gebhart/patrepeval huggingface dataset:
Surfactants Used in Food Industry: A Review (2009)

The understanding of the formation, structures, and properties of emulsions is essential to the creation and stabilization of structures in food. The increasing use of surfactants, the identification of compounds with low toxicity and good surface activity properties is of great interest. The relevance of the major end points specified in the Organisation for Economic Co-operation and Development (OECD) guidelines for the hazard assessment of food chemicals is critically analyzed and main parameters are acute toxicity, subacute repeated studies, allergy, reproductive toxicity, long-term studies, and mutagenicity tests. We focus this article on surfactant association structures and food colloids. There is almost infinite number of combinations are organized and arranged in very complex internal microstructures with various types of assemblies such as dispersions, emulsions, foams, gels, etc. Low-mass surfactants are very mobile at the interface and they are particularly efficient reducing the interfacial tension. As a result, they rapidly coat the freshly created oil-water interface during emulsification. In this category, we mainly mentioned monoglycerides, lecithins, glycolipids, fatty alcohols and fatty acids. High-mass surfactants cover protein and polysacharide groups. The protein molecule may interpenetrate in the lipid phase to various degrees. The specific binding is predominantly electrostatic: The headgroups of the surfactants bind to groups of opposite charge on the protein. The saturation binding for anionic surfactants is pH-independent and seems to be controlled by the cooperative hydrophobic interactions. Polysaccharides and smallmolecule surfactants are two of the predominant groups of amphiphilic materials that have been explored for the stabilization of emulsions. One of the most important aspects of polymer-surfactant systems is their ability to control stability and rheology over a wide range of composition. Biocompatible, biodegradable, and/or nontoxic emulsion-based formulations have great potential for applications in the food. The combination of particular characteristics such as emulsifying, anti-adhesive and antimicrobial activities presented by biosurfactants suggests potential application as multipurpose ingredients or additives.
Ozanimod (RPC1063) is a potent sphingosine‐1‐phosphate receptor‐1 (S1P 1 ) and receptor‐5 (S1P 5 ) agonist with autoimmune disease‐modifying activity (2016)

S1P receptor selectivity, favourable PK properties and efficacy in three distinct disease models supports the clinical development of RPC1063 for the treatment of relapsing multiple sclerosis and inflammatory bowel disease, differentiates RPC1063 from other S1P receptor agonists, and could result in improved safety outcomes in the clinic.
Recent advances in the understanding of inherited sideroblastic anaemia (2008)

Sideroblastic anaemia includes a heterogeneous group of rare conditions, characterized by decreased haem synthesis and mitochondrial iron overload, which are diagnosed by the presence of ringed sideroblasts in the bone marrow aspirate. The most frequent form is X-linked sideroblastic anaemia, caused by mutations of delta-aminolevulinic acid synthase 2 (ALAS2), the enzyme that catalyses the first and regulatory step of haem synthesis in erythroid precursors and is post-transcriptionally controlled by the iron regulatory proteins. Impaired haem production causes variable degrees of anaemia and mitochondrial iron accumulation as ringed sideroblasts. The heterogeneity and complexity of sideroblastic anaemia is explained by an increasing number of recognized molecular defects. New forms have been recognized as being linked to the deficient function of mitochondrial proteins involved in iron-sulphur cluster biogenesis, such as ABCB7 and GLRX5, which are extremely rare but represent important biological models. Local mitochondrial iron overload is present in all sideroblastic anaemias, whereas systemic iron overload occurs only in the forms because of primary or secondary deficiency of ALAS2.
Hemolysin patterns of Actinobacillus pleuropneumoniae (1990)

The secreted hemolytic activities produced by the reference strains and field isolates of the 12 serotypes and 2 subtypes of Actinobacillus pleuropneumoniae were analyzed. Serotype 1 produced a Ca2(+)-inducible hemolysin, which was previously characterized as a 105-kilodalton protein and was named hemolysin I (HlyI). Serotypes 2, 4, 6, 7, and 8 produced a different hemolytic activity that was not inducible by Ca2+ but required this ion for its activity. The hemolytic activity produced by these serotypes was much weaker than that found in serotype 1 and was not neutralized by rabbit antibodies against HlyI. It was, however, neutralized by serum from pigs that were experimentally infected with a serotype 2 strain and was called hemolysin II (HlyII). Serotypes 5a, 5b, 9, 10, and 11 produced both HlyI and HlyII. In these strains, HlyI was the major contributor to the hemolytic activity. The remaining serotypes, 3 and 12, produced a very weak hemolytic activity, which was not further analyzed. Immunoblot analysis of the culture supernatants from all 12 serotypes with rabbit polyclonal antibodies directed against HlyI revealed reactions with a protein in the 105-kilodalton size range for all serotypes, indicating that HlyI and HlyII might be serologically related. Strains producing active HlyI seem to belong to serotypes that are generally considered to be virulent types and that are frequently isolated from pigs in severe pleuropneumonia outbreaks.
Peptidyl transferase activity catalyzed by protein-free 23S ribosomal RNA remains elusive (1999)

In two recent articles by Nitta et al. (1998a, 1998b), evidence was presented that in vitro-transcribed protein-free 23S rRNA of Escherichia coli (and its individual domains) can catalyze peptide bond formation. The implications of these studies are considerable because demonstration of catalytic activity associated with protein-free 23S rRNA would be fundamental to our understanding of the mechanism and evolution of protein synthesis (Noller et al., 1992; Khaitovich et al., 1999).
[Childhood sexual abuses among 1307 adult students and analysis on results of Symptom Checklist-90 test]. (2006)

Childhood sexual abuse among students is not rare. The female students' incidence was obviously higher than that among the male students (chi(2) = 11.8, P = 0.001). About half of the abusers were the victims' close relatives, neighbors and teachers who live or study together with them. Personal experience of childhood sexual abuses may be one of the important factors influencing the victims' results of SCL-90 test.
Molecular and functional analysis of genes required for expression of group IB K antigens in Escherichia coli : characterization of the his‐region containing gene clusters for multiple cell‐surface polysaccharides (1997)

Escherichia coli group I capsular K antigens are found in two forms on the cell surface. The K(LPS) form is linked to lipopolysaccharide lipid A core, whereas the high-molecular-weight capsular form is assembled independently of lipid A core. Subgroup IB K antigens are generally co-expressed with either the O8 or O9 antigen and, under the appropriate conditions, with the exopolysaccharide, colanic acid. To examine the relationships between the genetic loci and the synthetic pathways for these various cell-surface polymers, the gene cluster responsible for expression of a prototype group IB K antigen (serotype K40) was cloned and the flanking chromosomal regions characterized. Analysis of the six orfs within the cluster indicates features typical of Wzy (Rfc)-dependent O antigens. Synthesis of group IB K antigens is initiated by WecA (Rfe), a UDP-GlcNAc::undecaprenylphosphate GlcNAc-1-phosphate transferase, and the chain length of K40LPS is determined by the wzz gene product. The his-region of the E. coli O8:K40 prototype is almost exclusively devoted to the expression of three different surface polysaccharides. The rfbK40 cluster is located adjacent to the cps (colanic acid synthesis) and rfbO8 (O8 antigen synthesis) loci in the gene order: his-rfbO8/O9-wzz-ugd-gnd-rfbK40-galF-cps. Thus, rfbK40 is in the location occupied by other Wzy-dependent rfb gene clusters, and rfbO8/O9 represents an additional locus.
Sol–gel process: influence of the temperature on the textural properties of organosilsesquioxane materials (2000)

The hydrolytic sol–gel polymerization of a variety of molecular precursors, (RO)3Si–X–Si(OR)3 with different structural features, has been investigated varying the temperature from −20 to +110 °C. "Rigid" precursors (R = Me, X = 1,4-C6H4, ferrocene-1,1′-diyl), "semi-rigid" precursors (R = Me, X = CH2CH2-1,4-C6H4CH2CH2; R = Et, X = CH2CH2CHCHCHCHCH2CH2) and alkylene-bridged precursors [R = Me, X = (CH2)6, (CH2)10; R = Et, X = (CH2)2, (CH2)14] were studied. A molecular precursor containing three Si(OMe)3 groups, 1,3,5-(MeO)3SiC6H3, was also considered. The reactions were performed using ionic and non-ionic catalysts. The ionic ones were a nucleophile [tetrabutylammonium fluoride (TBAF)], an acid (HCl) and a base (NaOH), and the non-ionic ones were nucleophiles [dimethylaminopyridine (DMAP), N-methylimidazole (NMI)]. The solvent employed was THF. Reactions were studied in MeOH only with TBAF as catalyst. In all cases the temperature appeared to be a fundamental parameter and had a drastic influence on the specific surface area and the porosity of the resulting solids. Particularly at low temperatures (−20 to 0 °C), the solids were mainly microporous with a weak mesoporous contribution without narrow pore size distribution. At higher temperature (20 to +110 °C), the solids exhibited very high specific surface areas and were mesoporous with a narrow pore size distribution. The specific surface area, the porosity and the pore size were highly dependent on the temperature. This work came in our study on the kinetic control of the texture.
Lysophosphatidylcholine as a Ligand for the Immunoregulatory Receptor G2A (2001)

Although the biological actions of the cell membrane and serum lipid lysophosphatidylcholine (LPC) in atherosclerosis and systemic autoimmune disease are well recognized, LPC has not been linked to a specific cell-surface receptor. We show that LPC is a high-affinity ligand for G2A, a lymphocyte-expressed G protein-coupled receptor whose genetic ablation results in the development of autoimmunity. Activation of G2A by LPC increased intracellular calcium concentration, induced receptor internalization, activated ERK mitogen-activated protein kinase, and modified migratory responses of Jurkat T lymphocytes. This finding implicates a role for LPC-G2A interaction in the etiology of inflammatory autoimmune disease and atherosclerosis.
Visualizing the structure of RNA-seq expression data using grade of membership models (2017)

Grade of membership models, also known as "admixture models", "topic models" or "Latent Dirichlet Allocation", are a generalization of cluster models that allow each sample to have membership in multiple clusters. These models are widely used in population genetics to model admixed individuals who have ancestry from multiple "populations", and in natural language processing to model documents having words from multiple "topics". Here we illustrate the potential for these models to cluster samples of RNA-seq gene expression data, measured on either bulk samples or single cells. We also provide methods to help interpret the clusters, by identifying genes that are distinctively expressed in each cluster. By applying these methods to several example RNA-seq applications we demonstrate their utility in identifying and summarizing structure and heterogeneity. Applied to data from the GTEx project on 53 human tissues, the approach highlights similarities among biologically-related tissues and identifies distinctively-expressed genes that recapitulate known biology. Applied to single-cell expression data from mouse preimplantation embryos, the approach highlights both discrete and continuous variation through early embryonic development stages, and highlights genes involved in a variety of relevant processes-from germ cell development, through compaction and morula formation, to the formation of inner cell mass and trophoblast at the blastocyst stage. The methods are implemented in the Bioconductor package CountClust.
Block Replacement Scheme based on Reuse Interval for Hybrid SSD System (2015)

최근 SSD(Solid State Drive)는 빠른 읽기/쓰기, 저전력 등 다양한 장점을 가지고 있어 스마트폰, 노트북, 서버 등의 저장장치로 사용 영역이 확대되고 있다. 하지만, 플래시 메모리의 읽기 및 쓰기의 비대칭적 성능과 제한된 쓰기 횟수가 SSD의 수명을 단축시키는 문제가 있어서 캐쉬(cache)로 사용되는 SSD의 내용을 변경시키는 블록 교체 기법(block replacement policy)이 매우 중요하다. Hybrid SSD의 수명을 향상 시킬 수 있는 방법 중 하나로 LARC 기법이 있으나, LARC는 SSD블록 관리를 위해 기존 LRU알고리즘을 사용하기 때문에 빈번히 참조되는 블록이 오래된 블록 대신 교체되어 SSD 미스율을 증가시킴으로써 시스템의 성능이 저하되는 문제점이 발생한다. 따라서, 본 논문에서는 다양한 데이터 읽기, 쓰기 환경에 효과적으로 대응하기 위해 블록의 재사용 간격을 고려한 새로운 블록 교체 기법을 제안한다. 제안된 기법은 블록 재사용 간격(Reuse interval)과 Age를 기반으로 최근성(Recency)을 추출하고 참조빈도(Frequency)를 같이 고려하여 블록을 교체한다. Workload 기반 Trace를 이용한 실험결과, 제안하는 기법은 여러가지의 기존 블록 교체 기법 및 LARC 알고리즘과 비교하여 쓰기 횟수 감소와 히트율 향상을 통해 시스템 성능과 SSD의 수명을 연장시킨다. Due to the advantages of fast read/write operation and low power consumption, SSD(Solid State Drive) is now widely adopted as storage device of smart phone, laptop computer, server, etc. However, the shortcomings of SSD such as limited number of write operations and asymmetric read/write operation lead to the problem of shortened life span of SSD. Therefore, the block replacement policy of SSD used as cache for HDD is very important. The existing solutions for improving the lifespan of SSD including the LARC scheme typically employ the LRU algorithm to manage the SSD blocks, which may increase the miss rate in SSD due to the replacement of frequently used block instead of rarely used block. In this paper we propose a novel block replacement scheme which considers the block reuse interval to effectively handle various data read/write patterns. The proposed scheme replaces the block in SSD based on the recency decided by reuse interval and age along with hit ratio. Computer simulation using workload trace files reveals that the proposed scheme consistently improves the performance and lifespan of SSD by increasing the hit ratio and decreasing the number of write operations compared to the existing schemes including LARC.
Photochemical internalisation increases the cytotoxic effect of the immunotoxin MOC31-gelonin (2000)

Photochemical internalisation (PCI) was recently demonstrated as a unique procedure for site-specific delivery of several types of membrane impermeable macromolecules from endocytotic vesicles to the cytosol (Berg et al., 1999). The technology is based on the cytosolic release of endocytosed macromolecules from endosomes and lysosomes upon exposure of cells to photosensitising compounds, which became localised to these vesicles, and light. In our study the possibility to increase the cytotoxic effect of the immunotoxin MOC31-gelonin by PCI was examined. The type I ribosome-inactivating protein gelonin was covalently linked to the monoclonal IgG1 antibody MOC31, directed against epithelial glycoprotein-2 (EGP-2), an antigen expressed on most carcinoma cells. Five different cell lines, of which 4 expressed EGP-2, were treated with MOC31-gelonin and endosomal and lysosomal localising photosensitisers, followed by exposure to light. Insignificant cytotoxicity of the MOC31-gelonin was observed when the cells were incubated with the immunotoxin alone. However, in combination with endosomal and lysosomal localising photosensitizers, we demonstrate synergistic toxic effect of the MOC31-gelonin conjugate in a light-dependent manner. Our results indicate that PCI is a promising tool for increasing the cytotoxicity of immunotoxins, which is important for further improvement of the PCI concept towards possible use in cancer therapy.
The fetal form of the acetylcholine receptor distinguishes rhabdomyosarcomas from other childhood tumors. (1998)

The fetal nicotinic acetylcholine receptor (AChR) of muscle is an oligomeric membrane protein with subunit composition alpha2betadeltagamma. After birth, the adult form, in which an epsilon-subunit replaces the gamma-subunit, predominates, and expression of the fetal form is limited to thymic myoid cells, extraocular muscles, and denervated striated muscle. We looked for expression of AChR in rhabdomyosarcomas and other childhood tumors by reverse transcription polymerase chain reaction and immunohistochemistry. mRNA for the AChR gamma-subunit was detected in all embryonal and alveolar rhabdomyosarcomas tested (n = 16) and in some tumors with a rhabdomyomatous component (n = 2) but not in other nonrhabdomyomatous tumors of childhood and adults (n = 45). The fetal form of the AChR was detected immunohistochemically in five of eight embryonal and four of eight alveolar rhabdomyosarcomas and in two Wilms' tumors with a rhabdomyomatous component but not in other tumors or in normal muscle. We conclude that reverse transcription polymerase chain reaction for AChR gamma-subunit could be useful for the diagnosis of rhabdomyosarcoma of childhood and for the detection of micrometastases and minimal residual disease. In addition, the fetal AChR protein is the first extracellular tumor marker that can distinguish rhabdomyosarcomas from nonrhabdomyomatous tumors and from normal muscle. Our findings, therefore, imply that the fetal AChR may be a target for in vivo imaging and, as AChR internalization and degradation is increased by antibody-induced cross-linking, may also provide a sensitive and specific target for immunotherapeutic strategies.
Adaptive control of a variable-impedance ankle-foot orthosis to assist drop-foot gait (2004)

An active ankle-foot orthoses (AAFO) is presented where the impedance of the orthotic joint is modulated throughout the walking cycle to treat drop-foot gait. During controlled plantar flexion, a biomimetic torsional spring control is applied where orthotic joint stiffness is actively adjusted to minimize forefoot collisions with the ground. Throughout late stance, joint impedance is minimized so as not to impede powered plantar flexion movements, and during the swing phase, a torsional spring-damper control lifts the foot to provide toe clearance. To assess the clinical effects of variable-impedance control, kinetic and kinematic gait data were collected on two drop-foot participants wearing the AAFO. For each participant, zero, constant, and variable impedance control strategies were evaluated and the results were compared to the mechanics of three age, weight, and height matched normals. We find that actively adjusting joint impedance reduces the occurrence of slap foot allows greater powered plantar flexion and provides for less kinematic difference during swing when compared to normals. These results indicate that a variable-impedance orthosis may have certain clinical benefits for the treatment of drop-foot gait compared to conventional ankle-foot orthoses having zero or constant stiffness joint behaviors.
Molecular adhesion development in a neural cell monolayer forming in an ultrasound trap (2005)

A 2-dimensional aggregate of C6 neural cells was formed rapidly (within 30 s) in suspension in a recently developed 1.5 MHz ultrasound standing wave trap. A typical 1 mm diameter aggregate contained about 3,500 cells. Spreading of membrane occurred between the aggregated cells. The rate of spreading of the tangentially developing intercellular contact area was 0.19 microm/min. The form of the suspended aggregate changed from one of a hexagonal arrangement of cells to one of a cell-monolayer-like continuous sheet of mostly quadrilateral and pentagonal cells as in a cell monolayer on a solid substratum. A range of fluorescent indicators showed that the >99% viability of the cells did not change during 1 h exposures; therefore cell viability was not compromised during the monolayer development. The average integral intensities from stained actin filaments at the spreading cell-cell interfaces after 1, 8 and 30 min were 14, 25 and 46 microm(2) respectively. The cells in this work progressed from physical aggregation, through molecular adhesion, to displaying the intracellular consequences of receptor interactions. The ability to form mechanically strong confluent monolayer structures that can be monitored in situ or harvested from the trap provides a technique with general potential for monitoring the synchronous development of cell responses to receptor-triggered adhesion.
Regulated Expansion and Survival of Chimeric Antigen Receptor-Modified T Cells Using Small Molecule-Dependent Inducible MyD88/CD40 (2017)

Anti-tumor efficacy of T cells engineered to express chimeric antigen receptors (CARs) is dependent on their specificity, survival, and in vivo expansion following adoptive transfer. Toll-like receptor (TLR) and CD40 signaling in T cells can improve persistence and drive proliferation of antigen-specific CD4<sup>+</sup> and CD8<sup>+</sup> T cells following pathogen challenge or in graft-versus-host disease (GvHD) settings, suggesting that these costimulatory pathways may be co-opted to improve CAR-T cell persistence and function. Here, we present a novel strategy to activate TLR and CD40 signaling in human T cells using inducible MyD88/CD40 (iMC), which can be triggered in vivo via the synthetic dimerizing ligand, rimiducid, to provide potent costimulation to CAR-modified T cells. Importantly, the concurrent activation of iMC (with rimiducid) and CAR (by antigen recognition) is required for interleukin (IL)-2 production and robust CAR-T cell expansion and may provide a user-controlled mechanism to amplify CAR-T cell levels in vivo and augment anti-tumor efficacy.
Purification and amino-terminal sequence of an insulin-like growth factor-binding protein secreted by rat liver BRL-3A cells. (1986)

A protein preparation that specifically binds insulin-like growth factors (IGFs) I and II was purified from medium conditioned by rat liver BRL-3A cells using molecular sieve chromatography in 1 M acetic acid followed by affinity chromatography on IGF-II-agarose. The affinity-purified IGF-binding protein exhibits a single major band with apparent Mr = 36,300 under reducing conditions on sodium dodecyl sulfate-polyacrylamide gels. The IGF-binding protein is efficiently and specifically cross-linked to either 125I-IGF-I (human) or 125I-IGF-II (rat) using disuccinimidyl suberate. An IGF-binding protein of similar apparent molecular weight was also affinity purified from rat hepatoma H-35 cell conditioned medium and found to differ from the BRL-3A protein such that potent polyclonal antisera prepared in rabbits against the purified BRL-3A IGF-binding protein exhibited a much lower titer for the H-35 protein in an enzyme-linked immunosorbent assay and upon immunoblotting. In order to determine whether a single BRL-3A IGF-binding protein is present in the affinity-purified preparation, the protein was prepared for sequencing on a Sephacryl S-300 column in 6 M guanidine HCl after reduction and alkylation. The amino acid composition (expressed in percentages) of this IGF-binding protein was determined to be: Cys = 5.5, Lys = 4.8, His = 2.8, Arg = 7.8, Asx = 10.2, Thr = 5.1, Ser = 3.9, Glx = 15.7, Gly = 17.4, Ala = 7.3, Val = 4.6, Met = 1.4, Ile = 2.4, Leu = 8.3, Tyr = 1.0, Phe = 1.9. Sequencing of the NH2-terminal portion of this protein led to the identification of 31 amino acids in the following order: Phe-Arg-Cys-Pro-Pro-Cys-Thr-Pro-Glu-Arg-Leu-Ala-Ala-Cys-Gly-Pro-Pro-Pro- Asp-Ala-Pro-Cys-Ala-Glu-Leu-Val-Arg-Glu-Pro-Gly-Cys. We conclude that rat liver BRL-3A cells secrete a single major IGF-binding protein capable of binding both IGF-I and IGF-II.