gebhart/patrepeval huggingface dataset:
Raman spectroscopy characterization of antibody phases in serum (2014)

When administered in serum, an efficacious therapeutic antibody should be homogeneous to minimize immune reactions or injection site irritation during administration. Monoclonal antibody (mAb) phase separation is one type of inhomogeneity observed in serum, and thus screening potential phase separation of mAbs in serum could guide lead optimization. However, serum contains numerous components, making it difficult to resolve mAb/serum mixtures at a scale amenable to analysis in a discovery setting. To address these challenges, a miniaturized assay was developed that combined confocal microscopy with Raman spectroscopy. The method was examined using CNTO607, a poorly-soluble anti-interleukin-13 human mAb, and CNTO3930, a soluble anti-respiratory syncytial virus humanized mAb. When CNTO607 was diluted into serum above 4.5 mg/mL, phase separation occurred, resulting in droplet formation. Raman spectra of droplet phases in mixtures included bands at 1240 and 1670 cm(-1), which are typical of mAb β-sheets, and lacked bands at 1270 and 1655 cm(-1), which are typical of α-helices. The continuous phases included bands at 1270 and 1655 cm(-1) and lacked those at 1240 and 1670 cm(-1). Therefore, CNTO607 appeared to be sequestered within the droplets, while albumin and other α-helix-forming serum proteins remained within the continuous phases. In contrast, CNTO3930 formed only one phase, and its Raman spectra contained bands at 1240, 1670, 1270 and 1655 cm,(-1) demonstrating homogeneous distribution of components. Our results indicate that this plate-based method utilizing confocal Raman spectroscopy to probe liquid-liquid phases in mAb/serum mixtures can provide a screen for phase separation of mAb candidates in a discovery setting.
[The prevalence of Cryptosporidium spp. in calves in Erzurum province]. (2008)

This study was carried out between March and April, 2007 to determine the prevalence of Cryptosporidium spp. in calves. The study was performed in 30 farms of 12 different localities of Erzurum and vicinity. The fecal samples were taken directly from the rectums of calves which were no more than three months old. The samples were centrifuged and examined under microscope by using the modified acid-fast technique. The prevalence of Cryptosporidium spp. was found to be 22.8% (43/189). The rate of infection was 30.3% (36/119) in calves with diarrhea and 10% (7/70) in healthy calves. The prevalence of the protozoan was 91.7% (11/12) and 53.3% (16/30) in localities and farms respectively. The prevalence was 17.3% (18/104) in state farms and 29.4% in village farms. During the research period, the presence of Cryptosporidiosis was suspected in 16 calves on two different farms. Fourteen of 16 calves (87.5%) were found to be infected with Cryptosporidium spp.
Missions to Phobos and Other Minor Bodies (2002)

Abstract A space mission to Mars’ moon Phobos with a space vehicle of new generation currently developed by the Russian Aerospace Agency is discussed. The vehicle design incorporates innovative SEP technology focused on small propulsion electric engines which significantly improve the mission energetic capability. The project is optimized around a sample return (PSR) from Phobos and also offers an opportunity for rendezvous/sample return missions from several asteroids, comets, and NEO. Scenario, rationale, and basic profile of PSR mission are presented.
Evolution of cooperation facilitated by reinforcement learning with adaptive aspiration levels (2011)

Repeated interaction between individuals is the main mechanism for maintaining cooperation in social dilemma situations. Variants of tit-for-tat (repeating the previous action of the opponent) and the win-stay lose-shift strategy are known as strong competitors in iterated social dilemma games. On the other hand, real repeated interaction generally allows plasticity (i.e., learning) of individuals based on the experience of the past. Although plasticity is relevant to various biological phenomena, its role in repeated social dilemma games is relatively unexplored. In particular, if experience-based learning plays a key role in promotion and maintenance of cooperation, learners should evolve in the contest with nonlearners under selection pressure. By modeling players using a simple reinforcement learning model, we numerically show that learning enables the evolution of cooperation. We also show that numerically estimated adaptive dynamics appositely predict the outcome of evolutionary simulations. The analysis of the adaptive dynamics enables us to capture the obtained results as an affirmative example of the Baldwin effect, where learning accelerates the evolution to optimality.
Determining the Singularities for the Observation of Three Image Lines (2016)

The determination of the singularity cases in the observation of image features is a complicated problem, which is still open, apart from image points. For the first time, we provide the singularity cases in the observation of three image lines. We show that a concept named the “hidden robot,” which was formerly used for understanding the singularities of a vision-based controller dedicated to parallel robots and, more recently, which proved to be efficient for finding the singularity cases in the observation of image points, can be used for interpreting the singularities in the observation of three image lines. The hidden robot concept considerably simplifies the analysis by using geometric interpretations of the mapping degeneracy and tools provided by the mechanical engineering community. We prove that in the most complicated case where three general lines in space are observed, singularities appear when the origin of the observed object frame is either on a quadric or a cubic surface whose location in space depends on the configuration of the observed lines. In simpler cases where at least two lines belong to the same plane, these two surfaces can degenerate into simpler geometrical loci (e.g., planes, cylinders, and lines).
16° Journée IRPF de Chimie: “Facing New Trends in Drug Discovery”, Institut de Recherche Pierre Fabre, Sorèze, Constitutional Dynamic Chemistry for Bioorganic and Medicinal Purposes.Lycée Freppel, De la Matière à la Vie. (2009)

International audience
Evaluating Symptoms to Improve Quality of Life in Patients with Chronic Stable Angina (2013)

Chronic stable angina (CSA) is a significant problem in the United States that can negatively impact patient quality of life (QoL). An accurate assessment of the severity of a patient's angina, the impact on their functional status, and their risk of cardiovascular complications is key to successful treatment of CSA. Active communication between the patient and their healthcare provider is necessary to ensure that patients receive optimal therapy. Healthcare providers should be aware of atypical symptoms of CSA in their patients, as patients may continue to suffer from angina despite the availability of multiple therapies. Patient questionnaires and symptom checklists can help patients communicate proactively with their healthcare providers. This paper discusses the prevalence of CSA, its impact on QoL, and the tools that healthcare providers can use to assess the severity of their patients' angina and the impact on QoL.
Dual Memory of Enantiomeric Helices in Poly(phenylacetylene)s Induced by a Single Enantiomer through Helix Inversion and Dual Storage of the Enantiomeric Helicity Memories (2015)

A series of stereoregular poly(phenylacetylene)s carrying prochiral phosphonic acid monoesters as the pendant groups (monophenyl ester: poly-1a; monoethyl ester: poly-1b; monoisopropyl ester: poly-1c) were synthesized. The polymers formed a preferred-handed helical conformation upon complexation with nonracemic amines, whose helix senses were inverted by temperature or solvent composition. The resulting diastereomeric right- and left-handed helices induced by chiral amines were retained or memorized after the chiral amines were completely replaced with achiral diamines, thus producing the corresponding enantiomeric helices. The helicity memory, however, is temporary and will be gradually lost due to its inherently dynamic nature. In order to permanently store or save the helicity memory, the phosphorus residues of the polymers were methyl esterified with diazomethane, which proceeded in an enantioselective way to generate a chiral center at the phosphorus residues with optical activity due to chirality transfer from the induced or memorized helical chirality of the polymer backbones, which enabled the storage of both the right- and left-handed macromolecular helices induced by the single enantiomer of the chiral amines. The enantioselectivity was significantly affected by the structures of the pendant phosphonate groups, and poly-1c bearing a monoisopropyl ester group showed the highest enantioselectivity, which further induced one of the helices of the polymer main chain with significant amplification of the helical chirality.
Coat colour in dogs: identification of the Merlelocus in the Australian shepherd breed (2006)

This study has identified the locus for the merle coat colour in dogs to be at the centromeric end of CFA10. Genetic studies on other breeds segregating the merle phenotype should allow the locus to be defined more accurately with the aim of identifying the gene. This work shows the power of the canine system to search for the genetic bases of mammalian pigmentation and developmental pathways.
Surface Chemistry Guides the Orientations of Adhering E. coli Cells Captured from Flow (2021)

Motivated by observations of cell orientation at biofilm-substrate interfaces and reports that cell orientation and adhesion play important roles in biofilm evolution and function, we investigated the influence of surface chemistry on the orientation of <i>Escherichia coli</i> cells captured from flow onto surfaces that were cationic, hydrophobic, or anionic. We characterized the initial orientations of nonmotile cells captured from gentle shear relative to the surface and flow directions. The broad distribution of captured cell orientations observed on cationic surfaces suggests that rapid electrostatic attractions of cells to oppositely charged surfaces preserve the instantaneous orientations of cells as they rotate in the near-surface shearing flow. By contrast, on hydrophobic and anionic surfaces, cells were oriented slightly more in the plane of the surface and in the flow direction compared with that on the cationic surface. This suggests slower development of adhesion at hydrophobic and anionic surfaces, allowing cells to tip toward the surface as they adhere. Once cells were captured, the flow was increased by 20-fold. Cells did not reorient substantially on the cationic surface, suggesting a strong cell-surface bonding. By contrast, on hydrophobic and anionic surfaces, increased shear forced cells to tip toward the surface and align in the flow direction, a process that was reversible upon reducing the shear. These findings suggest mechanisms by which surface chemistry may play a role in the evolving structure and function of microbial communities.
MEASURING SYSTEMS AND INSTRUMENTATION FOR EVALUATING PAVEMENT MAINTENANCE. INTERIM REPORT. EXECUTIVE SUMMARY (1989)

Chapter 1 of this report briefly discusses what is required for Pavement Management Systems (PMS) and then points out that PMS has not been geared toward maintenance managers. Chapter 2 develops the pavement characteristics data and measurements needed to study maintenance effectiveness. Chapter 3 deals with the technologies needed to make all measurements and introduces new technologies and new applications of technologies already in use. Chapter 4 is a sensitivity analysis and chapter 5 identifies the equipment used throughout the developed countries of the world. Chapter 6 identifies nonexisting highway equipment that can be transferred from other fields, discusses several feasibility studies already conducted, and outlines further testing necessary to complete evaluations of the technology and equipment identified. Chapter 7, the final chapter, makes recommendations based on the work completed during the first year of this research.
Chemical engineering of the peptidyl transferase center reveals an important role of the 2'-hydroxyl group of A2451 (2005)

The main enzymatic reaction of the large ribosomal subunit is peptide bond formation. Ribosome crystallography showed that A2451 of 23S rRNA makes the closest approach to the attacking amino group of aminoacyl-tRNA. Mutations of A2451 had relatively small effects on transpeptidation and failed to unequivocally identify the crucial functional group(s). Here, we employed an in vitro reconstitution system for chemical engineering the peptidyl transferase center by introducing non-natural nucleosides at position A2451. This allowed us to investigate the peptidyl transfer reaction performed by a ribosome that contained a modified nucleoside at the active site. The main finding is that ribosomes carrying a 2'-deoxyribose at A2451 showed a compromised peptidyl transferase activity. In variance, adenine base modifications and even the removal of the entire nucleobase at A2451 had only little impact on peptide bond formation, as long as the 2'-hydroxyl was present. This implicates a functional or structural role of the 2'-hydroxyl group at A2451 for transpeptidation.
Electron beam-induced deposition of platinum from Pt(CO)2Cl2 and Pt(CO)2Br2 (2020)

Two platinum precursors, Pt(CO)<sub>2</sub>Cl<sub>2</sub> and Pt(CO)<sub>2</sub>Br<sub>2</sub>, were designed for focused electron beam-induced deposition (FEBID) with the aim of producing platinum deposits of higher purity than those deposited from commercially available precursors. In this work, we present the first deposition experiments in a scanning electron microscope (SEM), wherein series of pillars were successfully grown from both precursors. The growth of the pillars was studied as a function of the electron dose and compared to deposits grown from the commercially available precursor MeCpPtMe<sub>3</sub>. The composition of the deposits was determined using energy-dispersive X-ray spectroscopy (EDX) and compared to the composition of deposits from MeCpPtMe<sub>3</sub>, as well as deposits made in an ultrahigh-vacuum (UHV) environment. A slight increase in metal content and a higher growth rate are achieved in the SEM for deposits from Pt(CO)<sub>2</sub>Cl<sub>2</sub> compared to MeCpPtMe<sub>3</sub>. However, deposits made from Pt(CO)<sub>2</sub>Br<sub>2</sub> show slightly less metal content and a lower growth rate compared to MeCpPtMe<sub>3</sub>. With both Pt(CO)<sub>2</sub>Cl<sub>2</sub> and Pt(CO)<sub>2</sub>Br<sub>2</sub>, a marked difference in composition was found between deposits made in the SEM and deposits made in UHV. In addition to Pt, the UHV deposits contained halogen species and little or no carbon, while the SEM deposits contained only small amounts of halogen species but high carbon content. Results from this study highlight the effect that deposition conditions can have on the composition of deposits created by FEBID.
The Lead Anode in Alkaline Solutions: I . The Initial Oxidation Processes (1987)

The initial reactions occurring at a Pb anode in alkaline solutions have been investigated using cyclic voltammetry and steady‐state and transient potentiostatic methodologies. It has been found that the first step in the reaction is the formation of a surface intermediate, followed by the deposition of a thin film on the Pb surface. A major portion of this film dissolves to form and the measured Tafel slope of 27 mV/decade of current density is consistent with the dissolution step being the rate‐determining step. With the use of the rotating ring disk electrode technique, in which the disk current is separated into that due to the formation of an insoluble surface product and that due to a dissolution reaction, it was found that some of the film dehydrates to form a thin film. At more positive potentials, further film growth occurs, but by a nucleation and growth mechanism.
Ascorbic acid as negative effector of the peroxidase‐catalyzed degradation of indole‐3‐acetic acid (1982)

Ascorbic acid is a strong inhibitor of indole‐3‐acetic oxidation catalyzed by commercial horse‐radish peroxidase. In the presence of excess ascorbic acid, the indole‐acetic acid oxidation catalysis is apparently blocked. The activity of peroxidase for indoleacetic acid at pH 3.7 and 33°C, in the presence of 2,4‐dichlorophenol and MnCl 2 as promotors was measured by polarographic technique. The K m was 0.27 m M and the maximum velocity was 1.02 mmol O 2 (mg protein) −1 min −1 . Dixon plots lead to an apparent K i of 1.25 (μ M for ascorbic acid and the inhibition was apparently competitive. Ascorbic acid, besides appearing to be a strong inhibitor of the IAA oxidase activity of peroxidase, seemed to protect IAA from total degradation. Addition of more than 5 μ M ascorbic acid produced both an exponential increase in the lag time before the onset of reaction and, at the end, an oxidation protection of 26 μ M IAA when 111 μ M IAA was present at the stawrt. The possibility of ascorbic acid‐IAA auxin from endogenous oxidation in plants, is proposed.
Design of a magnetic actuation system for a microbiota-collection ingestible capsule (2021)

Minimally invasive wireless devices, allowing the sampling of gut&#x2019;s bacteria, are needed for a longitudinal understanding of the role of the microbiota on the human health. Herein, we present a novel magnetic actuation system fitting inside a 11.5 &#x00D7; 30.5 mm wireless ingestible capsule. Lacking any electronic components, the capsule robot is designed for the collection of microbiota&#x2019;s samples through mechanical brushing. Wireless activation and in situ sampling are enabled by an external permanent magnetic source. This component, when approaching the capsule, progressively allows: (1) the adhesion of the device to the mucosa, (2 the exposure of the brushes, and (3) the sampling by multiple rotations. Numerical and analytical models were developed for dimensioning the system, and were validated by benchtop experiments.
Formulation and Pharmacokinetics Evaluation of Puerarin Nanocrystals for Intravenous Delivery (2012)

Puerarin is a very widely used drug for treating coronary heart disease. Owing to its poor water solubility and the adverse drug reactions caused by cosolvents having been confirmed by SFDA, the aim of present study was to construction and evaluation the puerarin nanocrystals in vitro and in vivo. The nanocrystals prepared were characterized using PCS, AFM, TEM, SEM and DSC. For the assessment of the pharmacokinetic parameters the developed formulations have been intravenous administered to beagle dogs. Results revealed that a narrow size distributed nanocrystals composed of crystallized spherical particles with a mean particle size of 423.6 +/- 17.3 nm, a poly-dispersity index of 0.13 +/- 0.07 and a negative charges around -30 mV was obtained. Puerarin dissolution velocity and saturation solubility were enhanced by the nanocrystals. DSC analysis revealed that the crystallinity of the puerarin was preserved during the high pressure homogenization and freeze-drying processes. Administration of the nanocrystals led to a mean plasma profile with almost similarly low variations in comparison to the reference solution, however with no initial blood peak as observed with the solution formulation. The puerarin nanocrystals exhibited a significantly (P < 0.05) reduced Cmax and clearance, and a significantly (P < 0.05) greater MRT, clearance and elimination half-life compared to the puerarin solution. These results revealed the opportunity to formulate puerarin in nanocrystals for intravenous delivery with higher safety.
A3 CROHN’S DISEASE PROTEOLYTIC MICROBIOTA ENHANCES INFLAMMATION THROUGH PAR2 PATHWAY IN GNOTOBIOTIC MICE (2023)

Abstract Background An imbalance in host proteases has been implicated in inflammatory bowel disease (IBD). Recent evidence implicates microbial proteolytic activity (PA) in ulcerative colitis but whether it also plays a role in Crohn’s disease (CD) remains unclear. Purpose We therefore investigated the colitogenic potential and underlying pathways of proteolytic CD microbiota. Method Adult germ-free (GF) C57BL/6 mice were colonized with CD microbiota selected based on high (CD-HPA) or low fecal proteolytic activity (CD-LPA), and from healthy controls with LPA (HC-LPA), after which total fecal proteolytic, elastolytic and mucolytic activity were analyzed in the mice. Microbial community was assessed by 16S rRNA gene sequencing. Immune function and colonic injury were investigated by inflammatory gene expression (NanoString) and histology. Colitis severity and underlying pathways were investigated in C57BL/6, Nucleotide-binding Oligomerization Domain-2 knock-out (Nod2-/-), and Protease-Activated Receptor 2 (PAR2) cleavage resistant mice (R38E-PAR2) subjected to 2% dextran sodium sulfate in drinking water for 5 days followed by 2 days on water. Result(s) Colonization with HC-LPA or CD-LPA lowered baseline fecal proteolytic activity compared with GF mice, which was paralleled by lower acute inflammatory cell infiltrate. CD-HPA further increased proteolytic activity compared with GF mice. Fecal supernatants from CD-LPA or HC-LPA colonized mice had lower in vitro PAR2 cleavage compared to supernatants from GF and CD-HPA colonized mice. Several genes, such as Map kinases, Rhoa, Myd88, and Tollip, were increased in GF mice compared to colonized mice. 18 genes related to inflammation and barrier function (e.g., Mapk2k6, Tnf, Claudin1) were differentially expressed between CD-LPA and CD-HPA. CD-HPA mice had lower alpha diversity, distinct microbial profiles, and higher fecal proteolytic activity compared with CD-LPA. Abundance of several beneficial species (e.g., Akkermansia muciniphilia) was decreased while other taxa were increased (e.g., Hungattella hathewayi) in CD-HPA compared to CD-LPA. H. hathewayi as well as the serine protease K04772 were transcriptionally increased in fecal samples from CD-HPA colonized mice. C57BL/6 and Nod2-/- mice, but not R38E-PAR2 mice, colonized with CD-HPA developed earlier and more severe colitis compared with mice colonized with CD-LPA. Conclusion(s) CD proteolytic microbiota is proinflammatory through a PAR2 pathway. H. hathewayi correlates with the proinflammatory phenotype through the serine protease K04772 in this model. The results support a role of microbial PA in CD, which could constitute a biomarker for identifying patients who would benefit from anti-proteolytic therapies. Disclosure of Interest None Declared
Change Detection for High Resolution Remote Sensing Image Based on Co-saliency Strategy (2019)

Change detection for remote sensing image is of great significance to a diverse range of applications. From the point of object-based method, this paper provides a change detection algorithm based on co-saliency strategy for multitemporal high resolution images. Firstly, the final difference image fused by difference feature and log difference feature, is generated, and feature image including spatial and contextual information is obtained by Gabor wavelet transform. Secondly, co-saliency strategy is performed via cluster-based method, combining the final difference image with feature difference image at each temporal data, and highlighting the common regions as the changed directly. Finally, actual change map is extracted by fuzzy local information C-means clustering algorithm (FLICM) and decision-voted method. The experiments show the method proposed in this paper has a superior performance in change detection for high resolution remote sensing images.