gebhart/patrepeval huggingface dataset:
CSF-1 and its receptor in breast carcinomas and neoplasms of the female reproductive tract (1997)

The expression and function of CSF-1 and its receptor were studied in tumors of the human breast, ovary, and endometrium. CSF-1 and its receptor, initially implicated as essential to normal monocyte development and trophoblastic implantation, have been more recently shown to be expressed by carcinomas of the breast and other epithelia of the female reproductive tract where activation of the receptor by ligand produced either by the tumor cells or by stromal elements stimulates tumor cell invasion by a urokinase-dependent mechanism. Breast carcinomas express wild-type CSF-1 receptors (CSF-1R) at levels comparable to those observed in trophoblast and monocytes. Ovarian and endometrial carcinomas express significantly lower levels of wild-type, functional CSF-1Rs, while ovarian carcinomas also express unusual transcripts that diverge from the wild-type CSF-1R transcript in their 5' extracellular domain sequences. Tumor cell expression of CSF-1R is under the control of several steroid hormones (glucocorticoids and progestins) and the binding of several bHLH transcription factors, while tumor cell expression of CSF-1 appears to be regulated by other hormones, some of which are involved in normal lactogenic differentiation. In addition, tumor cells often produce CSF-1 at such high levels that the cytokine spills into the extracellular fluid and circulation. Measurements of circulating levels of CSF-1 have proved useful in patients with ovarian, endometrial, and breast carcinoma both for disease detection and monitoring of response to therapy. CSF-1 and its receptor appear to be an important receptor/ligand pair in the biology of breast cancers and tumors of the female reproductive tract where they may regulate functions similar to those they control during macrophage activation and placental implantation.
Amplification and Overexpression of CTTN ( EMS1 ) Contribute to the Metastasis of Esophageal Squamous Cell Carcinoma by Promoting Cell Migration and Anoikis Resistance (2006)

Gain of chromosome 11q13 is a common event in esophageal squamous cell carcinoma (ESCC). The cortactin gene (CTTN, also EMS1), located at 11q13, plays a pivotal role in coupling membrane dynamics to cortical actin assembly. This gene has been implicated in the motility of several types of cells. In the present study, we found that the amplification and overexpression of the CTTN gene was associated with lymph node metastasis in ESCC. Functional analysis by small interfering RNA-mediated silencing of CTTN revealed that in addition to the effect on cell migration, CTTN influenced cell invasiveness by anoikis resistance. In vivo assay showed that inhibition of CTTN expression also decreased tumor growth and lung metastasis of ESCC cells. At the molecular level, we showed for the first time that the protective role of CTTN in anoikis resistance was correlated with the activation of the phosphatidylinositol 3-kinase/Akt pathway. Overall, the data suggest that CTTN is an oncogene in the 11q13 amplicon and exerts functions on tumor metastasis in ESCC.
Current clinical development of PI3K pathway inhibitors in glioblastoma (2012)

Glioblastoma (GBM) is the most common and lethal primary malignant tumor of the central nervous system, and effective therapeutic options are lacking. The phosphatidylinositol 3-kinase (PI3K) pathway is frequently dysregulated in many human cancers, including GBM. Agents inhibiting PI3K and its effectors have demonstrated preliminary activity in various tumor types and have the potential to change the clinical treatment landscape of patients with solid tumors. In this review, we describe the activation of the PI3K pathway in GBM, explore why inhibition of this pathway may be a compelling therapeutic target for this disease, and provide an update of the data on PI3K inhibitors in clinical trials and from earlier investigation.
Development of the cardiac coronary vascular endothelium, studied with antiendothelial antibodies, in chicken-quail chimeras. (1993)

The endothelium of the coronary vascular system has been described in the literature as originating from different sources, varying from aortic endothelium for the main coronary stems, endocardium for the intramyocardial network, and sinus venosus lining for the venous part of the coronary system. Using an antibody against quail endothelial cells (alpha-MB1), we investigated the development of the coronary vascular system in the quail (Hamburger and Hamilton stages 15 to 35) and in a series of 36 quail-chicken chimeras. In the chimeras, pieces of quail epicardial primordium and/or liver tissue were transplanted into the pericardial cavity of a chicken host. The results showed that the coronary vascular endothelial distribution closely followed the formation of the epicardial covering of the heart. However, pure epicardial primordium transplants did not lead to endothelial cell formation, whereas a liver graft with or without an epicardial contribution did have this capacity. The first endothelial cells were seen to reach the heart at the sinus venosus region, subsequently spreading through the inner curvature to the atrioventricular sulcus and the outflow tract and, last of all, over the ventricular surfaces. At these sites, the precursor cells and small vessels were seen to invade the sinus venosus wall, the ventricular and atrial myocardium, and the mesenchymal border of the aortic orifice. Connections with the endocardium of the heart tube were only observed in the right ventricular outflow region. Initially, the connections with the aortic endothelium were multiple, but later in development only two of these connections persisted to form the proximal part of the two main coronary arteries. Connections to the pulmonary orifice were never observed. Our transplantation data showed that the entire coronary endothelial vasculature originated from an extracardiac source. Moreover, using the developing subepicardial layer as a matrix, we showed that the endothelial cells reached the heart from the liver region. Ingrowth into the various cardiac segments was also observed. Implications for the relation to specific congenital cardiac malformations are discussed.
Cultivation of Schistosoma mansoni In vitro. I. Establishment of Cultures from Cercariae and Development until Pairing (1981)

Procedures are described for mass cultivation of Schistosoma mansoni. Cercariae were pooled, concentrated, and axenized through a series of washes in base medium containing antibiotics. Cercariae were sheared through a double-Luer-ended needle connected to two syringes, and tails separated and discarded. Young schistosomules were grown in a medium based upon BME augmented with lactalbumin hydrolysate, glucose, hormones, and other amendments and supplemented with human serum. Human blood cells (Type O) were added to cultures. Intestinal pigment was seen on the 5th day and gut cecal fusion began on day 11. Schistosomules developed steadily to pairing, which was seen first during the 7th wk of culture. Pairing occurred somewhat later in relation to development in vivo.
Mitochondrial Morphology and Intracellular Calcium Homeostasis in Cytochrome Oxidase-Deficient Human Fibroblasts (1997)

Mitochondrial encephalomyopathies arise from mutations in the mitochondrial or nuclear genome and result in defective energy metabolism. Investigation of cellular pathophysiology in these disorders has been limited to nonneuronal explant cultures such as fibroblasts and myoblasts. While investigating mitochondrial structure and function in fibroblasts obtained from control and cytochrome oxidase-deficient (COX) patients, we observed possible abnormalities by vital dye confocal microscopy. Most notable were swelling, reticulation (e.g., intricate fusion of mitochondria), and proliferation of mitochondria. However, a detailed quantitative comparison of mitochondrial morphology in age-, sex-, and passage-matched cultures revealed no significant differences between control and cytochrome oxidase-deficient fibroblasts, nor any differences with passage. In addition, COX fibroblasts exhibited no obvious impairment of intracellular calcium handling, measured by fura-2. These results indicate that cytochrome oxidase deficiency, at the level in these cultures, does not produce structural or ionic concentration alterations in fibroblasts. Future investigation of the pathophysiology of this respiratory chain disorder may require excitable tissue.
TIPS‐Tetracene‐ and TIPS‐Pentacene‐Annulated Poly(norbornadiene)s: Synthesis and Properties (2013)

The synthesis of tetracene- and pentacene-annulated norbornadienes, formed through the Diels-Alder reaction of a dehydroacene with cyclopentadiene is reported. Ring-opening metathesis polymerization (ROMP) leads to polymers that are investigated with respect to their physical, optical, and electronic properties by gel permeation chromatography (GPC), UV-vis spectroscopy, and cyclic voltammetry. The pentacene-containing polymer P1 is successfully integrated into an organic field-effect transistor (OFET); the tetracene-containing polymer P2 is integrated into an organic light-emitting diode (OLED).
SIMILARITY‐BASED RETRIEVAL WITH STRUCTURE‐SENSITIVE SPARSE BINARY DISTRIBUTED REPRESENTATIONS (2012)

We present an approach to similarity‐based retrieval from knowledge bases that takes into account both the structure and semantics of knowledge base fragments. Those fragments, or analogues, are represented as sparse binary vectors that allow a computationally efficient estimation of structural and semantic similarity by the vector dot product. We present the representation scheme and experimental results for the knowledge base that was previously used for testing of leading analogical retrieval models MAC/FAC and ARCS. The experiments show that the proposed single‐stage approach provides results compatible with or better than the results of two‐stage models MAC/FAC and ARCS in terms of recall and precision. We argue that the proposed representation scheme is useful for large‐scale knowledge bases and free‐structured database applications.
Studies on Retinal and Retinal Pigment Epithelial Gene Expression (2003)

The 'completion' of the murine and human genomes and creation of high-density expressed sequence tag (EST) databases from multiple tissues and multiple species, coupled with the development of high-throughput expression profiling approaches such as microarrays and Serial Analysis of Gene Expression (SAGE), is making possible the in-depth analysis of gene expression patterns in health and disease to an extent that was not previously possible. Such new information is providing insight into normal function, and into how normal function is altered in disease. Efforts have begun, and are accelerating, in the application of expression profiling to the study of the retina and retinal pigment epithelium (RPE). In this chapter we will review progress in this area. We will also discuss technical issues that make expression studies of the RPE particularly challenging, and share our experience in methodological approaches to overcome these challenges.
Evidence for Novel Hepaciviruses in Rodents (2013)

Hepatitis C virus (HCV) is among the most relevant causes of liver cirrhosis and hepatocellular carcinoma. Research is complicated by a lack of accessible small animal models. The systematic investigation of viruses of small mammals could guide efforts to establish such models, while providing insight into viral evolutionary biology. We have assembled the so-far largest collection of small-mammal samples from around the world, qualified to be screened for bloodborne viruses, including sera and organs from 4,770 rodents (41 species); and sera from 2,939 bats (51 species). Three highly divergent rodent hepacivirus clades were detected in 27 (1.8%) of 1,465 European bank voles (Myodes glareolus) and 10 (1.9%) of 518 South African four-striped mice (Rhabdomys pumilio). Bats showed anti-HCV immunoblot reactivities but no virus detection, although the genetic relatedness suggested by the serologic results should have enabled RNA detection using the broadly reactive PCR assays developed for this study. 210 horses and 858 cats and dogs were tested, yielding further horse-associated hepaciviruses but none in dogs or cats. The rodent viruses were equidistant to HCV, exceeding by far the diversity of HCV and the canine/equine hepaciviruses taken together. Five full genomes were sequenced, representing all viral lineages. Salient genome features and distance criteria supported classification of all viruses as hepaciviruses. Quantitative RT-PCR, RNA in-situ hybridisation, and histopathology suggested hepatic tropism with liver inflammation resembling hepatitis C. Recombinant serology for two distinct hepacivirus lineages in 97 bank voles identified seroprevalence rates of 8.3 and 12.4%, respectively. Antibodies in bank vole sera neither cross-reacted with HCV, nor the heterologous bank vole hepacivirus. Co-occurrence of RNA and antibodies was found in 3 of 57 PCR-positive bank vole sera (5.3%). Our data enable new hypotheses regarding HCV evolution and encourage efforts to develop rodent surrogate models for HCV.
The mechanics of non-Euclidean plates (2010)

Non-Euclidean plates are plates (“stacks” of identical surfaces) whose two-dimensional intrinsic geometry is not Euclidean, i.e. cannot be realized in a flat configuration. They can be generated via different mechanisms, such as plastic deformation, natural growth or differential swelling. In recent years there has been a concurrent theoretical and experimental progress in describing and fabricating non-Euclidean plates (NEP). In particular, an effective plate theory was derived and experimental methods for a controlled fabrication of responsive NEP were developed. In this paper we review theoretical and experimental works that focus on shape selection in NEP and provide an overview of this new field. We made an effort to focus on the governing principles, rather than on details and to relate the main observations to known mechanical behavior of ordinary plates. We also point out to open questions in the field and to its applicative potential.
Arenavirus Genome Rearrangement for the Development of Live Attenuated Vaccines (2015)

ABSTRACT Several members of the Arenaviridae family cause hemorrhagic fever disease in humans and pose serious public health problems in their geographic regions of endemicity as well as a credible biodefense threat. To date, there have been no FDA-approved arenavirus vaccines, and current antiarenaviral therapy is limited to an off-label use of ribavirin that is only partially effective. Arenaviruses are enveloped viruses with a bisegmented negative-stranded RNA genome. Each genome segment uses an ambisense coding strategy to direct the synthesis of two viral polypeptides in opposite orientations, separated by a noncoding intergenic region. Here we have used minigenome-based approaches to evaluate expression levels of reporter genes from the nucleoprotein (NP) and glycoprotein precursor (GPC) loci within the S segment of the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV). We found that reporter genes are expressed to higher levels from the NP than from the GPC locus. Differences in reporter gene expression levels from the NP and GPC loci were confirmed with recombinant trisegmented LCM viruses. We then used reverse genetics to rescue a recombinant LCMV (rLCMV) containing a translocated viral S segment (rLCMV/TransS), where the viral NP and GPC open reading frames replaced one another. The rLCMV/TransS showed slower growth kinetics in cultured cells and was highly attenuated in vivo in a mouse model of lethal LCMV infection, but immunization with rLCMV/TransS conferred complete protection against a lethal challenge with wild-type LCMV. Attenuation of rLCMV/TransS was associated with reduced NP expression levels. These results open a new avenue for the development of arenavirus live attenuated vaccines based on rearrangement of their viral genome. IMPORTANCE Several arenaviruses cause severe hemorrhagic fever in humans and also pose a credible bioterrorism threat. Currently, no FDA-licensed vaccines are available to combat arenavirus infections and antiarenaviral therapy is limited to the off-label use of ribavirin, which is only partially effective and associated with side effects. Here we describe, for the first time, the generation of a recombinant LCMV where the viral protein products encoded by the S RNA segment (NP and GPC) were swapped to generate rLCMV/TransS. rLCMV/TransS exhibited reduced viral multiplication in cultured cells and was highly attenuated in vivo while conferring protection, upon a single immunization dose, against a lethal challenge with wild-type LCMV. Our studies provide a proof of concept for the rational development of safe and protective live attenuated vaccine candidates based on genome reorganization for the treatment of pathogenic arenavirus infections in humans.
Synthesis and Evaluation Of 2″-Modified MMI Linked Dimers in Antisense Constructs (1997)

Abstract Synthesis of four methylene(methylimino) (MMI) linked dimers modifed at the 2′-position with fluoro and/or methoxy groups and their incorporation into different sequences has been accomplished. From these dimers, bis 2′-OMe MMI dimer was selected for further studies based on its synthetic accessibility, conformational study by NMR, and Tm analysis. Several chimeric antisense oligomers containing bis 2′-OMe dimers have been synthesized on a 10 μmol scale for in vivo studies.
REACTIONS OF 2,2,2-TRIFLUOROETHOXY- AND 2 , 2,2-TRIFLUOROETHYLTHIOBENZENE WITH LITHIUM DIALKYLAMIDES. THE FORMATION OF PHENYLTHIOYNAMINES (1976)

Abstract Reactions of 2,2,2-trifluoroethoxy-(2) and 2,2,2-trifluoroethylthiobenzene (3) with excess lithium dialkylamides afforded the difluorovinyl ether (4) and the phenylthioynamines (5) , respectively. Thus the latter reaction provides a convenient method for preparing these particular ynamines. Such striking difference in reaction course between 2 and 3 is discussed in terms of the relative stability of carbanions involved.
Reduced C9orf72 protein levels in frontal cortex of amyotrophic lateral sclerosis and frontotemporal degeneration brain with the C9ORF72 hexanucleotide repeat expansion (2014)

An intronic G(4)C(2) hexanucleotide repeat expansion in C9ORF72 is a major cause of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Several mechanisms including RNA toxicity, repeat-associated non-AUG translation mediated dipeptide protein aggregates, and haploinsufficiency of C9orf72 have been implicated in the molecular pathogenesis of this disorder. The aims of this study were to compare the use of two different Southern blot probes for detection of repeat expansions in an amyotrophic lateral sclerosis and frontotemporal lobar degeneration pathological cohort and to determine the levels of C9orf72 transcript variants and protein isoforms in patients versus control subjects. Our Southern blot studies identified smaller repeat expansions (250-1800 bp) that were only detectable with the flanking probe highlighting the potential for divergent results using different Southern blotting protocols that could complicate genotype-phenotype correlation studies. Further, we characterize a new C9orf72 antibody and show for the first time decreased C9orf72 protein levels in the frontal cortex from patients with a pathological hexanucleotide repeat expansion. These data suggest that a reduction in C9orf72 protein may be a consequence of the disease.
The phenylketonuria-associated substitution R68S converts phenylalanine hydroxylase to a constitutively active enzyme but reduces its stability (2019)

The naturally occurring R68S substitution of phenylalanine hydroxylase (PheH) causes phenylketonuria (PKU). However, the molecular basis for how the R68S variant leads to PKU remains unclear. Kinetic characterization of R68S PheH establishes that the enzyme is fully active in the absence of allosteric binding of phenylalanine, in contrast to the WT enzyme. Analytical ultracentrifugation establishes that the isolated regulatory domain of R68S PheH is predominantly monomeric in the absence of phenylalanine and dimerizes in its presence, similar to the regulatory domain of the WT enzyme. Fluorescence and small-angle X-ray scattering analyses establish that the overall conformation of the resting form of R68S PheH is different from that of the WT enzyme. The data are consistent with the substitution disrupting the interface between the catalytic and regulatory domains of the enzyme, shifting the equilibrium between the resting and activated forms ∼200-fold, so that the resting form of R68S PheH is ∼70% in the activated conformation. However, R68S PheH loses activity 2 orders of magnitude more rapidly than the WT enzyme at 37 °C and is significantly more sensitive to proteolysis. We propose that, even though this substitution converts the enzyme to a constitutively active enzyme, it results in PKU because of the decrease in protein stability.
54.2: Thin Plastic Electrophoretic Displays Fabricated by a Novel Process (2005)

Abstract We have developed a new way of making flexible, plastic active matrix displays using standard amorphous silicon TFT fabrication facilities. Using this technique we have made electrophoretic displays with three micron thick plastic a‐Si TFT backpanes. We believe that these are the thinnest plastic displays ever made.
A New Class of Potent Vascular Endothelial Growth Factor Receptor Tyrosine Kinase Inhibitors:  Structure−Activity Relationships for a Series of 9-Alkoxymethyl-12-(3-hydroxypropyl)indeno[2,1-a]pyrrolo[3,4-c]carbazole-5-ones and the Identification of CEP-5214 and Its Dimethylglycine Ester Prodrug Clinical Candidate CEP-7055 (2003)

A series of potent vascular endothelial growth factor R2 (VEGF-R2) tyrosine kinase inhibitors from a new indenopyrrolocarbazole template is reported. The structure-activity relationships for a series of 9-alkoxymethyl-12-(3-hydroxypropyl)indeno[2,1-a]pyrrolo[3,4-c]carbazole-5-ones revealed an optimal R9 substitution with ethoxymethyl 19 (VEGF-R2 IC(50) = 4 nM) and isopropoxymethyl 21 (VEGF-R2 IC(50) = 8 nM) being the most potent inhibitors in the series. The VEGF-R2 activity was reduced appreciably by increasing the size of the R9 alkoxy group or by alpha-methyl branching adjacent to the ring. The combined R9 alkoxymethyl and N12 hydroxypropyl substitutions were required for potent VEGF-R2 activity, and the corresponding thioether analogues were weaker than their ether counterparts. Compound 21 (R9 isopropoxymethyl, CEP-5214) was identified as a potent, low-nanomolar pan inhibitor of human VEGF-R tyrosine kinases, displaying IC(50) values of 16, 8, and 4 nM for VEGF-R1/FLT-1, VEGF-R2/KDR, and VEGF-R3/FLT-4, respectively, with cellular activity equivalent to the isolated enzyme activity. Compound 21 exhibited good selectivity against numerous tyrosine and serine/threonine kinases including PKC, Tie2, TrkA, CDK1, p38, JNK, and IRK. To increase water solubility and oral bioavailability, the N,N-dimethylglycine ester 40 was prepared. In pharmacokinetic studies in mice and rats, increased plasma levels of 21 were observed after oral administration of 40. Compound 21 demonstrated significant in vivo antitumor activity in numerous tumor models and was advanced into phase I clinical trials as the water-soluble N,N-dimethylglycine ester prodrug 40 (CEP-7055).