gebhart/patrepeval huggingface dataset:
Supplementary Figure S2 from Circulating Mitochondrial DNA Level, a Noninvasive Biomarker for the Early Detection of Gastric Cancer (2023)

&lt;p&gt;Supplementary Figure S2 : Analyses of the influence of age on peripheral leukocytes mtDNA content and on serological level of IL-8 in peripheral blood in cohorts 1 and 2. A) In cohort 1 Pearson correlation did not show any significant effect of age on mtDNA content when considering healthy, NAG and GC groups independently; however the analysis on the whole cohort showed a weak influence (p-value=0.04). Importantly, when considering together healthy plus NAG patients (shown as insert in the graph cohort 1) no significant correlation was observed, despite the presence of several older individuals within these patients. These data suggest that the correlation observed in the whole cohort was due to the significantly higher levels of mtDNA found in GC patients compared to healthy and NAG groups. B) No influence of age was observed on IL-8 levels when considering neither each disease group independently nor the whole cohort 1. C) In cohort 2, as in cohort 1, the Pearson correlation analysis did not show any significant correlation with age and mtDNA content when considering NAG, IM or GC groups independently. However, in the whole cohort a weak influence of age on mtDNA was observed (p-value=0.04). As for cohort 1, when the analysis included only NAG plus IM patients (shown as insert in the graph cohort 2), no significant correlation was observed despite the advanced age of some patients in these groups, specially among IM patients for which mean age was similar to GC patients.&lt;/p&gt;
Applying velocity profiling technology to flow measurement at the Orinda water treatment plant (1998)

A new type of flow measurement technology, velocity profiling, was tested in the South Channel of the Orinda Water Treatment Plant. This new technology allowed installation in the difficult hydraulic conditions of the South Channel, without interrupting plant operation. The advanced technology of velocity profiling enables flow measurements to be obtained in sites normally unusable by more traditional methods of flow rate measurement.
Preakuammicine: A long awaited missing link in the biosynthesis of monoterpene indole alkaloids (2016)

Preakuammicine is considered as a key intermediate in the biosynthesis of monoterpene indole alkaloids since the 1970's. Indeed, preakuammicine plays a crucial role in the biosynthesis of strychnan, type II, type III monoterpene indole alkaloids. According to the seminal hypothesis, preakuammicine would originate from a complex rearrangement of the akuammilan skeleton (such as rhazimol) but neither the structure of preakuammicine, nor the direct conversion from akuammillan alkaloids have been described [1]. Given the piecemeal spectral description of the molecule [2], questions about its structure and in particular a non matching C-16 stereochemistry between different monoterpene indole alkaloid series [ex: rhazimol (16R), stemmadenine (16S)]. The conversion of akuammilan-type into strychnan-type alkaloids was therefore studied, with the aim of characterizing this "missing link" [3] for the first time.
Molecular imaging of brain localization of liposomes in mice using MALDI mass spectrometry (2016)

Phospholipids have excellent biocompatibility and are therefore often used as main components of liposomal drug carriers. In traditional bioanalytics, the in-vivo distribution of liposomal drug carriers is assessed using radiolabeled liposomal constituents. This study presents matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) as an alternative, label-free method for ex-vivo molecular imaging of liposomal drug carriers in mouse tissue. To this end, indocyanine green as cargo and two liposomal markers, 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG) and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine conjugated with monodisperse polyethylene glycol (PEG36-DSPE) were incorporated into liposomal carriers and administered to mice. We used MALDI MSI of the two lipid markers in both positive and negative ion mode for visualization of liposome integrity and distribution in mouse organs. Additional MSI of hemoglobin in the same tissue slice and pixel-by-pixel computational analysis of co-occurrence of lipid markers and hemoglobin served as indicator of liposome localization either in parenchyma or in blood vessels. Our proof-of-concept study suggests that liposomal components and indocyanine green distributed into all investigated organs.
Fluid Mechanics in the Next Century (1996)

We consider here the future of some of the physical sciences that are developed enough for problems to be well posed mathematically even though, due to their complexity, analytical solutions are not possible. Such problems are typically approached through a combination of physical and numerical experiments, the latter increasing in scope and range as more computing power becomes available. Will they take over the former? Many areas in mechanics, and in particular fluid mechanics, appear to be at this stage. In a letter addressed to George G Stokes dated December 20, 1857, William Thomson wrote, "Now I think hydrodynamics is to be the root of all physical science, and is at present second to none in the beauty of its mathematics." Since we do not disagree with Lord Kelvin's assessment of the importance of fluid dynamics, we focus on this subject as a quintessential example for the rest of this perspective.
High-resolution 3D visualization of nanomedicine distribution in tumors (2019)

To improve the clinical translation of anti-cancer nanomedicines, it is necessary to begin building specific insights into the broad concept of the Enhanced Permeability and Retention (EPR) effect, using detailed investigations of the accumulation, distribution and retention of nanomedicines in solid tumors. Nanomedicine accumulation in preclinical tumors has been extensively studied; however, treatment efficacy will be heavily influenced by both the quantity of drug-loaded nanomedicines reaching the tumor as well as their spatial distribution throughout the tumor. It remains a challenge to image the heterogeneity of nanomedicine distribution in 3 dimensions within solid tumors with a high degree of spatial resolution using standard imaging approaches. <b>Methods:</b> To achieve this, an ex vivo micro computed tomography (µCT) imaging approach was developed to visualize the intratumoral distribution of contrast agent-loaded PEGylated liposomes. Using this semi-quantitative method, whole 3-dimensional (3D) tumor liposome distribution was determined with 17 µm resolution in a phenotypically diverse panel of four preclinical xenograft and patient-derived explant (PDX) tumor models. <b>Results:</b> High-resolution ex vivo μCT imaging revealed striking differences in liposome distribution within tumors in four models with different vascular patterns and densities, stromal contents, and microenvironment morphologies. Following intravenous dosing, the model with the highest density of pericyte-supported vessels showed the greatest liposome accumulation, while the model with vessels present in regions of high α-smooth muscle actin (αSMA) content presented with a large proportion of the liposomes at depths beyond the tumor periphery. The two models with an unsupported vascular network demonstrated a more restricted pattern of liposome distribution. <b>Conclusion:</b> Taken together, vessel distribution and support (the latter indicative of functionality) appear to be key factors determining the accumulation and distribution pattern of liposomes in tumors. Our findings demonstrate that high-resolution 3D visualization of nanomedicine distribution is a useful tool for preclinical nanomedicine research, providing valuable insights into the influence of the tumor vasculature and microenvironment on nanomedicine localization.
Extraction de surface physiquement plausible de simulations de fluides par particules (Journées de l'AFIG 2014) (2014)

International audience
Alterations in expression of S6K1 isoforms in MCF7 cells have a strong impact on the locomotor activity as well as on S6K1 and Akt signaling (2020)

To generate and characterize MCF-7 cell lines with altered expression of p85, p70 and p60 S6K1 isoforms: p85-/p70-/p60-MCF-7 and p85-/p70-/p60+MCF-7. Methods. CRISPR/ Cas9 gene editing, western blot analysis, immunofluorescence analysis, scratch assay. Results. Modified MCF-7 cells with knocked down expression of p85, p70, p60 or only p85 and p70 S6K1 isoforms were generated. Selective inhibition of only p85 and p70 isoforms in p85-/p70-/p60+MCF-7 cells was accompanied by actin cytoskeleton rearrangements, appearance of fibroblast-like cell morphology and significantly increased cell locomotor activity. Downregulation of all three S6K1 isoforms in p85-/p70-/p60 -MCF-7 cells inhibited cell migration with no changes in the cell morphology. Alterations in had a different impact on the ribosomal protein S6 phosphorylation and Akt signaling. Conclusion. Analysis of the modified MCF-7 cell lines revealed different impact of expression of S6K1 isoforms on MCF7 cell locomotor activity and the S6K1-and Akt-dependent signaling. Our data suggest that p60-S6K1 could be involved in regulation of the cell migration. The generated cells can be used for further analysis of functional activity of the S6K1 isoforms.
Data continuation in the presence of caustics: A synthetic data example (2004)

In data continuation, the information present in the collected data is used to estimate data at new positions. We investigate two examples of data continuation: data healing and dip moveout. By composing a modeling operator with an imaging operator we can construct an operator to perform each of the tasks. We review the theory and present an algorithm for data continuation specifically directed at these two examples. This algorithm is able to continue data in the presence of caustics. To demonstrate the performance of this algorithm, we use a synthetic example in which there are caustics.
Risks of Primary Extracolonic Cancers Following Colorectal Cancer in Lynch Syndrome (2012)

Carriers of MMR gene mutations who have already had a colorectal cancer are at increased risk of a greater range of cancers than the recognized spectrum of Lynch syndrome cancers, including breast and prostate cancers.
Intracochlear Perfusion of Synthetic Perilymph: Controls and Applications (1972)

The utilization of cochlear perfusion as a tool for the study of cochlear physiology is not new. Both perilymphatic and endolymphatic perfusions have been done. However in these studies little or no data were given to indicate that the cochleas involved in these experiments were damaged. For our studies a “synthetic perilymph” solution containing the following ingredients (millimoles/liter) was prepared daily just prior to use: NaCl, 136.8; KCL, 5.6; CaCl2, 2.16; NaHCO3, 11.9; MgCl2, 0.491; Na2HPO4, 0.352; glucose, 4.44. The pH of the final solution was 7.95–8.05. For perfusion, glass pipets were inserted into both scala media and scala tympani of the basal turn of the guinea pig cochlea. Perfusion of the perilymphatic space at a speed of 0.1 milliliters/min was continued for 2 min. The ac cochlear potential and/or the N1-evoked potential was monitored from a round-window electrode. In order to check for procedural damage, an electrophysiological assessment of the cochlea was made before and after drilling the cochlea for the insertion of the perfusing pipets, as well as before and after perfusing with the synthetic perilymph. Data on the effect of perfusing solutions containing neomycin, Na salicylate, and Na cyanide will be presented. In addition, the effect of temperature of the perfusing solution on cochlea electrophysiology will be discussed.
DArT markers: diversity analyses and mapping in Sorghum bicolor (2008)

We have successfully developed DArT markers for Sorghum bicolor and have demonstrated that DArT provides high quality markers that can be used for diversity analyses and to construct medium-density genetic linkage maps. The high number of DArT markers generated in a single assay not only provides a precise estimate of genetic relationships among genotypes, but also their even distribution over the genome offers real advantages for a range of molecular breeding and genomics applications.
High Conductance Calcium-Activated Potassium Channels (1995)

Potassium channels represent a vast and diverse family of ion channel proteins which are found in many different types of tissues [1, 2]. These channels modulate the electrical excitability of certain cells, such as those derived from neuronal, endocrine and muscle sources. They also control the resting plasma membrane potential of a large variety of cells, regardless of whether the cells display electrically excitable or nonexcitable properties. K+ channels are routinely categorized according to their biophysical and pharmacological properties. However, these proteins may also be sub-divided into two major classifications depending on whether they are activated by changes in membrane potential (voltage-sensitive channels), or by an interaction with small molecule modulators (ligand-gated channels). Unfortunately, when compared with other types of ion channels, such as with the members of the voltage-gated Na+ and Ca2+ channel families [3], the biochemistry and molecular pharmacology of K+ channels is still rather undeveloped.
Generation and characterization of genetically stable heterohybridomas producing foot-and-mouth disease virus-specific porcine monoclonal antibodies (2020)

This report covers the methodology for generation of stable heterohybridoma clones producing Foot-and-mouth disease virus (FMDV) reactive porcine monoclonal antibodies (mAbs). Swine received five inoculations of an inactivated O1 Manisa FMDV vaccine prior to the harvest of splenocytes. Due to the lack of a species-specific hybridoma fusion partner, the Sp2/0 murine myeloma cell line was utilized for the formation of porcine-murine heterohybridoma clones. Twenty-nine FMDV-reactive parental clones were generated. Following sub-cloning and monitoring of reactivity over 20 serial passages, eleven subclones derived from unique parental origins were characterized and are reported herein. This methodology demonstrated the production of porcine mAbs by fusion of porcine splenocytes from immunized pigs with murine myeloma cells to generate heterohybridomas. The porcine immune response may differ from the murine immune response in relation to recognized epitopes. Therefore, application of this methodology may provide valuable resources for swine immunology and enhance the understanding of the mechanisms for antibody based protection from diseases in swine.
Acid‐Doped Polybenzimidazole as the Membrane of Electrochemical Hydrogen Sensors (1997)

A protonic polymer electrolyte based on polybenzimidazole is proposed for use in a hydrogen sensor, operating at room temperature, in air. The potentiometric response in inert gas containing hydrogen obeys the Nernst equation. In air, the EMF is a mixed potential which results from the hydrogen oxidation and the oxygen reduction. The response time is of the order of 30 s whatever the hydrogen concentration step within the hydrogen partial pressure range from to 1 atm.
Metabolite Profiling of Cerebrospinal Fluid Derived from MS Patients (P5.238) (2015)

Objective: To identify unique metabolic determinants in cerebrospinal fluid (CSF) of patients with progressive MS. Background: Disease progression in MS is poorly understood and there is a need to investigate the biochemical abnormalities specifically associated with progressive MS. Design/methods: CSF was obtained from healthy controls (n=15, untreated secondary progressive MS (SPMS; N=15)and untreated primary progressive MS (PPMS; N=15) patients with informed consent under an IRB-approved protocol. CSF was analyzed on the GC/MS and LC/MS/MS platforms by Metabolon (Durham, NC. Results: Fifty metabolites were found to be significantly altered in the MS cohort as compared to controls. Additionally, the analysis revealed the differential metabolite profiles of PPMS and SPMS populations (18 with a p≤0.05). These notably included changes in metabolites related to carbohydrate metabolism, specifically through glycolysis and the pentose phosphate pathway (PPP). In particular, increased levels of the biochemical indicator of glucose utilization lactate, as well as elevations in several pentose sugars that may be obtained from the diet or synthesized through the PPP (ribulose, ribitol, xylonate, xylose, xylitol, arabinose, and threitol) were noted in both MS patient groups. Moreover, higher levels of metabolites involved in alternative pathways of glucose utilization, such as sorbitol and fructose, along with increased levels of the sugar alcohol mannitol and its derivative mannose were observed in the MS groups. Arginine metabolism was also found significantly affected with changes in creatine and creatinine as well as elevations in two biochemical markers of extracellular matrix (ECM) remodeling namely trans-4-hydroxyproline) and pro-hydroxy-pro, especially in PPMS patients. This indicates a differential contribution of ECM remodeling in PPMS disease. The study also found changes in the neuroactive amino acids, and additional “isolated” metabolites. Conclusion This study revealed perturbations in the CSF metabolome that were both consistent and different when comparing patients with PPMS or SPMS and warrant further investigation.
Oscillating Crystallization of (+) and (–) Enantiomers during Resolution by Entrainment of 2‐Azabicyclo[2.2.1]hept‐5‐en‐3‐one (1996)

Lamellar twinning of opposite enantiomers explains why the enantiomeric composition of a supersaturated solution oscillates during resolution by preferential crystallization of the bicyclic lactam (1; see diagram on the right).
Reversible universal quantum computation within translation-invariant systems (2006)

We show how to perform reversible universal quantum computation on a translationally invariant pure state, using only global operations based on next-neighbor interactions. We do not need to break the translational symmetry of the state at any time during the computation. Since the proposed scheme fulfills the locality condition of a quantum cellular automata, we present a reversible quantum cellular automaton capable of universal quantum computation.
A hybrid virtual bass system for optimized steady-state and transient performance (2010)

Bandwidth extension of a constrained loudspeaker system is regularly achieved employing nonlinear bass synthesis. The method operates on the doctrine of the missing fundamental whereby humans infer the presence of a fundamental tone when presented with a signal consisting of higher harmonics of said tone. Nonlinear devices and phase vocoders are commonly used for signal generation; both exhibiting deficiencies. A system is proposed where the two approaches are used in tandem via a mixing algorithm to suppress these deficiencies. Mixing is performed by signal transient content analysis in the frequency domain using constant-Q transforms. The hybrid approach is rated subjectively against various nonlinear device and phase vocoder techniques using the MUSHRA test method.
Determining fracture properties of reclaimed asphalt pavement-based cement mortar using semicircular bending test (2020)

While critical stress intensity factor ( K I c s https://s3-euw1-ap-pe-df-pch-content-public-p.s3.eu-west-1.amazonaws.com/9781003027362/6aa7412f-8b72-468d-8f65-f251e01b3a69/content/inline-math83_001.tif"/> ) and critical crack tip opening displacement ( C T O D c https://s3-euw1-ap-pe-df-pch-content-public-p.s3.eu-west-1.amazonaws.com/9781003027362/6aa7412f-8b72-468d-8f65-f251e01b3a69/content/inline-math83_002.tif"/> ) are conventionally tested using single edge notched beam (SEN(B)) specimens, the test method suffers some drawbacks. A new test to characterize the fracture properties of the two-parameter fracture model (TPFM) using semi-circular bending (SCB) specimens has recently been developed by the authors. In comparison with the SEN(B) specimens, the SCB specimens can be readily made in lab from the commonly used cylindrical specimens. The geometry is also more suitable for field applications due to the ease of extracting cylinder specimens from concrete structures. In this study, the fracture properties of the TPFM for a reclaimed asphalt pavement (RAP) based cement mortar and a plain mortar at different curing ages were characterized using the SCB fracture test. The test results show that the RAP-Mortar (cement mortar containing 100% RAP) has lower K I c s https://s3-euw1-ap-pe-df-pch-content-public-p.s3.eu-west-1.amazonaws.com/9781003027362/6aa7412f-8b72-468d-8f65-f251e01b3a69/content/inline-math83_001.tif"/> than the CON-Mortar (cement mortar containing 100% natural sand). However, the reduction of K I c s https://s3-euw1-ap-pe-df-pch-content-public-p.s3.eu-west-1.amazonaws.com/9781003027362/6aa7412f-8b72-468d-8f65-f251e01b3a69/content/inline-math83_001.tif"/> is less significant than that of the compressive strength or splitting tensile strength. On the other hand, the RAP-Mortar was found to have higher C T O D c https://s3-euw1-ap-pe-df-pch-content-public-p.s3.eu-west-1.amazonaws.com/9781003027362/6aa7412f-8b72-468d-8f65-f251e01b3a69/content/inline-math83_002.tif"/> than the CON-Mortar. The increased C T O D c https://s3-euw1-ap-pe-df-pch-content-public-p.s3.eu-west-1.amazonaws.com/9781003027362/6aa7412f-8b72-468d-8f65-f251e01b3a69/content/inline-math83_002.tif"/> indicates that cement mortar containing RAP could potentially have a higher capacity to sustain cracking.
Bispecific CD8 Treg modulators regulate a novel regulatory CD8 T cell network and eliminate pathogenic CD4 T cells in live cell co-culture system (2022)

Abstract INTRODUCTION Others have described a subset of CD8 T cells (CD8 Treg) with immunosuppressive characteristics in inflammatory disease settings. CD8 Treg activation through canonical T cell receptors results in their oligoclonal expansion and perforin dependent elimination of pathogenic CD4 T cells. We have described the CD8 Treg network in Celiac patients and its potential to eliminate pathogenic CD4 T cells. Here we describe bispecific CD8 Treg modulators that activate CD8 Tregs, resulting in pathogenic CD4 T cell death. METHODS Novel bispecific CD8 Treg modulators were tested for target specificity by Octet and cell binding. The functional impact of CD8 Treg modulators was evaluated using flow and Luminex assays, and in a live cell co-culture system using Celiac patient derived CD8 Tregs and gliadin activated CD4 T cell targets. CD8 Treg modulators with specific molecular formats were then ranked for functional efficacy. RESULTS We tested a panel of bispecific CD8 Treg modulators with monovalent binding affinities in the low nanomolar range that selectively bind the CD8 Treg subset. Within 48 hours of CD8 Treg modulator addition to T cell co-cultures, CD8 Tregs had a rapid increase of cytolytic markers and degranulation in response to CD4 T cell targets. We observed a concomitant increase of activated CD4 T cell death and decrease of pro-inflammatory cytokines. CONCLUSIONS Our results indicate that a targeted approach to engage and activate CD8 Treg reduces pathogenic CD4 T cells. As this newly described CD8 Treg cell network is observed in many autoimmune diseases, we postulate that bispecific CD8 T cell modulators may represent a novel, selective and broadly applicable therapeutic approach for the treatment of human autoimmune diseases.