gebhart/patrepeval huggingface dataset:
Layer-by-Layer Coated Digitally Encoded Microcarriers for Quantification of Proteins in Serum and Plasma (2007)

The "layer-by-layer" (LbL) technology has been widely investigated for the coating of flat substrates and capsules with polyelectrolytes. In this study, LbL polyelectrolyte coatings applied at the surface of digitally encoded microcarriers were evaluated for the quantitative, sensitive, and simultaneous detection of proteins in complex biological samples like serum, plasma, and blood. LbL coated microcarriers were therefore coupled to capture antibodies, which were used as capture agents for the detection of tumor necrosis factor (TNF-alpha), P24, and follicle stimulating hormone (FSH). It was found that the LbL coatings did not disassemble upon incubating the microcarriers in serum and plasma. Also, nonspecific binding of target analytes to the LbL coating was not observed. We showed that the LbL coated microcarriers can reproducibly detect TNF-alpha, P24, and FSH down to the picogram per milliliter level, not only in buffer but also in serum and plasma samples. Microcarrier-to-microcarrier intratube variations were less then 30%, and interassay variations less than 8% were observed. This paper also shows evidence that the LbL coated digitally encoded microcarriers are ideally suited for assaying proteins in "whole" blood in microfluidic chips, which are of high interest for "point-of-care" diagnostics.
Super Vector ! (2009)

Concevoir de nouveaux systèmes pharmaceutiques, développer des nanomédicaments... porte-drapeau des nanotechnologies à usage biomédical, Patrick Couvreur revient, non sans une pointe d’humour, sur son parcours « galéniste » et sur les gélules devenues nanomédicaments.
High expression of CD26 accurately identifies human bacteria‐reactive MR1‐restricted MAIT cells (2015)

Mucosa-associated invariant T (MAIT) cells express the semi-invariant T-cell receptor TRAV1-2 and detect a range of bacteria and fungi through the MHC-like molecule MR1. However, knowledge of the function and phenotype of bacteria-reactive MR1-restricted TRAV1-2(+) MAIT cells from human blood is limited. We broadly characterized the function of MR1-restricted MAIT cells in response to bacteria-infected targets and defined a phenotypic panel to identify these cells in the circulation. We demonstrated that bacteria-reactive MR1-restricted T cells shared effector functions of cytolytic effector CD8(+) T cells. By analysing an extensive panel of phenotypic markers, we determined that CD26 and CD161 were most strongly associated with these T cells. Using FACS to sort phenotypically defined CD8(+) subsets we demonstrated that high expression of CD26 on CD8(+) TRAV1-2(+) cells identified with high specificity and sensitivity, bacteria-reactive MR1-restricted T cells from human blood. CD161(hi) was also specific for but lacked sensitivity in identifying all bacteria-reactive MR1-restricted T cells, some of which were CD161(dim) . Using cell surface expression of CD8, TRAV1-2, and CD26(hi) in the absence of stimulation we confirm that bacteria-reactive T cells are lacking in the blood of individuals with active tuberculosis and are restored in the blood of individuals undergoing treatment for tuberculosis.
Mechanical response and rheological properties of polycarbonate layered‐silicate nanocomposites (2004)

Abstract The effect of clay loading on the mechanical behavior and melt state linear viscoelastic properties of intercalated polycarbonate (PC) nanocomposites was investigated. At low frequencies, the linear dynamic oscillatory moduli data revealed diminished frequency dependence with increasing nanoclay loading. The 3.5 and 5 wt% clay nanocomposites exhibited dramatically altered relaxation behavior, from liquid‐like to pseudo‐solid–like, compared to the pure PC and the 1.5 wt% clay nanocomposite. Thermal degradation of PC resulted from the melt compounding of organo‐modified nanoclays was evident from the reduction in the glass transition temperature and molecular weight of the PC nanocomposites. These nanocomposites also exhibited a significant decrease in the extent of tensile elongation and ductility with respect to the nanoclay incorporation. A concomitant decrease in the rheological properties at high frequencies was also observed, and was consistent with the lowering of the molecular weight of PC, particularly near or above the percolation threshold of nanoclay. These nanocomposites, nevertheless, exhibited elastic‐plastic deformation in compression, regardless of nanoclay content. Polym. Eng. Sci. 44:825–837, 2004. © 2004 Society of Plastics Engineers.
Write-a-video (2019)

We present Write-A-Video , a tool for the creation of video montage using mostly text-editing. Given an input themed text and a related video repository either from online websites or personal albums, the tool allows novice users to generate a video montage much more easily than current video editing tools. The resulting video illustrates the given narrative, provides diverse visual content, and follows cinematographic guidelines. The process involves three simple steps: (1) the user provides input, mostly in the form of editing the text, (2) the tool automatically searches for semantically matching candidate shots from the video repository, and (3) an optimization method assembles the video montage. Visual-semantic matching between segmented text and shots is performed by cascaded keyword matching and visual-semantic embedding, that have better accuracy than alternative solutions. The video assembly is formulated as a hybrid optimization problem over a graph of shots, considering temporal constraints, cinematography metrics such as camera movement and tone, and user-specified cinematography idioms. Using our system, users without video editing experience are able to generate appealing videos.
Fluorinated barbituric acid derivatives (1994)

The structures of 5,5-difluorobarbituric acid, C 4 H 2 F 2 N 2 O 3 (1), and 5-fluoro-5-phenylbarbituric acid, C 10 H 7 FN 2 O 3 (2), have been determined [barbituric acid is 2,4,6(1H,3H,5H-pyrimidinetrione]. Both compounds have the expected keto structure. The C-C bonds in the heterocyclic ring [1.526 (8) A for (1), 1.525 (6) and 1.537 (6) A for (2)] are elongated relative to those of the parent compounds, consistent with the electron-withdrawing power of the F-atom substituent(s). There is extensive intermolecular hydrogen bonding in both compounds
Feedback-based coding algorithms for broadcast erasure channels with degraded message sets (2012)

We consider single-hop broadcast packet erasure channels (BPEC) with degraded message sets and instantaneous feedback regularly available from all receivers, and demonstrate that the main principles of the virtual-queue-based algorithms in [1], which were proposed for multiple unicast sessions, can still be applied to this setting and lead to capacity-achieving algorithms. Specifically, we propose a generic class of algorithms and intuitively describe its rationale and properties that result in its efficiency. We then apply this class of algorithms to three examples of BPEC channels (with different numbers of users and 2 or 3 degraded message sets) and show that the achievable throughput region matches a known capacity outer bound, assuming feedback availability through a separate public channel. If the feedback channel is not public, all users can still decode their messages, albeit at some overhead which results in an achievable throughput that differs from the outer bound by O(N/L), where L is the packet length. These algorithms do not require any prior knowledge of channel statistics for their operation.
Organosilicate Spin-On Glasses (2004)

Porous copolymer films were synthesized from a methylsilsequioxane:1,2-bis(trimethoxysilyl)ethane (MSSQ:BTMSE) matrix and either an aromatic-core or aliphatic-core porogen at 10, 20, or 30 wt % porogen loading. Films were characterized using scanning electron microscopy (SEM), IR spectroscopy, and ellipsometry. Depth-sensing indentation experiments were performed to measure apparent film modulus, E, and hardness, H. Indentation load-displacement traces and SEM images were used to determine the threshold load for cracking, Pc. The aliphatic-core porogen produced a greater porosity film than the aromatic-core porogen for 10 wt % loading and smaller porosity films for 20 and 30 wt % loadings. IR spectra, normalized for film thickness and density, indicated decreased O-Si-O networking in porous MSSQ:BTMSE films. The combination of increased porosity and decreased O-Si-O networking led to a decreased apparent E and H relative to the unmodified MSSQ:BTMSE film. However, low-porosity (approximately 7%), aliphatic-porogen MSSQ:BTMSE films are optimized relative to unmodified MSSQ with smaller dielectric constant and greater E and H.
Bisphosphonates in development for metabolic bone disease (1994)

Bisphosphonates are analogues of endogenous pyrophosphate and exhibit profound effects on bone metabolism. These compounds have been shown to inhibit the recruitment and/or activity of osteoclasts (bone-resorbing cells) and to increase bone mass by reducing both the activation frequency of new bone remodelling units and the depth to which osteoclasts resorb bone. In animal studies, several bisphosphonates (etidronate, tiludronate, pamidronate, and cimadronate (YM-175) have also produced beneficial biomechanical effects on bone (increases in bone strength, stiffness and fracture load) in conjunction with increases in bone mass. Because of the bisphosphonates' high affinity for bone, very few soft-tissue effects or toxicities are observed. Bisphosphonates have shown clinical efficacy in metabolic bone diseases such as Paget's disease, metastatic hypercalcaemia and postmenopausal osteoporosis, and their use is under investigation in other diseases of abnormal bone turnover such as glucocorticoid-induced osteoporosis, hyperthyroidism, hyperparathyroidism and rheumatoid arthritis. Future work with these important therapeutic agents will optimise desired effects and identify and minimise adverse effects.
Acute renal failure in Eastern India (1995)

The present study included 426 patients with acute renal failure age range 7 months to 85 years, during 8-year period (1984-1992). Medical, surgical and obstetric causes were responsible for ARF in 68.3, 17.8, and 14% of cases respectively. The main aetiological factors encountered were volume depletion secondary to gastrointestinal fluid loss (35.2%), acute glomerulonephritis (10.3%), nephrotoxin (8.6%), falciparum malaria (4.2%), obstructive uropathy (13%), post-abortal (10.5%), and miscellaneous factors (1.4%) of patients. The overall mortality was 19.2%. Thus our observation revealed that diarrhoeal diseases (35.2%), obstructive uropathy (13.3%), and septic abortion (10.5%) were the main causes for ARF in medical, surgical, and obstetric groups respectively. In contrast to our studies, acute renal failure associated with diarrhoeal diseases, septicaemia, falciparum malaria and septic abortion are rare in European countries.
Fast Pyrolysis of Hydrolysis Lignin in Fluidized Bed Reactors (2021)

Fast pyrolysis of hydrolysis lignin was studied in fluidized bed units. Hydrolysis lignin, a bioproduct from the lignocellulosic ethanol production process (St1 Cellunolix), was processed in bench scale bubbling fluidized bed (BFB) and pilot scale circulating fluidized bed (CFB) units. Utilization of steam and ethanol as hydrogen sources was tested in a BFB unit. Major technical challenges identified were related to slow reaction rates of lignin degradation and the rapid secondary reactions in the vapor phase resulting in deposit formation and pressure buildup in product gas lines. The carbohydrate content of hydrolysis lignin had a clear correlation to its processability. More challenges with clogging and bed agglomeration were observed with lignin feedstock having lower carbohydrate content. The challenges with the bed agglomeration in the BFB unit were overcome by adding a rapidly rotating mixer in the reactor to break the agglomerates. With the CFB unit, bed agglomeration was not a problem, due to high gas velocities and forces applied to sand and lignin particles. In the BFB unit, the screw feeder was cooled and no significant melting problems were observed. In the CFB unit, melting problems were avoided by feeding the raw material in the cold section of reactor. However, severe increases in the pressure buildup and deposit formation rates were observed in both units. Steam and ethanol was tested, separately, in the BFB unit, to provide excess hydrogen in the system. Based on the product analyses both added hydrogen into the system, but hydrogen ended up mostly in the gas phase. To enhance the hydrogen transfer to the organic liquid, a catalyst active in hydrogen transfer is probably needed.
Self-Reactive CFTR T Cells in Humans: Implications for Gene Therapy (2013)

Cystic fibrosis (CF) is one of the most common autosomal recessive lethal disorders affecting white populations of northern European ancestry. To date there is no cure for CF. Life-long treatments for CF are being developed and include gene therapy and the use of small-molecule drugs designed to target specific cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations. Irrespective of the type of molecular therapy for CF, which may include gene replacement, exon skipping, nonsense suppression, or molecular correctors, because all of these modulate gene expression there is an inherent risk of activation of T cells against the wild-type version of CFTR. Here we report the validation of the human interferon-γ enzyme-linked immunospot assay and its application for the analysis of CFTR-specific T cell responses in patients with CF and in non-CF subjects. We found non-CF subjects with low levels of self-reactive CFTR-specific T cells in the United States and several patients with CF with low to high levels of self-reactive CFTR-specific T cells in both the United States and the United Kingdom.
Frequency, electric field and temperature dependence of piezoelectric constant of Pb(Zr,Ti)O3based ceramics under high electric field (1997)

Abstract Frequency, electric field and temperature dependence of piezoelectric constants d31 were measured under strong electric fields by a static method based on a linear response theory for Pb(Zr0.5Ti0.5)O3 (PZT) and Pb(Zr0.5Ti0.5)O3+0.3wt% MnO2 (Mn-PZT) ceramics. The result shows that the piezoelectric relaxation exists around 0.1Hz for the PZT and tens of heltz for the Mn-PZT at a room temperature. The d31 of the PZT decreases about 35% from 0.01Hz to 400Hz under an electric field of 20kV/cm and decreases about 20% from electric fields of 20kV/cm to 0kV/cm at 400Hz. It is confirmed that the d31 at 400Hz extrapolated to 0kV/cm is almost the same as that measured by the resonance-antiresonance method for the PZT. Temperature dependence of the d31 was also discussed.
Experience with Formal Specifications Using an Extended State Transition Model (1982)

Experience with the use of formal descriptions of communication services and protocols is described. The paper focuses on the experience of the authors with the extended state transition model which is proposed as a standard formal description technique (FDT) for the services and protocols in the OSI environment. The first part of the paper refers to various example specifications, including transport protocol and service specifications, and discusses the suitability of the specification method and possible extensions. In the remaining part, the use of such formal specifications during the phases of system design, implementation, and testing is described. Various approaches to protocol design validation, implementation, and assessment of implementations are discussed, with emphasis on the last point. The experience with several of these approaches is described in the paper, and further details may be found in the references.
AAV-Mediated TAZ Gene Replacement Restores Mitochondrial and Cardioskeletal Function in Barth Syndrome (2018)

Barth syndrome (BTHS) is a rare mitochondrial disease that affects heart and skeletal muscle and has no curative treatment. It is caused by recessive mutations in the X-linked gene TAZ, which encodes tafazzin. To develop a clinically relevant gene therapy to restore tafazzin function and treat BTHS, three different adeno-associated virus serotype 9 vectors were tested and compared to identify the optimal promoter-cytomegalovirus (CMV), desmin (Des), or a native tafazzin promoter (Taz)-for TAZ expression following intravenous administration of 1 × 10<sup>13</sup> vector genomes/kilogram to a mouse model of BTHS as either neonates (1-2 days of age) or adults (3 months of age). At 5 months of age, evaluations of biodistribution and TAZ expression levels, mouse activity assessments, fatigue in response to exercise, muscle strength, cardiac function, mitochondrial structure, oxygen consumption, and electron transport chain complex activity assays were performed to measure the extent of improvement in treated mice. Each promoter was scored for significant improvement over untreated control mice and significant improvement compared with the other two promoters for every measurement and within each age of administration. All three of the promoters resulted in significant improvements in a majority of the assessments compared with untreated BTHS controls. When scored for overall effectiveness as a gene therapy, the Des promoter was found to provide improvement in the most assessments, followed by the CMV promoter, and finally Taz regardless of injection age. This study provides substantial support for translation of an adeno-associated virus serotype 9-mediated TAZ gene replacement strategy using a Des promoter for human BTHS patients in the clinic.
Novel PCA-VIP scheme for ranking MRI protocols and identifying computer-extracted MRI measurements associated with central gland and peripheral zone prostate tumors (2014)

PCA-VIP identified relatively stable subsets of MRI features that performed well in localizing prostate cancer on MRI.
A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations (2017)

Summary Though the added value of proteomic measurements to gene expression profiling has been demonstrated, profiling of gene expression on its own remains the dominant means of understanding cellular responses to perturbation. Direct protein measurements are typically limited due to issues of cost and scale; however, the recent development of high-throughput, targeted sentinel mass spectrometry assays provides an opportunity for proteomics to contribute at a meaningful scale in high-value areas for drug development. To demonstrate the feasibility of a systematic and comprehensive library of perturbational proteomic signatures, we profiled 90 drugs (in triplicate) in six cell lines using two different proteomic assays — one measuring global changes of epigenetic marks on histone proteins and another measuring a set of peptides reporting on the phosphoproteome — for a total of more than 3,400 samples. This effort represents a first-of-its-kind resource for proteomics. The majority of tested drugs generated reproducible responses in both phosphosignaling and chromatin states, but we observed differences in the responses that were cell line-and assay-specific. We formalized the process of comparing response signatures within the data using a concept called connectivity, which enabled us to integrate data across cell types and assays. Furthermore, it facilitated incorporation of transcriptional signatures. Consistent connectivity among cell types revealed cellular responses that transcended cell-specific effects, while consistent connectivity among assays revealed unexpected associations between drugs that were confirmed by experimental follow-up. We further demonstrated how the resource could be leveraged against public domain external datasets to recognize therapeutic hypotheses that are consistent with ongoing clinical trials for the treatment of multiple myeloma and acute lymphocytic leukemia (ALL). These data are available for download via the Gene Expression Omnibus (accession GSE101406), and web apps for interacting with this resource are available at https://clue.io/proteomics . Highlights First-of-its-kind public resource of proteomic responses to systematically administered perturbagens Direct proteomic profiling of phosphosignaling and chromatin states in cells for 90 drugs in six different cell lines Extends Connectivity Map concept to proteomic data for integration with transcriptional data Enables recognition of unexpected, cell type-specific activities and potential translational therapeutic opportunities
Low power networks &#x2014; The ZigBee competition (2009)

The IEEE standard 802.15.4 for low-rate wireless personal area networks and ZigBee will play an important role for low power networks. From the authors' point of view, ZigBee might even become a key technology for such networks. A low complexity and low power implementation of a ZigBee receiver which is driven by zero-crossing demodulation (ZXD), an irregular sampling technique, will be introduced in this document.
Unusual forms of low density lipoprotein receptors in hamster cell mutants with defects in the receptor structural gene. (1986)

The structure and processing of low density lipoprotein (LDL) receptors in wild-type and LDL receptor-deficient mutant Chinese hamster ovary cells was examined using polyclonal anti-receptor antibodies. As previously reported for human LDL receptors, the LDL receptors in wild-type Chinese hamster ovary cells were synthesized as precursors which were extensively processed by glycosylation to a mature form. In the course of normal receptor turnover, an apparently unglycosylated portion of the cysteine-rich N-terminal LDL binding domain of the receptor is proteolytically removed. The LDL receptor-deficient mutants fall into four complementation groups, ldlA, ldlB, ldlC, and ldlD; results of the analysis of ldlB, ldlC, and ldlD mutants are described in the accompanying paper (Kingsley, D. M., K. F. Kozarsky, M. Segal, and M. Krieger, 1986, J. Cell. Biol, 102:1576-1585). Analysis of ldlA cells has identified three classes of mutant alleles at the ldlA locus: null alleles, alleles that code for normally processed receptors that cannot bind LDL, and alleles that code for abnormally processed receptors. The abnormally processed receptors were continually converted to novel unstable intracellular intermediates. We also identified a compound-heterozygous mutant and a heterozygous revertant which indicate that the ldlA locus is diploid. In conjunction with other genetic and biochemical data, the finding of multiple mutant forms of the LDL receptor in ldlA mutants, some of which appeared together in the same cell, confirm that the ldlA locus is the structural gene for the LDL receptor.