gebhart/patrepeval huggingface dataset:
Platelet-activating factor and anti-platelet-aggregating factor in acute reduction of blood pressure following percutaneous transluminal renal angioplasty in patients with renovascular hypertension. (1988)

The mechanism of the acute fall of BP following percutaneous transluminal renal angioplasty (PTRA) was studied in four patients with renovascular hypertension caused by fibromuscular dysplasia. One hour after PTRA, systemic blood pressure and plasma renin activity in the ipsilateral renal venous blood decreased significantly (P less than 0.05), but the plasma noradrenaline level in ipsilateral renal venous blood increased significantly (P less than 0.05). At the same time, a platelet-activating factor (PAF) and an unidentified factor that inhibited the aggregation of rabbit platelets induced by PAF, arachidonic acid or ADP were detected in the ipsilateral renal venous blood, but were not found in the contralateral renal venous blood. Plasma noradrenaline level in cubital venous blood decreased significantly (P less than 0.05) after 24 hours as compared with that before PTRA and BP also maintained the normal level. These results suggest that the reduction in plasma renin activity is associated with the acute reduction in BP following PTRA. PAF and an unidentified factor blocking the aggregation of platelets may be involved in ipsilateral renal venous blood following PTRA in patients with renovascular hypertension. The reduction in plasma noradrenaline level is an additional mechanism involved in maintaining normal BP following PTRA in the late stage.
Selective Production of Single-Wall Carbon Nanohorn Aggregates and Their Formation Mechanism (2002)

Single-wall carbon nanohorn (SWNH) aggregates can be produced by CO2 laser vaporization of carbon, and a single aggregate can take either a “dahlia-like” or “bud-like” form. We found that “dahlia-like” SWNH aggregates were produced with a yield of 95% when Ar at 760 Torr was used as the buffer gas, while “bud-like” SWNH aggregates were formed with a yield of 70 or 80% when either He or N2 at 760 Torr was used. The internal structures of both aggregates were studied by partially burning them in an O2 atmosphere. We were then able to examine the mechanism for the formation of SWNH aggregates.
Relations between approved platinum drugs and non-coding RNAs in mesothelioma (2018)

Malignant mesothelioma diseases feature an increasing risk due to their severe forms and their association with asbestos exposure. Platinum(II) complexes such as cisplatin and carboplatin are clinically approved for the therapy of mesothelioma often in combination with antimetabolites such as pemetrexed or gemcitabine. It was observed that pathogenic properties of mesothelioma cells and the response of mesothelioma tumors towards platinum-based drugs are strongly influenced by non-coding RNAs, in particular, by small microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). These non-coding RNAs controlled drug sensitivity and the development of tumor resistance towards platinum drugs. An overview of the interactions between platinum drugs and non-coding RNAs is given and the influence of non-coding RNAs on platinum drug efficacy in mesothelioma is discussed. Suitable non-coding RNA-modulating agents with potentially beneficial effects on cisplatin treatment of mesothelioma diseases are mentioned. The understanding of mesothelioma diseases concerning the interactions of non-coding RNAs and platinum drugs will optimize existing therapy schemes and pave the way to new treatment options in future.
Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs (2020)

Human induced pluripotent stem cells (hiPSCs) are a powerful model of neural differentiation and maturation. We present a hiPSC transcriptomics resource on corticogenesis from 5 iPSC donor and 13 subclonal lines across 9 time points over 5 broad conditions: self-renewal, early neuronal differentiation, neural precursor cells (NPCs), assembled rosettes, and differentiated neuronal cells. We identify widespread changes in the expression of both individual features and global patterns of transcription. We next demonstrate that co-culturing human NPCs with rodent astrocytes results in mutually synergistic maturation, and that cell type-specific expression data can be extracted using only sequencing read alignments without cell sorting. We lastly adapt a previously generated RNA deconvolution approach to single-cell expression data to estimate the relative neuronal maturity of iPSC-derived neuronal cultures and human brain tissue. Using many public datasets, we demonstrate neuronal cultures are maturationally heterogeneous but contain subsets of neurons more mature than previously observed.
Frequency Tuning and Chirping of a Pulsed CO2Laser by an Intracavity Prism (1989)

Abstract Based on results of TEA-CO2 laser-frequency tuning by an intracavity dispersive prism, the feasibility of CO2 laser-frequency chirping by a nonlinear intracavity prism or due to self-bending effects is discussed. The proposed scheme is shown to be superior to other nonlinear optics methods for CO2 laser-frequency chirping.
Catheter simulation system CathI: from patient data generation to cardiological training systems. (2004)

In this paper we discuss a new approach to generate 3D models for a simulation system for training an angioplasty. The underlying data for these models are obtained from angiograms that are captured during routine interventions in cardiology. For the extraction of the arteries we use a non-linear classificatory with features based on vesselness information (using a scale-space approach), the gray value, and motion information of the arteries. As result we can correctly find 80% of the arteries in the image and we have 4% pixels incorrectly classified as arteries. These models serve for a virtual catheter laboratory that is based on original instruments like catheters, wires, control instruments for the X-ray, syringes, and pressure pumps for the balloon catheter but instead of a patient an input instrument is used. This instrument sends positional and pressure data to a PC that simulates the patient. The cardiologist then obtains the visual and haptic feedback as if we operated a real patient.
An EMI-Immune PAM-4 Transmitter With Input Level Shifter in 130-nm BiCMOS Technology (2021)

This work presents a design of an electromagnetic interference (EMI)-immune pulse amplitude modulation-4 (PAM-4) transmitter. The traditional PAM-4 transmitters are prone to failing in the presence of EMI, which is experimentally verified. The proposed PAM-4 shows superior performance over the traditional PAM-4 transmitter, in the presence of EMI, by using an Input Level Shifter (ILS). ILS minimises the effect of EMI on a PAM-4 signal by reducing the input common-mode level of the transmitter and renders it compatible with the previous logic state. The proposed PAM-4 transmitter is fabricated in 130-nm BiCMOS technology with a chip area of 580 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{m}\,\,\times $ </tex-math></inline-formula> 915 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> . EMI-immunity measurements are aligned with the IEC 62132-2 standard by using a transverse electromagnetic (TEM) cell for radiated EMI-immunity. In the presence of a wide range of EMIs, the proposed PAM-4 transmitter operates at a data rate of 6.5 Gbps and maintains the minimum required eye-opening of 70 mV as per the standard IEEE 802.2bs. The proposed EMI-immune transmitter can withstand EMI powers of 0–16 dBm in frequencies ranging from 1 MHz to 1.5 GHz.
Sorbent Extraction of Pb(II), Cu(II), Ni(II), and Fe(III) Ions as 2-(5-Bromo-2-Pyridylazo)-5-Diethylamino-Phenol Chelates on Single-Walled Carbon Nanotube Disks Prior to Their Flame Atomic Absorption Spectrometric Determinations in Animal Feeds and Natural Water Samples (2012)

A sorbent extraction procedure for Pb(II), Cu(II), Ni(II), and Fe(III) ions on single-walled carbon nanotube disks has been established. Analyte ions were converted to 2-(5-bromo-2-pyridylazo)-5-diethylamino-phenol chelates, then adsorbed on the disk. Adsorbed chelates were easily desorbed from the disk by using 10 mL 2 M HNO3. The various analytical parameters, including pH and reagent amounts that were effective for the recoveries of the analytes on nanotube disks, were optimized. The influence of matrix ions was also studied. The LOD values based on 3sigma were in the 0.3-4.6 microg/L range. Validation of the proposed SPE procedure was carried out by the determination of analytes in certified reference materials (TMDA-54.4 fortified lake water and HR-1 Humber River sediment). Spiking and recovery experiments for the analyte ions in real samples gave good results. Application of the procedure was illustrated by the determination of analyte contents in some animal feeds and water samples from Turkey.
Molecular Characterization of Esophageal Squamous Cell Carcinoma Using Quantitative Proteomics (2023)

Esophageal squamous cell carcinoma (ESCC) is a heterogeneous cancer associated with a poor prognosis in advanced stages. In India, it is the sixth most common cause of cancer-related mortality. In this study, we employed high-resolution mass spectrometry-based quantitative proteomics to characterize the differential protein expression pattern associated with ESCC. We identified several differentially expressed proteins including PDPN, TOP2A, POSTN and MMP2 that were overexpressed in ESCC. In addition, we identified downregulation of esophagus tissue-enriched proteins such as SLURP1, PADI1, CSTA, small proline-rich proteins such as SPRR3, SPRR2A, SPRR1A, KRT4, and KRT13, involved in squamous cell differentiation. We identified several overexpressed proteins mapped to the 3q24-29 chromosomal region, aligning with CNV alterations in this region reported in several published studies. Among these, we identified overexpression of SOX2, TP63, IGF2BP2 and RNF13 that are encoded by genes in the 3q26 region. Functional enrichment analysis revealed proteins involved in cell cycle pathways, DNA replication, spliceosome, and DNA repair pathways. We identified the overexpression of multiple proteins that play a major role in alleviating ER stress, including SYVN1 and SEL1L. The SYVN1/SEL1L complex is an essential part of the ER quality control machinery clearing misfolded proteins from the ER. SYVN1 is an E3 ubiquitin ligase that ubiquitinates ER-resident proteins. Interestingly, there are also other non-canonical substrates of SYVN1 which are known to play a crucial role in tumor progression. Thus, SYVN1 could be a potential therapeutic target in ESCC.
Probing the interactions between air bubbles and (bio)-interfaces at the molecular scale using FluidFM technology (2021)

International audience
Interaction of Cationic Antimicrobial Peptides with Model Membranes (2001)

A series of natural and synthetic cationic antimicrobial peptides from various structural classes, including alpha-helical, beta-sheet, extended, and cyclic, were examined for their ability to interact with model membranes, assessing penetration of phospholipid monolayers and induction of lipid flip-flop, membrane leakiness, and peptide translocation across the bilayer of large unilamellar liposomes, at a range of peptide/lipid ratios. All peptides were able to penetrate into monolayers made with negatively charged phospholipids, but only two interacted weakly with neutral lipids. Peptide-mediated lipid flip-flop generally occurred at peptide concentrations that were 3- to 5-fold lower than those causing leakage of calcein across the membrane, regardless of peptide structure. With the exception of two alpha-helical peptides V681(n) and V25(p,) the extent of peptide-induced calcein release from large unilamellar liposomes was generally low at peptide/lipid molar ratios below 1:50. Peptide translocation across bilayers was found to be higher for the beta-sheet peptide polyphemusin, intermediate for alpha-helical peptides, and low for extended peptides. Overall, whereas all studied cationic antimicrobial peptides interacted with membranes, they were quite heterogeneous in their impact on these membranes.
TNF: its potential as an antitumour agent. (1988)

Tumour Necrosis Factor (TNF) was discovered on the basis of its capability to induce necrosis of certain tumours in vivo. A brief overview is given of the pleiotropic effects of TNF on a variety of cells, either transformed cells or normal, diploid cells. Many transformed cells are killed by TNF, especially in the presence of interferon-gamma or inhibitors of transcription or translation. Various activities of TNF on normal cells have been studied, especially those on the endothelial system; these effects may be relevant to an understanding of its toxicity. TNF presumably acts by activation of phospholipase-A2. A number of genes are induced by TNF and, for example, many cells produce interleukin-6. The latter acts on B-cells, on T-cells, on bone marrow cells and, last but not least, on hepatocytes, which results in the synthesis of acute phase proteins. Although the toxicity of TNF, especially in the presence of interferon, limits its wide applicability, it can nevertheless lead to complete tumour curing in experimental animals. Reduction of its toxicity, e.g. by indomethacin treatment, opens new possibilities for TNF as an antitumour drug, alone or in combination with interferon.
Radioimmunotherapy (RIT) with 131l-L19SIP in solid cancers (SC) and lymphoproliferative diseases: Final results of the first human trial. (2010)

2523 Background: The extradomain B of fibronectin (EDBF) is a promising target for cancer therapies due to its selective expression in newly formed blood vessels of SC and lymphomas. L19 is a human recombinant antibody that selectively binds EDBF. This phase I study investigated the whole-body distribution, tumor localization, and RIT potential of 131I-L19SIP, which is the L19-small immunoprotein (SIP, variable regions of L19) linked to 131I. Methods: Patients (pts) underwent RIT after dosimetry, based on dual-head gamma-camera planar imaging, only with lesion/red marrow absorbed dose ratio ≥10. 131I-L19SIP doses were diagnostic 5 mCi or RIT 3.7 GBq (100 mCi; n=16) or 5.5 GBq (150 mCi; n=10). Response and toxicity were assessed by RECIST and CTC-AE. Results: Fifty-one pts have been treated: 39 SC, 12 hematologic malignancies (HEM), median age 59 yrs (range 23-82), ECOG PS 0/1 74.5%/23.5%, ≥3 prior regimens in 35% of SC pts, 92% of HEM pts; peripheral blood stem cell transplant in 75% of HEM pts. The mono-exponential blood elimination profile of 131I-L19SIP gave a T1/2 ∼ 10 h, with low inter-patient variability. Median absorbed doses to healthy organs were within the safety threshold TD5/5 with maximum doses 50/5 in all pts. Approximately half of pts received RIT (20 SC, 6 HEM). Only hematologic toxicities were observed: grade 3-4 thrombocytopenia in 30% and 66% of SC and HEM pts, respectively (median duration 12 d; range 1- 56); platelet transfusion required in 4 pts; grade 4 neutropenia in 4 pts (>7 d, 2 pts). Imaging showed 131I-L19SIP selectively localized to tumor lesions and revealed lesions undetected by MRI or CT in some patients. In pts with Hodgkin's lymphoma (HL), 3/6 maintained partial responses for 5.3, >5.5, and 14 m, with complete disappearance of 21/25 and 6/11 lesions after repeated RIT in 2 pts, 1 of whom with a completely negative FDG-PET-CT. Also, 6 SC pts experienced disease stabilization sustained in 3 cases by repeated RIT (mesothelioma in 2 pts, thymoma in 1 pt). Conclusions: RIT with up to 5.5 GBq 131I-L19SIP is feasible and safe in SC and HEM, inducing sustained responses in 50% of treated HL pts and confirming EDBF as a promising neoangiogenic target for antibody-based therapies. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Bayer Shering Pharma, Philogen Bayer Onix, Philogen Bayer Schering Pharma, Philogen Philogen SpA
DNA Sequencing by Capillary Array Electrophoresis (2003)

On May 9,1998, PE Biosystems announced that they would introduce a new instrument based on “breakthrough DNA analysis technology” (1). Over 700 orders for the new sequencer were received in the first 5 mo of production, which make this instrument one of the most successful new products in the history of analytical instrumentation. This new instrument is based on capillary array electrophoresis (CAE) with a sheath-flow cuvet detector. This detection technology provides nearly 100% duty cycle, where every capillary is monitored simultaneously without the need for a scanning detector system. By use of this instrument, the Drosophila melanogaster sequence will be completed in less than 5 mo (2), and the sequence of the human genome will be substantially complete by the time that this book is in print.
A case of esophageal schwannoma treated by thoracoscopic enucleation (2012)

症例は63歳，女性．乳癌の術後経過観察中に胸部CTにて胸部上部食道に20mm大の腫瘤を指摘され，内視鏡検査にて胸部上部食道の粘膜下腫瘍と診断された．EUSガイド下のFNAにてS100陽性の腫瘍細胞を認めた．FDG-PETでは，腫瘍に一致してSUV max 5.28の異常集積を認めた．その後のCTにて腫瘍径25mmと増大傾向を認めたため，食道神経鞘腫の診断のもとに胸腔鏡下核出術を施行した．切除標本では腫瘍径は30×22×24mm，割面は黄白色調を呈していた．H.E. 染色では楕円形の核を有する紡錘形細胞が柵状かつ縦横に錯綜しながら増殖し，免疫染色にてvimentin(+)，S100(+)，α-SMA(-)，KIT(-)，CD34(-)の結果を得て，神経鞘腫と診断した．本邦における胸部食道の神経鞘腫の報告34例の臨床病理学的因子を，平滑筋腫のそれと比較した考察とともに報告する．
Synthesis of a new family of acyclic nucleoside phosphonates, analogues of TPases transition states (2012)

A 6-step procedure was developed for the synthesis of a new family of acyclic nucleoside phosphonates (ANPs), "PHEEPA" [(2-pyrimidinyl-2-(2-hydroxyethoxy)ethyl)phosphonic acids] in overall yields ranging from 4.5% to 32%. These compounds, which possess on one side a hydroxy function and on the other side a phosphonate group, can be considered either as potential antiviral agents or as transition state analogues of nucleoside phosphorylases such as thymidine phosphorylase.
Full Frequency Reuse Multibeam SatComs: Frame Based Precoding and User Scheduling (2014)

peer reviewed
ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions (2018)

Numerous in vitro studies have yielded a refined picture of the structural and molecular associations between Cyclic-AMP receptor protein (Crp), the DNA motif, and RNA polymerase (RNAP) holoenzyme. In this study, high-resolution ChIP-exonuclease (ChIP-exo) was applied to study Crp binding in vivo and at genome-scale. Surprisingly, Crp was found to provide little to no protection of the DNA motif under activating conditions. Instead, Crp demonstrated binding patterns that closely resembled those generated by σ70. The binding patterns of both Crp and σ70 are indicative of RNAP holoenzyme DNA footprinting profiles associated with stages during transcription initiation that occur post-recruitment. This is marked by a pronounced advancement of the template strand footprint profile to the +20 position relative to the transcription start site and a multimodal distribution on the nontemplate strand. This trend was also observed in the familial transcription factor, Fnr, but full protection of the motif was seen in the repressor ArcA. Given the time-scale of ChIP studies and that the rate-limiting step in transcription initiation is typically post recruitment, we propose a hypothesis where Crp is absent from the DNA motif but remains associated with RNAP holoenzyme post-recruitment during transcription initiation. The release of Crp from the DNA motif may be a result of energetic changes that occur as RNAP holoenzyme traverses the various stable intermediates towards elongation complex formation.
Supplementary Legends for Supplementary Figures S1-S4 from Exploring the Biomechanical Properties of Brain Malignancies and Their Pathologic Determinants <i>In Vivo</i> with Magnetic Resonance Elastography (2023)

&lt;p&gt;Supplementary Legends for Supplementary Figures S1-S4.&lt;/p&gt;
Organization of the gene encoding common acute lymphoblastic leukemia antigen (neutral endopeptidase 24.11): multiple miniexons and separate 5' untranslated regions. (1989)

The common acute lymphoblastic leukemia antigen (CALLA) is a 749-amino acid type II integral membrane protein that has been identified recently as the neutral endopeptidase 24.11 [NEP (EC 3.4.24.11)]. Herein, we characterize the organization of the human CALLA/NEP gene and show that it spans more than 80 kilobases (kb) and is composed of 24 exons. Exons 1 and 2 encode 5' untranslated sequences; exon 3 [170 base pairs (bp)] encodes the initiation codon and transmembrane and cytoplasmic domain; 20 short exons (exons 4-23), ranging in size from 36 to 162 bp, encode most of the extracellular portion of the enzyme; and exon 24 (approximately 3400 bp) encodes the COOH-terminal 32 amino acids of the protein and contains the entire 3' untranslated region (UTR). Of note, the pentapeptide sequence (His-Glu-Ile-Thr-His) associated with metalloprotease zinc binding and substrate catalysis is encoded within a single exon (exon 19). Three types of CALLA/NEP cDNAs have been identified: these clones contain 5' UTR sequences differing from one another upstream of exon 3. These human 5' sequences are homologous to those found in rat brain and rabbit kidney NEP cDNAs. The three human CALLA cDNA types result from alternative splicing of exons 1, 2a, or 2b to the common exon 3. Moreover, exons 2a and 2b share the same 5' sequence but differ from each other by the use of two distinct donor splice sites 171 bp apart in the gene. The substantial conservation of 5' untranslated sequences among species and the existence of 5' alternative splicing suggest that CALLA gene expression may be differentially controlled in a tissue-specific and/or developmentally regulated fashion.
Preparation of saturated and unsaturated fatty acid hydrazides and long chain C-glycoside ketohydrazones (2010)

A method is described to prepare both saturated and unsaturated fatty acid acyl hydrazides using a lipase as a catalyst. Hydrazides were generated from fatty acid methyl esters as well as directly from vegetable oils, and an organic co-solvent was not needed to maintain the integrity of the unsaturated fatty acids. Both C. antarctica lipase immobilized on acrylic resin and immobilized M. miehei lipase were used to catalyze the reaction, and they provided the desired acyl hydrazides with similar yields of 82.8% and 84.6%, respectively. Analysis of the products by MALDI-TOF-MS and GC-MS fragmentation pathways shows pure products free of starting methyl esters or triacylglycerols. These hydrazide molecules have been used, in conjunction with carbohydrate C-glycoside ketones, to prepare long chain C-glycoside ketohydrazones. This preparation does not require protecting groups or anomeric activation, and various C-glycoside ketohydrazones that retain the closed ring conformation of the parent sugars are described. These compounds have potential as renewable, sugar-based detergents in which the sugar moiety serves as the polar head group while the hydrazide alkyl chain is the non-polar component.