gebhart/patrepeval huggingface dataset:
Transcriptomic Differences between Primary Colorectal Adenocarcinomas and Distant Metastases Reveal Metastatic Colorectal Cancer Subtypes (2019)

Approximately 20% of colorectal cancer patients with colorectal adenocarcinomas present with metastases at the time of diagnosis, and therapies that specially target these metastases are lacking. We present a novel approach for investigating transcriptomic differences between primary colorectal adenocarcinoma and distant metastases, which may help to identify primary tumors with high risk for future dissemination and to inform the development of metastasis-targeted therapies. To effectively compare the transcriptomes of primary colorectal adenocarcinoma and metastatic lesions at both the gene and pathway levels, we eliminated tissue specificity of the "host" organs where tumors are located and adjusted for confounders such as exposure to chemotherapy and radiation, and identified that metastases were characterized by reduced epithelial-mesenchymal transition (EMT) but increased MYC target and DNA-repair pathway activities. <i>FBN2</i> and <i>MMP3</i> were the most differentially expressed genes between primary tumors and metastases. The two subtypes of colorectal adenocarcinoma metastases that were identified, EMT inflammatory and proliferative, were distinct from the consensus molecular subtype (CMS) 3, suggesting subtype exclusivity. In summary, this study highlights transcriptomic differences between primary tumors and colorectal adenocarcinoma metastases and delineates pathways that are activated in metastases that could be targeted in colorectal adenocarcinoma patients with metastatic disease. SIGNIFICANCE: These findings identify a colorectal adenocarcinoma metastasis-specific gene-expression signature that is free from potentially confounding background signals coming from treatment exposure and the normal host tissue that the metastasis is now situated within.
Chelation as a Driving Force in Organic Reactions. IV.1 Synthesis of α-Nitro Acids by Control of the Carboxylation-Decarboxylation Equilibrium2 (1963)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChelation as a Driving Force in Organic Reactions. IV.1 Synthesis of α-Nitro Acids by Control of the Carboxylation-Decarboxylation Equilibrium2Herman L. Finkbeiner and Martin. StilesCite this: J. Am. Chem. Soc. 1963, 85, 5, 616–622Publication Date (Print):March 1, 1963Publication History Published online1 May 2002Published inissue 1 March 1963https://pubs.acs.org/doi/10.1021/ja00888a031https://doi.org/10.1021/ja00888a031research-articleACS PublicationsRequest reuse permissionsArticle Views1830Altmetric-Citations104LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Finding Genes That Underlie Complex Traits (2002)

Phenotypic variation among organisms is central to evolutionary adaptations underlying natural and artificial selection, and also determines individual susceptibility to common diseases. These types of complex traits pose special challenges for genetic analysis because of gene-gene and gene-environment interactions, genetic heterogeneity, low penetrance, and limited statistical power. Emerging genome resources and technologies are enabling systematic identification of genes underlying these complex traits. We propose standards for proof of gene discovery in complex traits and evaluate the nature of the genes identified to date. These proof-of-concept studies demonstrate the insights that can be expected from the accelerating pace of gene discovery in this field.
Fabrication of polymeric large-core waveguides for optical interconnects using a rubber molding process (2000)

Polymeric large-core (47 μm×41 μm) optical waveguides for optical interconnects have been fabricated by using a rubber molding process. For low-cost low-loss large-core waveguides, our newly developed thick-photoresist patterning process is used for a master fabrication. Also a low-loss thermocurable polymer, perfluorocyclobutane (PFCB), is used in fabricating optical waveguides by rubber molding for the first time. The propagation loss is measured to be 0.4 dB/cm at the wavelength of 1.3 μm, and 0.7 dB/cm at the wavelength of 1.55 μm.
Non-Contact Skin Moisture Measurement Based on Near-Infrared Spectroscopy (2004)

Non-contact skin moisture measurement based on near-infrared (NIR) spectroscopy is proposed in the spectral range from 1300 to 2000 nm. A gap is introduced between the optical fiber probe and the skin surface in order to avoid occluding surface vapor. In vitro and in vivo experiments for measuring the water content of skin are implemented. The measured absorbance spectra are processed by multivariate analyses. Processed results are compared with the water content values obtained by a capacitance method. The correlations between the optical method and the capacitance method obtained by partial-least squares regression are higher than those obtained by multiple linear regression. In addition, a Monte Carlo simulation is implemented to evaluate measurement depths of the optical methods. It is presented that the measurement depth of the optical method depends largely on the water absorption. The simulation result also shows that the measurement depth of the optical method is much deeper than the depth of the capacitance method, especially in the spectral range where water absorption is relatively weak.
Modeling Nonstationary Processes Through Dimension Expansion (2012)

In this article, we propose a novel approach to modeling nonstationary spatial fields. The proposed method works by expanding the geographic plane over which these processes evolve into higher-dimensional spaces, transforming and clarifying complex patterns in the physical plane. By combining aspects of multidimensional scaling, group lasso, and latent variable models, a dimensionally sparse projection is found in which the originally nonstationary field exhibits stationarity. Following a comparison with existing methods in a simulated environment, dimension expansion is studied on a classic test-bed dataset historically used to study nonstationary models. Following this, we explore the use of dimension expansion in modeling air pollution in the United Kingdom, a process known to be strongly influenced by rural/urban effects, amongst others, which gives rise to a nonstationary field.
Molecular Beacons: A Novel DNA Probe for Nucleic Acid and Protein Studies (2000)

A new concept has been introduced for molecular beacon DNA molecules. Molecular beacons are a new class of oligonucleotides that can report the presence of specific nucleic acids in both homogeneous solutions and at the liquid-solid interface. They emit an intense fluorescent signal only when hybridized to their target DNA or RNA molecules. Biotinylated molecular beacons have been designed and used for the development of ultrasensitive DNA sensors and for DNA molecular interaction studies at a solid-liquid interface. Molecular beacons have also been used to study protein-DNA interactions. They have provided a variety of exciting opportunities in DNA/RNA/protein studies.
Overexpression of the BCRP/MXR/ABCP gene in a topotecan-selected ovarian tumor cell line. (1999)

Topotecan- or mitoxantrone-selected cell lines (T8 and MX3, respectively), derived from the human IGROV1 ovarian cancer cell line, were resistant to the topoisomerase I inhibitors topotecan, SN-38 (the active metabolite of irinotecan), and 9-aminocamptothecin, as well as to the topoisomerase II drug mitoxantrone. In both resistant cell lines, decreased accumulation of topotecan and mitoxantrone was observed, caused by enhanced energy-dependent efflux of the drugs involved. In both cell lines, we found that the breast cancer resistance protein/mitoxantrone resistance/placenta-specific ATP binding cassette (BCRP/MXR/ABCP) gene was overexpressed. Furthermore, BCRP/MXR/ABCP expression levels in various partially revertant T8 cells correlated with the levels of resistance to topotecan, SN-38, and mitoxantrone, strongly suggesting BCRP/MXR/ABCP to be the transporter responsible for the enhanced efflux. Pharmacodynamic analysis demonstrated that BCRP/MXR/ABCP is a very efficient transporter of topotecan; in vitro, 70% of the intracellular topotecan pool was transported out of the T8 or MX3 cells within 30 s. In conclusion, we report for the first time that BCRP/MXR/ABCP can also be up-regulated upon exposure of tumor cells to the clinically important drug topotecan, and that BCRP-mediated efflux of topotecan is very efficient. This highly efficient efflux of topotecan by BCRP/MXR/ABCP may have clinical relevance for patients being treated with topotecan.
Synthesis and Magnetic Behavior of Periodic Nickel Sphere Arrays (2003)

Inverse opal polymer replicas serve as excellent templates for the formation of metal sphere arrays (see Figure). Here nickel sphere arrays have been prepared by electrodeposition into poly(methyl methacrylate) templates. Angle‐dependent magnetic measurements indicate that these properties are dominated by shape anisotropy.
Unexpected development of autoimmunity in BAFF‐R‐mutant MRL‐lprmice (2006)

BAFF-R is the predominant receptor that mediates B-cell activating factor (BAFF)-dependent B-cell signalling and plays a critical role in late-stage B-cell maturation and survival. BAFF has been implicated in the development of autoimmunity and systemic lupus erythematosus (SLE). To define the role of BAFF-R in autoimmunity and SLE, we crossed A/WySnJ mice with MRL-lpr mice and generated BAFF-R-mutant MRL-lpr mice. The BAFF-R mutation markedly impaired the development of immature, mature and marginal zone B cells in the spleens of MRL-lpr mice. Unexpectedly, the BAFF-R mutation in MRL-lpr mice did not result in decreased autoantibody production, hypergammaglobulinaemia or immune complex-mediated glomerulonephritis. Rather, the ability of BAFF-R-mutant lpr splenic B cells to produce immunoglobulins in vitro was not decreased, although germinal centre formation, antibody response and B-cell proliferation were impaired. Further studies found increased numbers of B cells in the bone marrow of BAFF-R-mutant MRL-lpr mice compared to the BAFF-R-intact lupus mice. ELISPOT analysis revealed that BAFF-R-mutant MRL-lpr mice had more antibody-secreting cells in their bone marrow than the control mice. Thus, these findings could explain the development of autoimmunity and hypergammaglobulinaemia observed in BAFF-R-mutant MRL-lpr mice.
Survival of Patients with Newly Diagnosed Glioblastoma Treated with Radiation and Temozolomide in Research Studies in the United States (2010)

Newly diagnosed glioblastoma treated recently with RT + TMZ and talampanel, poly-ICLC, or cilengitide had significantly longer survival than similar patients treated with only RT + TMZ accrued internationally from 2000 to 2002. These differences could result from the novel agents or changing patterns of care. Until the reasons for these different survival rates are clarified, comparisons of outcomes from phase II studies with published RT + TMZ survival data should be interpreted with caution.
Interactive Navigation and Bronchial Tube Tracking in Virtual Bronchoscopy (1999)

An interactive virtual environment for simulation of bronchoscopy is developed. Medical doctor can safely plan their surgical bronchoscopy using the virtual environment without any invasive diagnosis which may risk the patient's health. The 3D pen input device of the system allows the doctor to navigate and visualize the bronchial tree of the patient naturally and interactively. To navigate the patient's bronchial tree, a vessel tracking process is required. While manual tracking is tedious and labor-intensive, fully automatic tracking may not be reliable. We propose a semi-automatic tracking technique called Intelligent Path Tracker which provides automation and enough user control during the vessel tracking. To support an interactive frame rate, we also introduce a new volume rendering acceleration technique, named as IsoRegion Leaping. The volume rendering is further accelerated by distributed rendering on a TCP/IP-based network of low-cost PCs. With these approaches, a 256 x 256 x 256 volume data of human lung, can be navigated and visualized at a frame rate of over 10 Hz in our virtual bronchoscopy system.
The primary structure of the human leukocyte antigen CD37, a species homologue of the rat MRC OX-44 antigen. (1989)

Comparison of NH2-terminal protein sequence from the rat OX-44 antigen with the sequence of the human CD37 antigen deduced from a cDNA clone shows that these antigens are species homologues. The CD37 sequence is 244 amino acids in length and lacks a conventional leader sequence. The molecule is likely to have an NH2-terminal cytoplasmic domain followed by three transmembrane sequences that lie within the first 110 amino acids. The rest of the molecule is hydrophillic and contains three sites for N-linked glycosylation.
Acylation-stimulating Protein (ASP)/Complement C3adesArg Deficiency Results in Increased Energy Expenditure in Mice (2004)

Acylation-stimulating protein (ASP) acts as a paracrine signal to increase triglyceride synthesis in adipocytes. In mice, C3 (the precursor to ASP) knock-out (KO) results in ASP deficiency and leads to reduced body fat and leptin levels yet they are hyperphagic. In the present study, we investigated the mechanism for this energy repartitioning. Compared with wild-type (WT) mice, male and female C3(-/-) ASP-deficient mice had elevated oxygen consumption (VO2) in both the active (dark) and resting (light) phases of the diurnal cycle: +8.9% males (p < 0.05) +9.4% females (p < 0.05). Increased physical activity (movement) was observed during the dark phase in female but not in male KO animals. Female WT mice moved 16.9 +/- 2.4 m whereas KO mice moved 30.1 +/- 5.4 m, over 12 h, +78.4%, p < 0.05). In contrast, there was no difference in physical activity in male mice, but a repartitioning of dietary fat following intragastric fat administration was noted. This was reflected by increased fatty acid oxidation in liver and muscle in KO mice, with increased UCP2 (inguinal fat) and UCP3 (muscle) mRNA expression (p = 0.005 and 0.036, respectively). Fatty acid uptake into brown adipose tissue (BAT) and white adipose tissue (WAT) was reduced as reflected by a decrease in the fatty acid incorporation into lipids (BAT -68%, WAT -29%. The decrease of FA incorporation was normalized by intraperitoneal administration of ASP at the time of oral fat administration. These results suggest that ASP deficiency results in energy repartitioning through different mechanisms in male and female mice.
Endogenous Sonic Hedgehog limits inflammation and angiogenesis in the ischaemic skeletal muscle of mice (2018)

Although ectopic administration of Shh has previously been shown to promote ischaemia-induced angiogenesis, the present study reveals that endogenous Shh does not promote ischaemia-induced angiogenesis. On the contrary, the absence of Shh leads to aberrant ischaemic tissue inflammation and a transiently increased angiogenesis.
Noise and Bias Error Due to Polarization Coupling in a Fiber Optic Gyroscope (2015)

This paper reports a comprehensive model of the noise and drift induced by polarization coupling in a fiber optic gyroscope (FOG) interrogated with a laser of arbitrary linewidth. It includes the effects of dynamic phase biasing, a realistic description of the laser phase noise and polarization-dependent loss. This model yields concise analytical expressions for the noise and drift dependencies on the laser linewidth, the fiber length and holding parameter h, and the fractional power launched into the unwanted polarization at the input to the sensing coil. For all realistic FOG parameter sets, the polarization-coupling noise is found to be insignificant. For a 1-km coil, a typical holding parameter (h = 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-5</sup> ) and push-pull modulation, the drift is only ~1 μ rad up to a linewidth of~100 MHz, which is far lower than previously believed. The drift decreases to even lower values for larger linewidths. Experimental measurements of the noise and drift in a 150-m FOG and their dependence on laser linewidth support these predictions. Birefringence modulation can be brought to bear to reduce this residual drift enough to meet the requirement for aircraft inertial navigation. Ultimately, this analysis shows that low-polarization coupling error can be obtained without the use of a broadband source.
Induction of Indefinite Cardiac Allograft Survival Correlates With Toll-Like Receptor 2 and 4 Downregulation After Serine Protease Inhibitor-1 (Serp-1) Treatment (2007)

Observed suppressive effects of Serp-1 on early innate immune response components such as TLR-2 and 4, and on adaptive responses such as T-cell intragraft infiltration suggests that Serp-1 may modulate the transition from innate to adaptive immunity, exhibiting a synergistic effect on allograft survival when used in combination with a subtherapeutic dose of CsA.
Electrical Impedance of Cardiac Muscle (1961)

Impedances of cat cardiac muscle and frog sartorius muscle were compared at several frequencies before and after interspace ion depletion. Strips of parallel fibers were obtained from papillary muscles and ventricular trabeculae. The impedances were measured in the direction of fiber orientation. Interspace ion concentrations were reduced by soaking the tissues in isotonic sucrose solution. The D.C. specific resistance of cardiac muscle compared to skeletal muscle was previously reported to be two times as large in Binger's and over five times as large in 0.1 Ringer "s-suerose solution. In the present study, the relative impedances of cardiac muscle at 10.000 c.p.s. compared to that at 10 c.p.s. were 75 and 48 per cent in Ringer's and sucrose solutions, respectively. The impedance of skeletal muscle was independent of frequency in Ringer's and in sucrose solutions. These results suggest the presence of transverse membranes (perhaps the intercalated discs) of high resistance and high capacitance.
Evaluation of the anti-cardiolipin antibody test: report of an international workshop held 4 April 1986. (1987)

Thirty laboratories from institutions in Britain, France, Italy, The Netherlands, New Zealand, Sweden and the USA participated in a workshop to evaluate the anti-cardiolipin (aCL) test. Participants were asked to measure IgG and IgM aCL in seven samples on each of three separate days. The seven samples were prepared so that IgG and IgM aCL concentrations were known before distribution. Twenty-three of 30 laboratories measuring IgG aCL had significant regression slopes (P less than 0.001) when optical absorbance readings or counts per minute were compared with IgG aCL concentration. Twenty-four of 28 laboratories measuring IgM aCL had significant regression slopes (P less than 0.001). Coefficient of determination (R2) ranged from 81.1% to 98.7% for laboratories with valid IgG aCL assays and from 48.0% to 96.7% for valid IgM aCL assays. Valid assays had in common the use of 10% fetal calf or 10% adult bovine serum in PBS. Assays that were not valid had in common the use of PBS, PBS-Tween, or 0.3% gelatin as diluents. All laboratories with valid assays defined samples with high and moderate aCL levels as positive but there was no consensus about low positive samples. This study shows that properly performed ELISA or SRIA assays can be used to provide an accurate, reproducible, and quantitative measure of IgG and IgM aCL concentration in serum samples.
Unraveling the Molecular Complexity of O-Glycosylated Endogenous (N-Terminal) pro–B-Type Natriuretic Peptide Forms in Blood Plasma of Patients with Severe Heart Failure (2016)

Our results directly demonstrate for the first time a rather complex distribution of the endogenously circulating glycoforms by mass spectrometric analysis in HF patients, and show 9 glycosites in human (NT-) proBNP. This information may also have an impact on commercial immunoassays applying antibodies specific for the central region of (NT-) proBNP, which detect mostly nonglycosylated forms.
On the Relation Between Sparse Sampling and Parametric Estimation (2009)

We consider the relationship between parameter estimation of an additive model and sparse inversion of an under-determined matrix (dictionary) in a linear system. The dictionary is constructed by sampling parameters of the additive model. Parameters and model order are estimated using regularized least-squares inversion. We investigate equi-spaced and Fisher information inspired parameter sampling methods for dictionary construction, and present an example quantifying parameter estimation error performance for the different sampling methods. These results indicate that estimation performance is degraded by sampling the parameter space either too finely or too coarsely.
The Transcriptional Factor Egr-1 Is Synthesized by Baculovirus-Infected Insect Cells in an Active, DNA-Binding Form (1991)

The Egr-1 (zfp-6) gene encodes a zinc-finger-containing nuclear protein that is rapidly and transiently induced in quiescent cells treated with mitogens. We have constructed baculovirus vectors that synthesize mouse Egr-1 protein initiating at two putative ATG start sites. The ATG site producing the larger protein (Mr, 80,000) is similar, if not identical, to Egr-1 synthesized by serum-stimulated quiescent mouse fibroblasts, thus identifying the likely site for translation. The protein synthesized by the insect cells is active as assayed by its ability to bind to a specific DNA sequence that has been identified as an Egr-1 binding site. The insect cell system will allow further studies of the structure and function of the Egr-1 product, a protein that appears to be an important "master switch" for other genes.
Reconstitution of a Protein Disulfide Catalytic System (1998)

Disulfide bonds are important for the structure and stability of many proteins. In prokaryotes their formation is catalyzed by the Dsb proteins. The DsbA protein acts as a direct donor of disulfides to newly synthesized periplasmic proteins. Genetic evidence suggests that a second protein called DsbB acts to specifically reoxidize DsbA. Here we demonstrate the direct reoxidation of DsbA by DsbB. We have developed a fluorescence assay that allows us to directly follow the reoxidation of DsbA. We show that membranes containing catalytic amounts of DsbB can rapidly reoxidize DsbA to completion. The reaction strongly depends on the presence of oxygen, implying that oxygen serves as the final electron acceptor for this disulfide bond formation reaction. Membranes from a dsbB null mutant display no DsbA reoxidation activity. The ability of DsbB to reoxidize DsbA fits Michaelis-Menten behavior with DsbA acting as a high affinity substrate for DsbB with a Km = 10 microM. The in vitro reconstitution described here is the first biochemical analysis of DsbB and allows us to study the major pathway of disulfide bond formation in Escherichia coli.