gebhart/patrepeval huggingface dataset:
Thioguanosine Conversion Enables mRNA‐Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC‐seq DUAL) (2020)

Temporal information about cellular RNA populations is essential to understand the functional roles of RNA. We have developed the hydrazine/NH<sub>4</sub> Cl/OsO<sub>4</sub> -based conversion of 6-thioguanosine (6sG) into A', where A' constitutes a 6-hydrazino purine derivative. A' retains the Watson-Crick base-pair mode and is efficiently decoded as adenosine in primer extension assays and in RNA sequencing. Because 6sG is applicable to metabolic labeling of freshly synthesized RNA and because the conversion chemistry is fully compatible with the conversion of the frequently used metabolic label 4-thiouridine (4sU) into C, the combination of both modified nucleosides in dual-labeling setups enables high accuracy measurements of RNA decay. This approach, termed TUC-seq DUAL, uses the two modified nucleosides in subsequent pulses and their simultaneous detection, enabling mRNA-lifetime evaluation with unprecedented precision.
Piezotronics and piezo-phototronics (2012)

Piezoelectricity, a phenomenon known for centuries, is an effect that is about the production of electrical potential in a substance as the pressure on it changes. The most well known material that has piezoelectric effect is the provskite structured Pb(Zr, Ti)O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> (PZT), which has found huge applications in electromechanical sensors, actuators and energy generators. But PZT is an electric insulator and it is less useful for building electronic devices. Wurtzite structures, such as ZnO, GaN, InN and ZnS, also have piezoelectric properties but they are not extensively used as much as PZT in piezoelectric sensors and actuators due to their small piezoelectric coefficients. In fact, due to the polarization of ions in a crystal that has non-central symmetry, a piezoelectric potential (piezopotential) is created in the crystal by applying a stress. For materials such as ZnO, GaN, InN in the wurtzite structure family, the effect of piezopotential to the transport behavior of charge carriers is significant due to their multiple functionalities of piezoelectricity, semiconductor and photon excitation. By utilizing the advantages offered by these properties, a few new fields have been created. Electronics fabricated by using inner-crystal piezopotential as a “gate” voltage to tune/control the charge transport behavior is named piezotronics, with applications in strain/force/pressure triggered/controlled electronic devices, sensors and logic units. Piezo-phototronic effect is a result of three-way coupling among piezoelectricity, photonic excitation and semiconductor transport, which allows tuning and controlling of electro-optical processes by strain induced piezopotential. The objective of this talk is to introduce the fundamentals of piezotronics and piezo-phototronics and to give an updated progress about their applications in energy science (LED, solar cell), electronics and sensors.
From protein domains to molecular nanoparticles: what can giant molecules learn from proteins? (2016)

Synthetic polymers are still considered as primitive as compared to the sophisticated polymeric machines like proteins.
Enhanced expression of the protein kinase substrate annexin in human hepatocellular carcinoma (1996)

Annexin (AX) constitutes a new family of Ca2+-dependent membrane-binding proteins; 13 of them have been described. Among these, annexin-1 (AX-I) has displayed many biological functions in vitro. Its actual role in vivo, however, remains unknown. We already reported that AX-I was expressed in proliferating (regenerating) hepatocytes at both protein and messenger RNA (mRNA) levels. The role of AX-I in human hepatocellular carcinoma (HCC) remains obscure. In this study, the amounts of AX-I at protein and mRNA levels, as well as its localization, have been determined in the normal human liver, chronic hepatitis liver, and nontumorous and tumorous portions of HCC. AX-I was rarely found in normal and chronic liver tissues, whereas it is overexpressed at both the transcriptional and translational levels in tumorous and nontumorous regions of HCC. In addition, more AX-I was expressed in the tumorous portion than the nontumorous portion of HCC. AX-I was present in the hepatocytes and HCC cells, localized mainly in the cytoplasm. AX-I was expressed in poorly differentiated cancer cells. Furthermore, AX-I was tyrosine-phosphorylated in HCC. We also found that some of the AX-I- positive hepatocytes in the nontumorous tissues were derived from a particular subset of parenchymal cells (stem or oval cells). These results indicate that AX-I plays an important role in the malignant transformation process leading to HCC and that it is closely related to the histological grade of HCC. HCC would offer a novel tool with which to study the function of AX-I in malignant transformation.
Non linear microwave characterization and modelization of carbon nanotube FETs (2007)

International audience
Cerebral Blood Flow and Blood Pressure: Dependent or Codependent?* (2019)

Department of Anesthesiology, The University of Texas Medical Branch at Galveston, Galveston, TX *See also p. 960. Dr. Prough received support for article research from the Moody Foundation. Dr. DeWitt has disclosed that he does not have any potential conflicts of interest.
Study of the Influence of the Dielectric Composition of Al/Ti/ZrO<sub>2</sub>:Al<sub>2</sub>O<sub>3</sub>/TiN/Si/Al Structures on the Resistive Switching Behavior for Memory Applications (2018)

The memory behavior of Al/Ti/ZrO2:Al2O3/TiN/Si/Al devices is investigated in this work. They are adequate to be used as resistive switching memories, with two clearly different states. Besides, intermediate states are also accessible in a controllable manner. The electrical characterization in terms of admittance parameters provides relevant complementary information. The cation ratio influences the memory maps and can be changed to obtain specifically sized shape of the maps. © The Electrochemical Society.
A comparison of the effectiveness of cyclosporine A, D, and G in the treatment of experimental autoimmune uveitis in rats. (1986)

Cyclosporine A (CsA), one compound in the family of cyclosporines, has effectively modulated the course of S-antigen induced experimental autoimmune uveitis (EAU). Cyclosporines G (CsG) and D (CsD), related to CsA in structure, were evaluated in their ability to prevent or modulate EAU in Lewis rats. 10 mg/kg/day IM of CsA effectively prevented the expression of EAU when therapy began on the day of immunization, while the same dosage of CsG prevented EAU in 81% of animals, and CsD only in 33%. Higher concentrations of CsG (40 mg/kg/day) did effectively block manifestations of the disease. Topical administration of CsG did not prevent the expression of disease but local protection was seen when the 500 micrograms CsG was placed intracamerally into only one eye. The in vitro comparison of these cyclosporines' capacity to alter proliferation and IL-2 release of a rat T-cell line capable of inducing EAU showed marked differences. CsA appeared to be most effective at abrogating these cellular functions at all concentrations tested, while CsD was least effective. CsG, however, approached the effectiveness of CsA. CsG is felt to be markedly less nephrotoxic than CsA, the secondary effect that is most commonly encountered, and could potentially be useful in the treatment of human intra-ocular inflammatory disease.
Synthesis of α-Branched Amines by Three- and Four-Component C–H Functionalization Employing a Readily Diversifiable Hydrazone Directing Group (2021)

Efficient syntheses of α-branched amines by three- and four-component C-H functionalization employing a diversifiable hydrazone directing group have been developed. The hydrazone in the α-branched amine products has been readily converted to multiple desirable functionalities such as a nitrile, a carboxylic acid, alkenes, and heterocycles using diverse heterolytic chemistry and homolytic transition metal- or photoredox-catalyzed processes. This study represents the first example of a four-component C-H functionalization reaction.
50 years of electrical-stress control in cable accessories (2013)

Maxwell and Felici developed the theoretical basis of geometrical stress control during the period 1846 to 1862. The first practical implementation, however, was that of Nagel in Germany in 1906 (Figure 1). He developed the socalled Nagel-bushing on the basis of conductive layers [1]. Around the same time, the Swiss professor Kuhlmann invented the refractive method [2]. His aim was to decrease the electrical stress at the points where it was highest, rather than distributing it to other areas. The famous Rogowski profile was introduced in 1923. The basic principles are the same today, although the applications have become more complex, and stress control is still an important research area in HV engineering. Developments in stress control during the last 50 years (Figure 1) have been due mainly to new materials and production processes, and modern technologies, which have made possible to create cable accessories of more compact design and to improve their reliability. These developments have included impedance stress control based on heat-shrinkable tubing, and nonlinear stress control. In both cases the driving force was the need to improve the stress-control system of cable accessories.
Scaffolds and Stem Cells for Patient-Tailored Aortic Heart Valve Tissue Engineering (2012)

Abstract Valve reconstruction or regeneration with living tissue is a daunting project for biomedical engineers and surgeons alike. Our translational approach to development of living valve replacements embraces three main principles: a) the accurate replication of each patient’s 3D aortic valve architecture for optimal functionality, b) layered scaffolds that mimic the aortic valve fibrosa, ventricularis and spongiosa to prevent buckling and enhance mechanical durability and c) the presence of autologous, valvular interstitial cells (VICs) to maintain matrix homeostasis. To create anatomically correct constructs, we used digital image processing of patient chest CT images and generated solid aortic valve root 3D structures using a stereo-lithography printer. Collagenous scaffolds to be used as the fibrosa and ventricularis layers were prepared from acellular porcine pericardium and collagen/GAG hydrogels to be used as the spongiosa layer. Layered scaffolds were attached to the molds, dried, stabilized with a non-toxic polyphenolic agent, rehydrated, the spongiosa seeded with human mesenchymal stem cells and valves subjected to functionality tests in a physiological heart valve bioreactor in sterile culture medium. Engineered valves exhibited excellent functional characteristics; most cells were alive, elongated significantly and stained positive for vimentin and actin, among other markers, suggestive of mechanical stimuli-induced stem cell differentiation into VICs. Ongoing studies are focused on endothelialization of the novel valve surfaces using stem cell-derived endothelial cells and rotational 3D seeding devices. In conclusion, autologous stem cell-seeded tri-layered collagenous scaffolds shaped to recapitulate the aortic heart valve shape and mechanics may provide future foundations for patient-tailored heart valve tissue engineering.
Theory-Guided Exploration of the Sr<sub>2</sub>Nb<sub>2</sub>O<sub>7</sub> System for Increased Dielectric and Piezoelectric Properties and Synthesis of Vanadium-Alloyed Sr<sub>2</sub>Nb<sub>2</sub>O<sub>7</sub> (2022)

Ab initio methods provide a powerful tool in the search for novel polar materials. In particular, there has been a surge to identify lead-free piezoelectric materials to replace PbZr0.52Ti0.48O3. This study examines a computational strategy to identify increased piezoelectric and dielectric responses of alloy systems based on the linear interpolation of force constants, Born effective charges, and internal strain tensors from their end-point compounds. We choose the ferroelectric layered perovskite Sr2Nb2O7as a parent structure and employ this alloying strategy for 19 potential cation substitutions, targeting thermodynamically metastable alloys with high piezoelectric response. From this screening, we identify Sr2Nb2-2xV2xO7as a promising polar system. We conduct large-unit-cell calculations of Sr2Nb2-2xV2xO7at x = 0.0625, 0.125 for multiple cation orderings and find a significant 184% enhanced piezoelectric response. The solid solution system is synthesized as single-crystalline thin-film heterostructures using pulsed-laser deposition, and an enhanced dielectric response is observed at x = 0.05 and at x = 0.1. We present the Sr2Nb2-2xV2xO7alloy system designed through high-throughput computational screening methods with a large calculated piezoelectric response and experimentally verified increased dielectric response. Our methodology is provided as a high-throughput screening tool for novel materials with enhanced polarizability and alloy systems with potential morphotropic phase boundaries.
Pathology from hydroxyapatite deposits in periarticular tissues. First conclusions on etiopathogenesis. (1994)

Biopsies of periarticular tissues from patients with episodes of chronic periarthritis were examinated by histological, ultrastructural and chemico-crystallographic methods. In all samples the mineralogical observations at the optical microscope, showed aggregates of microcrystalline incrustations, whose ultrastructural morphology has been characterized by SEM. The histological observations showed necrosis of collagen fibres and microcrystallization process in cavities and in metaplastic fibrocartilage. The HA deposits in the periarticular tissues, in the next stage of the process, are surrounded and demolished by macrophages and multinucleated giant cells. At the same time granulation tissue carries out the repair process, that begins with the formation of thin parallel collagen fibers interposed with many fibroblasts and numerous small vessels.
SU-8 microchannels for live cell dielectrophoresis improvements (2015)

In this work a novel SU-8 fabrication technology is employed to construct microfluidic devices for sensitive dielectrophoretic (DEP) manipulation of budding yeast cells. Identical devices were produced with standard soft-lithography processes. In comparison to standard PDMS based soft-lithography, an SU-8 layer was used to construct the microchannel walls sealed by a flat sheet of PDMS to obtain the microfluidic channels. Direct bonding of PDMS to SU-8 surface was achieved by efficient wet chemical silanization combined with oxygen plasma treatment of the contact surface. The presented fabrication process significantly improved the alignment of the microstructures. In addition, PDMS delamination above electrode topologies was significantly decreased over standard soft-lithography devices. The fabrication time and costs of the proposed methodology were found to be roughly the same. Sensitivity of the devices was tested by discriminating Saccharomyces cerevisiae cells in the G1 phase from cells in the S/G2/M phase using dielectrophoresis. This level of sensitivity necessitated high precision electrode structure that was designed using an FEM model based approach. Attaining such high precision using standard soft-lithography can be difficult due to additional requirements of an alignment stage and its associated tight timing limits.
Regenerative Engineering of the Human Using Convergence (2018)

The field of tissue engineering can be described as the application of biological, chemical, and engineering principles toward the repair, restoration, or regeneration of living tissues using materials, cells, and factors alone or in combination. The definition of regenerative engineering has undergone slight modifications over time but has stayed true to the notion that it is a Convergence field. This chapter discusses aspects of the use of regenerative engineering technologies, techniques, and approaches for the regeneration of bone and soft tissue. Regenerative Engineering can be viewed as a true Convergence field where the coming together of insights and approaches from originally distinct fields fuels the work done in Regenerative Engineering. This new field &quot;Regenerative Engineering&quot; is the convergence of advanced materials science, stem cell science, physics, developmental biology, and clinical translation to answer the grand challenge, i.e., to regenerate complex multicellular organs.
Discovery of New <i>Trichophyton</i> Members, T. persicum and T. spiraliforme spp. nov., as a Cause of Highly Inflammatory Tinea Cases in Iran and Czechia (2021)

Pathogens from the Trichophyton benhamiae complex are one of the most important causes of animal mycoses with significant zoonotic potential. In light of the recently revised taxonomy of this complex, we retrospectively identified 38 <i>Trichophyton</i> isolates that could not be resolved into any of the existing species. These strains were isolated from Iranian and Czech patients during molecular epidemiological surveys on dermatophytosis and were predominantly associated with highly inflammatory tinea corporis cases, suggesting possible zoonotic etiology. Subsequent phylogenetic (4 markers), population genetic (10 markers), and phenotypic analyses supported recognition of two novel species. The first species, Trichophyton persicum sp. nov., was identified in 36 cases of human dermatophytosis and one case of feline dermatophytosis, mainly in Southern and Western Iran. The second species, Trichophyton spiraliforme sp. nov., is only known from a single case of tinea corporis in a Czech patient who probably contracted the infection from a dog. Although the zoonotic sources of infections summarized in this study are very likely, little is known about the host spectrum of these pathogens. Awareness of these new pathogens among clinicians should refine our knowledge about their poorly explored geographic distribution. <b>IMPORTANCE</b> In this study, we describe two novel agents of dermatophytosis and summarize the clinical manifestation of infections. These new pathogens were discovered thanks to long-term molecular epidemiological studies conducted in Czechia and Iran. Zoonotic origins of the human infections are highly probable, but the animal hosts of these pathogens are poorly known. Further research is needed to refine our knowledge about these new dermatophytes.
<b>Protein F2, a novel fibronectin‐binding protein from <i>Streptococcus pyogenes</i>, possesses two binding domains</b> (1996)

Binding of the group A streptococcus (GAS) to respiratory epithelium is mediated by the fibronectin (Fn)-binding adhesin, protein F1. Previous studies have suggested that certain GAS strains express Fn-binding proteins that are different from protein F1. In this study, we have cloned, sequenced, and characterized a gene (prtF2) from GAS strain 100076 encoding a novel Fn-binding protein, termed protein F2. Insertional inactivation of prtF2 in strain 100076 abolishes its high-affinity Fn binding. prtF2-related genes exist in most GAS strains that lack prtF1 (encoding protein F1) but bind Fn with high affinity. These observations suggest that protein F2 is a major Fn-binding protein in GAS. Protein F2 is highly homologous to Fn-binding proteins from Streptococcus dysgalactiae and Streptococcus equisimilis, particularly in its carboxy-terminal portion. Two domains are responsible for Fn binding by protein F2. One domains (FBRD) consists of three consecutive repeats, whereas the other domain (UFBD) resides on a non-repeated stretch of approximately 100 amino acids and is located 100 amino acids aminoterminal of FBRD. Each of these domains is capable of binding Fn when expressed as a separate protein. In strain 100076, protein F2 activity is regulated in response to alterations in the concentration of atmospheric oxygen.
EFFECT OF HEAD SIZE AND CROSSLINKING ON WEAR IN POLYETHYLENE ACEATABULAR COMPONENTS (2004)

Polyethylene (PE) wear affects survivorship in the long term while dislocation remains a significant factor in the short term. Increasing head size can reduce impingement and dislocation. However, this increases wear rates and reduces the net thickness of the liner. Several reports have demonstrated significant reduction in wear in cross-linked PE. This study reports wear rates in crosslinked PE liners with increased head size. Four groups of PE liners were tested against cobalt-chrome heads in a hip wear simulator: highly crosslinked liners with head size 28mm (28XPE) and 32mm (32XPE), and minimally crosslinked liners with head size 28mm (28PE) and 32mm (32PE). Additional liners were used as load-soak controls to monitor weight gain due to fluid absorption. Gravimetric analysis was performed every 500,000 cycles for a total of 5,000,000 cycles. 28PE and 32PE liners had mean wear rates of 12.5(±1.0) and 17.45 (±2.6) mg/million cycles. Both highly crosslinked PE liners (28XPE and 32XPE) had significant less wear rates that regular polyethylene 1.49 (±0.72) and 2.55 (±0.19) mg/million cycles respectively. Increasing head size resulted in increased wear, which is consistent with previous reports. Highly crosslinked PE significantly reduced wear rates in both head sizes. Although there was a small increase in wear in the 32XPE group compared to the 28XPE group, wear was significantly less than both 32PE and 28PE groups. These encouraging results suggest that a dual benefit (reduced wear and reduced dislocation rate) might be achieved using 32XPE liners. Further studies that evaluate fatigue damage, crack propagation and impingement are necessary.
Allelic Analysis for<i>bar</i>Gene from Different Rice Transformation Events (2006)

Abstract Mechanism(s) of gene transformation and integration in rice (Oryza sauva L.) is/are not currently well understood. This research was conducted to determine whether a transgene is inserted into the rice genome specifically or randomly. Seven homozygous transgenic Taipei (T) 309 and Nipponbare plants with the bar transgene from different rice transformation events were crossed. The segregation of F2 and F3 populations from a total of 21 crosses was studied in a greenhouse and field to determine if the genes were allelic or non-allelic. Five genomic locations appeared to be involved among the seven transgenic plants. An additional 20 homozygous transgenic T309 plants, with the bar transgene from different transformation events, were crossed reciprocally with the previous seven plants. One hundred and fifteen crosses made during 1999 and 2000 were analyzed for allelism. In some combinations, the genes were allelic, but most of them were non-allelic, with two or more pairs of genes being expressed. Twenty loci among the 27 transgenic plants were involved and some plants had several inserted genes expressed. Genes in nine out of 27 transformed plants were allelic. We concluded that the functional foreign (bar) gene was restrictively/preferentially inserted into the rice genome in some cases and was not completely randomly inserted and expressed in the rice genome. If the mechanism(s) for preferential insertion were identified, rice researchers could possibly control insertion sites of transgenes to optimize gene expression.