gebhart/patrepeval huggingface dataset:
1A2-O03 A Study on an Exoskeletal Microarm (2007)

This paper reports the design and fabrication process of an exoskeletal microarm. The research of the microarm is part of a new concept of endoscopes designed for endoscopic submucosal dissection (ESD) operation. This novel ESD endoscope has two suction grippers to hold the lesion skin, and a cautery knife to cut. The grippers and cautery knife need to be manipulated at the end of the endoscope, thus a powerful yet small arm is needed. We focused on the shape memory alloy (SMA) for its high work output unit volume and its high power/mass ratio. However, the previously researched SMA actuated microarm bends by deforming its entire body. This mechanism makes it difficult to calculate the position of its end tip, necessary for the control of the grippers and the knife. Here, we propose an exoskeletal microarm. Polydimethylsiloxane (PDMS) elastomer is used to fabricate the microarm using a photolithography technique. The microarm is coated with hardening epoxy polymer, leaving only the joint part of the microarm uncoated. By placing an angle sensor at the joint, we are able to calculate the position of the microarm end. Selection and placement of the angle sensor and other parts of the new ESD endoscope is to be studied in the future.
Abstract 4534: Theory and methodology for the design and analysis of PDX mouse clinical trials (2017)

Abstract Patient-derived xenograft (PDX) is a well-accepted experimental cancer model mimicking original patients in histo- &amp; molecular pathology, as well as drug response. Mouse clinical trials (MCT) using PDX becomes increasingly prevalent in oncology research, yet the theory and methodology for trial design and analysis is underdeveloped. By analyzing tumor growths of 34081 PDX mice, we showed that majority of them can be satisfactorily modeled by exponential growth kinetics, based on which we derived a new drug response readout called the AUC ratio that is superior to the tumor growth inhibition (TGI) and its variants. We outlined a bootstrap algorithm to calculate its confidence interval, and showed that a 4:4 (4 mice in both treatment groups) or up design sharply increases measurement accuracy over the lesser design. Next, we introduce three approaches for drug evaluation and biomarker discovery in MCTs. In the end-point based analysis, we used a cohort of gastric PDXs to show a positive correlation between EGFR mRNA expression and cetuximab efficacy, in agreement with clinical trial results. We then used linear mixed models (LMMs) to describe MCTs as clustered longitudinal studies that capture the growth and drug response heterogeneities across PDXs and among mice within a PDX. Further, LMMs can separate prognostic and predictive biomarker effects, quantify response difference to a drug for multiple cancers, or efficacy difference of multiple drugs to a cohort of PDXs. Thirdly, we used additive frailty models to perform survival analysis on MCTs. We defined survival endpoints of PFS and OS in PDXs, and showed that hazard ratios can be more accurately estimated. We revealed an inherent connection between frailty and growth rate for PDXs. We performed computational simulations for the last two methods to show that statistical power improves tremendously with a 3:3 or up design. This work lays the foundation for rational design and analysis of PDX mouse clinical trials. Citation Format: Sheng Guo, Binchen Mao, Henry Q. Li. Theory and methodology for the design and analysis of PDX mouse clinical trials [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4534. doi:10.1158/1538-7445.AM2017-4534
Efficacy and Safety of Warfarin for the Treatment of Venous Thromboembolism　― A Multicenter Prospective Observational Cohort Study in Japan (AKAFUJI Study) ― (2023)

Warfarin therapy with an appropriate PT-INR according to Japanese guidelines is effective without increasing bleeding complications, regardless of patient characteristics.
Molecular Cytogenetic Characterization of a Critical Region in Bands 7q35-q36 Commonly Deleted in Malignant Myeloid Disorders (1998)

Abstract Loss of chromosome 7 (−7) or deletion of the long arm (7q−) are recurring chromosome abnormalities in myeloid leukemias. The association of −7/7q− with myeloid leukemia suggests that these regions contain novel tumor suppressor gene(s), whose loss of function contribute to leukemic transformation or tumor progression. Based on chromosome banding analysis, two critical regions have been identified, one in band q22 and another in bands q32-q35. Presently there are no data available on the molecular delineation of the distal critical region. In this study we analyzed bone marrow and blood samples from 13 patients with myeloid leukemia (de novo myelodysplastic syndrome [MDS] , n = 3; de novo acute myeloid leukemia [AML], n = 9; therapy-related (t-) AML, n = 1) which, on chromosome banding analysis, exhibited deletions (n = 12) or in one case a balanced translocation involving bands 7q31-qter using fluorescence in situ hybridization (FISH). As probes we used representative clones from a contig map of yeast artificial chromosome (YAC) clones that spans chromosome bands 7q31.1-qter. In the 12 cases with loss of 7q material, we identified a commonly deleted region of approximately 4 to 5 megabasepairs in size encompassing the distal part of 7q35 and the proximal part of 7q36. Furthermore, the breakpoint of the reciprocal translocation from the patient with t-AML was localized to a 1,300-kb sized YAC clone that maps to the proximal boundary of the commonly deleted region. Interestingly, in this case both homologs of chromosome 7 were affected: one was lost (−7) and the second exhibited the t(7q35). The identification and delineation of translocation and deletion breakpoints provides the first step toward the identification of the gene(s) involved in the pathogenesis of 7q35-q36 aberrations in myeloid disorders.
Electromagnetic active source sounding near the East Pacific Rise (1981)

An active source electrical conductivity sounding was carried out near the East Pacific Rise at 21°N. The average electrical conductivity from 2 km beneath the seafloor into the upper mantle was found to be about 0.004 S/m. There is no evidence of fully molten magma at a distance of 7 km from the spreading axis. The inferred conductivity with depth of the crustal rock is consistent with Brace’s model of connected, seawater filled pores in rocks heated from beneath.
Large‐scale extrusion processing and characterization of hybrid nylon‐6/SiO2nanocomposites (2004)

Abstract Solution impregnations, pulltrusion and film stacking are widely used methods to prepare thermoplastic composite materials. Extruders are used to melt the polymer and to incorporate fibers into the polymer in order to modify physical properties. In this article, the compounding of colloidal silica nanoparticles filled polyamide‐6 (PA‐6) is achieved using a twin‐screw extruder, which has a significant market share due to its low cost and easy maintenance. The experiments were performed at 250 rpm and the bulk throughput was 6 kg h −1 with a pump pressure of 30 bars. The composites were characterized with nuclear magnetic resonance (NMR), wide angle X‐ray diffraction (WAXD), differential scanning calorimetry (DSC) and transmission electron microscopy (TEM). As determined by WAXD, the PA‐6 showed higher amounts of γ ‐phase when compared to other synthesis methods such as in situ polymerization. TEM pictures showed that the silica particles aggregated nevertheless, upon addition of 14% (w/w) silica the E‐modulus increased from 2.7 to 3.9 GPa indicating that an effective mechanical coupling with the polymer was achieved. The behavior, illustrated with dynamic mechanical analysis (DMA) curves, indicated that in general when a filled system is compared to unfilled material, the values of the moduli (E′ and E″) increased and tan δ decreased. Determination of molecular mass distribution of the samples by means of size exclusion chromatography (SEC) coupled to a refractive index (RI), viscosity (DV) and light scattering (LS) detector revealed that the addition of silica did not decrease the average molecular weight of the polymer matrix, which is of importance for composite applications. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Barrier-to-Autointegration Factor 1 Protects against a Basal cGAS-STING Response (2020)

Although the pathogen recognition receptor pathways that activate cell-intrinsic antiviral responses are well delineated, less is known about how the host regulates this response to prevent sustained signaling and possible immune-mediated damage. Using a genome-wide CRISPR-Cas9 screening approach to identify host factors that modulate interferon-stimulated gene (ISG) expression, we identified the DNA binding protein Barrier-to-autointegration factor 1 (Banf1), a previously described inhibitor of retrovirus integration, as a modulator of basal cell-intrinsic immunity. Ablation of Banf1 by gene editing resulted in chromatin activation near host defense genes with associated increased expression of ISGs, including <i>Oas2</i>, <i>Rsad2</i> (viperin), <i>Ifit1</i>, and <i>ISG15</i> The phenotype in Banf1-deficient cells occurred through a cGAS-, STING-, and IRF3-dependent signaling axis, was associated with reduced infection of RNA and DNA viruses, and was reversed in Banf1 complemented cells. Confocal microscopy and biochemical studies revealed that a loss of Banf1 expression resulted in higher level of cytosolic double-stranded DNA at baseline. Our study identifies an undescribed role for Banf1 in regulating the levels of cytoplasmic DNA and cGAS-dependent ISG homeostasis and suggests possible therapeutic directions for promoting or inhibiting cell-intrinsic innate immune responses.<b>IMPORTANCE</b> Although the interferon (IFN) signaling pathway is a key host mechanism to restrict infection of a diverse range of viral pathogens, its unrestrained activity either at baseline or in the context of an immune response can result in host cell damage and injury. Here, we used a genome-wide CRISPR-Cas9 screen and identified the DNA binding protein Barrier-to-autointegration factor 1 (Banf1) as a modulator of basal cell-intrinsic immunity. A loss of Banf1 expression resulted in higher level of cytosolic double-stranded DNA at baseline, which triggered IFN-stimulated gene expression via a cGAS-STING-IRF3 axis that did not require type I IFN or STAT1 signaling. Our experiments define a regulatory network in which Banf1 limits basal inflammation by preventing self DNA accumulation in the cytosol.
Stimulated Innate Resistance of Lung Epithelium Protects Mice Broadly against Bacteria and Fungi (2009)

Pneumonia is a serious problem worldwide. We recently demonstrated that innate defense mechanisms of the lung are highly inducible against pneumococcal pneumonia. To determine the breadth of protection conferred by stimulation of lung mucosal innate immunity, and to identify cells and signaling pathways activated by this treatment, mice were treated with an aerosolized bacterial lysate, then challenged with lethal doses of bacterial and fungal pathogens. Mice were highly protected against a broad array of Gram-positive, Gram-negative, and class A bioterror bacterial pathogens, and the fungal pathogen, Aspergillus fumigatus. Protection was associated with rapid pathogen killing within the lungs, and this effect was recapitulated in vitro using a respiratory epithelial cell line. Gene expression analysis of lung tissue showed marked activation of NF-kappaB, type I and II IFN, and antifungal Card9-Bcl10-Malt1 pathways. Cytokines were the most strongly induced genes, but the inflammatory cytokines TNF and IL-6 were not required for protection. Lung-expressed antimicrobial peptides were also highly up-regulated. Taken together, stimulated innate resistance appears to occur through the activation of multiple host defense signaling pathways in lung epithelial cells, inducing rapid pathogen killing, and conferring broad protection against virulent bacterial and fungal pathogens. Augmentation of innate antimicrobial defenses of the lungs might have therapeutic value for protection of patients with neutropenia or impaired adaptive immunity against opportunistic pneumonia, and for defense of immunocompetent subjects against a bioterror threat or epidemic respiratory infection.
Bone Implant Interface (1994)

A comprehensive reference, this book provides an up-to-date study of the most widely used biomaterials in implant surgery. Practical and accessible, it provides theoretical and technical background essential for orthopaedic surgeons to meet the needs of arthroplasty successfully - specifically to relieve pain, provide motion with stability, and to correct deformity. It discusses biomaterials and prosthetic design as they pertain to specific physiological and medical situations. Emphasis is placed on longevity, stress and the overall success rate of implants, with an evaluation of prosthetic devices covering bone structure, anatomy, bioengineering, biomaterials, tribology and factors affecting successful implantation. The book is intended for orthopaedic surgeons, biomaterial scientists and bioengineers.
Microfluidic Gas Sensors: Detection Principle and Applications (2022)

With the rapid growth of emerging point-of-use (POU)/point-of-care (POC) detection technologies, miniaturized sensors for the real-time detection of gases and airborne pathogens have become essential to fight pollution, emerging contaminants, and pandemics. However, the low-cost development of miniaturized gas sensors without compromising selectivity, sensitivity, and response time remains challenging. Microfluidics is a promising technology that has been exploited for decades to overcome such limitations, making it an excellent candidate for POU/POC. However, microfluidic-based gas sensors remain a nascent field. In this review, the evolution of microfluidic gas sensors from basic electronic techniques to more advanced optical techniques such as surface-enhanced Raman spectroscopy to detect analytes is documented in detail. This paper focuses on the various detection methodologies used in microfluidic-based devices for detecting gases and airborne pathogens. Non-continuous microfluidic devices such as bubble/droplet-based microfluidics technology that have been employed to detect gases and airborne pathogens are also discussed. The selectivity, sensitivity, advantages/disadvantages vis-a-vis response time, and fabrication costs for all the microfluidic sensors are tabulated. The microfluidic sensors are grouped based on the target moiety, such as air pollutants such as carbon monoxide and nitrogen oxides, and airborne pathogens such as <i>E. coli</i> and SARS-CoV-2. The possible application scenarios for the various microfluidic devices are critically examined.
A distributed computational search strategy for the identification of diagnostics targets: Application to finding aptamer targets for methicillin-resistant staphylococci (2014)

The rapid and cost-effective identification of bacterial species is crucial, especially for clinical diagnosis and treatment. Peptide aptamers have been shown to be valuable for use as a component of novel, direct detection methods. These small peptides have a number of advantages over antibodies, including greater specificity and longer shelf life. These properties facilitate their use as the detector components of biosensor devices. However, the identification of suitable aptamer targets for particular groups of organisms is challenging. We present a semi-automated processing pipeline for the identification of candidate aptamer targets from whole bacterial genome sequences. The pipeline can be configured to search for protein sequence fragments that uniquely identify a set of strains of interest. The system is also capable of identifying additional organisms that may be of interest due to their possession of protein fragments in common with the initial set. Through the use of Cloud computing technology and distributed databases, our system is capable of scaling with the rapidly growing genome repositories, and consequently of keeping the resulting data sets up-to-date. The system described is also more generically applicable to the discovery of specific targets for other diagnostic approaches such as DNA probes, PCR primers and antibodies.
A male sterility-associated cytotoxic protein ORF288 in Brassica juncea causes aborted pollen development (2011)

Cytoplasmic male sterility (CMS) is a widespread phenomenon in higher plants, and several studies have established that this maternally inherited defect is often associated with a mitochondrial mutant. Approximately 10 chimeric genes have been identified as being associated with corresponding CMS systems in the family Brassicaceae, but there is little direct evidence that these genes cause male sterility. In this study, a novel chimeric gene (named orf288) was found to be located downstream of the atp6 gene and co-transcribed with this gene in the hau CMS sterile line. Western blotting analysis showed that this predicted open reading frame (ORF) was translated in the mitochondria of male-sterile plants. Furthermore, the growth of Escherichia coli was significantly repressed in the presence of ORF288, which indicated that this protein is toxic to the E. coli host cells. To confirm further the function of orf288 in male sterility, the gene was fused to a mitochondrial-targeting pre-sequence under the control of the Arabidopsis APETALA3 promoter and introduced into Arabidopsis thaliana. Almost 80% of transgenic plants with orf288 failed to develop anthers. It was also found that the independent expression of orf288 caused male sterility in transgenic plants, even without the transit pre-sequence. Furthermore, transient expression of orf288 and green fluorescent protein (GFP) as a fused protein in A. thaliana protoplasts showed that ORF288 was able to anchor to mitochondria even without the external mitochondrial-targeting peptide. These observations provide important evidence that orf288 is responsible for the male sterility of hau CMS in Brassica juncea.
AMMONIUM ADSORPTION ON NATURAL ZEOLITE (CLINOPTILOLITE): ADSORPTION ISOTHERMS AND KINETICS MODELING (2012)

A batch sorption process for removal of ammonium ions from aqueous solution using natural zeolite was studied. Tree different particle sizes of zeolite (1-2 mm, 2-4 mm and 4-10 mm) were used in the experiments. Sorption of ammonium ions on natural zeolite were carried out at 298 K with the initial concentrations of ammonium in the range of 1000 – 7000 mg NH4+-N/dm3. Equilibrium data were fitted by Freundlich and Langmuir isotherm and sorption kinetic data by pseudo-first and second order. The parameters were estimated by linear and non-linear method. Results show that non-linear method may be superior way to compute the parameters. The Langmuir isotherm model fitted better the experimental data with a maximum monolayer adsorption capacity of 58.36 mg NH4+-N/g (1-2 mm), 49.02 mg NH4+-N/g (2-4 mm) and 46.46 mg NH4+-N/g (4-10 mm), respectively. Also, the pseudo-second-order kinetic model was the best applicable model to describe the sorption kinetics. The obtained results suggest that the natural zeolite is a good adsorbent for removal of ammonium ions from aqueous solution and that ion exchange increased with decreasing of particle sizes of natural zeolite.
Interaction of modified oligonucleotides with nuclear proteins, formation of novel nuclear structures and sequence-independent effects on RNA processing (2018)

Abstract Oligonucleotides and nucleic acid analogues that alter gene expression are showing therapeutic promise for selected human diseases. The modification of synthetic nucleic acids to protect against nuclease degradation and to influence drug function is common practice, however, such modifications may also confer unexpected physicochemical and biological properties. Here we report backbone-specific effects of modified oligonucleotides on subnuclear organelles, altered distribution of nuclear proteins, the appearance of novel structured nuclear inclusions, and modification of RNA processing in cultured cells transfected with antisense oligonucleotides on a phosphorothioate backbone. Phosphodiester and phosphorodiamidate morpholino oligomers elicited no such consequences. Disruption of subnuclear structures and proteins elicit severe phenotypic disturbances, revealed by transcriptomic analysis of fibroblasts exhibiting such disruption. These data suggest that the toxic effects and adverse events reported after clinical evaluation of phosphorothioate nucleic acid drugs may be mediated, at least in part, by non-specific interaction of nuclear components with the phosphorothioate backbone.
Nanosized Prussian blue analogues as theranostic agents (2018)

International audience
Direct access to heterocyclic scaffolds by new multicomponent Ugi Smiles coupling (2006)

International audience
Microwave Sintering and Dielectric Properties of BaTiO3 Ceramics-Effect of liquid phase (2006)

Effects of liquid phase on microwave sintering with a frequency of 2.45 GHz of BaTiO3 ceramics were investigated. The additives to form the liquid were BaCO3, H3BO3 and BaB2O4. Addition of the liquid phase in microwave sintering promotes densification of BaTiO3 ceramics significantly, and densified ceramics were obtained by lower applied power and shorter processing time. Furthermore, electric resistivity of dense ceramics with BaCO3+2H3BO3 addition was different by sintering techniques, and a sample obtained by microwave sintering showed the dielectric, while one obtained by conventional sintering showed the semiconducting properties. Such different result is considered to be relating to presence of liquid phase with strong microwave absorption.
CDH1 and IL1-beta expression dictates FAK and MAPKK-dependent cross-talk between cancer cells and human mesenchymal stem cells (2015)

Dynamic interaction exists between hMSCs and cancer cells. CDH1 and IL1-Beta expression by cancer cells mediates the crosstalk between hMSCs and cancer cells. We propose a model where hMSCs act as the first line of defense against cancer cell growth and spread.
Using the Drosophila melanogaster D17-c3 cell culture system to study cell motility (2020)

Cultured Drosophila melanogaster S2 and S2R + cell lines have become important tools for uncovering fundamental aspects of cell biology as well as for gene discovery. Despite their utility, these cell lines are nonmotile and cannot build polarized structures or cell-cell contacts. Here we outline a previously isolated, but uncharacterized, Drosophila cell line named Dm-D17-c3 (or D17). These cells spread and migrate in culture, form cell-cell junctions and are susceptible to RNA interference (RNAi). Using this protocol, we describe how investigators, upon receiving cells from the Bloomington stock center, can culture cells and prepare the necessary reagents to plate and image migrating D17 cells; they can then be used to examine intracellular dynamics or observe loss-of-function RNAi phenotypes using an in vitroscratch or wound healing assay. From first thawing frozen ampules of D17 cells, investigators can expect to begin assaying RNAi phenotypes in D17 cells within roughly 2–3 weeks.