gebhart/patrepeval huggingface dataset:
Ultra-large chemical libraries for the discovery of high-affinity peptide binders (2020)

High-diversity genetically-encoded combinatorial libraries (10<sup>8</sup>-10<sup>13</sup> members) are a rich source of peptide-based binding molecules, identified by affinity selection. Synthetic libraries can access broader chemical space, but typically examine only ~ 10<sup>6</sup> compounds by screening. Here we show that in-solution affinity selection can be interfaced with nano-liquid chromatography-tandem mass spectrometry peptide sequencing to identify binders from fully randomized synthetic libraries of 10<sup>8</sup> members-a 100-fold gain in diversity over standard practice. To validate this approach, we show that binders to a monoclonal antibody are identified in proportion to library diversity, as diversity is increased from 10<sup>6</sup>-10<sup>8</sup>. These results are then applied to the discovery of p53-like binders to MDM2, and to a family of 3-19 nM-affinity, α/β-peptide-based binders to 14-3-3. An X-ray structure of one of these binders in complex with 14-3-3σ is determined, illustrating the role of β-amino acids in facilitating a key binding contact.
<title>Brand new method for magneto-optical signal detection with ultraresolution</title> (1995)

We have developed a brand-new method using a gyrator for magneto-optical pickup. This method provides a simple optical pickup with some unique characteristics. It achieves both higher optical coupling efficiency, higher readout signal level, and improved modulation transfer function called ultra-resolution. In this paper, we describe the principle of MO signal readout, theoretical analysis, some results of simulation and experiments.
Multifrequency Pulsed Electron Paramagnetic Resonance on Metalloproteins (2009)

Metalloproteins often contain metal centers that are paramagnetic in some functional state of the protein; hence electron paramagnetic resonance (EPR) spectroscopy can be a powerful tool for studying protein structure and function. Dipolar spectroscopy allows the determination of the dipole-dipole interactions between metal centers in protein complexes, revealing the structural arrangement of different paramagnetic centers at distances of up to 8 nm. Hyperfine spectroscopy can be used to measure the interaction between an unpaired electron spin and nuclear spins within a distance of 0.8 nm; it therefore permits the characterization of the local structure of the paramagnetic center's ligand sphere with very high precision. In this Account, we review our laboratory's recent applications of both dipolar and hyperfine pulsed EPR methods to metalloproteins. We used pulsed dipolar relaxation methods to investigate the complex of cytochrome c and cytochrome c oxidase, a noncovalent protein-protein complex involved in mitochondrial electron-transfer reactions. Hyperfine sublevel correlation spectroscopy (HYSCORE) was used to study the ligand sphere of iron-sulfur clusters in complex I of the mitochondrial respiratory chain and substrate binding to the molybdenum enzyme polysulfide reductase. These examples demonstrate the potential of the two techniques; however, they also highlight the difficulties of data interpretation when several paramagnetic species with overlapping spectra are present in the protein. In such cases, further approaches and data are very useful to enhance the information content. Relaxation filtered hyperfine spectroscopy (REFINE) can be used to separate the individual components of overlapping paramagnetic species on the basis of differences in their longitudinal relaxation rates; it is applicable to any kind of pulsed hyperfine or dipolar spectroscopy. Here, we show that the spectra of the iron-sulfur clusters in complex I can be separated by this method, allowing us to obtain hyperfine (and dipolar) information from the individual species. Furthermore, performing pulsed EPR experiments at different magnetic fields is another important tool to disentangle the spectral components in such complex systems. Despite the fact that high magnetic fields do not usually lead to better spectral separation for metal centers, they provide additional information about the relative orientation of different paramagnetic centers. Our high-field EPR studies on cytochrome c oxidase reveal essential information regarding the structural arrangement of the binuclear Cu(A) center with respect to both the manganese ion within the enzyme and the cytochrome in the protein-protein complex with cytochrome c.
The disulfide oxidoreductase SdbA is active in Streptococcus gordonii using a single C‐terminal cysteine of the CXXC motif (2015)

Recently, we identified a novel disulfide oxidoreductase, SdbA, in the oral bacterium Streptococcus gordonii. Disulfide oxidoreductases form disulfide bonds in nascent proteins using a CXXC catalytic motif. Typically, the N-terminal cysteine interacts with substrates, whereas the C-terminal cysteine is buried and only reacts with the first cysteine of the motif. In this study, we investigated the SdbA C(86) P(87) D(88) C(89) catalytic motif. In vitro, SdbA single cysteine variants at the N or C-terminal position (SdbAC86P and SdbAC89A ) were active but displayed different susceptibility to oxidation, and N-terminal cysteine was prone to sulfenylation. In S. gordonii, mutants with a single N-terminal cysteine were inactive and formed unstable disulfide adducts with other proteins. Activity was partially restored by inactivation of pyruvate oxidase, a hydrogen peroxide generator. Presence of the C-terminal cysteine alone (in the SdbAC86P variant) could complement the ΔsdbA mutant and restore disulfide bond formation in recombinant and natural protein substrates. These results provide evidence that certain disulfide oxidoreductases can catalyze disulfide bond formation using a single cysteine of the CXXC motif, including the buried C-terminal cysteine.
Increase of sensitivity of sputum cytology using high‐resolution image cytometry: Field study results (2002)

Lung cancer remains the leading cause of cancer deaths in the developed world. There is no widely accepted method to screen for this cancer. The most commonly used method remains conventional sputum cytology, but this method is hampered by low sensitivity. We tested the hypothesis that sensitivity of sputum cytology for early lung cancer can be greatly improved by using image analysis of sputum cells, at a modest reduction of specificity. The study was double-blinded and used sputum samples from subjects with well-characterized clinical diagnoses. There were 177 cancers, 98 dysplasias, and 558 normals. The study samples were separated into two independent sets: training set and test set. Sputum samples were collected prospectively from subjects with a high probability of having lung cancer. Seven institutions from five countries participated in the study. All subjects had complete clinical diagnoses which included, as a minimum, negative chest x-rays for all negative cancers, while all cancers had confirmed tissue pathology. Samples were prepared according to the Saccomanno method. For conventional cytology, slides were stained using Papanicolaou stain. For image analysis, slides were stained using a DNA-specific (Feulgen-Thionin) stain. An automated, high-resolution image cytometer was used for measurements. At 90% specificity, sensitivity of 60% can be achieved for adenocarcinoma, compared to only 14% sensitivity of conventional cytology (at 99% specificity). Similarly, 45% sensitivity at 90% specificity can be reached for stages 0 and I lung cancer, compared to only 14% (at 99% specificity) using conventional cytology.Cytometry combined with conventional cytology shows an increase in sensitivity to early-stage cancer and to adenocarcinomas compared to conventional cytology alone. While the results are encouraging, the sensitivity to detect early lung cancer should be further improved to 70-80% at 90-95% specificity before this test can be considered for screening of high-risk individuals for lung cancer. Cytometry (Clin. Cytometry) 50:168-176, 2002.
Synthesis, physical characterization, and acetone sorption kinetics in random copolymers of poly(ethylene terephthalate) and poly(ethylene 2,6-naphthalate) (1998)

Random copolymers of poly(ethylene terephthalate) (PET) and poly(ethylene 2,6-naphthalate) (PEN) were synthesized by melt condensation. In a series of thin, solvent cast films of varying PEN content, acetone diffusivity and solubility were determined at 35°C and an acetone pressure of 5.4 cm Hg. The kinetics of acetone sorption in the copolymer films are well described by a Fickian model. Both solubility and diffusivity decrease with increasing PEN content. The acetone diffusion coefficient decreases 93% from PET to PET/85PEN, a copolymer in which 85 weight percent of the dimethyl terephthalate in PET has been replace by dimethyl naphthalate 2,6-dicarboxylate. The acetone solubility coefficient in the amorphous regions of the polymer decreases by approximately a factor of two over the same composition range. The glass/rubber transition temperatures of these materials rise monotonically with increasing PEN content. Copolymers containing 20 to 80 wt % PEN are amorphous. Samples with <20% or >80% PEN contain measurable levels of crystallinity. Estimated fractional free volume in the amorphous regions of these samples is lower in the copolymers than in either of the homopolymers. Relative free volume as probed by positron annihilation lifetime spectroscopy (PALS) decreases systematically with increasing PEN content. Acetone diffusion coefficients correlate well with PALS results. Infrared spectroscopy suggests an increase in the fraction of ethylene glycol units in the trans conformation in the amorphous phase as the concentration of PEN in the copolymer increases. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 2981–3000, 1998
Time management in a co-housed social rodent species (Arvicanthis niloticus) (2018)

Sociality has beneficial effects on fitness, and timing the activities of animals may be critical. Social cues could influence daily rhythmic activities via direct effects on the circadian clock or on processes that bypass it (masking), but these possibilities remain incompletely addressed. We investigated the effects of social cues on the circadian body temperature (Tb) rhythms in pairs of co-housed and isolated grass rats, Arvicanthis niloticus (a social species), in constant darkness (DD). Cohabitation did not induce synchronization of circadian Tb rhythms. However, socio-sexual history did affect circadian properties: accelerating the clock in sexually experienced males and females in DD and advancing rhythm phase in the females in a light-dark cycle. To address whether synchronization occurs at an ultradian scale, we analyzed Tb and activity rhythms in pairs of co-housed sisters or couples in DD. Regardless of pair type, co-housing doubled the percentage of time individuals were simultaneously active without increasing individual activity levels, suggesting that activity bouts were synchronized by redistribution over 24 h. Together, our laboratory findings show that social cues affect individual "time allocation" budgets via mechanisms at multiple levels of biological organization. We speculate that in natural settings these effects could be adaptive, especially for group-living animals.
Different Profiles in Specific IgE to rBet v 1 and rBet v 2 in Patients Allergic to Birch Pollen from Six Countries (1997)

There are differences in IgE reactivity to rBet v 1 and rBet v 2 among allergic patients from the six countries studied. The complexity of the reactivity profile tends to be greater in individuals from the central/southern parts of Europe compared to Sweden and Finland. There is a good agreement between in vitro diagnosis with Pharmacia CAP System and Skin prick testing when using the same reagents, rBet v 1 and rBet v 2.
Exposure to the gut microbiota from cigarette smoke-exposed mice exacerbates cigarette smoke extract-induced inflammation in zebrafish larvae (2021)

Abstract Cigarette smoke (CS)-induced inflammation leads to a range of diseases including chronic obstructive pulmonary disease and cancer. The gut microbiota is a major modifying environmental factor that determine the severity of cigarette smoke-induced pathology. Microbiomes and metabolites from CS-exposed mice exacerbate lung inflammation via the gut-lung axis of shared mucosal immunity in mice but these systems are expensive to establish and analyse. Zebrafish embryos and larvae have been used to model the effects of cigarette smoking on a range of physiological processes and offer an amenable platform for screening modifiers of cigarette smoke-induced pathologies with key features of low cost and rapid visual readouts. Here we exposed zebrafish larvae to cigarette smoke extract (CSE) and characterised a CSE-induced leukocytic inflammatory phenotype with increased neutrophilic and macrophage inflammation in the gut. The CSE-induced phenotype was exacerbated by co-exposure to microbiota from the faeces of CS-exposed mice, but not control mice. Microbiota could be recovered from the gut of zebrafish and studied in isolation in a screening setting. This demonstrates the utility of the zebrafish-CSE exposure platform for identifying environmental modifiers of cigarette smoking-associated pathology and demonstrates that the CS-exposed mouse gut microbiota potentiates the inflammatory effects of CSE across host species.
The use of simulation in the off-line programming of robots (1985)

The general requirements of a robot simulation system are discussed and the benefits of integrating such a system with a solid modeller are indicated. The status of a robot simulator integrated with the BUILD solid modelling system is examined. The application example cited is the Condition Number analysis for optimum positioning of a workpiece in a robot&apos;s workspace. The robot simulator is used to verify that no interference takes place between the robot and workpiece in the optimum position.
Copper wire in automotive: Key challenges and robust validation (2016)

Opportunities and challenges of copper wire bonding implementation in the automotive context are presented from two different viewpoints: manufacturability and reliability. Compared to gold, copper offers better thermal and electrical properties, but its higher hardness imposes a tighter process control and a dedicated approach to process setup, optimization and validation. Compatibility with the plastic package direct materials and process flow has to be addressed, too. From a reliability standpoint, intrinsic ageing mechanisms like separation of Cu-Al Inter-Metallic Compounds (IMC), bond thermal fatigue in presence of molding compound delamination, copper or Cu-Al IMC corrosion have to be characterized in terms of lifetime margin versus severe application-specific environmental conditions typical of the automotive field. The key pillars of a robust qualification methodology are proposed, where the dominant failure mechanisms are prevented through a “copper-compatible” design, and their impact on product wear-out verified by extended stress testing in corner conditions.
A direct transform for the nuclear magnetic resonance chemical shift anisotropy (1999)

A direct transform of the NMR chemical shift anisotropy, operating on data acquired under magic angle spinning conditions, yielding rotationally invariant quantities, is potentially a source of increased resolution in solid state NMR. The mathematical basis for such a transform is discussed by exploiting an analogy with projection reconstruction. A specific example of the kind of pulse sequence required is given, and optimal sampling of the data is discussed.
Layout planning in assembly line kitting - a constraint programming approach (2021)

In truck manufacturing, an assembly line is typically used to produce many models and variations of trucks in any desired order. Thus, stations are fed with specific sets of parts, known as kits, depending on what truck is next in line. This paper focuses on how to automate the layout planning for placing parts on a kitting wagon. Layout planning resembles the pallet loading problem, but differences include that there is no layering, there may be constraints on how each part can be placed (orientation) and there may be predefined layout hints suggesting positions. A layout planner based on constraint programming is presented. The objective is to facilitate a decision support loop where an engineer may add placement hints as constraints (e.g., for enhancing the workflow at assembly stations) and reuse placements from similar kits to provide recognition. The layout planner automatically generates layout proposals. Finally, it is the engineer that approves the layout plan. There may be many acceptable solutions that have different scores (i.e., levels of quality). We show some approaches to reduce the search space to improve performance. The evaluations show the score and time needed for finding results on some problem instances that are optimally solvable. In the general case, however, finding an optimal solution may be unnecessary or even intractable.
Improved surface morphology and texture of Ag films on indium tin oxide via Cu additions (2007)

The surface and texture properties of Ag(Cu) alloy thin films on indium tin oxide (ITO) has been investigated and compared to pure Ag thin films on ITO. Atomic force microscopy (AFM) and x-ray diffraction results of annealed films show differences in the evolution of surface morphology and texture with annealing. The presence of Cu atoms in the silver alters the alloy’s surface energy and surface diffusion. This results in Ag and Ag(Cu) alloy having the very different surface morphology and crystallographic texture. The (111) texture of the Ag(Cu) is enhanced when compared to that of pure Ag films. The resistivity of Ag(Cu) films annealed at high temperatures (∼up to 600°C for 1h in vacuum) remained constant due to absence of agglomeration.
ACTR-18. A PHASE IB/II CLINICAL TRIAL OF DODECAFLUOROPENTANE EMULSION (DDFPE) AS A RADIOSENSITIZER IN GLIOBLASTOMA (2019)

Abstract BACKGROUND Tumor hypoxia decreases the response of glioblastoma multiforme (GBM) to radiotherapy (RT) and chemotherapy (temozolomide[TMZ]). The purpose of this study was to evaluate the safety and efficacy of a novel oxygen therapeutic, dodecafluoropentane emulsion (DDFPe), in chemoradiation treatment of GBM and stratify the results based on predicted TMZ response. METHODS With ethics approval and informed consent, 11 adult GBM patients were enrolled. Patients were administered DDFPe via IV infusion (2% w/vol at doses of 0.05, 0.1 or 0.17 mL/kg) within 5–30 minutes prior to each 2 Gy fraction of RT (30 fractions over 6-weeks) while breathing supplemental oxygen. Patients also received standard concurrent and adjuvant TMZ. To evaluate the reversal of tumor hypoxia, patients underwent oxygen-sensitive (TOLD) MRI before and after DDFPe administration. Patients were also studied with serial MRI scans per standard of care and followed for survival. RESULTS The non-serious adverse events considered by the investigator to be possibly, probably, or definitely related to DDFPe administration included fatigue (n=4), headache (n=2) and decrease in platelet count (n=2). Serious adverse events included two patients with symptomatic radiation necrosis: one patient at each of dose levels 0.1 and 0.17 mL/kg. Enrollment continued at the 0.1 mL/kg dose without additional significant DDFPe-related toxicity. Historically, the average overall survival for GBM patients is about 14.6 months. The median overall survival for the study was 591 days, or 19.4 months. According to independent review of the serial MR images, the median time to progression was 555 days, or 18 months, compared to a historical control of 6.9 months. TOLD MRI showed a trend in improved tumor oxygenation. CONCLUSION Although small, this trial shows that DDFPe used as a radiosensitizer appears to be safe and may provide some survival benefit. The FDA has allowed a Phase II clinical trial to assess its effectiveness.
No evidence of a link between influenza vaccines and Guillain–Barre syndrome–associated antiganglioside antibodies (2011)

Although the correlation between antiganglioside antibody cross-reactivity and glycosylation of viruses suggests the role of shared carbohydrate epitopes, no correlation was observed between hemagglutinin-inhibition titers and the induction of antiganglioside antibodies after influenza vaccination.
Guest Editorial: Special Section on the 48th European Solid-State Circuits Conference (ESSCIRC) (2019)

This Special Section of the IEEE Journal of Solid-State Circuits (JSSC) features expanded versions of papers selected from those presented at the 48th ESSCIRC Conference, held at Technische Universität Dresden, Dresden, Germany, during September 3–6, 2018.
Gapping by Squashing: Metal-Insulator and Insulator-Metal Transitions in Collapsed Carbon Nanotubes (2000)

Squashing brings circumferentially separated areas of a carbon nanotube into close proximity, drastically altering the low-energy electronic properties and (in some cases) reversing standard rules for metallic versus semiconducting behavior. Such a deformation mode, not requiring motion of tube ends, may be useful for devices. Uniaxial stress of a few kbar can reversibly collapse a small-radius tube, inducing a 0.1 eV gap with a very strong pressure dependence, while the collapsed state of a larger tube is stable. The low-energy electronic properties of chiral tubes are surprisingly insensitive to collapse.
ChemInform Abstract: Relaxant Activity of 4‐Amido‐3,4‐dihydro‐2H‐1‐benzopyran‐3‐ols and 4‐ Amido‐2H‐1‐benzopyrans on Guinea Pig Isolated Trachealis. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Conception d’une chaîne d’amplification de puissance commutée à faible temps d’établissement pour applications ultra large bande faible consommation en technologie CMOS 65 nm (2015)

National audience
Developing diagnostic assessment of breast lumpectomy tissues using radiomic and optical signatures (2021)

High positive margin rates in oncologic breast-conserving surgery are a pressing clinical problem. Volumetric X-ray scanning is emerging as a powerful ex vivo specimen imaging technique for analyzing resection margins, but X-rays lack contrast between non-malignant and malignant fibrous tissues. In this study, combined micro-CT and wide-field optical image radiomics were developed to classify malignancy of breast cancer tissues, demonstrating that X-ray/optical radiomics improve malignancy classification. Ninety-two standardized features were extracted from co-registered micro-CT and optical spatial frequency domain imaging samples extracted from 54 breast tumors exhibiting seven tissue subtypes confirmed by microscopic histological analysis. Multimodal feature sets improved classification performance versus micro-CT alone when adipose samples were included (AUC = 0.88 vs. 0.90; p-value = 3.65e-11) and excluded, focusing the classification task on exclusively non-malignant fibrous versus malignant tissues (AUC = 0.78 vs. 0.85; p-value = 9.33e-14). Extending the radiomics approach to high-dimensional optical data-termed "optomics" in this study-offers a promising optical image analysis technique for cancer detection. Radiomic feature data and classification source code are publicly available.