gebhart/patrepeval huggingface dataset:
Identification and validation of gene expression subtypes in a large set of colorectal cancer samples. (2012)

3511 Background: From a clinical perspective colorectal cancer (CRC) is a heterogeneous disease whose biological background is insufficiently understood. In order to adapt targeted treatment to biologically different categories of CRC patients, in depth understanding of the molecular mechanisms involved in CRC heterogeneity is urgently needed. Methods: Consensus cluster analysis of 1113 stage II-III CRC gene expression profiles from PETACC3 and 4 public datasets defined a set of subtypes which were confirmed in an independent set of 720 samples. The similarity between tumors was based on a set of 54 meta-genes. This approach improves the robustness to measurement noise and gives equal chances to each biological process to be accounted for in the subtype definition. We tested the association of the subtypes with clinical variables, molecular markers and patient survival. Results: We identified and validated 5 major subtypes A-E, with different levels of expression in 6 main molecular processes: epithelial-mesenchymal transition (EMT), immune response, colon crypt differentiation, proliferation, Wnt signaling and chromosome 20q. Significant differences in survival and an enrichment for markers such as MSI, BRAF mutation, site or p53 status were found between the subtypes. In addition, the new subtype classification uncovered heterogeneity within groups defined by these commonly used markers. Survival analysis showed significant prognostic value for meta-genes connected to EMT, proliferation and differentiation. Identical data processing and clustering applied to the validation set on the same meta-genes resulted in subtypes with almost identical expression patterns. Conclusions: We identified and validated robust molecular subtypes in the largest set of stage II-III CRC samples as a combination of multiple molecular processes, that complement current disease stratification based on clinico-pathological variables and molecular markers. The biological relevance of these subtypes was reflected in significant differences in survival. These insights open new perspectives for improving prognostic models and rationalize the prediction of tumor-specific drug sensitivity.
Dispersion Methodology for Technical Lignin into Polyester Polyol for High-Performance Polyurethane Insulation Foam (2021)

The incorporation of lignin into rigid polyurethane foam (RPUF) has been explored for the last two decades for replacing petrochemical polyols and producing sustainable high-performance insulation materials. However, to date, the issues associated with the dispersion of technical lignin in the commonly used polyols for RPUF have highly limited the improvement in mechanical and thermal insulation performance. This study reports the enhanced dispersion of kraft lignin (KL) up to 75 wt % in the glycerol-substituted aromatic polyester polyol blend. The influence of significantly well-dispersed KL on RPUF in terms of loading levels, the viscosity of the polyol, the microstructure, and the thermal and mechanical properties of RPUF is discussed. The KL incorporated (0.5–6.0 wt %) in polyol afforded a remarkable reduction in thermal conductivity (32%–34%) of the resultant RPUF with minimal variation in density and insignificant change in compressive strength. The scale of this improvement, to the best of our knowledge, has not been reported to date in lignin-incorporated RPUF systems. Furthermore, the presence of the KL in the RPUF also resulted in a mild improvement in the flame retardance performance. This study provides insights into producing KL-incorporated RPUF for thermal insulation application.
Transcriptome Analysis and Identification of a Transcriptional Regulatory Network in the Response to H<sub>2</sub>O<sub>2</sub> (2019)

Hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) is a common signal molecule initiating transcriptional responses to all the known biotic and abiotic stresses of land plants. However, the degree of involvement of H<sub>2</sub>O<sub>2</sub> in these stress responses has not yet been well studied. Here we identify time-dependent transcriptome profiles stimulated by H<sub>2</sub>O<sub>2</sub> application in Arabidopsis (<i>Arabidopsis thaliana</i>) seedlings. Promoter prediction based on transcriptome data suggests strong crosstalk among high light, heat, and wounding stress responses in terms of environmental stresses and between the abscisic acid (ABA) and salicylic acid (SA) responses in terms of phytohormone signaling. Quantitative analysis revealed that ABA accumulation is induced by H<sub>2</sub>O<sub>2</sub> but SA is not, suggesting that the implied crosstalk with ABA is achieved through ABA accumulation while the crosstalk with SA is different. We identified potential direct regulatory pairs between regulator transcription factor (TF) proteins and their regulated TF genes based on the time-course transcriptome analysis for the H<sub>2</sub>O<sub>2</sub> response, in vivo regulation of the regulated TF by the regulator TF identified by expression analysis of mutants and overexpressors, and in vitro binding of the regulator TF protein to the target TF promoter. These analyses enabled the establishment of part of the transcriptional regulatory network for the H<sub>2</sub>O<sub>2</sub> response composed of 15 regulatory pairs of TFs, including five pairs previously reported. This regulatory network is suggested to be involved in a wide range of biotic and abiotic stress responses in Arabidopsis.
Tomographic image of prompt gamma ray from boron neutron capture therapy: A Monte Carlo simulation study (2014)

Purpose of paper is to confirm the feasibility of acquisition of three dimensional single photon emission computed tomography image from boron neutron capture therapy using Monte Carlo simulation. Prompt gamma ray (478 keV) was used to reconstruct image with ordered subsets expectation maximization method. From analysis of receiver operating characteristic curve, area under curve values of three boron regions were 0.738, 0.623, and 0.817. The differences between length of centers of two boron regions and distance of maximum count points were 0.3 cm, 1.6 cm, and 1.4 cm.
TNF Inhibits Notch-1 in Skeletal Muscle Cells by Ezh2 and DNA Methylation Mediated Repression: Implications in Duchenne Muscular Dystrophy (2010)

We propose that in dystrophic muscles, elevated levels of TNFalpha and NF-kappaB inhibit the regenerative potential of satellite cells via epigenetic silencing of the Notch-1 gene.
Monitoring struturants of fat blends with ultrasound based in‐line rheometry (ultrasonic velocity profiling with pressure difference) (2008)

Summary Ultrasonic velocity profiling with pressure difference (UVP‐PD) was demonstrated to be a successful, non‐invasive, in‐line measurement system for instantaneous velocity and rheological flow profiling of complex, opaque fat blends. Model systems of 25% Akomic, 75% rapeseed oil; and 25% Akomic, 74% rapeseed oil and 1% Grindsted ® Crystalliser 110 were compared under real process conditions with UVP‐PD. Results indicated that the sample containing the crystalliser had twice the viscosity of the control. These in‐line results are in agreement with previous off‐line results, and offer the chance to probe the mechanics of fat blend physics under real, dynamic conditions.
Conduction in Multiphase Particulate/Fibrous Networks (2003)

Several promising Li-ion battery technologies incorporate nanoarchitectured carbon networks, typically in the form of whisker/particle blends bonded with thermoplastic binders to form the anodes. Degradation of these materials is currently a persistent problem, with damage presenting as blistering and/or delamination of the electrode. Both material composition and morphology play a role in these critical failure modes, and are explored in the present work as they affect conduction in practical battery materials. Lawrence Berkeley National Laboratories and the Institut de Recherche d'Hydro-Quebec supplied the materials studied in this work. Our present approach builds on our previous numerical work, incorporating real material morphology and careful selection of boundary conditions to reduce the numerical difficulties posed by singularities in the field solution, due to phase contrast, sharp corners, etc. In order to allow use of these models for various shapes of particles, we provide a few simple geometrical relations for calculation of total surface area for various morphologies of electrode materials. A four-point-probe technique was employed to obtain the experimental conductivities. Although the existence of contact resistance is well known, there is little literature regarding a technique to measure its value; here, we also present a method for quantifying it, assuming that the anode layer is comprised of two layers. Voltage functions for each layer are determined by enforcement of voltage continuity at the interfaces, current intensities at the inlet and outlet on both sides of interface, and assumption of zero voltage in the second layer as The four-point-probe technique is suitable for the electrode materials tested, offering reasonable experimental precision in a simple setup. The results of this study offer some insight into the design of active materials. The model shows applicability to a wide variety of materials, including those comprised of fibers, particles, and flakes. Comparisons among simulation predictions and real material conductivities showed very good agreement. An obvious subject of future work is combined electrochemical, conduction, and mechanical modeling of these materials. © 2003 The Electrochemical Society. All rights reserved.
Front Cover: KRAS Binders Hidden in Nature (Chem. Eur. J. 52/2019) (2019)

Drug discovery is in essence the discovery of a molecular key (the drug) which fits into a lock (scientists call them pockets) on a disease-causing protein. The lock on KRAS is extremely small, making it almost impossible for chemists to find a key to fit tightly enough into it. Nature has solved this problem by making highly rigid chemical scaffolds (rigid keys) that are capable of binding tightly to such shallow pockets. This work reports the discovery of rigid keys from nature that bind to KRAS and are ideal starting points for the discovery of future KRAS cancer drugs. More information can be found in the Communication by D. B. McConnell et al. on page 12037.
Adaptive beamforming for weather observations using the atmospheric imaging radar (2013)

An advantage of phased-array radars that has not been fully investigated is the application of digital beamforming for weather observations. With adaptive beamforming, the radar can change the beam pattern to reduce the impact of ground clutter and other interference on the estimation of meteorological variables. Many adaptive beamforming methods have been developed for applications involving signals that can be modeled as point sources. However, the received signal by weather radars is from distributed targets, namely the hydrometeors that fill spaces much larger than the radar resolution volume. Thus, direct application of adaptive beamforming methods intended for point sources to weather radars could lead to significant biases in estimated signal parameters. An initial study to demonstrate the feasibility of utilizing adaptive beamforming for weather observation was conducted using data collected by the Atmospheric Imaging Radar. These data are the first high-resolution (both temporal and spatial) simultaneous cross-section measurements through rapidly evolving storms.
Ontogeny of adrenergic fibers in rat spinal cord in relationship to adrenal preganglionic neurons (1988)

Adrenergic neurons in the C1 cell group in the rostral ventrolateral medulla oblongata contain epinephrine, as well as its biosynthetic enzyme, phenylethanolamine N-methyltransferase (PNMT). These neurons send axons to regions of the central nervous system known to regulate autonomic function, including the sympathetic preganglionic nuclei of thoracic and upper lumbar spinal cord. Previous studies have shown that PNMT is expressed in neurons located in the medulla oblongata on embryonic day 14; however, the development of the projections from these cells has not been studied. With the aid of high-performance liquid chromatography (HPLC) to determine levels of catecholamines and immunocytochemistry to demonstrate PNMT, the ontogeny of the adrenergic bulbospinal pathway in the embryonic, postnatal, and adult rat has been studied. In addition, the relationship between PNMT-immunoreactive (IR) fibers and retrogradely labeled sympathetic preganglionic neurons projecting to adrenal medulla are described. PNMT-IR fibers were first observed in the caudal medulla oblongata and lateral funiculus of spinal cord on gestational day 15(E15). On E16, PNMT-IR fibers in the thoracic spinal cord were observed in the intermediate gray matter at the level of the lateral horn. Epinephrine was measureable in spinal cord on E20. Both the density of PNMT-IR fibers and the levels of epinephrine increased to a maximum during the second postnatal week and then declined to adult levels. These observations suggest that a period of adrenergic hyperinnervation of spinal sympathetic nuclei occurs during the neonatal period. PNMT-IR terminals in spinal cord were observed, primarily, although not exclusively, in sympathetic nuclei of thoracic cord and parasympathetic nuclei of upper sacral cord. Adrenergic fibers in the intermediolateral nucleus (IML) and the central autonomic nucleus (CAN) dorsal to the central canal were particularly dense during the second postnatal week in both midthoracic and upper sacral segments. In the neonate, a "ladder-like" pattern of PNMT-IR fiber staining was observed which represented transverse fiber bundles connecting IML with CAN and extensive longitundinal fiber bundles along the border of the funiculus in IML. At all spinal levels, adrenergic fibers were also observed adjacent to the ependyma dorsal or lateral to the central canal. The relationship between adrenal preganglionic neurons and PNMT-IR fibers in IML was examined on postnatal days 4, 15, and 60. With retrograde labeling from adrenal medulla, it was demonstrated that PNMT-IR fibers are associated with adrenal preganglionic neurons throughout postnatal development.(ABSTRACT TRUNCATED AT 400 WORDS)
Detecting Repeating Objects Using Patch Correlation Analysis (2016)

In this paper we describe a new method for detecting and counting a repeating object in an image. While the method relies on a fairly sophisticated deformable part model, unlike existing techniques it estimates the model parameters in an unsupervised fashion thus alleviating the need for a user-annotated training data and avoiding the associated specificity. This automatic fitting process is carried out by exploiting the recurrence of small image patches associated with the repeating object and analyzing their spatial correlation. The analysis allows us to reject outlier patches, recover the visual and shape parameters of the part model, and detect the object instances efficiently. In order to achieve a practical system which is able to cope with diverse images, we describe a simple and intuitive active-learning procedure that updates the object classification by querying the user on very few carefully chosen marginal classifications. Evaluation of the new method against the state-of-the-art techniques demonstrates its ability to achieve higher accuracy through a better user experience.
Interlaboratory study on the quantification of calcium phosphate phases by Rietveld refinement (2015)

An interlaboratory study (ILS, round robin) was conducted to assess the accuracy and precision of the phase quantification of calcium phosphate (CaP) bioceramics by X-ray diffraction (XRD) and Rietveld refinement. For that purpose, a mixture of hydroxyapatite and β -tricalcium phosphate, two CaP phases commonly used in synthetic bone graft substitutes, was prepared and sent to 12 laboratories for XRD analysis. Results from 26 different instruments were received and evaluated statistically according to ASTM E691 – 13. The statistical analysis revealed that the reproducibility standard deviation of phase quantities was approximately two times greater than the repeatability standard deviation, which is obtained by repeating the analysis on a single instrument configuration multiple times. The 95% reproducibility limit for phase quantities was R = ±1.67 wt%. The study also demonstrated that several participants overinterpreted their data in an attempt to refine crystallite sizes of the minor phase.
Spontaneous and lectin-dependent cellular cytotoxicity by lymphocyte subpopulations against cell lines susceptible or resistant to spontaneous cytotoxicity. (1978)

In the present study we have investigated whether cell lines, which are resistant to spontaneous cytotoxicity, can be killed by lectin-dependent cellular cytotoxicity (LDCC), the expression of EAC (7S) receptors on LDCC effector cells, and the relationship between spontaneous cytotoxicity and LDCC when EAC (7S) receptor-positive or -negative subpopulations are tested against different target cell lines. We found that target cells which are resistant to spontaneous cytotoxicity can, indeed, be killed by LDCC, and that there is an inverse relationship between spontaneous cytotoxicity and LDCC, both when unfractionated lymphocytes were tested against different target cells and when fractionated cells were tested against cell lines highly susceptible to spontaneous cytotoxicity. The implications of these findings, in relation to the relative specificity of the spontaneous cytotoxicity system, are discussed.
Overall survival in patients with lung adenocarcinoma harboring “niche” mutations: an observational study (2020)

<b>Objective:</b> In addition to the most common somatic lung cancer mutations (i. e., KRAS and EGFR mutations), other genes may harbor mutations that could be relevant for lung cancer. We defined BRAF, c-MET, DDR2, HER2, MAP2K1, NRAS, PIK3CA, and RET mutations as "niche" mutations and analyzed. The aim of this retrospective cohort study was to assess the differences in the overall survival (OS) of patients with lung adenocarcinoma harboring niche somatic mutations. <b>Results:</b> Data were gathered for 252 patients. Mutations were observed in all genes studied, except c-MET, DDR2, MAP2K1, and RET. The multivariable analysis showed that 1) niche mutations had a higher mortality than EGFR mutations (HR = 2.3; 95% CI = 1.2-4.4; <i>p</i> = 0.009); 2) KRAS mutations had a higher mortality than EGFR mutations (HR = 2.5; 95% CI = 1.4-4.5; <i>p</i> = 0.003); 3) niche mutations presented a similar mortality to KRAS mutations (HR = 0.9; 95% CI = 0.6-1.5; <i>p</i> = 0.797). <b>Methods:</b> Three cohorts of mutations were selected from patients with lung adenocarcinoma and their OS was compared. Mutations that were searched for, were 1) BRAF, c-MET, DDR2, HER2, MAP2K1, NRAS, PIK3CA, and RET; 2) K-RAS; and 3) EGFR. Differences in OS between these three cohorts were assessed by means of a multivariable Cox model that adjusted for age, sex, smoking habits, clinical stages, and treatments. <b>Conclusions:</b> Niche mutations exhibited an increased risk of death when compared with EGFR mutations and a similar risk of death when compared with KRAS mutations.
Flavonoids and biological activities of<b><i>Jussiaea repens</i></b> (2007)

A new acylated avicularin, namely avicularin 2''-(4'''-O-n-pentanoyl)-gallate (1) along with 12 metabolites have been isolated from the ethyl acetate extract of the aerial parts of Jussiaea repens L. (Onagraceae). Their structures were established as trifolin 2''-O-gallate (2), quercetrin (3), guaijaverin (4), reynoutrin (5), juglanin (6), avicularin (7), hyperin (8), trifolin (9), hyperin 2''-O-gallate (10), rutin (11), kaempferol (12) and quercetin (13) on the basis of their chromatographic properties, chemical and spectroscopic evidences. The investigated ethyl acetate extract was found to be non-toxic (LD(50) up to the maximum soluble dose 4 g kg(-1) body wt.) and had significant antioxidant, hepatoprotective, anti-inflammatory and antidiabetic activities. Also some of the isolated flavonoids showed cytotoxic activity against Ehrlich ascitis carcinoma cells.
Iron mediates catalysis of nucleic acid processing enzymes: support for Fe(II) as a cofactor before the great oxidation event (2017)

Life originated in an anoxic, Fe2+-rich environment. We hypothesize that on early Earth, Fe2+ was a ubiquitous cofactor for nucleic acids, with roles in RNA folding and catalysis as well as in processing of nucleic acids by protein enzymes. In this model, Mg2+ replaced Fe2+ as the primary cofactor for nucleic acids in parallel with known metal substitutions of metalloproteins, driven by the Great Oxidation Event. To test predictions of this model, we assay the ability of nucleic acid processing enzymes, including a DNA polymerase, an RNA polymerase and a DNA ligase, to use Fe2+ in place of Mg2+ as a cofactor during catalysis. Results show that Fe2+ can indeed substitute for Mg2+ in catalytic function of these enzymes. Additionally, we use calculations to unravel differences in energetics, structures and reactivities of relevant Mg2+ and Fe2+ complexes. Computation explains why Fe2+ can be a more potent cofactor than Mg2+ in a variety of folding and catalytic functions. We propose that the rise of O2 on Earth drove a Fe2+ to Mg2+ substitution in proteins and nucleic acids, a hypothesis consistent with a general model in which some modern biochemical systems retain latent abilities to revert to primordial Fe2+-based states when exposed to pre-GOE conditions.
ChemInform Abstract: 1‐Alkyl‐1,2,5,6‐tetrahydropyridine‐3‐carboxaldehyde‐O‐alkyl‐oximes: A New Class of Potent Orally Active Muscarinic Agonists Related to Arecoline. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Statistical Library Characterization using Belief Propagation across Multiple Technology Nodes (2015)

In this paper, we propose a novel flow to enable computationally efficient statistical characterization of delay and slew in standard cell libraries. The distinguishing feature of the proposed method is the usage of a limited combination of output capacitance, input slew rate and supply voltage for the extraction of statistical timing metrics of an individual logic gate. The efficiency of the proposed flow stems from the introduction of a novel, ultra-compact, nonlinear, analytical timing model, having only four universal regression parameters. This novel model facilitates the use of maximum-a-posteriori belief propagation to learn the prior parameter distribution for the parameters of the target technology from past characterizations of library cells belonging to various other technologies, including older ones. The framework then utilises Bayesian inference to extract the new timing model parameters using an ultra-small set of additional timing measurements from the target technology. The proposed method is validated and benchmarked on several production-level cell libraries including a state-of-the-art 14-nm technology node and a variation-aware, compact transistor model. For the same accuracy as the conventional lookup-table approach, this new method achieves at least 15x reduction in simulation runs.