using work stealing to preserve load balance. Our schedulers are simple, decentralized, and have extremely low overhead. Compared to a baseline round-robin scheduler, the best performing scheduler reduces average execution time and energy by 19% and 11%, respectively, in regular applications, and 10% and 8%, respectively, in irregular applications.
Pleurotus fungi produce mevinolin, an inhibitor of HMG CoA reductase (1993)

Fungi of the genus Pleurotus were shown to produce the 3-hydroxy-3-methylglutaryl-CoA reductase inhibitor mevinolin. Crude methanol extracts and purified inhibitor from three different species, P. sapidus, P. saca and P. ostreatus, were tested using the solubilized microsomal HMGCoA reductase from Chinese hamster ovary cells. The identity of the inhibitor was also confirmed by thin layer chromatography, high pressure liquid chromatography and mass spectroscopy.
Fitting Linear Mixed-Effects Models Using lme4 (2014)

(Uploaded by Plazi for the Bat Literature Project) Maximum likelihood or restricted maximum likelihood (REML) estimates of the parameters in linear mixed-effects models can be determined using the lmer function in the lme4 package for R. As for most model-fitting functions in R, the model is described in an lmer call by a formula, in this case including both fixed- and random-effects terms. The formula and data together determine a numerical representation of the model from which the profiled deviance or the profiled REML criterion can be evaluated as a function of some of the model parameters. The appropriate criterion is optimized, using one of the constrained optimization functions in R, to provide the parameter estimates. We describe the structure of the model, the steps in evaluating the profiled deviance or REML criterion, and the structure of classes or types that represents such a model. Sufficient detail is included to allow specialization of these structures by users who wish to write functions to fit specialized linear mixed models, such as models incorporating pedigrees or smoothing splines, that are not easily expressible in the formula language used by lmer.
Ultraviolet-light-induced deposition of gold films (1987)

Gold film has been deposited by ultaviolet-light-induced photolysis of ammonium tetrachloroaurate/nitrocellulose film. The minimum feature size achieve is about 1 μm, and the film exhibits good adhesion. The effect of temperature on the photolyzing rate has been examined.
The nature of risk: The risk management of everything (2004)

This is a briefing by the author on his PD Leake lecture given at the Chartered Accountants’ hall earlier in the year. In it he examines the rise and rise of the risk industry and assesses the changes it has wrought in business life. He argues that unless the rise is halted we will see the retreat of socially valuable intelligence from the public domain.
Severe immune checkpoint inhibitor-associated gastritis: A case series and literature review (2022)

<b>Background and study aims </b> Recent advances in cancer treatment have involved the clinical application of immune checkpoint inhibitors (ICIs) for various type of cancers. The adverse events associated with ICIs are generally referred to as immune-related adverse events (irAEs). Gastrointestinal irAEs are a major disorder, but gastritis is not frequently observed. The aims of this study were to elucidate the clinical, endoscopic, and histological characteristics of irAE gastritis. <b>Patients and methods </b> Information on patients treated with ICIs were collected from a single institute over 3 years. IrAE gastritis was identified based on the clinical course and endoscopic and histopathological findings. Of the 359 patients treated with ICIs, four cases of irAE gastritis were identified in clinical records from the endoscopy unit. The endoscopic and histopathological findings were analyzed, and further immunohistochemical studies with immune subtype markers and programmed cell death ligand-1 (PD-L1) antibody were conducted. <b>Results </b> Among four patients with irAE gastritis, the remarkable endoscopic characteristics were network-pattern erosion, erythematous and edematous mucosa with thick purulent discharge, and fragile mucosa. Corresponding histological features were fibrinopurulent exudate, severe inflammatory cell infiltration, and epithalaxia, respectively. The PD-L1 expression rate was ≥ 1 % in the gastric tissue of all patients with gastritis. These patients were treated with prednisolone (PSL) and their symptoms improved within a few days to 2 weeks. <b>Conclusions </b> IrAE gastritis were characterized by specific endoscopic findings. The appropriate endoscopic diagnosis may lead to effective treatment with PSL.
Essential role of Helicobacter pyloriγ‐glutamyltranspeptidase for the colonization of the gastric mucosa of mice (1999)

Constitutive expression of gamma-glutamyltranspeptidase (GGT) activity is common to all Helicobacter pylori strains, and is used as a marker for identifying H. pylori isolates. Helicobacter pylori GGT was purified from sonicated extracts of H. pylori strain 85P by anion exchange chromatography. The N-terminal amino acid sequences of two of the generated endo-proteolysed peptides were determined, allowing the cloning and sequencing of the corresponding gene from a genomic H. pylori library. The H. pylori ggt gene consists of a 1681 basepair (bp) open reading frame encoding a protein with a signal sequence and a calculated molecular mass of 61 kDa. Escherichia coli clones harbouring the H. pylori ggt gene exhibited GGT activity at 37 degrees C, in contrast to E. coli host cells (MC1061, HB101), which were GGT negative at 37 degrees C. GGT activity was found to be constitutively expressed by similar genes in Helicobacter felis, Helicobacter canis, Helicobacter bilis, Helicobacter hepaticus and Helicobacter mustelae. Western immunoblots using rabbit antibodies raised against a His-tagged-GGT recombinant protein demonstrated that H. pylori GGT is synthesized in both H. pylori and E. coli as a pro-GGT that is processed into a large and a small subunit. Deletion of a 700 bp fragment within the GGT-encoding gene of a mouse-adapted H. pylori strain (SS1) resulted in mutants that were GGT negative yet grew normally in vitro. These mutants, however, were unable to colonize the gastric mucosa of mice when orally administered alone or together (co-infection) with the parental strain. These results demonstrate that H. pylori GGT activity has an essential role for the establishment of the infection in the mouse model, demonstrating for the first time a physiological role for a bacterial GGT enzyme.
In situgrowth of luminescent silver nanoclusters inside bulk sol-gel silica glasses (2017)

International audience
Adiponitrile-LiTFSI solution as alkylcarbonate free electrolyte for LTO/NMC Li-ion batteries (2017)

Recently, dinitriles (NC(CH2)nCN) and especially adiponitrile (ADN, n=4) have attracted the attention as secure electrolyte solvents due to their chemical stability, high boiling points, high flash points and low vapor pressure. The good solvating properties of ADN toward lithium salts and its high electrochemical stability (~ 6V vs. Li/Li+) make it suitable for safer Li-ions cells without performances loss. In this study, ADN is used as a single electrolyte solvent with lithium bis(trimethylsulfonyl)imide (LiTFSI). This electrolyte allows the use of aluminum collectors as almost no corrosion occurs at voltages up to 4.2 V. Physico-chemical properties of ADN-LiTFSI electrolyte such as salt dissolution, conductivity and viscosity were determined. The cycling performances of batteries using Li4Ti5O12 (LTO) as anode and LiNi1/3Co1/3Mn1/3O2 (NMC) as cathode were determined. The results indicate that LTO/NMC batteries exhibit excellent rate capabilities with a columbic efficiency close to 100%. As an example, cells were able to reach a capacity of 165 mAh.g-1 at 0.1C and a capacity retention of more than 98% after 200 cycles at 0.5C. In addition, electrodes analyses by SEM, XPS and electrochemical impedance spectroscopy after cycling confirming minimal surface changes of the electrodes in the studied battery system
P010 Precision Dosing Tool Forecasts Trough Infliximab and Associates With Disease Status in Inflammatory Bowel Diseases (2021)

These data establish the value of our MIPD tool in forecasting trough IFX levels in patients with IBD. Serum TNF-α and CRP are reflective of inflammatory burden which impacts exposure.