gebhart/patrepeval huggingface dataset:
Ca2+-Dependent, Phospholipid-Binding Residues of Synaptotagmin Are Critical for Excitation–Secretion CouplingIn Vivo (2008)

Synaptotagmin I is the Ca(2+) sensor for fast, synchronous release of neurotransmitter; however, the molecular interactions that couple Ca(2+) binding to membrane fusion remain unclear. The structure of synaptotagmin is dominated by two C(2) domains that interact with negatively charged membranes after binding Ca(2+). In vitro work has implicated a conserved basic residue at the tip of loop 3 of the Ca(2+)-binding pocket in both C(2) domains in coordinating this electrostatic interaction with anionic membranes. Although results from cultured cells suggest that the basic residue of the C(2)A domain is functionally significant, such studies provide contradictory results regarding the importance of the C(2)B basic residue during vesicle fusion. To directly test the functional significance of each of these residues at an intact synapse in vivo, we neutralized either the C(2)A or the C(2)B basic residue and assessed synaptic transmission at the Drosophila neuromuscular junction. The conserved basic residues at the tip of the Ca(2+)-binding pocket of both the C(2)A and C(2)B domains mediate Ca(2+)-dependent interactions with anionic membranes and are required for efficient evoked transmitter release. Our results directly support the hypothesis that the interactions between synaptotagmin and the presynaptic membrane, which are mediated by the basic residues at the tip of both the C(2)A and C(2)B Ca(2+)-binding pockets, are critical for coupling Ca(2+) influx with vesicle fusion during synaptic transmission in vivo. Our model for synaptotagmin's direct role in coupling Ca(2+) binding to vesicle fusion incorporates this finding with results from multiple in vitro and in vivo studies.
Modulation of Vascular Human Endothelial and Rat Smooth Muscle Cell Growth by a Fucosylated Chondroitin Sulfate from Echinoderm (2000)

Fucosylated chondroitin sulfate is a glycosaminoglycan extracted from the sea cucumber Ludwigothurea grisea. This polysaccharide has the same structure as a mammalian chondroitin sulfate but some of the glucuronic acid residues display sulfated fucose branches. Anticoagulant and antithrombotic properties of fucosylated chondroitin sulfate have already been described. In order to further investigate its potential therapeutic use as an antithrombotic agent, we studied its effect on vascular smooth muscle cell (SMC) proliferation and endothelial cell proliferation, migration and Tissue Factor Pathway Inhibitor (TFPI) release. The experiments were performed on SMC from rat thoracic aorta and on human umbilical vein endothelial cell (HUVEC) in culture with or without added fibroblast growth factors (FGF-1 and FGF-2). Our results showed that: (i) fucosylated chondroitin sulfate had a strong inhibitory effect on SMC proliferation (IC50 =10 +/- 5 microg/ml) and (ii) no effect on HUVEC proliferation and migration assays, in the absence of exogenous FGF, while heparin had inhibitory effects; (iii) fucosylated chondroitin sulfate (10 microg/ml) enhanced FGF-1 and FGF-2 induced HUVEC proliferation by 45% (145.4 +/- 7.2%) and 27% (126.9 +/- 4.2%), respectively; (iv) on FGF-induced HUVEC migration, fucosylated chondroitin sulfate (10 microg/ml) had a strong enhancing effect with FGF-1, +122% (222.2 +/- 15.8%), three times higher than that of heparin, and a lower enhancing effect with FGF-2, +43% (142.7 +/- 4.6%), whereas heparin had no effect; (v) fucosylated chondroitin sulfate stimulated TFPI release, mainly on the free form. +98% (198.2 +/- 25%). In addition, the structural features of the polysaccharide associated with its biological activity were resolved using chemically modified fucosylated chondroitin sulfates. Sulfated fucose branches groups are essential to the potentiating effect of the polysaccharide on HUVEC proliferation and migration. Surprisingly, removal of fucose branches from the fucosylated chondroitin sulfate did not abolish TFPI release. Finally, partial reduction of the glucuronic acid carboxyl groups limited the potentiating effect on HUVEC proliferation and migration but did not affect TFPI release. In conclusion, this fucosylated chondroitin sulfate from invertebrate origin reveals useful properties for an antithrombotic agent: inhibition of SMC proliferation, enhancement of endothelium wound repair and TFPI release. These properties on vascular cells, associated with a low bleeding tendency and an antithrombotic activity, strongly suggest its potential use as a new therapeutic agent in arterial thrombosis and restenosis, with a more favorable effect than heparin.
Unsupervised learning of human body parts from video footage (2009)

Estimation of human body postures from video footage is still one of the most challenging tasks in computer vision. Even most recent approaches in this field rely strongly on domain knowledge provided by human supervisors and are nevertheless far from operating reliably under real-world conditions. We propose to overcome these issues by integrating principles of organic computing into the posture estimation cycle, thereby relegating the need for human intervention while simultaneously raising the level of system autonomy.
Liquid crystals with restricted molecular topologies: supermolecules and supramolecular assemblies (1998)

The term liquid crystal is often associated with fascinating compounds that exhibit unusual melting or solubilisation properties, however, it also represents a unique collection of mesophases that exist between the solid state and the amorphous liquid. As such, this unique state of matter can be accessed by a wide variety of materials from low molar mass to polymeric systems. In this Feature Article we describe some recent studies concerning the liquid-crystalline behaviour of ‘in-between’ materials that have discrete molecular structures, and which are oligomeric but not low molar mass or polymeric systems. Thus, these materials could be described as having supermolecular architectures. We examine some of their mesophase properties and their abilities to form supramolecular assemblies. The development of liquid crystals that have large molecular structures or consist of large scale assemblies is one step towards creating novel self-organising systems which are of a similar dimension to certain biological materials, such as proteins.
Low temperature reduction of hexavalent chromium by a microbial enrichment consortium and a novel strain of Arthrobacter aurescens (2006)

A. aurescens, indigenous to the subsurface, has the potential to be a predominant metal reducer in enhanced, in situ subsurface bioremediation efforts involving Cr(VI) and possibly other heavy metals and radionuclides.
Cusum modelling of the dynamics of process performance improvement programmes (2006)

Purpose To evaluate the Cusum model as a means of rapid trend detection and dynamic response classifier in a low signal/noise environment. Design/methodology/approach The method used was the design and implementation of an IT system for automatic on‐line monitoring of press operator performance. Findings Operators engaged following an in‐house skills enhancement programme display a wide range of performance profiles. Research limitations/implications Identifies opportunities for further management investigation of working practices identified as leading to regression plus operators obviously learning to “work smarter, not harder”. Practical implications A range of novel performance templates based on the Cusum model have been derived and tested on 18 press operators. Originality/value The Cusum model is already well established in the literature. This case study shows that the model can be readily exploited via automatic operator performance monitoring and subsequent classification.
Comparison of Field-Theoretic Approaches in Predicting Polymer Nanocomposite Phase Behavior (2017)

Because of the considerable parameter space, efficient theoretical and simulation methods are required to predict the morphology and guide experiments in polymer nanocomposites (PNCs). Unfortunately, theoretical and simulation methods are restricted in their ability to accurately map to experiments based on necessary approximations and numerical limitations. In this study, we provide direct comparisons of two recently developed coarse-grained approaches for modeling polymer nanocomposites (PNCs): polymer nanocomposite field theory (PNC-FT) and dynamic mean-field theory (DMFT). These methods are uniquely suited to efficiently capture mesoscale phase behavior of PNCs in comparison to other theoretical and simulation frameworks. We demonstrate the ability of both methods to capture macrophase separation and describe the thermodynamics of PNCs. We systematically test how the nanoparticle morphology in PNCs is affected by a uniform probability distribution of grafting sites, common in field-based methods, versus random discrete grafting sites on the nanoparticle surface. We also analyze the accuracy of the mean-field approximation in capturing the phase behavior of PNCs. Moreover, the DMFT method introduces the ability to describe nonequilibrium phase behavior while the PNC-FT method is strictly an equilibrium method. With the DMFT method we are able to show the evolution of nonequilibrium states toward their equilibrium state and a qualitative assessment of the dynamics in these systems. These simulations are compared to experiments consisting of polystyrene grafted gold nanorods in a poly(methyl methacrylate) matrix to ensure the model gives results that qualitatively agree with the experiments. This study reveals that nanoparticles in a relatively high matrix molecular weight are trapped in a nonequilibrium state and demonstrates the utility of the DMFT framework in capturing nonequilibrium phase behavior of PNCs. Both the PNC-FT and DMFT framework are promising methods to describe the thermodynamic and nonequilibrium phase behavior of PNCs.
Synthesis and Two‐Photon Properties of Multi‐Branched Fluorophores Composed of Ladder‐Type Conjugated Cores and Functionalized Diquinoxalinylamino Peripheries (2014)

Abstract Two multipolar fluorophores using ladder‐type oligo‐( p ‐phenylene) units as the central π‐bridges and functionalized diquinoxalinylamino moieties as the peripheral groups have been synthesized and experimentally shown to manifest strong two‐photon absorption (2PA) and medium‐high up‐converted emission properties in the near‐IR (NIR) spectral region under the irradiation of femtosecond laser pulses. Tentative analysis of the structure–2PA property revealed that in the presented structural combination, diquinoxalinylamino units are useful 2PA‐enhancing subunits when properly incorporated. The π‐conjugation length of the central oligo‐( p ‐phenylene) components was also found to be one of the key parameters that relates to the magnitude of the overall molecular 2PA properties in the studied molecular system, and this structural motif provides access to highly efficient two‐photon absorbers with large two‐photon action cross‐section values.
Poly(isophthalic acid)(ethylene oxide) as a Macromolecular Modulator for Metal–Organic Polyhedra (2016)

A new strategy was developed by using a polymer ligand, poly(isophthalic acid)(ethylene oxide), to modulate the growth of metal-organic polyhedra (MOP) crystals. This macromolecular modulator can effectively control the crystal habit of several different Cu24L24 (L = isophthalic acid derivatives) MOPs. The polymer also directed the formation of MOP structures under reaction conditions that only produce metal-organic frameworks in the absence of modulator. Moreover, the polymer also enabled the deposition of MOP crystals on glass surfaces. This macromolecular modulator strategy provides an innovative approach to control the morphology and assembly of MOP particles.
Using Transformer models for gender attribution in Polish (2022)

Gender identification is the task of predicting the gender of an author of a given text. Some languages, including Polish, exhibit gender-revealing syntactic expression. In this paper, we investigate machine learning methods for gender identification in Polish. For the evaluation, we use large (780M words) corpus "He Said She Said", created by grepping (for author's gender identification) gender-revealing syntactic expressions and normalizing all these expressions to masculine form (for preventing classifiers from using syntactic features). In this work, we evaluate TF-IDF based, fastText, LSTM and RoBERTa models, differentiating self-contained and non-selfcontained approaches. We also provide a human baseline. We report large improvements using pre-trained RoBERTa models and discuss the possible contamination of test data for the best pre-trained model.
Super-wideband fine spectrum quantization for low-rate high-quality MDCT coding mode of the 3GPP EVS codec (2015)

This article presents a low bit-rate super wideband MDCT coder, which is adopted as a part of the recently standardized codec for Enhanced Voice Services. To maximize codec performance at 13.2 kbps, existing algorithms are reviewed and several new tools are introduced into the low bit-rate MDCT coder to improve the performance of the coder while coding music and mixed content. A subjective listening test demonstrates the advantage of the proposed system for 13.2 kbps when compared to AMR-WB+.
Reactivity and Application of Soluble and Polymer-Supported Phase-Transfer Catalysts (1987)

A survey of molecules capable of working as phase-transfer catalysts is presented. Special attention is devoted to quaternary onium salts, crown-ethers and cryptands, all of which have a high lipophilicity ensured by aliphatic chains. An examination is made of the structural factors and reaction conditions ruling the reactivity of anions associated with these systems. Concentrated aqueous solutions of alkali hydroxides affect the hydration and hence the reactivity of anions transferred by lipophilic cations into the organic phase, an effect strongly enhanced in the case of OH-. Lipophilic cage ligands forming very stable complexes with sodium salts are particularly efficient catalysts for reactions promoted by highly hydrophilic and slightly polarizable anions, like CH3O-, OH-, F-, etc. Polymer-supported phase-transfer catalysts (quaternary salts, crown-ethers and cryptands) are examined and their reactivity is compared with that of the corresponding soluble systems. The possible application of immobilized phase-transfer catalysts, as an alternative to soluble ones, is also critically analysed.
Discovery of HSD-621 as a Potential Agent for the Treatment of Type 2 Diabetes (2012)

11β-Hydroxysteroid dehydrogenase type 1 (11β-HSD1) catalyzes the conversion of inactive glucocorticoid cortisone to its active form, cortisol. The glucocorticoid receptor (GR) signaling pathway has been linked to the pathophysiology of diabetes and metabolic syndrome. Herein, the structure-activity relationship of a series of piperazine sulfonamide-based 11β-HSD1 inhibitors is described. (R)-3,3,3-Trifluoro-2-(5-(((R)-4-(4-fluoro-2-(trifluoromethyl)phenyl)-2-methylpiperazin-1-yl)sulfonyl)thiophen-2-yl)-2-hydroxypropanamide 18a (HSD-621) was identified as a potent and selective 11β-HSD1 inhibitor and was ultimately selected as a clinical development candidate. HSD-621 has an attractive overall pharmaceutical profile and demonstrates good oral bioavailability in mouse, rat, and dog. When orally dosed in C57/BL6 diet-induced obesity (DIO) mice, HSD-621 was efficacious and showed a significant reduction in both fed and fasting glucose and insulin levels. Furthermore, HSD-621 was well tolerated in drug safety assessment studies.
Therapeutic vaccine for chronic diseases after the COVID-19 Era (2021)

There is currently a respiratory disease outbreak caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). After rapid development, RNA vaccines and adenoviral vector vaccines were approved within a year, which has demonstrated the strong impact of preventing infectious diseases using gene therapy technology. Furthermore, intensive immunological analysis has been performed to evaluate the efficiency and safety of these vaccines, potentially allowing for rapid progress in vaccine technology. After the coronavirus disease 2019 (COVID-19) era, the novel vaccine technology developed will expand to other vaccines. We have been developing vaccines for chronic diseases, such as hypertension, for >10 years. Regarding the development of vaccines against self-antigens (i.e., angiotensin II), the vaccine should efficiently induce a blocking antibody response against the self-antigen without activating cytotoxic T cells. Therefore, the epitope vaccine approach has been proposed to induce antibody production in response to a combination of a B cell epitope and exogenous T cell epitopes through major histocompatibility complex molecules. When these vaccines are established as therapeutic options for hypertension, their administration regimen, which might be a few times per year, will replace daily medication use. Thus, therapeutic vaccines for hypertension may be a novel option to control the progression of cerebrovascular diseases. Hopefully, the accumulation of immunological findings and vaccine technology advances due to COVID-19 will provide a novel concept for vaccines for chronic diseases.
In vivo free‐breathing DTI and IVIM of the whole human heart using a real‐time slice‐followed SE‐EPI navigator‐based sequence: A reproducibility study in healthy volunteers (2015)

The slice-following DWI SE-EPI sequence is a promising solution for clinical implementation, offering a robust improved workflow for further evaluation of DWI in cardiology. Magn Reson Med 76:70-82, 2016. © 2015 Wiley Periodicals, Inc.
Novel femtosecond pulse stretcher/ compressor systems with cubic phase and wavelength tunability, and decreased alignment sensitivity (1994)

Traditional grating CPA stretcher/compres- sor systems have relied on high groove densities (~2000 1/mm) for systems operating in the 800 nm wavelength regime. While this type of setup works well for pulse durations on the order of 100-fs, operation becomes prohibitive for shorter pulsewidths due to the alignment sensitivity.
Synthesis of 3-(carboxyarylalkyl)imidazo[2,1-f][1,2,4]triazines as potential inhibitors of AMP deaminase (2008)

C-Ribosyl 1,2,4-triazolo[1,2,4]triazines which are able to undergo covalent hydration are of interest as potential inhibitors of AMP deaminase. In a search for compounds with improved bioavailability we have synthesized compounds in which the sugar has been replaced by carboxyarylalkyl based ribose phosphate mimics. The target carboxyarylalkyl imidazotriazines 11 and 12 were synthesized using a linear seven step sequence starting from simple benzoate derivatives. Alternatively, the hydroxyethyl imidazotriazine 39 is available in five steps and this synthon was used to prepare the imidazotriazines 34 and 48 in a short convergent manner.
Measurement and prediction of the thermomechanical response of shape memory alloy hybrid composite beams (2005)

Previous work at NASA Langley Research Center (LaRC) involved fabrication and testing of composite beams with embedded, pre-strained shape memory alloy (SMA) ribbons within the beam structures. That study also provided comparison of experimental results with numerical predictions from a research code making use of a new thermoelastic model for shape memory alloy hybrid composite (SMAHC) structures. The previous work showed qualitative validation of the numerical model. However, deficiencies in the experimental-numerical correlation were noted and hypotheses for the discrepancies were given for further investigation. The goal of this work is to refine the experimental measurement and numerical modeling approaches in order to better understand the discrepancies, improve the correlation between prediction and measurement, and provide rigorous quantitative validation of the numerical analysis/design tool. The experimental investigation is refined by a more thorough test procedure and incorporation of higher fidelity measurements such as infrared thermography and projection moire interferometry. The numerical results are produced by a recently commercialized version of the constitutive model as implemented in ABAQUS and are refined by incorporation of additional measured parameters such as geometric imperfection. Thermal buckling, post-buckling, and random responses to thermal and inertial (base acceleration) loads are studied. The results demonstrate the effectiveness of SMAHC structures in controlling static and dynamic responses by adaptive stiffening. Excellent agreement is achieved between the predicted and measured results of the static and dynamic thermomechanical response, thereby providing quantitative validation of the numerical tool.
Human thrombin and FXa mediate porcine endothelial cell activation; modulation by expression of TFPI‐CD4 and hirudin‐CD4 fusion proteins (2001)

Aside from their critical role in thrombosis, activated coagulation factors also have inflammatory properties and these may be important during delayed xenograft rejection (DXR). This study assessed whether porcine EC could be activated by factor Xa (FXa) and thrombin (FIIa) and whether expression of tissue factor pathway inhibitor (TFPI)-CD4 and hirudin-CD4 fusion proteins could prevent such activation. Incubation of porcine EC with human FXa and FIIa induced cell surface expression of E-selectin, VCAM and tissue factor (TF) in a time-dependent and concentration-dependent manner. In contrast, porcine EC transfected with a human TFPI-CD4 fusion protein were selectively resistant to these pro-inflammatory effects of FXa but not FIIa. Likewise, the transfectants expressing the hirudin-CD4 fusion protein were selectively resistant to the pro-inflammatory effects of FIIa but not those of FXa. When combined, the FXa and FIIa had an additive effect on the activation of control EC. In contrast, coexpression of both hirudin-CD4 and TFPI-CD4 fusion proteins completely inhibited the upregulation of VCAM with the FXa/FIIa mix. These results indicate that expression of novel anticoagulant fusion proteins on the surface of porcine EC can protect against EC activation induced by human coagulation factors FXa and FIIa. In vivo, we anticipate that expression of these fusion proteins on the endothelium of transplanted xenografts, besides preventing intravascular thrombosis, will also protect against EC activation induced by trace amounts of FIIa and FXa, thereby further protecting the grafts from DXR.
Dissolution of man-made vitreous fibers in rat alveolar macrophage culture and Gamble's saline solution: influence of different media and chemical composition of the fibers. (1994)

The effect of different chemical compositions of man-made vitreous fibers (MMVF) on their dissolution by alveolar macrophages (AM) in culture and in Gamble's solution was studied. The fibers were exposed to cultured rat AMs, culture medium alone; or Gamble's saline solution for 2, 4, or 8 days. The dissolution of the fibers was studied by measuring the amount of silicon (Si), iron (Fe), and aluminum (Al) in each medium. The AMs in culture dissolved Fe and Al from the fibers but the dissolution of Si was more marked in the cell culture medium without cells and in the Gamble's solution. The dissolution of Si, Fe, and Al was different for different fibers, and increased as a function of time. The Fe and Al content of the fibers correlated negatively with the dissolution of Si by AMs from the MMVF, i.e., when the content of Fe and Al of the fibers increased the dissolution of Si decreased. These results suggest that the chemical composition of MMVFs has a marked effect on their dissolution. AMs seem to affect the dissolution of Fe and Al from the fibers. This suggests that in vitro models with cells in the media rather than only culture media or saline solutions would be preferable in dissolution studies of MMVFs.