gebhart/patrepeval huggingface dataset:
Molecular Mechanisms of Cryoprotection in Aqueous Proline:  Light Scattering and Molecular Dynamics Simulations (2008)

Free proline amino acid is a natural cryoprotectant expressed by numerous organisms under low-temperature stress. Previous reports have suggested that complex assemblies underlie its functional properties. We investigate here aqueous proline solutions as a function of temperature using combinations of Raman spectroscopy, Rayleigh-Brillouin light scattering, and molecular dynamics simulations with the view to revealing the molecular origins of the mixtures' functionality as a cryoprotectant. The evolution of the Brillouin frequency shifts and line widths with temperature shows that, above a critical proline concentration, the water-like dynamics is suppressed and viscoelastic behavior emerges: Here, the Landau-Placzek ratio also shows a temperature-independent maximum arising from concentration fluctuations. Molecular dynamics simulations reveal that the water-water correlations in the mixtures depend much more weakly on temperature than does bulk water. By contrast, the water OH Raman bands exhibit strong red-shifts on cooling similar to those seen in ices; however, no evidence of ice lattice phonons is observed in the low-frequency spectrum. We attribute this primarily to enhanced proline-water hydrogen bonding. In general, the picture that emerges is that aqueous proline is a heterogeneous mixture on molecular length scales (characterized by significant concentration fluctuations rather than well-defined aggregates). Simulations reveal that proline also appears to suppress the normal dependence of water structure on temperature and preserves the ambient-temperature correlations even in very cold solutions. The water structure in cold proline solutions therefore appears to be similar to that at a higher effective temperature. This, coupled with the emergence of glassy dynamics offers a molecular explanation for the functional properties of proline as a cryoprotectant without the need to invoke previously proposed complex aggregates.
Class III HD‐Zip gene regulation, the golden fleece of ARGONAUTE activity? (2004)

MicroRNAs, small noncoding RNAs, are implicated in gene regulation in both metazoans and plants. In plants, many of the targets of miRNA-mediated gene regulation encode transcription factors with functions in development, such as the Class III HD-Zip gene family whose members direct polarity establishment in leaves and vasculature. Three recent papers provide insight into how miRNAs, likely acting through a complex containing an Argonaute protein, regulate Class III HD-Zip gene expression in Arabidopsis and maize.1-3 While the precise biological activity of Argonaute proteins remains an enigma, ARGONAUTE1 in Arabidopsis is required for the proper regulation of miRNA165/166, which targets cleavage of Class III HD-Zip mRNAs. Consistent with their proposed role in negative regulation, expression of miRNA165/166 is complementary to that of Class III HD-Zip gene expression, but this is perturbed in agronaute1 mutants. Determining how these complementary patterns of expression are formed should lead us closer to an understanding of the molecular mechanisms by which asymmetry is established in developing leaves.
The Lymphocyte Metalloprotease MDC-L (ADAM 28) Is a Ligand for the Integrin α4β1 (2002)

The interaction of lymphocytes with other cells is critical for normal immune surveillance and response. MDC-L (ADAM 28), a member of the ADAM (a disintegrin and metalloprotease) protein family, is expressed on the surface of human lymphocytes. ADAMs possess a disintegrin-like domain similar in sequence to small non-enzymatic snake venom peptides that act as integrin antagonists. We report here that the disintegrin domain of MDC-L is recognized by the leukocyte integrin alpha(4)beta(1). Recombinant Fc fusion proteins possessing the disintegrin domain of MDC-L supported adhesion of the T-lymphoma cell line, Jurkat, in a concentration- and divalent cation-dependent manner. Adhesion of Jurkat cells to the disintegrin domain of MDC-L was inhibited by an anti-MDC-L monoclonal antibody (mAb), Dis1-1. The epitope for mAb Dis1-1 was localized within 59 residues of the disintegrin domain. Recombinant expression of this 59-residue fragment of the disintegrin domain also supported cell adhesion. Adhesion of Jurkat cells to the MDC-L disintegrin domain was specifically inhibited by anti-alpha(4) and anti-beta(1) function-blocking mAbs. Furthermore, adhesion of various cell lines to MDC-L correlated with expression of the integrin alpha(4)-subunit. Transfected K562 cells expressing alpha(4)beta(1) adhered to the disintegrin domain in contrast to non-transfected K562 cells. We further investigated the binding of recombinant MDC-L disintegrin domain (rDis-Fc) in solution. The rDis-Fc was found to bind to Jurkat cells in solution in a concentration-dependent and saturable manner. Both adhesion and solution binding of rDis-Fc was inhibited by the alpha(4)beta(1) ligand mimetic CS-1 peptide. Additionally, recognition of the MDC-L disintegrin domain required "activation" of lymphocyte beta(1) integrins. The interaction of MDC-L with alpha(4)beta(1) may potentially regulate metalloprotease function by targeting or sequestering the active protease on the cell surface. These results suggest a potential role for the lymphocyte ADAM, MDC-L, in the interaction of lymphocytes with alpha(4)beta(1)-expressing leukocytes.
Magnetization reversal in europium sulfide nanocrystals (2006)

The authors report the observation of the reversal in the magnetization hysteresis curve of europium sulfide nanocrystals. This phenomenon was investigated through the temperature-dependent magnetization of two classes of nanomaterials, nanocrystalline (2.0nm⩽dNCs⩽100nm) and quantum confined (dNCs⩽2.0nm), where dNCs is the diameter of the nanomaterial. The effect of the size of the nanomaterial on the magnetization is attributed to the competition between the magnetic properties of strained surface atoms and unstrained core atoms. Superconducting quantum interference device probed the magnetic response. Electron microscopy and X-ray diffraction spectroscopy revealed the crystallinity and monodispersivity of the nanomaterials.
Image retrieval with relevance feedback (2002)

The proposed system for image retrieval using multidimensional features (IRMF) characterises and matches image content in a high dimensional feature space of colour, texture and shape dimensions. By including the entire pyramid of low-, medium-, and high-level primitives, the semantics of image content at different feature levels can be represented and extracted efficiently for image retrieval. This provides accurate query formulation and improves the accuracy in the search results. By co-jointly matching image features in a multidimensional space rather than in separate independent feature spaces, the precision in image retrieval is improved from more than 50% to up to 90% for the top 10 most similar images retrieved. The impact of the information of the image's background has been mentioned in a very few published papers. Our experiments show that the efficient extraction of background information can improve the precision of image retrieval. To speed up the retrieval process, we also propose interactive relevance feedback to let the user participate in the process. The system is implemented for Internet Web access.
Site‐Targeted Interfacial Solid‐Phase Chemistry: Surface Functionalization of Organic Monolayers via Chemical Transformations Locally Induced at the Boundary between Two Solids (2016)

Effective control of chemistry at interfaces is of fundamental importance for the advancement of methods of surface functionalization and patterning that are at the basis of many scientific and technological applications. A conceptually new type of interfacial chemical transformations has been discovered, confined to the contact surface between two solid materials, which may be induced by exposure to X-rays, electrons or UV light, or by the application of electrical bias. One of the reacting solids is a removable thin film coating that acts as a reagent/catalyst in the chemical modification of the solid surface on which it is applied. Given the diversity of thin film coatings that may be used as solid reagents/catalysts and the lateral confinement options provided by the use of irradiation masks, conductive AFM probes or stamps, and electron beams in such solid-phase reactions, this approach is suitable for precise targeting of different desired chemical modifications to predefined surface sites spanning the macro- to nanoscale.
Exploiting static application knowledge in a Java compiler for embedded systems (2011)

Offering many benefits in terms of productivity and reliability, Java is becoming an attractive choice for the field of embedded computing. However, its programming model that relies on the capabilities of just-in-time compilation limits the opportunities to generate highly optimized code in an ahead-of-time compiler. In the KESO project, a Java VM for statically-configured deeply embedded systems, we have previously used static application knowledge to create a tailored runtime environment. In this paper, we present and discuss how this static knowledge can further be exploited by our compiler in order to perform advanced optimizations that would otherwise not be achievable. We conducted a case study with the CDx real-time benchmark in which we examined the peculiarities and challenges that arise, and evaluated the effectiveness of both standard and system-model-specific compiler optimizations in the context of a static embedded application model. Our results show that incorporating the available a-priori knowledge in the compiler provides significant improvements to both footprint and runtime, and can additionally help the system integrator to identify consistency problems between the code and a higher-level system specification at an early development stage.
Broad-Spectrum Antiviral Activity of the IMP Dehydrogenase Inhibitor VX-497: a Comparison with Ribavirin and Demonstration of Antiviral Additivity with Alpha Interferon (2000)

The enzyme IMP dehydrogenase (IMPDH) catalyzes an essential step in the de novo biosynthesis of guanine nucleotides, namely, the conversion of IMP to XMP. The major event occurring in cells exposed to competitive IMPDH inhibitors such as ribavirin or uncompetitive inhibitors such as mycophenolic acid (MPA) is a depletion of the intracellular GTP and dGTP pools. Ribavirin is approved as an inhaled antiviral agent for treatment of respiratory syncytial virus (RSV) infection and orally, in combination with alpha interferon (IFN-alpha), for the treatment of chronic hepatitis C virus (HCV) infection. VX-497 is a potent, reversible uncompetitive IMPDH inhibitor which is structurally unrelated to other known IMPDH inhibitors. Studies were performed to compare VX-497 and ribavirin in terms of their cytotoxicities and their efficacies against a variety of viruses. They included DNA viruses (hepatitis B virus [HBV], human cytomegalovirus [HCMV], and herpes simplex virus type 1 [HSV-1]) and RNA viruses (respiratory syncytial virus [RSV], parainfluenza-3 virus, bovine viral diarrhea virus, Venezuelan equine encephalomyelitis virus [VEEV], dengue virus, yellow fever virus, coxsackie B3 virus, encephalomyocarditis virus [EMCV], and influenza A virus). VX-497 was 17- to 186-fold more potent than ribavirin against HBV, HCMV, RSV, HSV-1, parainfluenza-3 virus, EMCV, and VEEV infections in cultured cells. The therapeutic index of VX-497 was significantly better than that of ribavirin for HBV and HCMV (14- and 39-fold, respectively). Finally, the antiviral effect of VX-497 in combination with IFN-alpha was compared to that of ribavirin with IFN-alpha in the EMCV replication system. Both VX-497 and ribavirin demonstrated additivity when coapplied with IFN-alpha, with VX-497 again being the more potent in this combination. These data are supportive of the hypothesis that VX-497, like ribavirin, is a broad-spectrum antiviral agent.
Insights into Acinetobacter War-Wound Infections, Biofilms, and Control (2010)

It is imperative to develop such effective measures as active and passive immunization to control multidrug-resistant and tenacious A baumannii infections and to prevent nonhealing wounds. The authors' understanding in immunization against burn wound-related infections by the model bacteria will facilitate research progress in the poorly explored area of immunization against war-wound biofilm infections.
APOE ε4: The most prevalent yet understudied risk factor for Alzheimer's disease (2014)

Brain pathology of Alzheimer's diseases (AD) and the genetics of autosomal dominant familial AD have been the "lamp posts" under which the AD field has been looking for therapeutic targets. Although this approach still remains valid, none of the compounds tested to date have produced clinically meaningful results. This calls for developing complementary therapeutic approaches and AD targets. The allele ε4 of apolipoprotein E4 (APOE ε4), is the most prevalent genetic risk factor for sporadic AD, and is expressed in more than half of the AD patients. However, in spite of its genetic prominence, the allele APOE ε4 and its corresponding protein product apoE4 have been understudied. We presently briefly discuss the reasons underlying this situation and review newly developed AD therapeutic approaches that target apoE4 and which pave the way for future studies.
Design and Development of a Software-Defined Underwater Acoustic Modem for Sensor Networks for Environmental and Ecological Research (2006)

This paper describes the design and successful development of an acoustic modem for potential use in underwater ecological sensor networks. The presentation includes theoretical study, design and development of both software and hardware, laboratory experiments, and the documentation and analysis of field-test results.
Origin and control of anisotropy in three dimensional printing of structural ceramics (1996)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 1996.
Lack of gurmarin sensitivity of sweet taste receptors innervated by the glossopharyngeal nerve in C57BL mice (1997)

Effects of a sweet response inhibitor, gurmarin, on responses of the chorda tympani and glossopharyngeal nerves were studied in the C57BL/KsJ strain of mice. The lingual application of gurmarin at 3.0 microg/ml (approxiamtely 0.7 microM) or more significantly suppressed chorda tympani responses to 0.5 M sucrose, as previously reported. The magnitude of gurmarin inhibition of the chorda tympani responses reached a plateau (approximately 45% of control) at 50 microg/ml (approximately 11.9 microM). In contrast, no such gurmarin inhibition of sucrose responses was observed in the glossopharyngeal nerve even at 100 microg/ml (approximately 23.8 microM). The lingual application of a proteolytic enzyme, pronase, suppressed sucrose responses to <20% of control in both chorda tympani and glossopharyngeal nerves. These results suggest differential sensitivity to gurmarin by sweet taste receptors innervated by the chorda tympani and the glossopharyngeal nerves. The former apparently possess gurmarin sensitivity, whereas most of the latter may be lacking sensitivity.
Ultrasound Biomicroscopy of the Aging Rhesus Monkey Ciliary Region (2001)

Ultrasound biomicroscopy of the living rhesus monkey ocular ciliary region was undertaken to identify age-dependent changes that might relate to the progression of presbyopia. Monkeys were anesthetized and pharmacologically cyclopleged, the eyelids were held open with a lid speculum, and sutures were placed beneath the medial and lateral rectus muscles. Ultrasound biomicroscopy imaging of the nasal and temporal quadrants of the eye were performed, and the live images were recorded to videotape. Subsequent image analysis was performed to obtain objective morphometric measurements of the ciliary body region. The ciliary body inner radius of curvature, outer radius of curvature, inner arc length, area, thickness, perimeter, zonular fiber length, and circumlental space were measured. Zonular space was calculated. The circumlental space decreased with increasing age in the temporal quadrant. The other morphologic measurements were not significantly correlated with age or body weight. Most morphologic measurements were significantly different comparing temporal vs. nasal quadrants. Bifurcation of the posterior zonular fibers was frequently observed. Although temporal circumlental space was the only measurement found to change with age, ultrasound biomicroscopy of the living rhesus ciliary region did identify distinct nasal vs. temporal asymmetries, which may reflect anatomical requirements for convergence-associated accommodation.
Anastomotic integrity after operations for large-bowel cancer: a multicentre study. (1980)

Clinically evident anastomotic dehiscence was studied in 1466 patients who had undergone resection of a large-bowel adenocarcinoma. The overall incidence of anastomotic leakage was 13%, but the incidence varied between surgeons (range 0.5% to over 30%). Morbidity and mortality were significantly higher in those patients in whom the anastomosis failed to heal primarily. If these results are extrapolated to the national level, it should be possible by achieving results closer to those in patients without leakage to reduce overall post-operative mortality after resection of large-bowel cancer by 2% and to achieve an appreciable reduction in morbidity. Both factors are clinically important and, taken together, could result in appreciable saving of revenue.
The epidermal growth factor receptor phosphorylates GTPase-activating protein (GAP) at Tyr-460, adjacent to the GAP SH2 domains. (1991)

GTPase-activating protein (GAP) stimulates the ability of p21ras to hydrolyze GTP to GDP. Since GAP is phosphorylated by a variety of activated or oncogenic protein-tyrosine kinases, it may couple tyrosine kinases to the Ras signaling pathway. The epidermal growth factor (EGF) receptor cytoplasmic domain phosphorylated human GAP in vitro within a single tryptic phosphopeptide. The same GAP peptide was also apparently phosphorylated on tyrosine in EGF-stimulated rat fibroblasts. Circumstantial evidence suggested that residue 460 might be the site of GAP tyrosine phosphorylation. This possibility was confirmed by phosphorylation of a synthetic peptide corresponding to the predicted tryptic peptide containing Tyr-460. Alteration of Tyr-460 to phenylalanine by site-directed mutagenesis diminished the in vitro phosphorylation of a bacterial GAP polypeptide by the EGF receptor. We conclude that Tyr-460 is a site of GAP tyrosine phosphorylation by the EGF receptor in vitro and likely in vivo. GAP Tyr-460 is located immediately C terminal to the second GAP SH2 domain, suggesting that its phosphorylation might have a role in regulating protein-protein interactions.
Tuning the Adsorption Properties of Zeolites as Adsorbents for CO2 Separation: Best Compromise between the Working Capacity and Selectivity (2014)

The choice of an appropriate adsorbent for CO2 separation by pressure-swing adsorption remains a field of intense research. In this work, several FAU and LTA zeolites with different Na contents (Si/Al ratios) are studied for the separation of CO2 from mixtures of CO2, CO, and CH4 by means of breakthrough experiments. The breakthrough experiments were carried out between 1 and 5 bar at 303 K using two feed mixtures: 50/50 (v/v) CO2/CH4 and 75/15/15 (v/v/v) CO2/CH4/CO. The most polar zeolites, i.e., those with high Na content, exhibit the highest adsorption capacity and selectivity for CO2, but their regeneration is difficult; hence, their working capacity is low. The opposite is true for the least polar zeolites, i.e., those with low Na content. In order to quantify the trade-off between the selectivity and working capacity, the Ruthven statistical model (RSM) was used. It satisfactorily reproduced the experimental trends. We, therefore, used the RSM to identify the properties of the adsorbent that lead to an optimal compromise between the working capacity and separation factor. The critical parameter is the concentration of extraframework cations, which, in turn, depends on the framework charge of the zeolites FAU and LTA. The optimal trade-off zone is defined in terms of the Henry constant of CO2 (KCO2). It is found that this zone is placed between KCO2 = 5 × 10–3 and 50 × 10–3 molecules·bar–1·Å–3. This interval corresponds to a heat of adsorption of CO2 at zero coverage between 27 and 32 kJ·mol–1. In our study, this optimal range of Henry constants was achieved for the zeolites Na-USY, SAPO-37, LTA (Si/Al = 5), and EMC-1.
The Same Immunoregulatory Molecules Contribute to Successful Pregnancy and Transplantation (2002)

Regulation of CD200 and MD-1 expression may control both pregnancy and allograft survival.
Advances in the Biology and Chemistry of Sialic Acids (2009)

Sialic acids are a subset of nonulosonic acids, which are nine-carbon alpha-keto aldonic acids. Natural existing sialic acid-containing structures are presented in different sialic acid forms, various sialyl linkages, and on diverse underlying glycans. They play important roles in biological, pathological, and immunological processes. Sialobiology has been a challenging and yet attractive research area. Recent advances in chemical and chemoenzymatic synthesis, as well as large-scale E. coli cell-based production, have provided a large library of sialoside standards and derivatives in amounts sufficient for structure-activity relationship studies. Sialoglycan microarrays provide an efficient platform for quick identification of preferred ligands for sialic acid-binding proteins. Future research on sialic acid will continue to be at the interface of chemistry and biology. Research efforts not only will lead to a better understanding of the biological and pathological importance of sialic acids and their diversity but also could lead to the development of therapeutics.
Enabling Anticancer Therapeutics by Nanoparticle Carriers: The Delivery of Paclitaxel (2011)

Anticancer drugs, such as paclitaxel (PTX), are indispensable for the treatment of a variety of malignancies. However, the application of most drugs is greatly limited by the low water solubility, poor permeability, or high efflux from cells. Nanoparticles have been widely investigated to enable drug delivery due to their low toxicity, sustained drug release, molecular targeting, and additional therapeutic and imaging functions. This review takes paclitaxel as an example and compares different nanoparticle-based delivery systems for their effectiveness in cancer chemotherapy.
A RIE process for submicron, silicon electromechanical structures (1992)

A reactive ion etching (RIE) process is used for the fabrication of submicron, movable single-crystal silicon (SCS) mechanical structures and capacitor actuators. The process is called SCREAM for single crystal reactive etching and metallization process. The RIE process gives excellent control of lateral dimensions (0.2 mu m approximately 2 mu m) while maintaining a large vertical depth (1 mu m approximately 4 mu m) for the formation of high aspect ratio, freely suspended SCS structures. The silicon etch processes are independent of crystal orientation and produce controllable vertical profiles. The process also incorporates process steps to form vertical, 4 mu m deep, aluminum, capacitor actuators. Using SCREAM, the authors have designed, fabricated and tested two-dimensional x-y microstages and circular SCS structures. For the x-y stage they measured a maximum displacement of +or-6 mu m in x and y with 40 V DC applied to either x or y, or both x and y actuators. The process technology offers the capability to use a structural stiffness as low as 10-2 N m-1.