gebhart/patrepeval huggingface dataset:
New Tubular-Design Ellipse With Backup Pressure (2018)

Summary This paper proposes a tubular-design ellipse dependent on backup pressure (internal pressure for collapse and external pressure for burst), so that the latest American Petroleum Institute (API) collapse-resistance equations (API TR 5C32015) with dependence on internal pressure can be shown simultaneously on the same plot with the ellipse. Unlike the current ellipse used widely in the industry for casing-and-tubing design, which is approximate, the proposed ellipse is exact for collapse, burst, and axial loads. Without the proposed ellipse, use of the approximate ellipse will continue, requiring separate plots for the API collapse-resistance equations. Example cases demonstrate the advantages of the proposed ellipse, including increased accuracy. Results help clarify questions regarding the origin and use of the 2015 API collapse-resistance equations.
Cyclin D1 gene contains a cryptic promoter that is functional in human cancer cells (2001)

A novel cyclin D1 (CCND1)-TROP2 fusion oncogene has been isolated from human cancer cells. Unexpectedly, the chimeric cDNA was found to express TROP2 in the absence of exogenous promoters. Mutagenesis of the TROP2 and CCND1 sequences and in vitro transcription/translation show that a cryptic promoter is present in the 3' coding region of CCND1. The CCND1 cryptic promoter is functional in luciferase assays, where it augments the basal expression levels by eightfold and efficiently cooperates with an SV-40 enhancer. The transcription start sites of the cryptic promoter map at bases 797 and 935 of CCND1, as determined by RNase protection assays. The cryptic promoter possesses canonical binding sites for ubiquitous transcription factors and W/S, X1, and CAAT/Y boxes that are characteristic of major histocompatibility complex class II gene promoters. Remarkably, the cryptic CCND1 promoter is active in human cancer cells and generates a truncated transcript that contains CCND1 instability sequences. Thus, this novel CCND1 transcription unit may play a role in the regulation of the expression of cyclin D1 and in tumor cell growth.
Supplementary Figure S14 from Evolution of Castration-Resistant Prostate Cancer in ctDNA during Sequential Androgen Receptor Pathway Inhibition (2023)

&lt;p&gt;Supplementary Figure S14 shows temporal changes in whole exome somatic mutation profiles in patients that had evidence for somatic mutation profile change based on 72-gene targeted sequencing.&lt;/p&gt;
Elucidating the role of surface chemistry on cationic phosphorus dendrimer–siRNA complexation (2018)

In the field of dendrimers targeting small interfering RNA (siRNA) delivery, dendrimer structural properties, such as the flexibility/rigidity ratio, play a crucial role in the efficiency of complexation. However, advances in organic chemistry have enabled the development of dendrimers that differ only by a single atom on their surface terminals. This is the case for cationic phosphorus dendrimers functionalized with either pyrrolidinium (DP) or morpholinium (DM) terminal groups. This small change was shown to strongly affect the dendrimer-siRNA complexation, leading to more efficient anti-inflammatory effects in the case of DP. Reasons for this different behavior can hardly be inferred only by biological in vitro and in vivo experiments due to the high number of variables and complexity of the investigated biological system. However, an understanding of how small chemical surface changes may completely modify the overall dendrimer-siRNA complexation is a significant breakthrough towards the design of efficient dendrimers for nucleic acid delivery. Herein, we present experimental and computational approaches based on isothermal titration calorimetry and molecular dynamics simulations to elucidate the molecular reasons behind different efficiencies and activities of DP and DM. Results of the present research highlight how chemical surface modifications may drive the overall dendrimer-siRNA affinity by influencing enthalpic and entropic contributions of binding free energy. Moreover, this study elucidates molecular reasons related to complexation stoichiometry that may be crucial in determining the dendrimer complexation efficiency.
Metabolic effects of combined glucagon receptor antagonism and glucagon-like peptide-1 receptor agonism in high fat fed mice (2022)

Ablation of glucagon receptor (GCGR) signalling is a potential treatment option for diabetes, whilst glucagon-like peptide-1 (GLP-1) receptor agonists are clinically approved for both obesity and diabetes. There is a suggestion that GCGR blockade enhances GLP-1 secretion and action, whilst GLP-1 receptor activation is known to inhibit glucagon release, implying potential for positive interactions between both therapeutic avenues. The present study has examined the ability of sustained GCGR antagonism, using desHis<sup>1</sup>Pro<sup>4</sup>Glu<sup>9</sup>-glucagon, to augment the established benefits of the GLP-1 mimetic, exendin-4, in high fat fed (HFF) mice. Twice-daily injection of desHis<sup>1</sup>Pro<sup>4</sup>Glu<sup>9</sup>-glucagon, exendin-4 or a combination of both peptides to groups of HFF mice for 10 days had no impact on body weight or energy intake. Circulating blood glucose and glucagon concentrations were significantly (P < 0.05-0.01) decreased by all treatment regimens, with plasma insulin levels elevated (P < 0.001) when compared to lean control mice. Intraperitoneal and oral glucose tolerance were improved (P < 0.05-0.01) by all treatments, despite lack of enhanced glucose-stimulated insulin secretion. Following exogenous glucagon administration, all HFF treatment groups displayed reduced (P < 0.05-0.001) glucose and insulin levels compared to HFF saline controls, although peripheral insulin sensitivity was largely unchanged across all animals. Interestingly, all treatments had tendency to increase pancreatic insulin content with pancreatic glucagon content significantly elevated (P < 0.05) by all interventions. These studies highlight the capacity of peptide-based GCGR inhibition, or GLP-1 receptor activation, to significantly improve metabolism in HFF mice but suggest no obvious additive benefits of combined therapy.
Intestinal Folate Absorption (1973)

These studies were designed to determine whether pteroylmonoglutamic acid (PGA) at physiologic concentrations is transported across the small intestine unaltered or is reduced and methylated to the circulating folate form (5-methyltetrahydrofolate [5-MeFH(4)]) during absorption. [(3)H]PGA was incubated in vitro on the mucosal side of rat jejunum. Of the folate transferred to the serosal side, the percent identified as 5-MeFH(4) by DEAE-Sephadex chromtography was inversely related to the initial mucosa PGA concentration: at 7, 20, and 2,000 nM, 44%, 34%, and 2%, respectively, was converted to 5-MeFH(4). In contrast, less than 4% of the folate transferred across ileal mucosa was 5-MeFH(4) when the initial mucosa concentration was 20 nM. Specific activity of dihydrofolate (DHF) reductase, the enzyme responsible for converting PGA to tetrahydrofolic acid, was measured in villus homogenates and was significantly greater in the jejunum than in the ileum. 1,000 nM methotrexate (MTX), a DHF reductase inhibitor, markedly inhibited PGA conversion to 5-MeFH(4) by the jejunum. Studies of transmural flux, initial rate of mucosal entry (influx) and mucosal accumulation (uptake) of folate were also performed. Although MTX did not alter the influx of PGA, MTX decreased jejunal mucosal uptake but increased transmural movement. Transmural folate movement across ileal mucosa was greater than across jejunal mucosa although mucosal uptake was greater in the jejunum than in the ileum. These results could explain previous studies which have failed to identify conversion of PGA to 5-MeFH(4) when intestinal preparations have been exposed to higher and less physiologic concentrations of PGA. Further, these studies suggest that 5-MeFH(4) may be retained by the jejunal mucosa.
Highly lethal H5N1 influenza virus in asia: Genesis and options for control. (2004)

Extract: Unprecedented animal epidemics of avian influenza viruses of the H5N1 subtype have been reported in Asia in 2004. These outbreaks resulted in the destruction of hundreds of millions of poultry. Of the 44 persons in Asia infected with H5N1 viruses, 32 died (20 in Vietnam and 12 in Thailand). It is impossible to predict whether H5 subtype viruses will acquire the ability to spread among humans and cause a new pandemic. The highly pathogenic Z genotype of H5N1 is now endemic in southeastern Asia and will continue to threaten veterinary and human public health. Influenza A viruses belong to the Orthomyxoviridae family and can be divided into 15 hemagglutinin (HA) and 9 neuraminidase (NA) subtypes on the basis of antigenic and sequence differences in these surface glycoproteins (proteins with sugar groups attached). In wild aquatic birds, influenza's natural hosts, the viruses cause no disease. Periodically, influenza viruses are transmitted to other hosts and cause transient infections and occasional deaths. Less frequently, influenza viruses are transmitted to other species and become adapted to the new hosts. Thus permanent lineages of influenza A viruses are established in humans, swine, horses, and domestic poultry.
Crown-Annelated 9,10-Bis(1,3-dithiol-2-ylidene)-9,10-dihydroanthracene Derivatives as Cation Sensors: Synthesis, X-ray Crystal Structures, Voltammetric and Spectroscopic Monitoring of Metal Complexation (2001)

The synthesis of O4S2-crown annelated derivatives of 9,10-bis(1,3-dithiol-2-ylidene)-9,10-dihydroanthracene using the novel Horner−Wadsworth−Emmons reagent 7 is reported. The bis- and mono-crown systems 9 and 12 function as efficient ligands in the voltammetric and UV/Vis spectroscopic recognition of Na+ and Ag+. Solution electrochemical studies reveal that metal complexation to the crown unit(s) leads to a significant positive shift in the potential of the first, two-electron oxidation wave of 9 and 12 [maximum shift E1ox = 115 mV for 9 in the presence of Ag+ (ca. 10 molar equivalents)]. Considerably smaller shifts (< 30 mV) were observed for complexation of Li+, K+ and Ba2+. UV/Vis spectrophotometric studies of metal binding (Na+ and Ag+) to 9 are consistent with the simultaneous formation of 1:1 and 1:2 complexes. The X-ray crystal structures of compounds 10 and 12·CH2Cl2 are reported. The anthracenediylidene moiety of 12 is U-shaped due to the boat conformation of the central (quinodimethane) ring and folding of both 1,3-dithiole rings, providing an overall saddle conformation. The folding in 10 is reduced as steric crowding is relieved by removal of one of the 1,3-dithiole units.
Abstract 4673: DCLK1 promotes hepatocellular carcinoma via atypical β-catenin-regulated signaling and immune suppression (2019)

Introduction: Genetic lineage tracing in mouse model has revealed that mature hepatocytes are the cell of origin of injury-induced hepatocellular carcinoma (HCC), the second most common cause of cancer-related deaths worldwide. Hepatocyte plasticity, defined as the ability to change cellular identity, plays a critical role in the repair process following liver injury. Inflammatory liver diseases often lead to cirrhosis and HCC. The molecular mechanisms that regulate the decision between hepatocyte injury repair and neoplastic initiation are unclear. Doublecortin-like kinase 1 (DCLK1), a microtubule-associated kinase, is expressed during liver injury, cirrhosis, and HCC, but not in normal liver. Here, we demonstrate a novel mechanism by which DCLK1 regulates injury-associated hepatocyte plasticity and immunosuppression in HCC.Methods: Cell culture, DEN/CCl4-induced injury in mouse livers, and humanized mouse model were used for analyzing hepatocyte plasticity and DCLK1+ cells-induced changes in hepatic cells and macrophages.Results: DCLK1-overexpressing primary human hepatocytes formed spheroids in 3D culture. DCLK1-overexpressing hepatoma cells exhibited a 48-kDa active β-catenin with preserved hypophosphorylated N-terminus, which interacted with TCF-4, resulting in enhanced luciferase reporter activity and cyclin D1 expression. Downregulation of DCLK1 using siRNAs inhibited expression of this β-catenin fragment. DCLK1 overexpression increased phosphorylation of GSK-3β at Ser9, thus preventing its complete proteasomal degradation. Liver tissues from patients with cirrhosis and HCC expressed the 48-kDa active β-catenin, DCLK1, cyclin D1, and 80-kDa E-cadherin ectodomain, suggesting a change in epithelial polarity. DCLK1-overexpressing primary human hepatocytes transplanted into FRG mice demonstrated β-catenin activation in the transplanted hepatocytes. Injury-induced DCLK1+ epithelial cells in mouse livers expressed PD-L1. DCLK1+ human hepatoma cells induced CD206 in macrophages in a dual co-culture assay.Conclusions: DCLK1 enhances hepatocyte plasticity, clonogenicity, and tumorigenic signaling via atypical β-catenin-dependent mechanism. DCLK1+ cells show ability to suppress the host anti-tumor immunity by expressing PD-L1 and inducing macrophage polarization.Citation Format: Naushad Ali, Parthasarathy Chandrakesan, Michael S. Bronze, Courtney W. Houchen. DCLK1 promotes hepatocellular carcinoma via atypical β-catenin-regulated signaling and immune suppression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4673.
A microbial metabolite synergizes with endogenous serotonin to triggerC. elegansreproductive behavior (2020)

Natural products are a major source of small-molecule therapeutics, including those that target the nervous system. We have used a simple serotonin-dependent behavior of the roundworm <i>Caenorhabditis elegans</i>, egg laying, to perform a behavior-based screen for natural products that affect serotonin signaling. Our screen yielded agonists of G protein-coupled serotonin receptors, protein kinase C agonists, and a microbial metabolite not previously known to interact with serotonin signaling pathways: the disulfide-bridged 2,5-diketopiperazine gliotoxin. Effects of gliotoxin on egg-laying behavior required the G protein-coupled serotonin receptors SER-1 and SER-7, and the G<sub>q</sub> ortholog EGL-30. Furthermore, mutants lacking serotonergic neurons and mutants that cannot synthesize serotonin were profoundly resistant to gliotoxin. Exogenous serotonin restored their sensitivity to gliotoxin, indicating that this compound synergizes with endogenous serotonin to elicit behavior. These data show that a microbial metabolite with no structural similarity to known serotonergic agonists potentiates an endogenous serotonin signal to affect behavior. Based on this study, we suggest that microbial metabolites are a rich source of functionally novel neuroactive molecules.
Data from Changes in CpG Islands Promoter Methylation Patterns during Ductal Breast Carcinoma Progression (2023)

&lt;div&gt;Abstract&lt;p&gt;Aberrant promoter methylation of several known or putative tumor suppressor genes occurs frequently during carcinogenesis, and this epigenetic change has been considered as a potential molecular marker for cancer. We examined the methylation status of nine genes (&lt;i&gt;APC, CDH1, CTNNB1, TIMP3, ESR1, GSTP1, MGMT, THBS1&lt;/i&gt;, and &lt;i&gt;TMS1&lt;/i&gt;), by quantitative methylation specific PCR. Synchronous preinvasive lesions (atypical ductal hyperplasia and/or ductal carcinoma &lt;i&gt;in situ&lt;/i&gt;) and invasive ductal breast carcinoma from 52 patients, together with pure lesions from 24 patients and 12 normal tissues paired to tumor and 20 normal breast distant from tumor were analyzed. Aberrant promoter methylation was detected in both preinvasive and invasive lesions for genes &lt;i&gt;APC, CDH1, CTNNB1, TIMP3, ESR1&lt;/i&gt;, and &lt;i&gt;GSTP1&lt;/i&gt;. However, hierarchical mixed model and Generalized Estimating Equations model analyses showed that only &lt;i&gt;APC, CDH1&lt;/i&gt;, and &lt;i&gt;CTNNB1&lt;/i&gt; promoter regions showed a higher frequency and methylation levels in pathologic samples when compared with normal breast. Whereas &lt;i&gt;APC&lt;/i&gt; and &lt;i&gt;CTNNB1&lt;/i&gt; did not show differences in methylation levels or frequencies, &lt;i&gt;CDH1&lt;/i&gt; showed higher methylation levels in invasive tumors as compared with preinvasive lesions (&lt;i&gt;P&lt;/i&gt; &lt; 0.04, Mann-Whitney test with permutation correction). The analysis of &lt;i&gt;APC, CDH1&lt;/i&gt;, and &lt;i&gt;CTNNB1&lt;/i&gt; methylation status was able to distinguish between normal and pathologic samples with a sensitivity of 67% (95% confidence interval, 60-71%) and a specificity of 75% (95% confidence interval, 69-81%). Our data point to the direct involvement of &lt;i&gt;APC, CDH1&lt;/i&gt;, and &lt;i&gt;CTNNB1&lt;/i&gt; promoter methylation in the early stages of breast cancer progression and suggest that they may represent a useful tool for the detection of tumor cells in clinical specimens. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2694–700)&lt;/p&gt;&lt;/div&gt;
Fa&#x0E7;ade Segmentation in a Multi-view Scenario (2011)

We examine a new method of façade segmentation in a multi-view scenario. A set of overlapping, thus redundant street-side images exists and each image shows multiple buildings. A semantic segmentation identifies primary areas in the image such as sky, ground, vegetation, and façade. Subsequently, repeated patterns are detected in image segments previous labeled as "façade areas" and are applied to separate specific facades from each other. Experimentation is based on an industrial street-view dataset from a moving car by well-designed, calibrated, automated cameras. High overlap images define a multi-view scenario. We achieve 97% pixel-wise segmentation effectiveness, outperforming current state-of-the-art methods.
Supplementary Figure Legend from Small-Molecule IAP Antagonists Sensitize Cancer Cells to TRAIL-Induced Apoptosis: Roles of XIAP and cIAPs (2023)

&lt;p&gt;PDF - 53KB, Legend for Supplementary Figure 1.&lt;/p&gt;
Linear classifier and textural analysis of optical scattering images for tumor classification during breast cancer extraction (2013)

Texture analysis of light scattering in tissue is proposed to obtain diagnostic information from breast cancer specimens. Light scattering measurements are minimally invasive, and allow the estimation of tissue morphology to guide the surgeon in resection surgeries. The usability of scatter signatures acquired with a micro-sampling reflectance spectral imaging system was improved utilizing an empirical approximation to the Mie theory to estimate the scattering power on a per-pixel basis. Co-occurrence analysis is then applied to the scattering power images to extract the textural features. A statistical analysis of the features demonstrated the suitability of the autocorrelation for the classification of notmalignant (normal epithelia and stroma, benign epithelia and stroma, inflammation), malignant (DCIS, IDC, ILC) and adipose tissue, since it reveals morphological information of tissue. Non-malignant tissue shows higher autocorrelation values while adipose tissue presents a very low autocorrelation on its scatter texture, being malignant the middle ground. Consequently, a fast linear classifier based on the consideration of just one straightforward feature is enough for providing relevant diagnostic information. A leave-one-out validation of the linear classifier on 29 samples with 48 regions of interest showed classification accuracies of 98.74% on adipose tissue, 82.67% on non-malignant tissue and 72.37% on malignant tissue, in comparison with the biopsy H and E gold standard. This demonstrates that autocorrelation analysis of scatter signatures is a very computationally efficient and automated approach to provide pathological information in real-time to guide surgeon during tissue resection.
Convolutional Coding and ARQ Schemes for Wireless Communications (1998)

Flexible and low-complexity variable rate coding schemes based on rate-compatible convolutional codes are presented. The codes have a wide range of code rates and are optimized for good performance on both AWGN and Rayleigh fading channels. Furthermore, the application of these codes for rate matching, combined coding and spreading in a DS-CDMA system and hybrid type-II ARQ schemes are demonstrated. Very long constraint length convolutional codes with sequential decoding is proposed and shown to be suitable for high performance services in wireless systems. 1 Introduction Since the introduction of cellular telephony in the early 80&amp;apos;s, virtually all markets and operators have seen a rapid increase in the number of subscribers. In the early 90&amp;apos;s the first generation analog systems were replaced by the second generation digital systems. These systems have higher capacity due to source (speech) coding, channel coding and the inherent robustness of digital transmission. Common for all thes...
Synthesis of star-comb PCE superplasticiser towards an understanding of its properties in cement pastes (2017)

Synthesis of the star-comb (also referred to as star-graft) copolymer architecture of a polycarboxylate ether or poly(acrylic acid)-co-poly(isoprenyl oxy poly(ethylene glycol) ether) (PCE) using a star chain transfer agent (CTA) with multiple mercapto groups by free radical polymerisation and its properties in cement pastes are discussed. By varying the number of mercapto groups of the star CTA, star-comb PCEs with a similar acid/ether ratio, molecular weight and anionic charge density but different arm numbers were prepared. The synthesised PCEs were characterised by proton nuclear magnetic resonance and gel permeation chromatography with a triple-detector system. It was proved that PCEs with star-comb topological structure could be successfully applied as superplasticisers. The effects of star-comb PCEs with different numbers of arms on cement paste fluidity, zeta potential and adsorption were studied. A theoretical model was developed to explain the differences in adsorption behaviour of linear-comb and star-comb PCEs on the surfaces of cement particles. This work provides useful guidance for the exploration of new topological structures of PCEs in future studies.