gebhart/patrepeval huggingface dataset:
Self-assembly of peptides to nanostructures (2014)

The formation of well-ordered nanostructures through self-assembly of diverse organic and inorganic building blocks has drawn much attention owing to their potential applications in biology and chemistry. Among all organic building blocks, peptides are one of the most promising platforms due to their biocompatibility, chemical diversity, and resemblance to proteins. Inspired by the protein assembly in biological systems, various self-assembled peptide structures have been constructed using several amino acids and sequences. This review focuses on this emerging area, the recent advances in peptide self-assembly, and formation of different nanostructures, such as tubular structures, fibers, vesicles, and spherical and rod-coil structures. While different peptide nanostructures have been discovered, potential applications are explored in drug delivery, tissue engineering, wound healing, and surfactants.
Influence of surface treatments developed for oral implants on the physical and biological properties of titanium. (I) Surface characterization. (1997)

We present an investigation of the physico-chemical surface properties of commercially pure titanium coverslips which were submitted to various treatments designed to optimize their topography in view of application in oral implantology. The surface microroughness, chemical composition and water wettability were analyzed on titanium coverslips prepared by mechanical polishing, acid attack in HCl/H2SO4, after mechanical polishing or sandblasting, and titanium plasma-spray. The chemical composition has been measured by Auger electron spectroscopy. The treatments have no major influence on the surface chemical composition and all the samples display a composition approaching that of TiO2 with minor amounts of carbon, sulfur, silicon and calcium as impurities. The roughness has been measured by scanning force microscopy on an area of 20 microns x 20 microns on each sample. Polished titanium is smooth (peak-to-valley roughness 81 nm), whereas the acid-attacked surfaces exhibit a micro-roughness in the microns range (2100 nm for polished and acid attacked; 3600 nm for sandblasted and acid attacked) which is quite reproducible over large areas of the sample. The acid attacked samples present a subsurface layer which contains hydrogen below the native passivating oxide layer. Water wettability measurement shows that all surfaces are hydrophobic with a slightly higher contact angle for the acid attacked surfaces. The different treatments analyzed in this study essentially influence the surface roughness by preserving the chemical composition and the wettability properties of titanium native oxide surface layer.
A novel method of selective epitaxial growth of InP by metalorganic chemical vapor deposition (1987)

A novel method of the selective epitaxy of InP was developed by employing a two-step growth in atmospheric pressure metalorganic chemical vapor deposition. By this method, selective epitaxy, without ridge and/or lateral growth, and with uniform deposition of the polycrystalline layer on the SiO2 mask, could be achieved. First, a thin uniform InP polycrystalline layer was deposited on a SiO2/InP substrate and a stripe pattern was formed by photolithography, and then selective epitaxial growth was performed. Selective epitaxial layers thus obtained were found to have a photoluminescence half width of ∼40 meV at room temperature, which was comparable to the one reported by other workers in homoepitaxial metalorganic chemical vapor deposition growth of InP. The resistivity of the polycrystalline layer was ∼700 Ω cm at room temperature, which was four orders of magnitude larger than that of the selective epitaxial layer. Therefore, electrical isolation may be sufficient for fabrication of InP planar devices.
Adaptor protein TDRD7 is co-localized with ribosomal protein S6 kinases S6K1 and S6K2 in cell lines of different tissue origin (2013)

Our previous studies have shown that S6K1 and S6K2 protein kinases form the complexes with newly identified adaptor protein TDRD7, which is involved in regulation of cytoskeleton dynamics, mRNA transport, protein translation, piRNAs processing and transposons silensing. Aim.Determination the subcellular localization of S6K1-TDRD7 and S6K2-TDRD7 protein complexes. Methods. Immunofluorescense microscopy was used to study co-localization of S6K1/S6K2 and TDRD7 in HEK293, HEPG2 cell lines as well as in rat primary hippocampal neurons using primary polyclonal anti-S6K1 antibodies, monoclonal anti-S6K2 and anti-TDRD7 antibodies. Results. It was found that S6K1 is co-localized with TDRD7 in perinuclear region of HEK293 cells. S6K1 and S6K2 were also co-localized with TDRD7 in perinuclear region of HEPG2 cells and in soma of primary rat hippocampal neurons. Conclusions. In this report we provide an additional experimental evidences of possible S6K1-TDRD7 and S6K2-TDRD7 complexes formation in cells of different tissue origins that may reflect their potential physiological importance. However, elucidation of the exact composition of these complexes and their role in cell physiology requires additional studies.
The Difference of Fatty Acid Composition in Plasma and Platelet Aggregation between Farming and Fishing Populations (1981)

A survey of the serum fatty acid composition and platelet aggregation in people living in fishing (Kawazu, Katsuura-city) and farming (Kamagaya-city) villeges in Chiba prefecture was undertaken.EPA (eicosapentaenoic acid), AA (arachidonic acid), DHA (docosahexaenoic acid) concentrations in plasma and EPA/AA value in the people living in the fishing village who eat a great deal of fish (fish consumption was 250g per day) were significantly higher than those in the people living in the farming village (fish consumption was only 90g per day). Platelet aggregation in the people in the fishing village was significantly lower than that in the farming village population. Although differences in the value of T-C, HDL-C, and AI (atherogenic index) between both areas were not significant, the value of TG in the people of the farming village was higher than that in the fishing village. Coefficients of correlation between DHA and either EPA, EPA/AA ratio were very high.
Neutral and ion thermochemistry: Its present status and significance (2009)

This short account outlines the sources of thermochemical data that are important for gas phase ion chemistry. It describes some of the relationships that have been identified for the empirical estimation of enthalpies among neutral molecules, free radicals, and odd and even electron ions. For neutral species, the additivity principle works well and this has been developed to cover a very wide range of structures and isomers. Ionization energies of homologous species depend inversely on molecular size, allowing estimates to be made for missing members. For ions, the effect of a group substitution (such as replacing a hydrogen atom by, e.g., a methyl or hydroxyl group) can easily be estimated, but such results are strongly dependent upon the position of the charge site, relative to that of the substitution. Special emphasis is given to the reliability of data collections and simple directions are provided as to how critically to assess and identify less-than-satisfactory values.
Can a Modified Anterior External Fixator Provide Posterior Compression of AP Compression Type III Pelvic Injuries? (2013)

This additive device may improve the initial anterior and posterior stability in the acute management of unstable and life-threatening pelvic ring injuries.
Influence of starch sources and dietary protein levels on intestinal functionality and intestinal mucosal amino acids catabolism in broiler chickens (2019)

Amino acid catabolism in the gut mucosa is subject to nutritional regulation. Given that amino acids can be spared from catabolism in the gut mucosa by supplementation of amylose, it follows their post-enteral availability would be improved and intestinal energy would be derived more efficiently from glucose.
Robust DNA repair in PAXX‐deficient mammalian cells (2018)

To ensure genome stability, mammalian cells employ several DNA repair pathways. Nonhomologous DNA end joining (NHEJ) is the DNA repair process that fixes double-strand breaks throughout the cell cycle. NHEJ is involved in the development of B and T lymphocytes through its function in V(D)J recombination and class switch recombination (CSR). NHEJ consists of several core and accessory factors, including Ku70, Ku80, XRCC4, DNA ligase 4, DNA-PKcs, Artemis, and XLF. Paralog of XRCC4 and XLF (PAXX) is the recently described accessory NHEJ factor that structurally resembles XRCC4 and XLF and interacts with Ku70/Ku80. To determine the physiological role of PAXX in mammalian cells, we purchased and characterized a set of custom-generated and commercially available NHEJ-deficient human haploid HAP1 cells, <i>PAXX</i><sup><i>Δ</i></sup><i>, XRCC4</i><sup><i>Δ</i></sup> , and <i>XLF</i><sup><i>Δ</i></sup> . In our studies, HAP1 <i>PAXX</i><sup><i>Δ</i></sup> cells demonstrated modest sensitivity to DNA damage, which was comparable to wild-type controls. By contrast, <i>XRCC4</i><sup><i>Δ</i></sup> and <i>XLF</i><sup><i>Δ</i></sup> HAP1 cells possessed significant DNA repair defects measured as sensitivity to double-strand break inducing agents and chromosomal breaks. To investigate the role of PAXX in CSR, we generated and characterized <i>Paxx</i><sup>-/-</sup> and <i>Aid</i><sup><i>-/-</i></sup> murine lymphoid CH12F3 cells. CSR to IgA was nearly at wild-type levels in the <i>Paxx</i><sup>-/-</sup> cells and completely ablated in the absence of activation-induced cytidine deaminase (AID). In addition, <i>Paxx</i><sup>-/-</sup> CH12F3 cells were hypersensitive to zeocin when compared to wild-type controls. We concluded that <i>Paxx</i>-deficient mammalian cells maintain robust NHEJ and CSR.
Endometriosis (2004)

Endometriosis affects a huge number of women throughout the world. It has been estimated that between 1% and 15% of women who are examined for pelvic pain and infertility may have endometriosis; the true prevalence is unknown because diagnosis can only be made with any accuracy by laparoscopic examination of the pelvis. This book provides clinicians with all the information they need in a succinct and clear text, with colour illustrations. Chapters cover: epidemiology and aetiology; diagnosis; investigation; medical treatment; and surgical treatment.
Author Correction: Novel multimodal molecular imaging of Vitamin H (Biotin) transporter activity in the murine placenta (2021)

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
MicroRNA-146a limits tumorigenic IL-17 signaling in colorectal cancer (2021)

Abstract Interleukin-17 (IL-17) is a major inflammatory cytokine implicated in colorectal cancer (CRC) development. However, the mechanisms that control tumorigenic IL-17 signaling are poorly understood. Recently, expression changes and polymorphisms in the small non-coding RNA, microRNA-146a (miR-146a), have been associated with clinical outcomes in inflammatory bowel disease and CRC patients. Here, we identified a novel role for miR-146a as a major negative regulator of colonic inflammation and tumorigenesis via modulation of IL-17 responses. MiR-146a-deficient mice are susceptible to both colitis-associated and sporadic CRC, and present with enhanced tumorigenic IL-17 signaling. Within myeloid cells, miR-146a targets RIPK2, an intermediate in NOD2 signaling, to limit myeloid cell-derived IL-17-inducing cytokines and restrict colonic IL-17 levels. Accordingly, myeloid cell-specific deletion of miR-146a leads to CRC susceptibility. Moreover, within intestinal epithelial cells (IECs), miR-146a targets TRAF6, an intermediate in IL-17R signaling, to restrict IEC responsiveness to IL-17. MiR-146a within IECs further suppresses CRC by targeting PTGES2, an enzyme for PGE2 synthesis. IEC-specific deletion of miR-146a confers marked CRC susceptibility. Importantly, preclinical administration of miR-146a mimic or direct inhibition of miR-146a targets, TRAF6/RIPK2 can ameliorate CRC. In conclusion, miR-146a prevents CRC by two interlinked mechanisms: 1) by limiting myeloid cell-mediated IL-17 production; and 2) by inhibiting tumorigenic IL-17R signaling in IECs. Overexpression of miR-146a may be a promising therapeutic approach for CRC to limit multiple pathways converging on tumorigenic IL-17 signaling.
Targeting strategies for mRNA delivery (2022)

mRNA gene therapy has recently emerged as a candidate to enable multiple therapeutic applications including protein replacement therapy, vaccine immunology, and regenerative medicine. Despite the extensive therapeutic potential, the successful clinical translation of mRNA gene therapies has been very limited in practice due to the inadequate understanding of how to target various organs or cell type for protein expression. Multiple studies in the past decade have demonstrated carrier material properties and routes of administration as significant parameters influencing the expression profile of mRNA therapeutics. However, the disparate nature of these reports has prevented critical and global understanding of how these factors contribute to organ targeting for mRNA delivery. Elucidation of trends and commonalities in materials achieving tissue specific mRNA delivery may enable the realization of the medical and commercial promise of therapeutic mRNA medicines. The purpose of this review is to provide a thorough and robust meta-analysis of the various materials that have been successfully used to target different organs for mRNA delivery. The article summarizes the distinct properties of the materials used as well as evaluates various routes of administration of mRNA therapeutics and the applications that can be achieved. This review will therefore serve as useful guide for the community in the development of future materials for mRNA delivery to enable the full potential of this nucleic acid modality for gene therapy.
Portal hypertensive gastropathy is associated with iron deficiency anemia (2020)

The CTP score but not HVPG or MELD were risk factors for severe PHG. Importantly, anemia and especially IDA are significantly more common in patients with severe PHG.
Infrared spectroscopic study of the interaction of cations in zeolites with simple molecular probes. Part 1.—Adsorption of molecular hydrogen on alkaline forms of zeolites as a test for localization sites (1991)

The localization sites for univalent cations in cationic forms of zeolites (A, X, Y, ZSM-5 and mordenite) have been investigated using the low-temperature adsorption of molecular hydrogen as a spectroscopic test. The extent of H—H bond polarization, estimated from the low-frequency shift of the fundamental stretching vibration of perturbed H2 molecules, was found to be strongly dependent on the basicity of the neighbouring oxygen atoms of the framework.
Data from Molecular Signature of MT1-MMP: Transactivation of the Downstream Universal Gene Network in Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Invasion-promoting MT1-MMP is directly linked to tumorigenesis and metastasis. Our studies led us to identify those genes, the expression of which is universally linked to MT1-MMP in multiple tumor types. Genome-wide expression profiling of MT1-MMP–overexpressing versus MT1-MMP–silenced cancer cells and a further data mining analysis of the preexisting expression database of 190 human tumors of 14 cancer types led us to identify 11 genes, the expression of which correlated firmly and universally with that of MT1-MMP (&lt;i&gt;P&lt;/i&gt; &lt; 0.00001). These genes included regulators of energy metabolism (NNT), trafficking and membrane fusion (SLCO2A1 and ANXA7), signaling and transcription (NR3C1, JAG1, PI3Kδ, and CK2α), chromatin rearrangement (SMARCA1), cell division (STK38/NDR1), apoptosis (DAPK1), and mRNA splicing (SNRPB2). Our subsequent extensive analysis of cultured cells, tumor xenografts, and cancer patient biopsies supported our data mining. Our results suggest that transcriptional reprogramming of the specific downstream genes, which themselves are associated with tumorigenesis, represents a distinctive “molecular signature” of the proteolytically active MT1-MMP. We suggest that the transactivation activity of MT1-MMP contributes to the promigratory cell phenotype, which is induced by this tumorigenic proteinase. The activated downstream gene network then begins functioning in unison with MT1-MMP to rework the signaling, transport, cell division, energy metabolism, and other critical cell functions and to commit the cell to migration, invasion, and, consequently, tumorigenesis. [Cancer Res 2008;68(11):4086–96]&lt;/p&gt;&lt;/div&gt;
Development and Application of an Integrated Dew Point and Glass Temperature Sensor (2001)

&lt;div class="htmlview paragraph"&gt;With the optimization of HVAC system controls for comfort, air quality and energy efficiency the potential for fogging the glass has increased. To maintain occupant safety, a method to predict when such fogging conditions exist is necessary to be able to execute proactive control corrections to prevent fogging. Windshield fog conditions are predicated on windshield surface temperature, cabin relative humidity and the reference temperature of the humidity sensor. This has driven a joint development project between Delphi Automotive Systems divisions to develop an Integrated Dew Point and Glass Temperature (IDGT) sensor. This sensor is a combination of three elements: a glass temperature sensor, a relative humidity sensor, and a humidity reference temperature sensor. Using this sensor package, the cabin dew point is calculated from the relative humidity and humidity reference temperature for comparison with the windshield glass temperature. When the windshield glass temperature drops to or is below the cabin dew point temperature, fog will form on the windshield. Utilizing this information, a proactive automatic climate control system implements corrections before the occurrence of fogging.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This paper discusses the following issues concerning this new technology:&lt;/div&gt; &lt;div class="htmlview paragraph"&gt; &lt;ul class="list disc"&gt; &lt;li class="list-item"&gt;&lt;div class="htmlview paragraph"&gt;Sensor design and development.&lt;/div&gt;&lt;/li&gt; &lt;li class="list-item"&gt;&lt;div class="htmlview paragraph"&gt;A comparison between the existing technologies and the new sensor design.&lt;/div&gt;&lt;/li&gt; &lt;li class="list-item"&gt;&lt;div class="htmlview paragraph"&gt;Vehicle / system integration of the sensor.&lt;/div&gt;&lt;/li&gt; &lt;/ul&gt; &lt;/div&gt;
Highly efficient high-order harmonic generation by metallic carbon nanotubes (1999)

High-order harmonic generation by metallic carbon nanotubes exposed to an intense ultrashort pulse has been theoretically investigated in the semiclassical approximation. The mechanism of nonlinearity provided by the motion of conduction electrons below the band of optical resonances has been considered. It has been shown that the high density of states of conduction electrons in metallic carbon nanotubes and the specific dispersion law inherent in hexagonal crystalline structure as well as the transverse quantization of the electron momentum result in a uniquely high efficiency of the current conversion to high-order harmonics.
Alginate/Xanthan gum hydrogels as forensic blood substitutes for bloodstain formation and analysis. (2023)

Understanding the behaviour of human blood outside of the body has important implications in forensic research, especially related to bloodstain pattern analysis (BPA). The design of forensic blood substitutes (FBSs) can provide many advantages, including the incorporation of multiple physiological components for use as safe and reliable materials for forensic applications. In this work, we present the design of synthetic alginate and xanthan gum-based hydrogels that contain electrosprayed microparticles (MPs) with and without crosslinked DNA. In addition to the MPs, the alginate/xanthan gum FBS materials include fillers to alter the physical appearance and fluid properties of the material. The optimized FBS consisted of alginate (1% w/v) and xanthan gum (5.0 x10-3 w/v %), 2 mM CaCl2, ferric citrate (0.5% w/v), magnesium silicate (0.25% w/v), Allura red (2% w/v), 0.025% v/v Tween 20 and 9.5% v/v MPs. The FBS was tested in passive dripping experiments relevant to BPA scenarios at various impact angles. The spreading ratio (Ds/D0) was determined for 90 degree stains made on a paper surface and compared to bovine blood where the FBS was shown to simulate accurate and predictable spreading behaviour. In addition, we simulated other common BPA scenarios (e.g., impact patterns) and evidence processing potential. The FBS could be swabbed, and the DNA could be extracted, amplified, and genotyped analogous to human blood evidence. A stability test was also conducted which revealed a shelf-life of up to 4 weeks where the material remains relevant to human blood at physiological temperature.
On modeling utility for cooperative slotted Aloha games (2008)

In this paper, we propose a generalized utility function model for cooperative slotted Aloha in a distributed system. Multiuser diversity gains are achieved by appropriately designing the Nash equilibrium thresholds for the selfish users. The network enforces fairness among different users by employing a pricing policy that favors equal access probabilities. This generalized game model provides the flexibility in designing the utility function associated with QoS. Our study on the impact of different utility function models shows that the multiuser diversity gains achieved by different models remain constant under the throughput optimization framework and vary slightly under the revenue optimization framework.
Comparison of decellularization techniques for preparation of extracellular matrix scaffolds derived from three‐dimensional cell culture (2012)

Extracellular matrix (ECM) scaffolds derived from cultured cells have drawn increasing attention for use in tissue engineering. We have developed a method to prepare cultured cell-derived ECM scaffolds by combining three-dimensional cell culture, decellularization, and selective template removal. Cell-ECM-template complexes were first formed by culture of cells in a poly(lactic-co-glycolic acid) (PLGA) mesh template to deposit their own ECM. The complexes were subsequently decellularized to remove cellular components. Finally, the PLGA template was selectively removed to obtain the ECM scaffolds. Seven decellularization methods were compared for their decellularization effects during scaffold preparation. They were: freeze-thaw cycling (-80°C, six times) with ammonia water (25 mM); 0.1% Triton™ X-100 (TX100) with 1.5M KCl aqueous solution; freeze-thaw cycling alone; ammonia water alone; TX100 extraction; osmotic shock with 1.5M KCl; and freeze-thaw cycling with 3M NaCl. Among these methods, the methods of freeze-thaw cycling with NH(4) OH and TX100 with 1.5M KCl showed the best effect on the removal of cellular components from the complexes, while the other five methods could only partially remove cellular components. The ECM scaffolds prepared by these two methods had similar gross appearances and microstructures. In vivo implantation of the ECM scaffolds prepared by these two methods induced mild host responses. The two decellularization methods were demonstrated to be effective for preparation of cultured cell-derived ECM scaffolds.