gebhart/patrepeval huggingface dataset:
Adventures in Sulfur−Nitrogen Chemistry (2006)

This account reviews our efforts over the past 37 years to understand the chemistry of a select group of sulfur-nitrogen compounds including sulfinimines (N-sulfinyl imines) and N-sulfonyloxaziridines. Our early exploration of the thermal properties of sulfenamides, a class of sulfur-nitrogen compounds about which little was known, resulted in a new procedure, the silver-assisted method, for the construction of sulfenimines (N-sulfenyl imines). Selective oxidations of these compounds resulted in the production of N-sulfinyl imines (sulfinimines) and N-sulfonyloxaziridines. N-Sulfonyloxaziridines turned out to be a new class of aprotic neutral oxidizing reagents. Enantiomerically pure examples afford high ee values in the oxidation of enolates to alpha-hydroxy carbonyl compounds and in the oxidation of sulfides and selenides to sulfoxides and selenoxides. Additions of organometallic reagents to enantiomerically pure sulfinimines provide the best and most versatile method for the asymmetric construction of the carbon-nitrogen stereocenters found in many biologically active compounds. Sulfinimine-derived chiral building blocks provide efficient access to many classes of nitrogen heterocycles including aziridines, 2H-azirines, pyrrolidines, and piperidines.
Effect of Estrogen Agonists and Antagonists on Induction of Progesterone Receptor in a Rat Hypothalamic Cell Line (1999)

Estrogen is essential in the hypothalamus for the central regulation of reproduction. To understand the molecular mechanism(s) of estrogen action in the hypothalamus, immortalized rat embryonic hypothalamic cell lines were characterized for steroid receptors and subcloned. Scatchard analysis of the D12 subclone demonstrated one high affinity estrogen receptor-binding site (Kd = 31.3+/-1.9 pM) with a Bmax of 30.8+/-0.8 fmol/mg. Estrogen receptor-alpha protein was identified by Western blot and gel shift analyses. Treatment with estradiol (48 h) stimulated progesterone receptor (PR) messenger RNA expression and binding to [3H]R5020, a synthetic progestin. Because the agonist or antagonist activity of estrogen mimetics can be cell type dependent, the activities of various estrogen mimetics were determined in D12 cells. ICI 182,780 (IC50 = 0.63 nM), raloxifene (IC50 = 1 nM), enclomiphene (IC50 = 77 nM), and tamoxifen (IC50 = 174 nM) inhibited the induction of PR by estradiol, and none of these compounds significantly stimulated PR when given alone. In contrast, 17alpha-ethynyl estradiol (EC50 = 0.014 nM), zuclomiphene (EC50 = 100 nM), and genistein (EC50 = 17.5 nM) functioned as estrogen agonists in these cells. In addition, the estrogen-induced progesterone receptor activated a progesterone response element reporter construct in response to progestins. Thus, the D12 rat hypothalamic cell line provides a useful model for characterizing tissue-selective estrogenic compounds, identifying estrogen- and progesterone-regulated hypothalamic genes, and understanding the molecular mechanisms of steroid action in various physiological processes mediated by the hypothalamus.
Urinary excretion of sulphated N-acetylhexosamines in patients with various mucopolysaccharidoses (1985)

Sulphated N-acetylhexosamines have been isolated from human urine and tentatively identified as N-acetylglucosamine 6-sulphate (GlcNAc6S), N-acetylgalactosamine 6-sulphate (GalNAc6S), N-acetylgalactosamine 4-sulphate (GalNAc4S) and N-acetylgalactosamine 4,6-disulphate (GalNAc4,6diS). Urine from mucopolysaccharidosis-Type-IIID, -IVA and -VI patients compared with that from normal individuals contains elevated levels of GlcNAc6S (380-fold), GalNAc6S (180-fold) and GalNAc4S (420-fold) respectively. Urine from mucopolysaccharidosis-Type-VI patients also contain more than 600 times the normal level of GalNAc4,6diS. Urine from a mucolipidosis-Type-II and a multiple-sulphatase-deficient patient, and, in general, all mucopolysaccharidosis patients studied, contain at least 5-10-fold elevations of sulphated N-acetylhexosamines over the levels detected in urine from normal controls and a alpha-mannosidosis patient. Urine from patients with clinically mild phenotypes contains less sulphated N-acetylhexosamines than isolated from urine of clinically severe mucopolysaccharidosis patients. The source of the four sulphated N-acetylhexosamines is not known. However, incubation of a series of oligosaccharide substrates, derived from keratan sulphate and chondroitin 6-sulphate and containing non-reducing-end beta-linked 6-sulphated N-acetylhexosamine residues, with homogenates of cultured human skin fibroblasts has indirectly been shown to release GlcNA6S and GalNAc6S respectively. Release of GalNAc4S could not be demonstrated in similar incubations of oligosaccharide substrates derived from chondroitin 4-sulphate and containing non-reducing-end beta-linked GalNAc4S residues. We propose that some, if not all, of the sulphated N-acetylhexosamine present in human urine is derived from the action of beta-N-acetylhexosaminidase on sulphated GlcNAc or GalNAc residues at the non-reducing end of keratan sulphate, dermatan sulphate or chondroitin sulphate.
Use of a BamHI polymorphism in the factor IX gene for the determination of hemophilia B carrier status (1986)

A BamHI polymorphism has been identified in the human factor IX gene. This polymorphism, which occurs in approximately 6% of X chromosomes, has been used to determine the carrier status of a female in a family with a history of hemophilia B. This family was uninformative for the previously reported TaqI and Xmnl polymorphisms in the factor IX gene.
QoE-driven Unsupervised Image Categorization for Optimized Web Delivery (2014)

Due to rapid growth in the richness of web applications and the multitude of wireless devices on which web content can be consumed, optimizing the content delivery of dynamic web applications represents an important technical challenge. One of the keys to solving the wireless web performance puzzle is that of efficient image content delivery. Since the critical factor in image delivery is the end-user experience, we propose a simple quantitative metric for characterizing the Quality of Experience (QoE) for any given image that gets sent through a web delivery service (WDS) pipeline. This quantitative signature, termed VoQS (\emph{variation of quality signature}), allows any two arbitrary images to be compared in the context of web delivery performance. We then use VoQS in conjunction with an unsupervised learning algorithm to group similarly performing images into coherent groups for optimized web delivery. Using a large database of images compiled from multiple content providers and diverse device-optimized formats, we demonstrate that our approach allows large image databases to be efficiently parsed into coherent groups in a content-dependent and device-targeted manner for optimized image content delivery. Our approach significantly decreases the average bits per image that need to be delivered across large image databases (by 43\% in our experiments) while preserving the perceptual quality across the entire image database. We also discuss how such a categorization approach can be leveraged for real-time web delivery of novel image data.
A Na+ channel agonist: a potential cardiotonic agent with a novel mechanism? (2004)

British Journal of Pharmacology (2004) 143 , 663–665. doi: 10.1038/sj.bjp.0705970
The Importance of Lys-352 of Human Immunoglobulin E in FcϵRII/CD23 Recognition (2004)

The interaction of immunoglobulin E (IgE) with its low affinity receptor (FcepsilonRII/CD23) plays a central role in the initiation and regulation of type I hypersensitivity responses. We have previously identified the importance of amino acid residues in the A-B loop of the Cepsilon3 domain of human IgE and implicated a region close to the glycosylation site at asparagine 371 as contributing to IgE-CD23 interaction. These residues were now targeted by site-directed mutagenesis. The IgE-CD23 interaction was assessed by semiquantitative flow cytometry. Replacement of the entire Cepsilon3 A-B loop (residues 341-356) with the homologous rat IgE sequence resulted in complete loss of human CD23 recognition, as did replacement of residues 346-353, indicating that class-specific effector residue(s) are contained within these eight amino acids. Lysine 352 within the A-B loop was identified as contributing directly to human CD23 interaction. Mutation to the rodent homologue glycine or glutamate resulted in a significant reduction in binding compared with native IgE, whereas conservative substitution with arginine effected a small, but statistically significant, enhancement of CD23 binding. Mutation of the Cepsilon3 glycosylation site at asparagine 371 to threonine or glutamine did not significantly affect CD23 recognition. Our results yield new insights into the structural basis of the hIgE-CD23 interaction and hold promise for the rational design of drugs that can manipulate IgE-mediated regulation of the allergic response.
Distributed visualization framework architecture (2009)

An architecture for distributed and collaborative visualization is presented. The design goals of the system are to create a lightweight, easy to use and extensible framework for reasearch in scientific visualization. The system provides both single user and collaborative distributed environment. System architecture employs a client-server model. Visualization projects can be synchronously accessed and modified from different client machines. We present a set of visualization use cases that illustrate the flexibility of our system. The framework provides a rich set of reusable components for creating new applications. These components make heavy use of leading design patterns. All components are based on the functionality of a small set of interfaces. This allows new components to be integrated seamlessly with little to no effort. All user input and higher-level control functionality interface with proxy objects supporting a concrete implementation of these interfaces. These light-weight objects can be easily streamed across the web and even integrated with smart clients running on a user's cell phone. The back-end is supported by concrete implementations wherever needed (for instance for rendering). A middle-tier manages any communication and synchronization with the proxy objects. In addition to the data components, we have developed several first-class GUI components for visualization. These include a layer compositor editor, a programmable shader editor, a material editor and various drawable editors. These GUI components interact strictly with the interfaces. Access to the various entities in the system is provided by an AssetManager. The asset manager keeps track of all of the registered proxies and responds to queries on the overall system. This allows all user components to be populated automatically. Hence if a new component is added that supports the IMaterial interface, any instances of this can be used in the various GUI components that work with this interface. One of the main features is an interactive shader designer. This allows rapid prototyping of new visualization renderings that are shader-based and greatly accelerates the development and debug cycle.
Wavelet multiscale representation and morphological filtering for texture segmentation (1993)

Images are typically composed of structures or features that are scale-invariant in some sense over different spatial scales. The authors first study two scale invariant measures, fractal dimension and a D-dimensional measure both estimated by morphological filtering and used as textural features for segmenting natural textures. They show that they are independent parameters and describe different local characteristics of the irregular intensity surface of a textured image. Further, they demonstrate that the D-dimensional measure gives better clustering in feature space than fractal dimension, at least for distinguishing rural and urban textures. This simplifies segmentation efficiently. However this method suffers from what the authors call an edge effect and they point out that it is difficult to obtain anisotropic information. This leads to segmentation errors. The second part of the paper presents a novel framework which combines wavelet multiresolution decomposition and morphological filtering to effectively reject isolated edges, thus exploiting the assumption that urban texture is isotropic. Examples are given throughout.<
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DistilBERT, a distilled version of BERT: smaller, faster, cheaper and lighter (2019)

As Transfer Learning from large-scale pre-trained models becomes more prevalent in Natural Language Processing (NLP), operating these large models in on-the-edge and/or under constrained computational training or inference budgets remains challenging. In this work, we propose a method to pre-train a smaller general-purpose language representation model, called DistilBERT, which can then be fine-tuned with good performances on a wide range of tasks like its larger counterparts. While most prior work investigated the use of distillation for building task-specific models, we leverage knowledge distillation during the pre-training phase and show that it is possible to reduce the size of a BERT model by 40%, while retaining 97% of its language understanding capabilities and being 60% faster. To leverage the inductive biases learned by larger models during pre-training, we introduce a triple loss combining language modeling, distillation and cosine-distance losses. Our smaller, faster and lighter model is cheaper to pre-train and we demonstrate its capabilities for on-device computations in a proof-of-concept experiment and a comparative on-device study.
[In situ hybridization with digoxigenin-labelling oligonucleotide: an practical approach to skeletal tissues]. (1998)

The purpose of this study was to investigate the in situ hybridization technique of paraffin-embedded skeletal tissues by non-radioactive labelling oligonucleotide, Five six-week-old male SD rats were selected and the proximal epiphyseal growth plates of bilateral tibiae were removed to be decalcified in 0.5 mol/L EDTA. The tissues were embedded by paraffin and the sections were treated and hybridized with RNase-free reagents. Control groups were set to testified the sensitivity and the specificity of the experiment. The results showed that this method preserved the integrate structures and effectively detected the mRNA of the tissues. These indicated that it was an efficient and practical approach to the biomolecular research of skeletal tissue.
Epitaxial Growth of Highly Luminescent CdSe/CdS Core/Shell Nanocrystals with Photostability and Electronic Accessibility (1997)

The synthesis of epitaxially grown, wurtzite CdSe/CdS core/shell nanocrystals is reported. Shells of up to three monolayers in thickness were grown on cores ranging in diameter from 23 to 39 Å. Shell growth was controllable to within a tenth of a monolayer and was consistently accompanied by a red shift of the absorption spectrum, an increase of the room temperature photoluminescence quantum yield (up to at least 50%), and an increase in the photostability. Shell growth was shown to be uniform and epitaxial by the use of X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), high resolution transmission electron microscopy (HRTEM), and optical spectroscopy. The experimental results indicate that in the excited state the hole is confined to the core and the electron is delocalized throughout the entire structure. The photostability can be explained by the confinement of the hole, while the delocalization of the electron results in a degree of electronic accessibility that makes these nanocrystals attractive for use in optoelectronic devices.
Human autoimmune diseases: a comprehensive update (2015)

There have been significant advances in our understanding of human autoimmunity that have led to improvements in classification and diagnosis and, most importantly, research advances in new therapies. The importance of autoimmunity and the mechanisms that lead to clinical disease were first recognized about 50 years ago following the pioneering studies of Macfarlane Burnett and his Nobel Prize-winning hypothesis of the 'forbidden clone'. Such pioneering efforts led to a better understanding not only of autoimmunity, but also of lymphoid cell development, thymic education, apoptosis and deletion of autoreactive cells. Contemporary theories suggest that the development of an autoimmune disease requires a genetic predisposition and environmental factors that trigger the immune pathways that lead, ultimately, to tissue destruction. Despite extensive research, there are no genetic tools that can be used clinically to predict the risk of autoimmune disease. Indeed, the concordance of autoimmune disease in identical twins is 12-67%, highlighting not only a role for environmental factors, but also the potential importance of stochastic or epigenetic phenomena. On the other hand, the identification of cytokines and chemokines, and their cognate receptors, has led to novel therapies that block pathological inflammatory responses within the target organ and have greatly improved the therapeutic effect in patients with autoimmune disease, particularly rheumatoid arthritis. Further advances involving the use of multiplex platforms for diagnosis and identification of new therapeutic agents should lead to major breakthroughs within the next decade.
Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model (1999)

Side-chain modeling has a widespread application in many current methods for protein tertiary structure determination, prediction, and design. Of the existing side-chain modeling methods, rotamer-based methods are the fastest and most efficient. Classically, a rotamer is conceived as a single, rigid conformation of an amino acid sidechain. Here, we present a flexible rotamer model in which a rotamer is a continuous ensemble of conformations that cluster around the classic rigid rotamer. We have developed a thermodynamically based method for calculating effective energies for the flexible rotamer. These energies have a one-to-one correspondence with the potential energies of the rigid rotamer. Therefore, the flexible rotamer model is completely general and may be used with any rotamer-based method in substitution of the rigid rotamer model. We have compared the performance of the flexible and rigid rotamer models with one side-chain modeling method in particular (the self-consistent mean field theory method) on a set of 20 high quality crystallographic protein structures. For the flexible rotamer model, we obtained average predictions of 85.8% for chi1, 76.5% for chi1+2 and 1.34 A for root-mean-square deviation (RMSD); the corresponding values for core residues were 93.0%, 87.7% and 0.70 A, respectively. These values represent improvements of 7.3% for chi1, 8.1% for chi1+2 and 0.23 A for RMSD over the predictions obtained with the rigid rotamer model under otherwise identical conditions; the corresponding improvements for core residues were 6.9%, 10.5% and 0.43 A, respectively. We found that the predictions obtained with the flexible rotamer model were also significantly better than those obtained for the same set of proteins with another state-of-the-art side-chain placement method in the literature, especially for core residues. The flexible rotamer model represents a considerable improvement over the classic rigid rotamer model. It can, therefore, be used with considerable advantage in all rotamer-based methods commonly applied to protein tertiary structure determination, prediction, and design and also in predictions of free energies in mutational studies.
HVAC Systems Design Handbook (1988)

A complete, fully revised HVAC design reference. Thoroughly updated with the latest codes, technologies, and practices, this all-in-one resource provides details, calculations, and specifications for designing efficient and effective residential, commercial, and industrial HVAC systems. HVAC Systems Design Handbook, Fifth Edition, features new information on energy conservation and computer usage for design and control, as well as the most recent International Code Council (ICC) Mechanical Code requirements. Detailed illustrations, tables, and essential HVAC equations are also included. This comprehensive guide contains everything you need to design, operate, and maintain peak-performing HVAC systems
Smooth motion-compensated video deinterlacing (2011)

In this paper a smooth motion-compensated approach for video deinterlacing is proposed. The algorithm combines intra-field interpolation with overlapped-block-based motion- compensated inter-field interpolation, alleviating thus the artifacts specific to block-based motion-compensated deinterlacing schemes. Our algorithm takes into account the high-frequency content of an area and adapts the interpolation approach accordingly, such that the contours are preserved in the resulted progressive frame. Moreover, our proposal is optimized to lower heavy computation, which is the main drawback of motion-compensated deinterlacing algorithms. Experiments demonstrate a significant gain in reconstruction quality as compared to other deinterlacing implementations.
Induction and characterization of cytotoxic T‐lymphocytes recognizing a mutated p21ras peptide presented by HLA‐A*0201 (1995)

The ras oncogene is frequently found to be activated in human cancer through point mutations at codons 12, 13 or 61. We explored whether these altered p21ras protein sequences contain peptide sequences that can activate naive CD8+ cytotoxic T lymphocytes (CTL). Several wild-type and mutated p21ras peptides were identified that carry a binding motif for human leukocyte antigen (HLA)-A*0201. Two peptides were found to bind strongly to this allele. CD8+ CTL bulk cultures specifically reacting with one of these peptides could be induced, using processing-defective T2 cells loaded with peptide CLLDILDTAGL as stimulators. The peptide is derived from p21ras, position 51-61, and carries a 61 Gln-->Leu mutation. In contrast, a 9-mer peptide CLLDILDTA corresponding to amino acid sequence 51-59 of wild-type p21ras did not yield reactive CTL cultures. T-cell clones with low affinity for the 11-mer peptide were isolated from CLLDILDTAGL-reactive bulk cultures. These T cells did not lyse melanoma cells transfected with 61-Leu N-ras, although lysis was found when these transfectants were pulsed with the 11-mer peptide. Possibly, T cells of higher affinity may be required to demonstrate processed peptide on the cell surface. The combined experiments suggest that a peptide derived from mutated p21ras can be recognized by HLA class I-restricted CTL, whereas an analogous wild-type p21ras peptide may not be immunogenic.