gebhart/patrepeval huggingface dataset:
In vivo murine left ventricular pressure-volume relations by miniaturized conductance micromanometry (1998)

The mouse is the species of choice for creating genetically engineered models of human disease. To study detailed systolic and diastolic left ventricular (LV) chamber mechanics in mice in vivo, we developed a miniaturized conductance-manometer system. alpha-Chloralose-urethan-anesthetized animals were instrumented with a two-electrode pressure-volume catheter advanced via the LV apex to the aortic root. Custom electronics provided time-varying conductances related to cavity volume. Baseline hemodynamics were similar to values in conscious animals: 634 +/- 14 beats/min, 112 +/- 4 mmHg, 5.3 +/- 0.8 mmHg, and 11,777 +/- 732 mmHg/s for heart rate, end-systolic and end-diastolic pressures, and maximum first derivative of ventricular pressure with respect to time (dP/dtmax), respectively. Catheter stroke volume during preload reduction by inferior vena caval occlusion correlated with that by ultrasound aortic flow probe (r2 = 0.98). This maneuver yielded end-systolic elastances of 79 +/- 21 mmHg/microliter, preload-recruitable stroke work of 82 +/- 5.6 mmHg, and slope of dP/dtmax-end-diastolic volume relation of 699 +/- 100 mmHg.s-1.microliter-1, and these relations varied predictably with acute inotropic interventions. The control normalized time-varying elastance curve was similar to human data, further supporting comparable chamber mechanics between species. This novel approach should greatly help assess cardiovascular function in the blood-perfused murine heart.
Rare ALK Expression but no ALK Rearrangement in Pancreatic Ductal Adenocarcinoma and Neuroendocrine Tumors (2013)

Objectives Anaplastic lymphoma kinase (ALK) gene rearrangements were first identified in anaplastic large cell lymphomas. Subsequently, they have been observed in other tumor types with ALK-rearranged tumors demonstrating responsiveness to ALK inhibitors. The aggressiveness of pancreatic ductal adenocarcinoma warrants the examination of ALK rearrangements in pancreatic cancer as a potential therapeutic target. Immunohistochemical expression of ALK1 correlates with ALK rearrangements in other tumors. We performed ALK immunohistochemistry on samples of pancreatic ductal adenocarcinoma and pancreatic neuroendocrine tumors using 2 tissue microarrays. Methods ALK1 expression was scored for each case as 0, 1+, 2+, or 3+ using established criteria. Fluorescence in situ hybridization using a break-apart assay with probes for ALK was performed to detect ALK rearrangement in ALK1-positive cases. Results All 46 neuroendocrine tumors were negative for ALK1. Of 140 ductal adenocarcinoma cases, 5 showed immunoreactivity for ALK1: 1 was 3+, 2 were 2+, and 2 were 1+. However, fluorescence in situ hybridization for ALK rearrangement was negative in all 5 cases. Conclusions The results demonstrate that ALK1 expression is uncommon in both pancreatic ductal adenocarcinoma and neuroendocrine tumors. Rare ALK1 expression is not induced by ALK translocation, and ALK is unlikely to be a therapeutic target in pancreatic tumors.
Linear-Energy-Transfer Effects on Polymers (1991)

Various polymers (polymethacrylonitrile, PMCN, polyvinylacetate, PVAc, poly(ethylene oxide), PEO, poly(ethylene-co-propylene), CP-EP, and polystyrene, PSt) have been irradiated at room temperature and in the absence of oxygen witn γ-rays, and various ions of different kinetic energy E. Thus, a wide range of electronic stopping power, dE/dx, from 2x10-4 to 2.5 MeV/µm was accessible. PMCN predominantly undergoes main-chain scission and, in analogy to the previously examined polymethylmethacrylate, PMMA, the corresponding radiation chemical yield G(S), decreases with increasing stopping power. PSt predominantly crosslinks and the corresponding yield, G(X), is small and independent of dE/dx. PVAc, PEO and CP-EP also crosslink predominantly under the action of ionizing radiation and the gel doses increase with increasing stopping power. This finding indicates that, for these polymers, both radiation chemical yields, G(S) and G(X) decrease with increasing dE/dx. Moreover, for PEO and PVAc, irradiated with 40Ar ions, the gel dose increases by a factor of 4 upon increasing
A low-cost microwave rotary joint (2014)

A simple and cheap coaxial microwave rotary joint covering frequencies from 1 to 21 GHz is described. Measured typical insertion loss is 0.7 dB, return loss stays better than 10 dB and the rotating torque requirement is 26 mNm. Maximum variation of attenuation as a function of rotating angle is 0.5 dB. Operation up to 37 GHz has been tried with loss values around 2 dB, typical.
A Soluble Form of α1,3-Galactosyltransferase Functions within Cells to Galactosylate Glycoproteins (1997)

It has been assumed that membrane-bound glycosyltransferases function within the Golgi apparatus to glycosylate glycoproteins. We now report, however, that a truncated, soluble recombinant form of the murine alpha1,3-galactosyltransferase expressed in human 293 cells is highly efficient and comparable to the full-length enzyme in alpha-galactosylating both newly synthesized membrane-associated and secreted glycoproteins. Although the soluble enzyme was secreted by cells as expected, we also found that the full-length, membrane-associated form was secreted. Unexpectedly, both secreted forms are cleaved identically at two primary sites within the stem region by endogenous protease(s) at the indicated positions in the sequence 73KDWW (downward arrow) FPS (downward arrow) WFKNG. These results demonstrate that the soluble alpha1,3-galactosyltransferase is functional within the cell and that specific proteolysis occurs in the stem region. The widespread occurrence of different soluble glycosyltransferases secreted by cells suggests that normal glycoconjugate biosynthesis may involve cooperation between membrane-bound and soluble enzymes.
The Fate of Adipocytes after Nonvascularized Fat Grafting (2012)

The authors show convincing evidence of very dynamic remodeling of adipose tissue after nonvascularized grafting. The authors observed three zones from the periphery to the center of the graft: the surviving area (adipocytes survived), the regenerating area (adipocytes died, adipose-derived stromal cells survived, and dead adipocytes were replaced with new ones), and the necrotic area (both adipocytes and adipose-derived stromal cells died).
Osmium-Based Pyrimidine Contrast Tags for Enhanced Nanopore-Based DNA Base Discrimination (2015)

Nanopores are a promising platform in next generation DNA sequencing. In this platform, an individual DNA strand is threaded into nanopore using an electric field, and enzyme-based ratcheting is used to move the strand through the detector. During this process the residual ion current through the pore is measured, which exhibits unique levels for different base combinations inside the pore. While this approach has shown great promise, accuracy is not optimal because the four bases are chemically comparable to one another, leading to small differences in current obstruction. Nucleobase-specific chemical tagging can be a viable approach to enhancing the contrast between different bases in the sequence. Herein we show that covalent modification of one or both of the pyrimidine bases by an osmium bipyridine complex leads to measureable differences in the blockade amplitudes of DNA molecules. We qualitatively determine the degree of osmylation of a DNA strand by passing it through a solid-state nanopore, and are thus able to gauge T and C base content. In addition, we show that osmium bipyridine reacts with dsDNA, leading to substantially different current blockade levels than exhibited for bare dsDNA. This work serves as a proof of principle for nanopore sequencing and mapping via base-specific DNA osmylation.
Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages (2012)

This first report on genome-wide binding of LXR in a human cell line provides new insights into the transcriptional network of LXR and its target genes with their link to physiological processes, such as apoptosis.The gene expression microarray and sequence data have been submitted collectively to the NCBI Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo under accession number GSE28319.
Genetic Variation associated with Ischemic Heart Failure: A HuGE Review and Meta-Analysis (2007)

The ischemic etiology of heart failure is an independent prognostic factor associated with worse long-term outcome. Recent evidence indicates a role for genetic susceptibility to ischemic heart failure. The authors systematically reviewed all known case-control studies that investigated the association between genetic variants and ischemic heart failure. Twenty-two articles, which examined 24 gene polymorphisms, were identified. In 22 polymorphisms, the variant form had a functional effect. Twenty-two polymorphisms were variants of genes involved in the maladaptive neurohormonal activation. Seven polymorphisms (ACE 1/D, AGT M235T, ADRA2C Del322-325, ADRB2 Arg16Gly, ADRB2 Gln27Glu, EDN1 Lys198Asn, VEGF G-405C) showed a significant association in individual studies. Five polymorphisms (ACE 1/D, ADRB1 Arg389Gly, ADRB2 Argl6Gly, ADRB2 Gln27Glu, TNF G308A) were examined by more than one study, and meta-analyses were performed. The meta-analyses showed no significant sign of heterogeneity. In all settings, there was no significant association, except for polymorphism ADRB2 Arg16Gly under a recessive model (fixed-effects odds ratio = 1.32, 95% confidence interval: 1.05, 1.65). Taking into account that ischemic heart failure is a complex disease with multifactorial etiology, a minor contributing pathogenetic role of the investigated gene polymorphisms cannot be totally excluded. Case-control studies that investigate gene-gene and gene-environment interactions might further elucidate the genetics of ischemic heart failure.
Gene Networks and microRNAs Implicated in Aggressive Prostate Cancer (2009)

Prostate cancer, a complex disease, can be relatively harmless or extremely aggressive. To identify candidate genes involved in causal pathways of aggressive prostate cancer, we implemented a systems biology approach by combining differential expression analysis and coexpression network analysis to evaluate transcriptional profiles using lymphoblastoid cell lines from 62 prostate cancer patients with aggressive phenotype (Gleason grade >or= 8) and 63 prostate cancer patients with nonaggressive phenotype (Gleason grade <or= 5). From 13,935 mRNA genes and 273 microRNAs (miRNA) tested, we identified significant differences in 1,100 mRNAs and 7 miRNAs with a false discovery rate (FDR) of <0.01. We also identified a coexpression module demonstrating significant association with the aggressive phenotype of prostate cancer (P = 3.67 x 10(-11)). The module of interest was characterized by overrepresentation of cell cycle-related genes (FDR = 3.50 x 10(-50)). From this module, we further defined 20 hub genes that were highly connected to other genes. Interestingly, 5 of the 7 differentially expressed miRNAs have been implicated in cell cycle regulation and 2 (miR-145 and miR-331-3p) are predicted to target 3 of the 20 hub genes. Ectopic expression of these two miRNAs reduced expression of target hub genes and subsequently resulted in cell growth inhibition and apoptosis. These results suggest that cell cycle is likely to be a molecular pathway causing aggressive phenotype of prostate cancer. Further characterization of cell cycle-related genes (particularly, the hub genes) and miRNAs that regulate these hub genes could facilitate identification of candidate genes responsible for the aggressive phenotype and lead to a better understanding of prostate cancer etiology and progression.
Enlèvement du phosphore des eaux usées par traitement à base de tourbe dopée aux boues rouges (1999)

Abstract L'ajout d'un agent dopant à base d'aluminium et de fer, soit les boues rouges issues de l'extraction de l'alumine de la bauxite, a été testé avec une tourbe horticole commerciale et ce, pour l'épuration d'eaux usées municipales provenant d'un traitement secondaire. Suite à des essais en colonnes, l'efficacité de déphosphatation est passée de 17 et 21% sur la tourbe uniquement à plus de 95% en présence de l'agent dopant. De même, l'utilisation de boues rouges a permis de réduire la concentration de P t de l'effluent à moins de 0.15 mg/L. L'effet dopant diminuait avec le temps et surtout pro‐portionnellement à la charge hydraulique appliquée. Pour une charge de 30 cm/j j la déphosphatation respectait les recommandations gouvemementales (P t , dans l'effluent &lt;1 mg/L) et ce, pour une période de 50 jours. Les performances sur les autres paramètres indicateurs classiques tels la DBO 5 , le DCO et l'enlèvement des coliformes ne furent pas altérés par l'emploi de l'agent dopant.
The Vascular Endothelial Growth Factor Family: Signalling for Vascular Development (1999)

Click to increase image sizeClick to decrease image sizeKey Words: Angiogenesisendothelial growth factorsgrowth factorsneuropilinPIGFreceptor protein tyrosine kinaseVEGF
Elevation of interferon beta-inducible proteins in ataxia telangiectasia cells. (1996)

The recently cloned ATM gene has been shown to bear considerable homology to phosphatidylinositol 3 kinases and, therefore, its product may function in signal transduction. In this study, we report constitutively elevated levels of two IFN-beta-inducible proteins, ubiquitin cross-reactive protein (UCRP), and low molecular weight protein (LMP2), in human fibroblasts with the inherited disease ataxia telangiectasia (AT). Using immunoblotting, it was found that a M(r) 15,000 band representing free UCRP was hardly detectable in normal cells, while it was the predominant band in AT cells. Similarly, the expression of a M(r) 23,000 protein, LMP2 was found to be higher in AT cells than in normal cells. Culturing three successive passages of the AT cell line in the presence of different concentrations of neutralizing antibodies against IFN-beta caused partial and complete reduction, respectively, of the free UCRP and LMP2 signals to normal levels. These results indicate that UCRP and LMP2 pools may be basally elevated in AT cells due to constitutive activation of the IFN-beta induction pathway and are in keeping with the recently reported constitutive activation of the NF-kappaB transcriptional activator in AT cells.
Identification of genes for reverse transcriptase–like enzymes in twoDrosophilaretrotransposons,412 and gypsy; a rapid detection method of reverse transcriptase genes using YXDD box probes (1986)

Using synthetic oligonucleotides corresponding to the amino acid sequences best conserved among retroviral reverse transcriptases, we developed a rapid method to detect cloned DNA fragments with the genes for reverse transcriptases. By this technique followed by nucleotide sequence determination, nucleotide sequences coding for reverse transcriptase-like enzymes were identified in two Drosophila retrotransposons, gypsy and 412. Our sequence analysis suggested that there are at least two major groups of retrotransposons in Drosophila with respect to putative reverse transcriptases and both gypsy and 412 belong to a category of retrotransposons which have putative reverse transcriptases very similar in amino acid sequence to the counterpart of Moloney murine leukaemia virus, a typical mammalian retrovirus.
Reduced oxygen tension and EDTA improve bovine zygote development in a chemically defined medium. (2000)

Bovine zygotes produced by in vitro oocyte maturation and fertilization were cultured for 7.5 d in a chemically defined medium without serum or proteins, except .12 IU/mL of insulin. In Exp. 1, embryos were cultured in approximately 20% oxygen (i.e., 5% CO2 in air) or 5% CO2; 5% O2; 90% N2, with the metal chelators EDTA or diethylenetetraaminopentaacetic acid (DTPA) at 0, 5, 25, or 125 microM. More (P < .01) embryos developed to blastocysts at 5% O2 (17%) than at -20% O2 (7%). Also, embryos grown at 5% O2 averaged more cells than embryos cultured at -20% O2 (38 vs 29 cells for morulae and blastocysts and 15 vs 12 cells including all embryos; P < .05). There were interactions (P < .01) among chelator, concentration of chelator, and oxygen tension. The most efficacious treatments were 5 microM EDTA at 5 or -20% O2 (24 and 20% blastocysts), 5 microM DTPA at 5% O2 (28% blastocysts), and 25 microM EDTA at 5% O2 (25% blastocysts). High concentrations of either chelator were detrimental, especially at -20% O2. In Exp. 2, a smaller range of chelator concentrations was compared (EDTA: 3, 9, 27, or 81 microM, DTPA: 3 or 15 microM) in 5% O2. More embryos developed to blastocysts and expanded blastocysts with 3 microM EDTA than the control without a chelator (20 and 16% vs 7 and 3%, respectively; P < .05). However, in Exp. 3, which concerned embryo development in .33, 1, 3, or 27 microM EDTA and .33, 1, or 3 microM DTPA, no concentration of either chelator was better (P > . 1) than the control.
Strider GhostBuster: Why It’s A Bad Idea For Stealth Software To Hide Files (2004)

File-hiding through lying APIs [HTB03, NTI04] is an advanced stealth technique used by many popular system-monitoring software such as RootKits, Trojans, and keyloggers (collectively called “ghostware ” in this paper) to make executables or data files invisible. Once the ghostware program is started, it intercepts all file queries at a very low level and uses filtering to ensure that a chosen subset of files are never revealed to any file query operations made by any program, not associated with the ghostware, running on the infected machine. This technique can defeat experienced system administrators who search the file system and Windows Registry for suspicious entries, as well as commonly used malware scanning tools that are based on known-bad file signatures. Most of the existing ghostware detection tools exploit the imperfection of today’s file-hiding implementations. Although such tools are necessary for combating today’s ghostware, they may essentially provide testing resources to help the evolution towards perfect ghostware. In contrast, the Strider GhostBuster targets the fundamental weakness of the file-hiding behavior and turns the problem into its own solution [WVR+04]. The basic idea is very simple: since the hidden files are visible before the ghostware is started and become invisible after that, a diff of the two file-system scans before and after should precisely capture all
Real-Time Regularized Ultrasound Elastography (2010)

This paper introduces two real-time elastography techniques based on analytic minimization (AM) of regularized cost functions. The first method (1D AM) produces axial strain and integer lateral displacement, while the second method (2D AM) produces both axial and lateral strains. The cost functions incorporate similarity of radio-frequency (RF) data intensity and displacement continuity, making both AM methods robust to small decorrelations present throughout the image. We also exploit techniques from robust statistics to make the methods resistant to large local decorrelations. We further introduce Kalman filtering for calculating the strain field from the displacement field given by the AM methods. Simulation and phantom experiments show that both methods generate strain images with high SNR, CNR and resolution. Both methods work for strains as high as 10% and run in real-time. We also present in vivo patient trials of ablation monitoring. An implementation of the 2D AM method as well as phantom and clinical RF-data can be downloaded.
Contributions of Fasting and Postprandial Plasma Glucose Increments to the Overall Diurnal Hyperglycemia of Type 2 Diabetic Patients (2003)

The relative contribution of postprandial glucose excursions is predominant in fairly controlled patients, whereas the contribution of fasting hyperglycemia increases gradually with diabetes worsening. These results could therefore provide a unifying explanation for the discrepancies as observed in previous studies.
Nitazoxanide vs. probiotics for the treatment of acute rotavirus diarrhea in children: a randomized, single-blind, controlled trial in Bolivian children (2008)

Treatment with nitazoxanide and probiotics is effective in the management of children with acute rotavirus diarrhea. Small differences in favor of nitazoxanide were found in comparison with probiotics. Nitazoxanide is an important treatment option for rotavirus diarrhea.
RNA-associated autoantigens activate B cells by combined B cell antigen receptor/Toll-like receptor 7 engagement (2005)

Previous studies (Leadbetter, E.A., I.R. Rifkin, A.H. Hohlbaum, B. Beaudette, M.J. Shlomchik, and A. Marshak-Rothstein. 2002. Nature. 416:603-607; Viglianti, G.A., C.M. Lau, T.M. Hanley, B.A. Miko, M.J. Shlomchik, and A. Marshak-Rothstein. 2003. Immunity. 19:837-847) established the unique capacity of DNA and DNA-associated autoantigens to activate autoreactive B cells via sequential engagement of the B cell antigen receptor (BCR) and Toll-like receptor (TLR) 9. We demonstrate that this two-receptor paradigm can be extended to the BCR/TLR7 activation of autoreactive B cells by RNA and RNA-associated autoantigens. These data implicate TLR recognition of endogenous ligands in the response to both DNA- and RNA-associated autoantigens. Importantly, the response to RNA-associated autoantigens was markedly enhanced by IFN-alpha, a cytokine strongly linked to disease progression in patients with systemic lupus erythematosus (SLE). As further evidence that TLRs play a key role in autoantibody responses in SLE, we found that autoimmune-prone mice, lacking the TLR adaptor protein MyD88, had markedly reduced chromatin, Sm, and rheumatoid factor autoantibody titers.
Detection of Ki-ras mutations in tissue and plasma samples of patients with pancreatic cancer using PNA-mediated PCR clamping and hybridisation probes (2005)

In the present study, we combined the PCR-clamping approach with melting curve analysis using mutant specific hybridisation probes and wild-type specific peptide nucleic acids (PNAs) to determine the genotypes of the most frequent point mutation in codon 12 of the proto-oncogene Ki-ras in tissue and plasma samples of patients with pancreatic cancer. The sensitivity of our assay was 1-5 x 10(-5). The melting curve analysis of tissue samples of four patients revealed two valine mutations, one none-valine mutation and one wild-type sequence. Ki-ras alterations were found in 28% of DNAs (18 out of 64) of nonrelated plasma samples of 10 patients with ductal adenocarcinoma of the pancreas. The valine mutation was the predominantly detected gene alteration (83%). Out of ten patients investigated, four patients (40%) became positive during clinical observation with respect to Ki-ras mutation. All four patients exhibited progressive disease and high levels of tumour marker CA 19-9. In conclusion, the one-step procedure discribed may be a useful clinical tool for analysing Ki-ras point mutations in tissue and plasmas samples. In addition, this method can be adapted for simultanous detection of multiple mutations and quantitation.