gebhart/patrepeval huggingface dataset:
The Streptococcus agalactiae complement interfering protein combines multiple complement‐inhibitory mechanisms by interacting with both C4 and C3 ligands (2018)

Group B Streptococcus (GBS) colonizes the human lower intestinal and genital tracts and constitutes a major threat to neonates from pregnant carrier mothers and to adults with underlying morbidity. The pathogen expresses cell-surface virulence factors that enable cell adhesion and penetration and that counteract innate and adaptive immune responses. Among these, the complement interfering protein (CIP) was recently described for its capacity to interact with the human C4b ligand and to interfere with the classical- and lectin-complement pathways. In the present study, we provide evidence that CIP can also interact with C3, C3b, and C3d. Immunoassay-based competition experiments showed that binding of CIP to C3d interferes with the interaction between C3d and the complement receptor 2/cluster of differentiation 21 (CR2/CD21) receptor on B cells. By B-cell intracellular signaling assays, CIP was confirmed to down-regulate CR2/CD21-dependent B-cell activation. The CIP domain involved in C3d binding was mapped via hydrogen deuterium exchange-mass spectrometry. The data obtained reveal a new role for this GBS polypeptide at the interface between the innate and adaptive immune responses, adding a new member to the growing list of virulence factors secreted by gram-positive pathogens that incorporate multiple immunomodulatory functions.-Giussani, S., Pietrocola, G., Donnarumma, D., Norais, N., Speziale, P., Fabbrini, M., Margarit, I. The Streptococcus agalactiae complement interfering protein combines multiple complement-inhibitory mechanisms by interacting with both C4 and C3 ligands.
Discrimination of Anionic Polysaccharides via Monomer-Excimer Switching and Photo-Induced Colorimetric Reaction of 1-Methyl-3-(N-(1,8-naphthalimidyl)ethyl)imidazolium (2018)

Abstract 1-Methyl-3-(N-(1,8-naphthalimidyl)ethyl)imidazolium can be a discriminator for anionic polysaccharides via monomer-excimer switching and photo-induced colorimetric reaction. In the system, the excimer fluorescence increases remarkably in the presence of sulfated polysaccharides. The degree of enhancement depends on the number of sulfate groups in its structure. In contrast, the degree of excimer enhancement is not significant in the presence of carboxylated polysaccharides probably due to a different photo-induced decay pathway. The solutions containing carboxylated polysaccharides certainly become yellow via a photo-induced colorimetric reaction.
Structure and View Estimation for Tomographic Reconstruction: A Bayesian Approach (2006)

This paper addresses the problem of reconstructing the density of a scene from multiple projection images produced by modalities such as x-ray, electron microscopy, etc. where an image value is related to the integral of the scene density along a 3D line segment between a radiation source and a point on the image plane. While computed tomography (CT) addresses this problem when the absolute orientation of the image plane and radiation source directions are known, this paper addresses the problem when the orientations are unknown - it is akin to the structure-from-motion (SFM) problem when the extrinsic camera parameters are unknown. We study the problem within the context of reconstructing the density of protein macro-molecules in Cryogenic Electron Microscopy (cryo-EM), where images are very noisy and existing techniques use several thousands of images. In a non-degenerate configuration, the viewing planes corresponding to two projections, intersect in a line in 3D. Using the geometry of the imaging setup, it is possible to determine the projections of this 3D line on the two image planes. In turn, the problem can be formulated as a type of orthographic structure from motion from line correspondences where the line correspondences between two views are unreliable due to image noise. We formulate the task as the problem of denoising a correspondence matrix and present a Bayesian solution to it. Subsequently, the absolute orientation of each projection is determined followed by density reconstruction. We show results on cryo-EM images of proteins and compare our results to that of Electron Micrograph Analysis (EMAN) - a widely used reconstruction tool in cryo-EM.
Synergistic Activity of Benzoyl Peroxide and Erythromycin (2000)

Radical activity of BP in tetraethylene glycol dimethacrylate is increased when tested in consort with several antibiotics, such as the macrolides. We propose that the tertiary amines contained on certain antibiotics are responsible for catalysis of BP radical formation. If increased radical formation correlates with enhanced biological effect, then these data reveal the possibility of a biological synergism in mixtures of BP and antibiotics. An understanding of the mechanism of catalysis of BP radical formation by antibiotics may lead to the discovery of improved treatments for acne.
Inference of a probabilistic finite state machine from its output (1995)

This paper addresses the problem of identifying a probabilistic FSM from its output. The authors propose a formal description of the FSM and its output, using a regular phrase-structured grammar. This description is associated with a cost measuring its information content. The authors then state the inference problem as a combinatorial optimization problem with an objective function define as the cost of the description of the FSM and its output. A heuristic algorithm is proposed which processes the output "on line" and yields a local minimum of the authors' criterion. At each step (i.e. as new data is observed and processed), the procedure searches locally through the space of non-probabilistic FSMs, i.e., the transitions are initially regarded as being only present or absent. When a non-probabilistic model has been generated, the transition probabilities are determined from their relative frequencies given the behavior indicated by the data. This yields maximum likelihood estimates of the probabilities. The costs of the obtained probabilistic FSMs are then computed, and the K minimum cost FSMs are kept as starting points for the next step search. At each step, the generation of the FSMs is done via a local search through the neighborhoods of the K best FSMs obtained at the previous step. This algorithm is compared with similar algorithms proposed previously, and tested on a range of examples. It is found to work for a wider range of FSMs than the previous methods, and it is much more practical for large problems than previously proposed exhaustive search techniques.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
1,4-Benzodiazepines as Inhibitors of Respiratory Syncytial Virus (2006)

Respiratory syncytial virus (RSV) is the cause of one-fifth of all lower respiratory tract infections worldwide and is increasingly being recognized as a serious threat to patient groups with poorly functioning immune systems. Our approach to finding a novel inhibitor of this virus was to screen a 20 000-member diverse library in a whole cell XTT assay. Parallel assays were carried out in the absence of virus in order to quantify any associated cell toxicity. This identified 100 compounds with IC(50)'s less than 50 muM. A-33903 (18), a 1,4-benzodiazepine analogue, was chosen as the starting point for lead optimization. This molecule was moderately active and demonstrated good pharmacokinetic properties. The most potent compounds identified from this work were A-58568 (47), A-58569 (44), and A-62066 (46), where modifications to the aromatic substitution enhanced potency, and A-58175 (42), where the amide linker was modified.
In situ study of the growth properties of Ni-rare earth silicides for interlayer and alloy systems on Si(100) (2012)

We report on the solid-phase reaction of thin Ni-rare earth films on a Si(100) substrate, for a variety of rare earth (RE) elements (Y, Gd, Dy, and Er). Both interlayer (Ni/RE/〈Si〉) and alloy (Ni-RE/〈Si〉) configurations were studied. The phase sequence during reaction was revealed using real-time x-ray diffraction whereas the elemental diffusion and growth kinetics were examined by real-time Rutherford backscattering spectrometry. All RE elements studied exert a similar influence on the solid phase reaction. Independent of the RE element or its initial distribution a ternary Ni2Si2RE phase forms, which ends up at the surface after NiSi growth. With respect to growth kinetics, the RE metal addition hampers the Ni diffusion process even for low concentrations of 2.5 at. %, resulting in the simultaneous growth of Ni-rich silicide and NiSi. Moreover, the formation of Ni2Si2RE during NiSi growth alters the Ni diffusion mechanism in the interlayer causing a sudden acceleration of the Ni silicide growth. Besides a significant effect on the silicide growth, we have found that adding 5 at. % Er (relative to Ni) lowers the NiSi Schottky barrier height on n-type Si(100) by approximately 0.1 eV for the interlayer and alloy configuration.
DNA−Block Copolymer Conjugates (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTDNA−Block Copolymer ConjugatesKeith J. Watson, So-Jung Park, Jung-Hyuk Im, , and Chad A. MirkinView Author Information Department of Chemistry, Northwestern University 2145 Sheridan Road, Evanston, Illinois 60208 Cite this: J. Am. Chem. Soc. 2001, 123, 23, 5592–5593Publication Date (Web):May 18, 2001Publication History Received16 February 2001Revised18 April 2001Published online18 May 2001Published inissue 1 June 2001https://pubs.acs.org/doi/10.1021/ja0156845https://doi.org/10.1021/ja0156845rapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views2078Altmetric-Citations87LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Chemical structure,Copolymers,Genetics,Melting,Polymers Get e-Alerts
Synthesis at the Interface of Chemistry and Biology (2014)

The feature that perhaps most distinguishes chemistry from the rest of the sciences is the ability of chemists to control the structure of matter at the molecular level. Unfortunately, we are not nearly as adept at the synthesis of molecules with defined functions as we are at the synthesis of molecules with defined structures. As the focus of chemistry increasingly shifts from structure to function, chemists will need to develop better strategies to efficiently generate molecules, and systems of molecules, with desired physical, chemical, or biological properties in order to meet the biomedical, energy, and environmental needs of the future. Indeed this challenge represents one of the great opportunities for synthesis in the coming years. One direction we can turn for help is Mother Nature: after all, living organisms carry out a remarkable array of complex functions using natural molecules and molecular assemblies. With this theme in mind, the focus of our work has been to exploit nature itself, i.e., use the synthetic strategies, molecules, and biosynthetic machinery of living organisms, together with more traditional chemical approaches, to generate molecules with properties that might be difficult to realize by chemical strategies alone.
Controlling Scratching in Cu Chemical-Mechanical Planarization (CuCMP) (2009)

In the manufacture of advanced semiconductor devices, undesirable scratches are produced during such fine-scale material removal processes as chemical-mechanical planarization (CMP). In this paper, the upper-bound loads for scratching in CMP at single-particle contacts are estimated and validated by AFM experiments on thin, homogeneous coatings. Additionally, the upper limits for the scratch width and depth are estimated and validated by polishing experiments. For a Cu surface polished on a Rohm and Haas IC1000 pad with Al2O3 or SiO2 abrasives the maximum scratch width is about one-half of the abrasive particle diameter.
Pregnane-x-receptor controls hepatic glucuronidation during pregnancy and neonatal development in humanized UGT1 mice (2012)

PXR is a key regulator of pregnancy induced glucuronidation capacity in addition to modulating the severity of neonatal jaundice.
Exact Expressions for the Far-Zone Electromagnetic Fields Radiated by Thin Elliptical Loop Antennas of Arbitrary Size (2018)

Circular loop antennas have received considerable attention over the years due to their wide range of practical applications. However, in comparison, surprisingly little research work has been devoted to the study of elliptical loop antennas, which provide designers with an additional degree of freedom to control their radiation properties. Here, a complete set of analytical expressions is derived for the vector potential and corresponding far-zone electromagnetic fields of a thin elliptical loop antenna of an arbitrary size based on a general Fourier cosine series representation of the current distribution. Furthermore, several important special cases of the general theory are considered including elliptical loop antennas with a constant and a cosinusoidal current distribution. It is also shown that for the special case when the lengths of the semimajor and semiminor axes are equivalent, the general expressions for the far-zone electromagnetic fields will reduce to well-known results for a circular loop. Finally, some example radiation pattern plots for elliptical loop antennas are generated using the exact theoretical expressions derived in this paper.
Graph Signal Compression via Task-Based Quantization (2021)

Graph signals arise in various applications, ranging from sensor networks to social media data. The high-dimensional nature of these signals implies that they often need to be compressed in order to be stored and conveyed. The common framework for graph signal compression is based on sampling, resulting in a set of continuous-amplitude samples, which in turn have to be quantized into a finite bit representation. In this work we study the joint design of graph signal sampling along with the quantization of these samples, for graph signal compression. We focus on bandlimited graph signals, and show that the compression problem can be represented as a task-based quantization setup, in which the task is to recover the spectrum of the signal. Based on this equivalence, we propose a joint design of the sampling and recovery mechanisms for a fixed quantization mapping, and present an iterative algorithm for dividing the available bit budget among the discretized samples. Our numerical evaluations demonstrate that the proposed scheme achieves reconstruction accuracy within a small gap of that achievable with infinite resolution quantizers, while compressing high-dimensional graph signals into finite bit streams.
Down-regulated MicroRNAs in Gastric Carcinoma May Be Targets for Therapeutic Intervention and Replacement Therapy (2021)

Gastric cancer is one of the leading types of cancer with an annual death toll of 700,000 worldwide. Despite the fact that several agents are approved for its treatment, high percentage of recurrence and intractability of metastatic disease remain a major problem. The identification of new targets and modalities for treatment are therefore of high priority. We have searched the literature for microRNAs down-regulated in gastric cancer with efficacy in gastric cancer-related murine xenograft models after reconstitution therapy. Among the identified miRs were 25 miRs targeting transcription factors, seven of them regulating cell-cycle and apotosis-related targets, and five of them regulating GTPase-related targets such as GAPs and GEFs. According to criteria such as prognostic impact, functional data, and tractability, miR-133 b/a (MCL1) and miR-518 (MDM2) are suggested as potentially valuable targets for further evaluation and possible treatment of gastric cancer.
Effect of plaunotol in combination with clarithromycin against clarithromycin-resistant Helicobacter pylori in vitro and in vivo (2007)

Objectives: Recently, there has been a decrease in the eradication rate of Helicobacter pylori due to the increase in antibiotic resistance of this bacterium. Plaunotol, a cytoprotective anti-ulcer agent, exhibits antibacterial activity against H. pylori. The purpose of the present study was to investigate the effect of plaunotol in combination with clarithromycin against clarithromycin-resistant H. pylori clinical isolates.
The value of stump split skin grafting following amputation for trauma in adult upper and lower limb amputees (1987)

One hundred and twenty adult patients were reviewed in whom split skin grafts were applied to the stump following traumatic amputation of the upper limb (44 amputees) or lower limb (76 amputees). The average follow-up period was seven and a half years after initial amputation. There was delay in prosthetic fitting in all patients. Approximately one third of patients complained of occasional minor ulceration, controlled by removing the prosthesis for a few days or modification of the prosthesis. Further revision surgery, including excision of the grafted skin often combined with proximal bone resection, but not removal of the proximal joint, was necessary in 29% of below-elbow amputees and approximately 50% of below and above-knee amputees. At the above-elbow level, use of skin grafts allowed prosthetic fitting because of preservation of sufficient length of the stump. Despite the fact that revision surgery may often be necessary, split skin grafting has a definite place in the early management of the stump following traumatic limb amputation in the adult. Preservation of stump length with the knee or elbow joint allows easier rehabilitation and lower energy expenditure when using the prosthesis. Partial foot amputation, when combined with skin grafting usually requires subsequent revision to a more proximal level to obtain a satisfactory result.
A Practical Synthesis of a High‐Loading Solid‐Supported IBX Amide for the Oxidation of Alcohols. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Modeling Air-flow in the Tracheobronchial Tree using Computational Fluid Dynamics (2007)

In this paper, we present a biomechanical framework to model air-flow inside the bronchus and deformations across the tracheobronchial tree, pipeline for the simulator, theory and initial steps to realize this framework on a highly parallel graphical processing unit (GPU). We discuss the main challenges expected and encountered to date. By using computational fluid dynamics (CFD) and computational solid dynamics (CSD) principles, we propose a numerical simulation framework that includes a biomechanical model of the tracheobronchial tree to simulate air flow inside the tree, on GPU in real-time. The proposed 3D biomechanical model to simulate the air inside the lungs coupled with a deformation model of the tracheobronchial tree, expressed through fluid-structure interaction, can be used to predict the transformations of the voxels from a 4D computed tomography (4DCT) dataset. Additionally, the proposed multi-functional CFD and CSD based framework is suitable for clinical applications such as adaptive lung radiotherapy, and a regional alveolar ventilation estimation.
Matériaux Polymères et Développement Durable (2010)

The second half of the 20th century, sometimes called the plastic age, knew a boom of polymer materials in all the sectors of industrial activity. Nowadays, although polymer production is continuously growing, all the developed countries are facing new challenges regarding the rarefaction of fossil resources and the sustainable development. Many research works performed in the institutions affiliated to the Fédération Gay-Lussac aim to contribute to this field by exploring some new aspects of polymer science. They include: unusual polymerization reactions, new types of tri-dimensional networks, valorization of natural polymers, biocomposites and nano-biocomposites, durability of polymeric products
Continuous Flow Vortex Fluidic Transformation of Kombucha Cellulose into More Compact and Crystalline Fibers (2022)

A chemical-free and scalable novel route for generating more compact and crystalline cellulose from cellulosic biofilms formed at the air–water interface as an otherwise waste byproduct from the kombucha tea beverage fermentation industry has been developed. This involves processing the byproduct by treatment with aqueous 1 M NaOH at 50 °C and then 1% glacial acetic acid followed by washing with distilled water until the pH of the washing water is 7, followed by continuous flow processing in the vortex fluidic device (VFD). This thin-film microfluidic platform houses a 20 mm outside diameter and 17.5 mm inside diameter quartz tube with a hemispherical base. The induced high shear mechanical energy arising from the topological fluid flows within the thin film when the tube is tilted at θ +45° and spun at ω 6k rpm converts the kombucha cellulose to smaller fiber diameters ∼70 nm cf. ∼127 nm preVFD processing. The material is characterized using dynamic light scattering, scanning electron microscopy, atomic force microscopy, X-ray diffraction, thermogravimetric analysis/differential scanning calorimetry, Fourier transform infrared, and Brunauer–Emmett–Teller. The modification of the cellulose is understood mechanistically by the high shear topological fluid flow from the Coriolis force from the base of the tube, forcing the individual cellulose polymer strands together in an ordered array. Such transient localized high shear flow associated with high temperatures and pressures over the fibers on the surface of the tube force the backbone long cellulose strands together resulting in increased crystallinity. The findings lay the foundation for transforming a byproduct from kombucha tea beverage fermentation into unique material for other applications.
Synthesis of 1-(3-Azido-2,3-Dideoxy-Beta-D-Ribo-Hexofuranosyl)Thymine (1993)

Abstract The nucleoside derivative 1-(3-azido-2,3-dideoxy-beta-D-ribo-hexofuranosyl)thymine has been synthesized from 3-0-benzyl-1,2-0-isopropylidene-alpha-D-glucofuranose-5,6-carbonate in an overall yield of 16%. The key step in the synthesis involves the selective deacetylation of a nucleoside derivative having a cyclic carbonate moiety.