gebhart/patrepeval huggingface dataset:
RollFISH achieves robust quantification of single-molecule RNA biomarkers in paraffin-embedded tumor tissue samples (2018)

Single-molecule RNA fluorescence in situ hybridization (smFISH) represents a promising approach to quantify the expression of clinically useful biomarkers in tumor samples. However, routine application of smFISH to formalin-fixed, paraffin-embedded (FFPE) samples is challenging due to the low signal intensity and high background noise. Here we present RollFISH, a method combining the specificity of smFISH with the signal boosting of rolling circle amplification. We apply RollFISH to quantify widely used breast cancer biomarkers in cell lines and FFPE samples. Thanks to the high signal-to-noise ratio, we can visualize selected biomarkers at low magnification (20 × ) across entire tissue sections, and thus assess their spatial heterogeneity. Lastly, we apply RollFISH to quantify HER2 mRNA in 150 samples on a single tissue microarray, achieving a sensitivity and specificity of detection of HER2-positive samples of ~90%. RollFISH is a robust method for quantifying the expression and intratumor heterogeneity of biomarkers in FFPE tissues.
Genetic Transformation of Streptococcus mutans (1981)

Three strains of Streptococcus mutans belonging to serotypes a, c, and f were transformed to streptomycin resistance by deoxyribonucleic acids derived from homologous and heterologous streptomycin-resistant strains of S. mutans and Streptococcus sanguis strain Challis. Homologous transformation of S. mutans was less efficient than heterologous transformation by deoxyribonucleic acids from other strains of S. mutans.
THE IMMUNOCHEMICAL CHARACTERISATION OF CIRCULATING IMMUNE COMPLEX CONSTITUENTS IN CANDIDA ALBICANS OSTEOMYELITIS BY ISOELECTRIC FOCUSING, IMMUNOBLOT, AND IMMUNOPRINT (1987)

Circulating immune complexes present in the serum of a patient with systemic lupus erythematosus, end-stage renal failure, and thoracic vertebral Candida albicans osteomyelitis were sequentially analysed by isoelectric focusing, immunoblotting, and immunoprinting. Candida antigens (including mannoproteins), Clq and C3 complement components, and specific anti-Candida antibody were detected within polyethylene glycol precipitated complexes. An antigen of 47K molecular weight was amongst those demonstrated by polyacrylamide gel electrophoresis to be present within the complexes. It has been proposed elsewhere that a serologic response to a 47K protein is predictive of recovery from Candida albicans infection. Free antibody had specificity for Candida antigens ranging in molecular weight from 18K to more than 100K including a 47K component. The analytical techniques employed allowed rapid and precise identification of the components of one particular immune complex system and will be widely applicable to the dissection of other diverse systems.
α‐Substituted Phosphonate Analogues of Lysophosphatidic Acid (LPA) Selectively Inhibit Production and Action of LPA (2007)

Isoform-selective agonists and antagonists of the lysophosphatidic acid (LPA) G-protein-coupled receptors (GPCRs) have important potential applications in cell biology and therapy. LPA GPCRs regulate cancer cell proliferation, invasion, angiogenesis, and biochemical resistance to chemotherapy- and radiotherapy-induced apoptosis. LPA and its analogues are also feedback inhibitors of the enzyme lysophospholipase D (lysoPLD, also known as autotaxin), a central regulator of invasion and metastasis. For cancer therapy, the ideal therapeutic profile would be a metabolically stabilized pan-LPA receptor antagonist that also inhibits lysoPLD. Herein we describe the synthesis of a series of novel alpha-substituted methylene phosphonate analogues of LPA. Each of these analogues contains a hydrolysis-resistant phosphonate mimic of the labile monophosphate of natural LPA. The pharmacological properties of these phosphono-LPA analogues were characterized in terms of LPA receptor subtype-specific agonist and antagonist activity using Ca(2+) mobilization assays in RH7777 and CHO cells expressing the individual LPA GPCRs. In particular, the methylene phosphonate LPA analogue is a selective LPA(2) agonist, whereas the corresponding alpha-hydroxymethylene phosphonate is a selective LPA(3) agonist. Most importantly, the alpha-bromomethylene and alpha-chloromethylene phosphonates show pan-LPA receptor subtype antagonist activity. The alpha-bromomethylene phosphonates are the first reported antagonists for the LPA(4) GPCR. Each of the alpha-substituted methylene phosphonates inhibits lysoPLD, with the unsubstituted methylene phosphonate showing the most potent inhibition. Finally, unlike many LPA analogues, none of these compounds activate the intracellular LPA receptor PPARgamma.
Developing a high-throughput screening method for threonine overproduction based on an artificial promoter (2015)

This method should play a functional role for continuous improvement of threonine industry. Additionally, the threonine sensor construction using promoters obtained by proteomics analyses is so convenient that it would be easily extended to develop HTS models for other biochemicals.
Biological effects of high energy radiation and ultra high dose rates (1991)

Recently a powerful electron accelerator, 50 MeV race-track microtron, has been taken into clinical use. This gives the opportunity to treat patients with higher x-ray and electron energies than before. Furthermore, treatments can be performed were the entire fractional dose can be delivered in parts of a second. The relative biological effectiveness (RBE) of high energy photons (up to 50 MV) was studied in vitro and in vivo. Oxygen enhancement ratio (OER) of 50 MV photons and RBE of 50 MeV electrons were investigated in vitro. Single-fraction experiments, in vitro, using V-79 Chinese hamster fibroblasts showed an RBE for 50 MV x-rays of approximately 1.1 at surviving fraction 0.01, with reference to the response to 4 MV x- rays. No significant difference in OER could be demonstrated. Fractionation experiments were carried out to establish the RBE at the clinically relevant dose level, 2 Gy. The RBE calculated for the 2 Gy/fraction experiments was 1.17. The RBEs for 20 MV x-rays and 50 MeV electrons were equal to one. In order to investigate the validity of these results, the jejunal crypt microcolony assay in mice was used to determine the RBE of 50 MV x-rays. The RBE for 50 MV x-rays in this case was estimated to be 1.06 at crypt surviving fraction 0.1. Photonuclear processes are proposed as one possible explanation to the higher RBE for 50 MV x-rays. Several studies of biological response to ionizing radiation of high absorbed dose rates have been performed, often with conflicting results. With the aim of investigating whether a difference in effect between irradiation at high dose rates and at conventional dose rates could be verified, pulsed 50 MeV electrons from a clinical accelerator were used for experiments with ultra high dose rates (mean dose rate: 3.8 x 10^ Gy/s) in comparison to conventional (mean dose rate: 9.6 x 10"^ Gy/s). V-79 cells were irradiated in vitro under both oxic and anoxic conditions. No significant difference in relative biological effectiveness (RBE) or oxygen enhancement ratio (OER) was observed for ultra high dose rates compared to conventional dose rates. A central issue in clinical radiobiological research is the prediction of responses to different radiation qualities. The choice of cell survival and dose response model greatly influences the results. In this context the relationship between theory and model is emphasized. Generally, the interpretations of experimental data are dependent on the model. Cell survival models are systematized with respect to their relations to radiobiological theories of cell kill. The growing knowledge of biological, physical, and chemical mechanisms is reflected in the formulation of new models. This study shows that recent modelling has been more oriented towards the stochastic fluctuations connected to radiation energy deposition. This implies that the traditional cell survival models ought to be complemented by models of stochastic energy deposition processes at the intracellular level.
A hydroxyproline-rich protein in the soybean cell wall. (1988)

A cDNA clone that hybridizes to an mRNA (1A10) that accumulates to a substantial level in the axis of the germinating soybean seed was sequenced. The amino acid sequence of the clone indicates an almost perfect repeat of Pro-Pro-Val-Tyr-Lys resulting in a protein containing 40% proline and lacking serine and histidine. On the likelihood that such a protein might be a hydroxyproline-rich cell-wall glycoprotein (HRGP), cell walls of a soybean cell culture were extracted by procedures used to obtain soluble basic cell-wall glycoproteins, and the proteins were fractionated and purified. A 33-kDa protein (and possibly a 28-kDa protein) was obtained that has an amino acid distribution similar to that of the cDNA clone. The protein lacks histidine and serine and contains 20% hydroxyproline and 20% proline. The HRGP is thus distinct both in its amino acid content and in its pentameric repeat of Pro-Pro-Val-Tyr-Lys, with half of the prolines being hydroxylated.
Neural network compensation of gear backlash hysteresis in position-controlled mechanisms (1995)

This paper demonstrates that artificial neural networks can be used to identify and compensate for hysteresis caused by gear backlash in precision position-controlled mechanisms. A major contribution of this research is that physical analysis of the system nonlinearities and optimal control are used to design the neural network structure. Network sizing and initializing problems are thus eliminated. This physically meaningful, modular approach facilitates the integration of this neural network with existing controllers; thus, initial performance matches that of existing control approaches and then is improved by refining the parameter estimates via further learning. The neural network operates by recognizing backlash and switching to a control which moves smoothly through the backlash when the torque transmitted to the output shaft must be reversed.
Integrated Analysis of DNA Methylation and RNA Transcriptome during In Vitro Differentiation of Human Pluripotent Stem Cells into Retinal Pigment Epithelial Cells (2014)

Using the paradigm of in vitro differentiation of hESCs/iPSCs into retinal pigment epithelial (RPE) cells, we have recently profiled mRNA and miRNA transcriptomes to define a set of RPE mRNA and miRNA signature genes implicated in directed RPE differentiation. In this study, in order to understand the role of DNA methylation in RPE differentiation, we profiled genome-scale DNA methylation patterns using the method of reduced representation bisulfite sequencing (RRBS). We found dynamic waves of de novo methylation and demethylation in four stages of RPE differentiation. Integrated analysis of DNA methylation and RPE transcriptomes revealed a reverse-correlation between levels of DNA methylation and expression of a subset of miRNA and mRNA genes that are important for RPE differentiation and function. Gene Ontology (GO) analysis suggested that genes undergoing dynamic methylation changes were related to RPE differentiation and maturation. We further compared methylation patterns among human ESC- and iPSC-derived RPE as well as primary fetal RPE (fRPE) cells, and discovered that specific DNA methylation pattern is useful to classify each of the three types of RPE cells. Our results demonstrate that DNA methylation may serve as biomarkers to characterize the cell differentiation process during the conversion of human pluripotent stem cells into functional RPE cells.
Comparative immunoperoxidase demonstration of T-antigens in human colorectal carcinomas and morphologically abnormal mucosa. (1985)

The T-antigen (Thomsen-Friedenreich antigen) is a well-characterized tumor-associated glycoprotein that is immunologically reactive in humans. In order to demonstrate the presence of T-antigens in colorectal tissue, benign and malignant tissue from 46 patients with colorectal cancer were examined by means of an immunoperoxidase method. Peanut agglutinin and a polyclonal immune rabbit antiserum were used to demonstrate T-antigens on 72% of formalin-fixed malignant specimens and on more than 92% of frozen malignant specimens. Both ligands bound to the cell membrane and secreted mucus, but only the rabbit serum showed routine staining of the cytoplasm. The T-antigen distribution was heterogeneous without relation to degree of differentiation. Transitional mucosa adjacent to malignant tissue showed a strong anti-T binding to secreted mucus. Slightly morphologically altered crypts remote from the carcinoma expressed T-antigens. Unexpectedly, both ligands bound to nerve cells of the enteric ganglia. These contain gangliosides with immunodominant oligosaccharides identical with those on the T-antigen. Therefore, cross-reactions might have occurred between the gangliosides and the used ligands. The T-antigens now seem to be present in various widespread cancers, and they probably occur early in malignant transformation.
Novel Real-Time Quantitative PCR Test for Trisomy 21 (2002)

The detection of gross chromosomal abnormalities is a major focus of invasive prenatal diagnosis testing, of which the most common cytogenetic anomaly in live births is trisomy 21 (Down syndrome). Classically these examinations are lengthy procedures relying on karyotypic analysis of cultured amniocytes or chorionic mesenchyme. More rapid alternatives, such as fluorescence in situ hybridization and quantitative fluorescent PCR on uncultured cells, are time- and labor-intensive. Here we describe a novel real-time PCR (1)(2) assay for the detection of trisomy 21 that is readily amenable to automation and high-throughput screening.

Real-time PCR can determine subtle alterations in gene dosage, such as hetero- or homozygosity of the RhD locus (3) and protooncogene amplification in breast cancer patients (4). We examined whether a real-time PCR assay could determine chromosomal ploidy, in particular for the prenatal detection of Down syndrome (trisomy 21). We examined the coamplification of a genetic locus (amyloid gene) in the Down’s region of chromosome 21 and a control locus [glyceraldehyde 3-phosphate dehydrogenase (GAPDH)] on chromosome 12. The amyloid gene locus on chromosome 21 was chosen because aberrant expression of this protein has been implicated in the physiologic lesions associated with Down syndrome (5). Furthermore, use of this locus should enable the detection of unbalanced Robertsonian translocations involving the Down’s region of chromosome 21, which occur in ∼4% of Down syndrome cases (6). No such cases were available during in this pilot study.

We used a …
Regeneration of Peroxiredoxins by p53-Regulated Sestrins, Homologs of Bacterial AhpD (2004)

Acting as a signal, hydrogen peroxide circumvents antioxidant defense by overoxidizing peroxiredoxins (Prxs), the enzymes that metabolize peroxides. We show that sestrins, a family of proteins whose expression is modulated by p53, are required for regeneration of Prxs containing Cys-SO(2)H, thus reestablishing the antioxidant firewall. Sestrins contain a predicted redox-active domain homologous to AhpD, the enzyme catalyzing the reduction of a bacterial Prx, AhpC. Purified Hi95 (sestrin 2) protein supports adenosine triphosphate-dependent reduction of overoxidized PrxI in vitro, indicating that unlike AhpD, which is a disulfide reductase, sestrins are cysteine sulfinyl reductases. As modulators of peroxide signaling and antioxidant defense, sestrins constitute potential therapeutic targets.
Algorithm-driven Artifacts in median polish summarization of Microarray data (2010)

We propose tRMA as a modification of RMA to normalize microarray experiments for correlation-based analysis.
Gonococcal Porin Vaccine Evaluation: Comparison of Por Proteosomes, Liposomes, and Blebs Isolated from rmp Deletion Mutants (1992)

The gonococcal major outer membrane protein, Por (protein I), is a potential vaccine candidate. A large-scale animal trial compared the immunogenicity of Por inserted in liposomes (mimicking its in vivo structure) with previously used vaccines containing Por. Por was purified from Rmp (protein III)-negative gonococcal mutants and made into five different formulations: proteosomes, proteosomes absorbed to alum, liposomes, gonococcal membrane blebs, and gonococcal membrane blebs absorbed to alum. Por liposomes induced the greatest amount of Por antibodies; proteosomes and both preparations of blebs induced minimal amounts of Por antibodies. Proteosomes absorbed to alum induced slightly lower amounts of Por antibodies than did liposomes, especially when protein IA was used. Whole-organism absorption studies revealed that a significantly greater percentage of liposome-induced Por antibodies recognized exposed portions of the protein than did proteosome- or proteosome/alum-induced antibodies.
Role of LPS/CD14/TLR4-mediated inflammation in necrotizing enterocolitis: Pathogenesis and therapeutic implications (2009)

LPS and distension are required to produce the histological and inflammatory features of NEC. A potential treatment option is blocking LPS activation and leukocyte infiltration.
Early effective suppression of inflammation in rheumatoid arthritis reduces radiographic progression (1998)

Early 'aggressive' drug treatment, using sulphasalazine and/or methotrexate, aimed at reduction of the CRP level, significantly reduces the (rate of) radiographic progression in RA.
EuroFlow: Resetting leukemia and lymphoma immunophenotyping. Basis for companion diagnostics and personalized medicine (2012)

Laboratory diagnostics in patients with a hematological malignancy has three major applications: establishing the diagnosis, prognostic classification and evaluation of treatment effectiveness. Immunophenotyping is currently recognized to provide essential information for all three applications. 2-9 Expression of individual immunophenotypic markers was initially assessed by microscopic techniques, but since the 90's multiparameter flow cytometric immunophenotyping has become the technique of choice, as it is the sole technique that fulfills the requirements for high speed, broad applicability at diagnosis and during follow-up, and accurate focusing on the malignant cell population using membrane-bound and intracellular proteins as targets. 9-14 6] In this regard, the weakest points of multiparameter flow cytometry relate to: (i) the design of the panels of markers to be applied, (ii) the evaluation of new versus 'classical' markers, (iii) the analysis of the data obtained from the flow cytometric measurements and (iv) interpretation of the results. In addition, it is a technological field that is continuously evolving, but where many traditional procedures are still in use, for example, for data analysis. Whereas industry invested significantly in developing and implementing further innovation of the flow cytometry instruments, the innovation in immunophenotyping reagents and in software for analysis of the progressively larger and complex data sets was much more limited or virtually absent, particularly in the area of leukemia and lymphoma typing.
The Subcellular Distribution of Calnexin Is Mediated by PACS-2 (2008)

Calnexin is an endoplasmic reticulum (ER) lectin that mediates protein folding on the rough ER. Calnexin also interacts with ER calcium pumps that localize to the mitochondria-associated membrane (MAM). Depending on ER homeostasis, varying amounts of calnexin target to the plasma membrane. However, no regulated sorting mechanism is so far known for calnexin. Our results now describe how the interaction of calnexin with the cytosolic sorting protein PACS-2 distributes calnexin between the rough ER, the MAM, and the plasma membrane. Under control conditions, more than 80% of calnexin localizes to the ER, with the majority on the MAM. PACS-2 knockdown disrupts the calnexin distribution within the ER and increases its levels on the cell surface. Phosphorylation by protein kinase CK2 of two calnexin cytosolic serines (Ser554/564) reduces calnexin binding to PACS-2. Consistent with this, a Ser554/564 Asp phosphomimic mutation partially reproduces PACS-2 knockdown by increasing the calnexin signal on the cell surface and reducing it on the MAM. PACS-2 knockdown does not reduce retention of other ER markers. Therefore, our results suggest that the phosphorylation state of the calnexin cytosolic domain and its interaction with PACS-2 sort this chaperone between domains of the ER and the plasma membrane.
Topical aminolevulinic acid‐photodynamic therapy for the treatment of acne vulgaris (2005)

ALA-PDT with red light was found to be effective in the reduction of the number of inflamed lesions in patients with mild-to-moderate acne vulgaris, with no significant short-term adverse effects.
From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways (2016)

The human body hosts an enormous abundance and diversity of microbes, which perform a range of essential and beneficial functions. Our appreciation of the importance of these microbial communities to many aspects of human physiology has grown dramatically in recent years. We know, for example, that animals raised in a germ-free environment exhibit substantially altered immune and metabolic function, while the disruption of commensal microbiota in humans is associated with the development of a growing number of diseases. Evidence is now emerging that, through interactions with the gut-brain axis, the bidirectional communication system between the central nervous system and the gastrointestinal tract, the gut microbiome can also influence neural development, cognition and behaviour, with recent evidence that changes in behaviour alter gut microbiota composition, while modifications of the microbiome can induce depressive-like behaviours. Although an association between enteropathy and certain psychiatric conditions has long been recognized, it now appears that gut microbes represent direct mediators of psychopathology. Here, we examine roles of gut microbiome in shaping brain development and neurological function, and the mechanisms by which it can contribute to mental illness. Further, we discuss how the insight provided by this new and exciting field of research can inform care and provide a basis for the design of novel, microbiota-targeted, therapies.
Specific Adsorption of Histidine-Tagged Proteins on Silica Surfaces Modified with Ni2+/NTA-Derivatized Poly(ethylene glycol) (2007)

Silica surfaces modified with nitrilotriacetic acid (NTA)-polyethylene glycol (PEG) derivatives were used to immobilize hexahistidine-tagged green fluorescent protein (His6-GFP), biotin/streptavidin-AlexaFluor555 (His6-biotin/SA-AF), and gramicidin A-containing vesicles (His6-gA). Three types of surface-reactive PEG derivatives-NTA-PEG3400-Si(OMe)3, NTA-PEG3400-vinylsulfone, and mPEG5000-Si(OMe)3 (control)-were grafted onto silica and tested for their ability to capture His6-tag species via His6/Ni2+/NTA chelation. The composition and thicknesses of the PEG-modified surfaces were characterized using X-ray photoelectron spectroscopy, contact angle, and ellipsometry. Protein capture efficiencies of the NTA-PEG-grafted surfaces were evaluated by measuring fluorescence intensities of these surfaces after exposure to His6-tag species. XPS and ellipsometry data indicate that surface adsorption occurs via specific interactions between the His6-tag and the Ni2+/NTA-PEG-grafted surface. Protein immobilization was most effective for NTA-PEG3400-Si(OMe)3-modified surfaces, with maximal areal densities achieved at 45 pmol/cm2 for His6-GFP and 95 fmol/cm2 for His6-biotin/SA-AF. Lipid vesicles containing His6-gA in a 1:375 gA/lipid ratio could also be immobilized on Ni2+/NTA-PEG3400-Si(OMe)3-modified surfaces at 0.5 mM total lipid. Our results suggest that NTA-PEG-Si(OMe)3 conjugates may be useful tools for immobilizing His6-tag proteins on solid surfaces to produce protein-functionalized surfaces.