gebhart/patrepeval huggingface dataset:
Single Cell Transcriptional Signatures of the Human Placenta in Term and Preterm Parturition (2019)

Abstract More than 135 million births occur each year; yet, the molecular underpinnings of human parturition in gestational tissues, and in particular the placenta, are still poorly understood. The placenta is a complex heterogeneous organ including cells of both maternal and fetal origin, and insults that disrupt the maternal-fetal dialogue could result in adverse pregnancy outcomes such as preterm birth. There is limited knowledge of the cell type composition and transcriptional activity of the placenta and its compartments during physiologic and pathologic parturition. To fill this knowledge gap, we used scRNA-seq to profile the placental villous tree, basal plate, and chorioamniotic membranes of women with or without labor at term and those with preterm labor. Significant differences in cell type composition and transcriptional profiles were found among placental compartments and across study groups. For the first time, two cell types were identified: 1) lymphatic endothelial decidual cells in the chorioamniotic membranes, and 2) non-proliferative interstitial cytotrophoblasts in the placental villi. Maternal macrophages from the chorioamniotic membranes displayed the largest differences in gene expression (e.g. NFKB1) in both processes of labor; yet, specific gene expression changes were also detected in preterm labor. Importantly, several placental scRNA-seq transcriptional signatures were modulated with advancing gestation in the maternal circulation, and specific immune cell type signatures were increased with labor at term (NK-cell and activated T-cell) and with preterm labor (macrophage, monocyte, and activated T-cell). Herein, we provide a catalogue of cell types and transcriptional profiles in the human placenta, shedding light on the molecular underpinnings and non-invasive prediction of the physiologic and pathologic parturition. One sentence summary The common molecular pathway of parturition for both term and preterm spontaneous labor is characterized using single cell gene expression analysis of the human placenta.
MUC13 EXPRESSION AND ITS IN VITRO FUNCTIONS IN OVARIAN CANCER (2007)

Mucins are attractive targets for cancer diagnosis. MUC13 is a recently identified mucin and is suggested to be over-expressed in ovarian cancer. We analyzed the expression profile and function of MUC13 to determine its role in ovarian cancer. A monoclonal antibody (clone PPZ0020) was used to determine the expression profile of MUC13 by immunohistochemistry, using an ovarian tissue microarray slide containing normal and cancerous samples. Additionally, MUC13 expression was also analyzed in 55 clinically proven ovarian tissue cancer samples. For functional analysis, a full-length MUC13 was exogenously expressed in a MUC13 null ovarian cancer cell line SKOV-3 and evaluated by means of cell proliferation and migration assays. Paired student t-tests were preformed for statistical analysis. MUC13 expression was undetectable in normal and benign ovarian samples and was significantly (p<0.005) higher in cancer samples. MUC13 expression was most frequent in mucinous types of ovarian cancer samples. Additionally, in functional studies the exogenous expression of MUC13 in SKOV-3 ovarian cancer cells increased cellular migration, cell proliferation, and the number of cells in S-phase of cell cycle. Furthermore, MUC13 expression reduced cell to cell aggregation. These results indicate that MUC13 is aberrantly expressed in ovarian cancer and may have a role in ovarian cancer pathogenesis.
Efficacy of Therapy with Bortezomib in Solid Tumors: A Review based on 32 Clinical Trials (2014)

The ubiquitin-proteasome system is a major pathway for protein degradation, so that proteasome is now considered as an important target for drug discovery. Bortezomib, the first US FDA-approved proteasome inhibitor now used as a front-line treatment for multiple myeloma. To better understand the effects of bortezomib in cancer treatment, we carried out a review based on 32 published clinical trials to determine whether bortezomib will benefit patients with solid tumors. Information of complete response, partial response, stable disease and objective response rate was collected to assess clinical outcomes. A lack of therapeutic effects was observed when bortezomib was used as a single agent. Meanwhile, when bortezomib treatment was combined with other agents, bortezomib offered no statistically significant response versus these agents alone. High-quality studies are required to better understand the clinically effects of bortezomib and the development of a new generation of proteasome inhibitors is absolutely necessary.
Optisch aktive Übergangsmetall-Komplexe, XLIII. (—)578-C5H5Mn(NO)(COC6H5)PN. Darstellung, Epimerisierung und Stereochemie des Ligandenaustauschs. (1976)

In the reaction of [C 5 H 5 Mn(NO)(CO)PN*]PF 6 (1) with LiC 6 H 5 5-exo-C 6 H 5 C 5 H 5 Mn(NO)-(CO)PN* (2) and C 5 H 5 Mn(NO)(COC 6 H 5 )PN* (3) are formed. If the reaction is carried out with optically active starting material 1 the optically active ring addition and benzoyl compounds 2 and 8 resp., are obtained. Whereas the ring addition product 2 is configurationally stable, the benzoyl complex 3 in solution epimerizes according to 1 st order kinetics. The change of configuration at the Mn atom occurs by PN* dissociation with formation of a chiral intermediate. This is demonstrated by the fact that exchange of PN* in (-) 578 -C 5 H 5 Mn(NO)(COC 6 H 5 )PN* (1a) with P(OC 2 H 5 ) 3 gives (+) 578 -C 5 H 5 Mn(NO)-(COC 6 H 5 )P(OC 2 H 5 ) 3 (4a), a reaction proceeding with retention of configuration at the metal atom
Activities of a Nitrofurazone-Containing Urinary Catheter and a Silver Hydrogel Catheter against Multidrug-Resistant Bacteria Characteristic of Catheter-Associated Urinary Tract Infection (1999)

The in vitro inhibitory activity of a nitrofurazone-coated urinary catheter (NFC) against 86 recently obtained susceptible and multidrug-resistant (MDR) clinical isolates of Escherichia coli, Klebsiella pneumoniae, Citrobacter freundii, Staphylococcus aureus, coagulase-negative staphylococci, and Enterococcus faecium, which are species implicated in catheter-associated urinary tract infection and which traditionally have been susceptible to nitrofuran derivatives, was determined using an agar diffusion assay. In a subset of these strains, the activity of the NFC was compared with that of a silver hydrogel urinary catheter (SHC), and the durability of each catheter's inhibitory activity was assessed during serial daily transfers of catheter segments to fresh culture plates. Except for vancomycin-resistant E. faecium, the NFC was active against all isolates tested and showed comparable inhibition zones with susceptible and MDR strains of each species. In contrast, the SHC inhibited only certain staphylococci (P < 0.01 versus the NFC), and among these strains, the SHC produced smaller inhibition zones than did the NFC (P < 0.01). Inhibition was evident for up to 5 days with the NFC, but for only 1 day (if at all) with the SHC (P < 0.01). These data document that, for most genera which traditionally have been susceptible to nitrofuran derivatives, the NFC remains active against contemporary MDR isolates. They also demonstrate that the in vitro antibacterial activity of the NFC is markedly superior to that of the SHC in several respects. Thus, the NFC shows promise for clinical use in the current era of MDR bacteria.
Exploring the Potential of a Genome-Reduced Escherichia coli Strain for Plasmid DNA Production (2023)

The global demand for nucleic acid-based vaccines, including plasmid DNA (pDNA) and mRNA vaccines, needs efficient production platforms. However, conventional hosts for plasmid production have encountered challenges related to sequence integrity due to the presence of insertion sequences (ISs). In this study, we explored the potential of a genome-reduced <i>Escherichia coli</i> as a host for pDNA production. This strain had been constructed by removing approximately 23% of the genome which were unessential genes, including the genomic unstable elements. Moreover, the strain exhibits an elevated level of NADPH, a coenzyme known to increase plasmid production according to a mathematical model. We hypothesized that the combination of genome reduction and the abundance of NADPH would significantly enhance pDNA production capabilities. Remarkably, our results confirmed a three-fold increase in pDNA production compared to the widely employed DH5α strain. Furthermore, the genome-reduced strain exhibited heightened sensitivity to various antibiotics, bolstering its potential for large scale industrial pDNA production. These findings suggest the genome-reduced <i>E. coli</i> as an exciting candidate for revolutionizing the pDNA industry, offering unprecedented efficiency and productivity.
VHF Radio Interferometry of Lightning (1991)

Abstract Lightning discharges radiate strongly at radio frequencies, and studies of the radiation provide valuable information on lightning breakdown processes. Interferometric techniques can be used to locate the numerous radiation events as a function of time during a discharge and to generate images of the developing lightning channels inside a storm, where they are obscured from view at optical wavelengths.
Percutaneous left atrial appendage occlusion using different technologies in the United Kingdom: A multicenter registry (2016)

LAAO can be performed safely in a real world setting with good implant success rates and procedural outcomes. The long-term benefits of the procedure are reassuring in terms of both ischemic events and avoidance of severe bleeding associated with anticoagulation in this patient group. © 2016 Wiley Periodicals, Inc.
Generation and propagation of high-power parabolic pulses in optical fibers (2000)

Summary form only given.We have verified that high power parabolic pulses as generated in high gain, normal dispersion fiber amplifiers, can be propagated over substantial fiber lengths in the presence of large self-phase modulation. The self-similar propagation of parabolic pulses is invaluable for the design of future highly integrated ultrafast laser systems. Even now, parabolic pulses are central to the design of ultrahigh power ultrafast amplifiers and compressors based on cladding-pumped Yb fibers, which can produce femtosecond pulses with optical efficiencies larger than 70% at several watts of average power.
A Class of Risk Neutral Densities with Heavy Tails (2001)

From observed bid and ask prices of European call and put options we estimate the risk neutral density of a stock at some future time $t>0$. We restrict attention to a class of densities with heavy tails and use a Bayesian formulation in order to study the variation in the distributions fitting the data. Heavy tails are here meant in the intuitive sense of being heavier than the tails of a normal distribution. From the fitted risk neutral density we also consider the inverse problem of finding the volatility in a diffusion model for the price process. Finally, we apply our methods to data on the S&P 500 index.
COVID-Net CXR-S: Deep Convolutional Neural Network for Severity Assessment of COVID-19 Cases from Chest X-ray Images (2021)

Abstract The world is still struggling in controlling and containing the spread of the COVID-19 pandemic caused by the SARS-CoV-2 virus. The medical conditions associated with SARS-CoV-2 infections have resulted in a surge in the number of patients at clinics and hospitals, leading to a significantly increased strain on healthcare resources. As such, an important part of managing patients with SARS-CoV-2 infections within the clinical workflow is severity assessment, which is often conducted with the use of chest x-ray (CXR) images. In this work, we introduce COVID-Net CXR-S, a convolutional neural network for predicting the airspace severity of a SARS-CoV-2 positive patient based on a CXR image of the patient's chest. More specifically, we leveraged transfer learning to transfer representational knowledge gained from over 16,000 CXR images from a multinational cohort of over 15,000 patient cases into a custom network architecture for severity assessment. Experimental results with a multi-national patient cohort curated by the Radiological Society of North America (RSNA) RICORD initiative showed that the proposed COVID-Net CXR-S has potential to be a powerful tool for computer-aided severity assessment of CXR images of COVID-19 positive patients. Furthermore, radiologist validation on select cases by two board-certified radiologists with over 10 and 19 years of experience, respectively, showed consistency between radiologist interpretation and critical factors leveraged by COVID-Net CXR-S for severity assessment. While not a production-ready solution, the ultimate goal for the open source release of COVID-Net CXR-S is to act as a catalyst for clinical scientists, machine learning researchers, as well as citizen scientists to develop innovative new clinical decision support solutions for helping clinicians around the world manage the continuing pandemic.
Adeno-Associated Virus–Mediated Delivery of CRISPR–Cas Systems for Genome Engineering in Mammalian Cells (2016)

The CRISPR-Cas9 system has emerged as a highly versatile platform for introducing targeted genome modifications into mammalian cells and model organisms. However, fully capitalizing on the therapeutic potential for this system requires its safe and efficient delivery into relevant cell types. Adeno-associated virus (AAV) vectors are a clinically promising class of engineered gene-delivery vehicles capable of safely infecting a broad range of dividing and nondividing cell types, while also serving as a highly effective donor template for homology-directed repair. Together, CRISPR-Cas9 and AAV technologies have the potential to accelerate both basic research and clinical applications of genome engineering. Here, we present a step-by-step protocol for AAV-mediated delivery of CRISPR-Cas systems into mammalian cells. Procedures are given for the preparation of high-titer virus capable of achieving a diverse range of genetic modifications, including gene knockout and integration.
Amorphous PAF-1: Guiding the Rational Design of Ultraporous Materials (2014)

A number of topological structures for PAF-1 are compared with an amorphous structure for PAF-1, reproducing the ultrahigh surface area and pore volume observed experimentally. We compare the porosity properties of these structures and discuss potential structural strategies for increasing porosity and gas uptake properties. The PAF-1 network formation mechanism is simulated through use of an automated generation process, revealing the importance of the solvent in the resulting network structure and porosity properties. This opens up new rational design strategies and considerations for developing the next generation of porous framework materials.
Hypsarrhythmia (1997)

To determine the frequency and significance of the EEG features of hypsarrhythmia, we analyzed the pre-ACTH records of 53 consecutive patients with infantile spasms for the severity of the following abnormalities: disorganization of background, slowing, high amplitude, spike activity, and for the presence or absence of each of the following patterns and variants: electrodecremental discharges, absence of normal sleep activity, relative normalization, hemihypsarrhythmia, burst suppression (BS), occipital hypsarrhythmia, interhemispheric asymmetry, and interhemispheric synchronization. We calculated a total score indicating the severity of the hypsarrhythmia for each record. The hypsarrhythmia variant patterns occurred frequently in up to 69% of the records. Patients with cerebral dysgenesis were more likely to have hemihypsarrhythmia or BS pattern persistent throughout the EEG. Patients with history of perinatal hypoxia-ischemia were more likely to have absence of normal sleep activity. The occurrence of each of the other variant patterns did not correlate with etiology. Favorable outcome did not correlate with the occurrence, or absence, of any of the variant patterns but was associated with faster background activity (< 75% delta), a lower total hypsarrhythmia score (< or = 10), and with absence of electrodecremental discharges on the pre-ACTH EEG. We conclude that variant patterns of hypsarrhythmia are frequent, generally do not correlate with prognosis, and thus are best included within the definition of hypsarrhythmia. The severity of the hypsarrhythmia, however, does have significant prognostic implications.
Stabilization mechanism of electrodeposited silicon thin films (2014)

Amorphous composite silicon thin films electrodeposited in tetrahydrofuran, containing up to 80 at% of Si and exhibiting an homogeneous dispersions of O, C and Cl in the amorphous Si matrix, have been successfully stabilized against oxidation using a post-annealing step in inert atmosphere. In order to understand the impact of the annealing step on their stabilization against oxidation, their composition and structure have been investigated upon heat treatments. It has been shown that the presence of impurities such as O, C and Cl does not have any impact on the stabilization process, which is rather linked to the presence of hydrogen in the Si composites. This conclusion has been drawn after a detailed analysis of the bonding structure of films annealed at different temperatures and dwell times by the mean of Raman spectroscopy. It has been shown that annealing the as-deposited films at 350 °C for a couple of hours or at higher temperatures induced a hydrogen evolution, characterized by the breaking of Si-H bonds and the formation of Si-Si bonds, which stabilized the silicon network. The understanding and the reproducibility of this stabilization process of silicon thin film electrodeposited in organic solvent paves the way for their use for many applications.
MICROMECHANICAL MODEL FOR THERMAL ANALYSIS OF PARTICULATE AND FIBROUS COMPOSITES (1998)

Thermal stresses occur at the micromechanical level of a particle-/fiber-reinforced composite caused by the mismatch of coefficients of thermal expansion (CTE) of the constituent materials like the particle/fiber and the matrix binder. The stresses affect the service envelope of a composite structure when it is subject to an external load. Thus, this ankle presented a simplified, analytical, three-dimensional, micromechanical model so as to compute microthermal stresses occurring in the constituent materials as well as the effective CTE of a composite based on their materials properties. The analytical solutions for both particulate and fibrous composites were compared to the results obtained from finite element analyses as well as other results if available. The comparison of the effective CTEs and the microthermal stresses between the present solutions and the finite element results showed an excellent agreement. In addition, a parametric study was conducted in order to determine the effects of each parameter of the constituent materials on the effective CTE, microthermal stresses, and the solution errors. The orthogonal array technique used in the Taguchi method was adopted for the parametric study.
Synergistic interaction of the two paralogous Arabidopsis genes LRX1 and LRX2 in cell wall formation during root hair development (2003)

LRR-extensins (LRX) form a family of structural cell wall proteins containing a receptor-like domain. The functional analysis of Arabidopsis LRX1 has shown that it is involved in cell morphogenesis of root hairs. In this work, we have studied LRX2, a paralog of LRX1. LRX2 expression is mainly found in roots and is responsive to factors promoting or repressing root hair formation. The function of LRX1 and LRX2 was tested by the expression of a truncated LRX2 and different LRX1/LRX2 chimaeric proteins. Using complementation of the lrx1 phenotype as the parameter for protein function, our experiments indicate that LRX1 and LRX2 are functionally similar but show differences in their activity. Genetic analysis revealed that single lrx2 mutants do not show any defect in root hair morphogenesis, but synergistically interact with the lrx1 mutation. lrx1/lrx2 double mutants have a significantly enhanced lrx1 phenotype, resulting in frequent rupture of the root hairs soon after their initiation. Analysis of the root hair cell wall ultrastructure by transmission electron microscopy (TEM) revealed the formation of osmophilic aggregates within the wall, as well as local disintegration of the wall structure in the double mutant, but not in wild-type plants. Our results indicate that LRX1 and LRX2 have overlapping functions in root hair formation, and that they likely regulate cell morphogenesis by promoting proper development of the cell wall.
Dose‐dependent bioavailability indicators for curcumin and two of its novel derivatives (2013)

Novel water-soluble curcumin derivatives have been developed to overcome low in vivo bioavailability of curcumin. The aim of this work is to assess the potential utility of certain downstream targets as bioavailability indicators of systemic activity of pure curcumin and two novel water-soluble curcumin derivatives (NCD) by constructing dose-dependent response curves and to prove whether this novel curcumin derivatives retained, improved, or abolished biological activity of pure curcumin when applied in vivo. Pure curcumin (CUR), curcumin-carboxy derivative (NCD-1), and curcumin protein conjugate (NCD-2) were administered orally to rats at escalating doses: 37, 74, 148, and 296 μM/kg body weight, respectively. Plasma levels of GST activity, cavernous tissue levels of cGMP, and enzymatic activity of both HO-1 and GST were assessed one and half and 24 hours after oral administration of curcumin formulae. This study showed that there was a progressive elevation of cavernous tissue levels of cGMP and enzymatic activity of both HO-1 and GST in a dose-dependent manner that was maintained for 24 h with CUR, NCD-1, and NCD-2. Plasma GST activity was decreased by the lowest doses on the curve. The three dose-dependent bioavailability indicators as surrogates of curcumin and two of its novel derivatives are valid in the studied range of concentration and extended time. The novel curcumin derivatives still conserve with improvement the biological activity of natural curcumin when applied in vivo.
An Electronic Current Transformer Based on Rogowski Coil (2008)

In the industrial world the quality of the electric power is becoming very critical. In order to verify this requirement, new measurement systems should be installed at various levels of the power network, capable to measure over a wide frequency range the current and voltage harmonics with a proper accuracy. When high voltage power systems are taken into account, this requirement is very difficult to achieve using traditional measurement devices, mainly due to the bandwidth limitations of this kind of transducers. For this reason in the last years several research activity have been especially focused on the study and the development of new measurement systems for high-voltage networks. In particular, in this paper a current transformer based on Rogowski coils for high voltage systems is presented, fulfilling the features required for power quality analysis. The adopted transformer architecture, which is based on digital processing techniques, permits to overcome the typical problem concerning the use of Rogowski coils as current transducer.