gebhart/patrepeval huggingface dataset:
Ionic Current Model of a Hypoglossal Motoneuron (2005)

We have developed a single-compartment, electrophysiological, hypoglossal motoneuron (HM) model based primarily on experimental data from neonatal rat HMs. The model is able to reproduce the fine features of the HM action potential: the fast afterhyperpolarization, the afterdepolarization, and the medium-duration afterhyperpolarization (mAHP). The model also reproduces the repetitive firing properties seen in neonatal HMs and replicates the neuron's response to pharmacological experiments. The model was used to study the role of specific ionic currents in HM firing and how variations in the densities of these currents may account for age-dependent changes in excitability seen in HMs. By varying the density of a fast inactivating calcium current, the model alternates between accelerating and adapting firing patterns. Modeling the age-dependent increase in H current density accounts for the decrease in mAHP duration observed experimentally, but does not fully account for the decrease in input resistance. An increase in the density of the voltage-dependent potassium currents and the H current is required to account for the decrease in input resistance. These changes also account for the age-dependent decrease in action potential duration.
A novel STK1-targeted small-molecule as an “antibiotic resistance breaker” against multidrug-resistant Staphylococcus aureus (2017)

Ser/Thr protein kinase (STK1) plays a critical role in cell wall biosynthesis of and drug resistance in methicillin-resistant Staphylococcus aureus (MRSA). MRSA strains lacking STK1 become susceptible to failing cephalosporins, such as Ceftriaxone and Cefotaxime. STK1, despite being nonessential protein for MRSA survival, it can serve as an important therapeutic agent for combination therapy. Here, we report a novel small molecule quinazoline compound, Inh2-B1, which specifically inhibits STK1 activity by directly binding to its ATP-binding catalytic domain. Functional analyses encompassing in vitro growth inhibition of MRSA, and in vivo protection studies in mice against the lethal MRSA challenge indicated that at high concentration neither Inh2-B1 nor Ceftriaxone or Cefotaxime alone was able to inhibit the growth of bacteria or protect the challenged mice. However, the growth of MRSA was inhibited, and a significant protection in mice against the bacterial challenge was observed at a micromolar concentration of Ceftriaxone or Cefotaxime in the presence of Inh2-B1. Cell-dependent minimal to no toxicity of Inh2-B1, and its abilities to down-regulate cell wall hydrolase genes and disrupt the biofilm formation of MRSA clearly indicated that Inh2-B1 serves as a therapeutically important "antibiotic-resistance-breaker," which enhances the bactericidal activity of Ceftriaxone/Cefotaxime against highly pathogenic MRSA infection.
Synthesis of Polymers with Well-defined Structures by Novel Ring-opening Reactions of Oxetanes (2006)

This article reports new ring-opening reactions of oxetane compounds with certain reagents such as acyl chlorides, carboxylic esters, phenols, and carboxylic acids using certain quaternary onium salts as catalysts. Reaction behavior of oxetanes was investigated based on kinetic study. These new reactions of oxetanes were also successfully applied to polymer synthesis. Polymers containing pendant reactive groups were obtained by polyaddition of bis (oxetane) s with certain difunctional monomers such as dicarboxylic chlorides, bis (phenol) s, or dicarboxylic acids. The reaction of oxetanes with cyclic carboxylic anhydrides proceeded in alternating ring-opening copolymerization mode to give copolymers with A-B sequence. The authors found new anionic ring-opening polymerization of oxetanes containing pendant hydroxyl groups using appropriate catalyst system. Hyperbranched polymers containing hydroxyl groups were prepared by the reactions of oxetanes. Alkali developable photopolymers were also obtained by the chemical modification of the hyperbranched polymers. The reactions of oxetanes with certain reagents were also useful for thermal curing reaction providing oxetane resins.
WATER AND MINERAL STRESSES, PRODUCTION YIELDS AND PHOTOACTIVITY OF CORIANDRUM SATIVUM L. (2010)

Coriander (Coriandrum sativum L.) antifungal activity against the phytopathogenic fungi C. cucumerinum, F. culmorum, B. cinerea and A. niger was evaluated using leaf extracts obtained with ethyl acetate or methanol. The relation between mineral supply and photobioactivity was not clear while the increasing of water deficit strongly enhanced the light dependent antifungal activity. On the whole the lack of P and a water deficit of about 50% enhanced the potential photoactivity of C. sativum comparatively to its ground state activity.
Minnesota Taconite Workers Health Study: Environmental Study of Airborne Particulate Matter - Development of Standard Operating Procedures for Particle Collection and Gravimetric Analysis (2013)

June 2013 Report of Investigations, NRRI/RI-2013/01; Project No. 1806-10416-20080. Natural Resources Research Institute, University of Minnesota Duluth, 5013 Miller Trunk Highway, Duluth MN 55811-1442
Use of Chemometrics and Laser-Induced Breakdown Spectroscopy for Quantitative Analysis of Major and Minor Elements in Aluminum Alloys (2007)

In the present work, quantitative analysis of major and minor elements in aluminum alloys is investigated using chemometrics and laser-induced plasma spectroscopy with a commercially available laser-induced breakdown (LIBS) spectrometer. Multivariate calibrations use the entire signal matrix for all elements in a single multivariate regression model. This enables accounting for the correlation between variables often referred to as matrix effects in conventional univariate modeling. Modeling the entire signal matrix improves robustness over traditional univariate calibration since it can compensate for matrix effects. Several nonlinear data pretreatment methods have been used to correct for nonlinear behaviors of the analytical signals prior to performing the multivariate calibration. The use of multivariate calibration in combination with cubic implicit nonlinear data pretreatment showed the most accurate results. The accuracy reported with the developed multivariate calibration is better than 5% for the major alloying elements. Based on the results obtained, the use of chemometrics and laser-induced plasma spectroscopy have been successfully applied to the quantitative analysis of major and minor alloying elements in aluminum.
A Study on Characteristics of Overhead Rigid Conductor System for Developing the High-speed System up to 250km/h (2015)

An overhead rigid conductor system is mainly applied to the subway and recently studies on the rigid system have been conducted for applications such as tunnels of high-speed line and speed improvement of a conventional lines up to 250km/h. Power feeding performance which is the most important in a rigid system can be measured by contact force and characteristics of this contact force are related to the shape and material of the R-BAR. In this paper, we analyze the measurements of contact force, current heating temperature, impedance of a rigid conductor which was developed in Korea, after that we compare static characteristics of home and abroad rigid conductors which have various shapes and materials.
Location and Functional Significance of Retinol-binding Sites on the Serine/Threonine Kinase, c-Raf (2005)

Redox activations of serine/threonine kinases represent alternate pathways in which vitamin A plays a crucial co-factor role. Vitamin A binds the zinc finger domain of c-Raf with nanomolar affinity. The retinoid-binding site has been mapped within this structure by scanning mutagenesis. The deduced contact sites were found anchored on Phe-8, counting from the 1st conserved histidine of the zinc finger. These sites agreed with contact amino acids identified by computational docking. The boundaries of a related binding pocket were identified by mutagenesis and partially confirmed by docking trials in the protein kinase C-alpha C1A zinc finger. They comprised Phe-7, Phe-8, and Trp-22. This trio was absent from the alphaC1B domain, explaining why the latter did not bind retinol. Reconfiguring at a minimum the two corresponding amino acids of alphaC1B, Thr-7 and Tyr-22, to conform to alphaC1A converted this domain to a binder. Deletion of the predicted retinoid-binding site in the full-length molecule created a mutant c-Raf that was deficient in retinol-dependent redox activation but fully responsive to epidermal growth factor. Our findings indicate that ligation of retinol to a specific site embedded in the regulatory domain is an important feature of c-Raf regulation in the redox pathway.
Intracellular Protein Aggregation Is a Proximal Trigger of Cardiomyocyte Autophagy (2008)

We conclude that protein aggregation is a proximal trigger of cardiomyocyte autophagy and that autophagic activity functions to attenuate aggregate/aggresome formation in heart. Findings reported here are the first to demonstrate that protein aggregation occurs in response to hemodynamic stress, situating pressure-overload heart disease in the category of proteinopathies.
Artery of Davidoff and Schechter: A Large Angiographic Case Series of Dural AV Fistulas (2021)

The artery of Davidoff and Schechter (ADS) is the only meningeal branch of the posterior cerebral artery (PCA), supplying the medial tentorial margin and posterior portions of the falx. Given its small size, it is rarely identified on angiographic studies, unless enlarged in pathologies such as dural arteriovenous fistulas (DAVFs) or vascularized masses. This artery was first described by Wollschlaeger and Wollschlaeger in 1965, and to date, only a few reports have described its significance. The objective of this study is to report our experience with the ADS in dural fistulas from 2 tertiary medical centers and to emphasize the importance of recognizing this artery during angiographic examination of vascular tentorial and posterior fossa lesions. To our knowledge, this report demonstrates the largest angiographic case series published to date, recognizing a total of 7 patients with ADS arising secondary to a posterior fossa or tentorial DAVF and one of the largest reported series of DAVFs supplied by the ADS treated by endovascular and surgical techniques. Our cases validate the importance of prompt identification of the ADS for the diagnosis as well as endovascular treatment of vascular malformations in the posterior fossa and tentorial region.
A Missing Solution to the Transport Equation and Its Effect on Estimation of Cloud Absorptive Properties (2002)

Most of the existing cloud radiation models treat liquid water drops of a variety of sizes as an ensemble of particles. The ensemble approach assumes that all drop sizes are well represented in an elementary volume, and its scattering and absorbing properties can be accurately specified through the use of the drop size probability density distribution function. The concentration of large drops, however, can be so low that a chance to capture them in the elementary volume is rare. Thus the drop ensemble assumption is not always true, though classical radiative transfer theory uses this assumption to simplify the radiative transfer process, as if scattering takes place from an ''average drop'' rather than from a particular drop. The theoretical analysis presented in this paper demonstrates that if a cumulative distribution function is used to describe drop size variability with jumps accounting for the probability of finding large drops in the elementary volume, one obtains an extra term, the Green's function, in the solution of the radiative transfer equation. The analysis of data on cloud drop size distribution acquired during the First International Satellite Cloud Climatology Project (ISCCP) Research Experiment (FIRE) field campaign clearly shows jumps in the cumulative drop size distribution; the magnitudes of the jumps are related to the frequencies of large drop occurrence. This discontinuity is primarily responsible for the additional terms that must be added to the solution to properly account for the photon interaction with the large drops. The enhancement of cloud absorption due to accounting for the ''missing solution'' exhibits a jump-like response to continuous variation in the concentration of large drops and may exceed the enhancement predicted by the ensemble-based models. The results presented here indicate that the missing term might be plausible to explain the enhanced value of the ratio of the shortwave cloud forcing at the surface to the forcing at top of the atmosphere.
Bioresponsive Polyphenol-Based Nanoparticles as Thrombolytic Drug Carriers (2022)

Thrombolytic (clot-busting) therapies with plasminogen activators (PAs) are first-line treatments against acute thrombosis and ischemic stroke. However, limitations such as narrow therapeutic windows, low success rates, and bleeding complications hinder their clinical use. Drug-loaded polyphenol-based nanoparticles (NPs) could address these shortfalls by delivering a more targeted and safer thrombolysis, coupled with advantages such as improved biocompatibility and higher stability in vivo. Herein, a template-mediated polyphenol-based supramolecular assembly strategy is used to prepare nanocarriers of thrombolytic drugs. A thrombin-dependent drug release mechanism is integrated using tannic acid (TA) to cross-link urokinase-type PA (uPA) and a thrombin-cleavable peptide on a sacrificial mesoporous silica template via noncovalent interactions. Following drug loading and template removal, the resulting NPs retain active uPA and demonstrate enhanced plasminogen activation in the presence of thrombin (1.14-fold; <i>p</i> < 0.05). Additionally, they display lower association with macrophage (RAW 264.7) and monocytic (THP-1) cell lines (43 and 7% reduction, respectively), reduced hepatic accumulation, and delayed blood clearance in vivo (90% clearance at 60 min vs 5 min) compared with the template-containing NPs. Our thrombin-responsive, polyphenol-based NPs represent a promising platform for advanced drug delivery applications, with potential to improve thrombolytic therapies.
Flavor visualization: Taste guidance in co-cooking system for coexistence (2010)

Currently we are developing a co-cooking system that helps users to make similar tasting dishes, even though users may all be in remote locations and potentially cooking at different times. Because it is difficult to explain verbally or through written media about cooking taste in the co-cooking interface system, we've researched a flavor visualization module that guides unique tastes with graphical information in the co-cooking interface system. To achieve this, firstly, we conducted literature studies to clarify the flavor and visualization. We executed user studies to extract linguistic vocabularies of flavor expressions and sensibility vocabularies from each of the expression elements of visualization and flavor. We then built connections between sensibility vocabularies from the expression elements in visualization and flavor through literature studies and user interviews. Based on this relationship grouping work, we could make a relationship table of flavor and visualization expressions that broadly contains the relationships between flavor expressions and visual expressions. We could then realize a real-time working prototype based on the relationship mapping table that we studied. This flavor visualization can tackle the task of augmenting, through cross modal interactions, feelings of tastes by visual means. In further research, we are thinking flavor visualization will express individual cooking signatures, as derived from a personal history of taste and physical cooking habits. Also, it can visualize cooking tastes that express an individual's unique taste signatures for a more precise and emotionally involved remote co-cooking experience. Through this, we are expecting possibilities for fostering intimacy and family communication using the memory triggers that come from tastes. We hope this will make us emotionally feel coexistent in separated locations, and even different times, by facilitating conversation and other sensory communication with family and friends.
The Epidemiology of Injury in ATV and Motocross Sports (2012)

Off-road motorsports are popular in rural and suburban areas, and allow for racing, recreation, and easy access to backcountry destinations. This chapter will review the incidence and types of injuries sustained in off-road motorsports. We completed a structured review of motocross and all-terrain vehicle (ATV) injuries, assessing for injury rates, risk factors, and mortality figures. Information for this study was obtained from a PubMed search under the terms 'motocross', 'motorcross', 'all-terrain vehicles', 'injury', 'motorcycle', 'ATV'. Abstracts and articles in the English language from 1980 onward were reviewed. Further statistics were obtained from the US Consumer Product Safety Commission publications. Operating vehicles off-road requires coordination, experience, and training. Motocross is an organized sport with national associations governing the competition of highly trained athletes. ATVs are used both recreationally and commercially, typically for farming and ranching. ATV use appears more dangerous that motocross, with a higher mortality rate, disproportionately for children. Both sports continue to have high rates of head, spinal cord, and extremity injury. Future prospective studies in off-road motorsports should evaluate the risk factors for injury and target specific areas for injury prevention. Improved training programs, use and improvement of safety helmets, and for ATV use, limiting access to minors, may improve the overall safety of off-road motorsports.
Enantioselective Catalytic Formation of 3-Substituted Dihydrocoumarin Derivatives (2019)

International audience
MAME: A compression function with reduced hardware requirements (2007)

Abstract. This paper describes a new compression function, MAME designed for hardware-oriented hash functions which can be used in applications with reduced hardware requirements. MAME takes a 256-bit message block and a 256-bit chaining variable as input and produces a 256-bit output. In the light of recent attacks on MD5 and SHA-1, our design strategy is very conservative, and we show that our compression function is secure against various kinds of widely known attacks with very large security margins. The simple logical operations and the hardware efficient S-boxes are used to achieve a hardware implementation of MAME requiring only 8.1 Kgates on 0.18 µm technology.
Hamster Polyomavirus Research: Past, Present, and Future (2021)

Hamster polyomavirus (Mesocricetus auratus polyomavirus 1, HaPyV) was discovered as one of the first rodent polyomaviruses at the end of the 1960s in a colony of Syrian hamsters (<i>Mesocricetus auratus</i>) affected by skin tumors. Natural HaPyV infections have been recorded in Syrian hamster colonies due to the occurrence of skin tumors and lymphomas. HaPyV infections of Syrian hamsters represent an important and pioneering tumor model. Experimental infections of Syrian hamsters of different colonies are still serving as model systems (e.g., mesothelioma). The observed phylogenetic relationship of HaPyV to murine polyomaviruses within the genus <i>Alphapolyomavirus,</i> and the exclusive detection of other cricetid polyomaviruses, i.e., common vole (Microtus arvalis polyomavirus 1) and bank vole (Myodes glareolus polyomavirus 1) polyomaviruses, in the genus <i>Betapolyomavirus</i>, must be considered with caution, as knowledge of rodent-associated polyomaviruses is still limited. The genome of HaPyV shows the typical organization of polyomaviruses with an early and a late transcriptional region. The early region encodes three tumor (T) antigens including a middle T antigen; the late region encodes three capsid proteins. The major capsid protein VP1 of HaPyV was established as a carrier for the generation of autologous, chimeric, and mosaic virus-like particles (VLPs) with a broad range of applications, e.g., for the production of epitope-specific antibodies. Autologous VLPs have been applied for entry and maturation studies of dendritic cells. The generation of chimeric and mosaic VLPs indicated the high flexibility of the VP1 carrier protein for the insertion of foreign sequences. The generation of pseudotype VLPs of original VP1 and VP2-foreign protein fusion can further enhance the applicability of this system. Future investigations should evaluate the evolutionary origin of HaPyV, monitor its occurrence in wildlife and Syrian hamster breeding, and prove its value for the generation of potential vaccine candidates and as a gene therapy vehicle.
Computational method to reduce the search space for directed protein evolution (2001)

We introduce a computational method to optimize the in vitro evolution of proteins. Simulating evolution with a simple model that statistically describes the fitness landscape, we find that beneficial mutations tend to occur at amino acid positions that are tolerant to substitutions, in the limit of small libraries and low mutation rates. We transform this observation into a design strategy by applying mean-field theory to a structure-based computational model to calculate each residue's structural tolerance. Thermostabilizing and activity-increasing mutations accumulated during the experimental directed evolution of subtilisin E and T4 lysozyme are strongly directed to sites identified by using this computational approach. This method can be used to predict positions where mutations are likely to lead to improvement of specific protein properties.
LOWERING THE WEAR OF PUMP TUBES BY STEM SLEEVES WITH A HARD ALLOY (1979)

The value of the wear of the tube samples was measured at six points of the friction path along the length of the stroke of the sleeve. The wear of the sleeves was determined from the decrease in the diameter at the bands. The experiments (whose results are given in Table 1) showed that the wear of stem sleeves with facing bands in both versions, and of the pump tubes working in a pair with them, decreased in comparison with massproduced sleeves hardened by a high-frequency current and with sleeves. As can be seen from Fig. 2, tubes working in a pair with faced sleeves have a smooth surface without damage, differing from the friction surface of a tube, with breaks and scorings, worn by sleeves; the friction surface of a tube tested in a pair with hardened sleeves, does not have this kind of impermissible damage. An analysis of the microstructure of the tubes constitutes evidence that, with the friction of hardened (including by a high-frequency current) sleeves, there is oxidational wear of the metals unlike the seizing of sleeves. A comparison of the results of the wear of sleeves faced with a hard alloy and hardened by a high- frequencycurrentwit h sleeves (with an analysis of the macrostructure of the samples) shows that this kind of facing greatly decreases the wear of a friction pair by the elimination of seizing of the untreated
In Search of Low- k Dielectrics (1999)

Within the next few years, high-performance chips containing as many as 0.5 billion transistors on a single chip will be produced, containing up to 10,000 meters of on-chip wiring. However, such increased device and wiring densities cannot be achieved with currently used materials. The search is now on for materials that can replace silicon dioxide as the insulator in these future devices. But despite a bewildering number of candidate materials under investigation, a clear winner has yet to emerge.