gebhart/patrepeval huggingface dataset:
Nonmonotonic Energy Dissipation in Microfluidic Resonators (2009)

Nanomechanical resonators enable a range of precision measurements in air or vacuum, but strong viscous damping makes applications in liquid challenging. Recent experiments have shown that fluid damping is greatly reduced in fluidic embedded-channel microcantilevers. Here we report the discovery of nonmonotonic energy dissipation due to the fluid in such devices, which leads to the intriguing prospect of enhancing the quality factor upon miniaturization. These observations elucidate the physical mechanisms of energy dissipation in embedded-channel resonators and thus provide the basis for numerous applications in nanoscience and biology.
Development of a helper-independent human adenovirus vector and its use in the transfer of the herpes simplex virus thymidine kinase gene (1986)

Approximately 2 kilobases (kb) of additional DNA can be packaged into wild-type virions of human adenovirus type 5 (Ad5). To extend this limit, a helper independent Ad5 cloning vector was constructed by deleting most of early region 3 (E3) from map coordinates 78.5 to 84.7 and essentially all of early region 1 (E1) from coordinates 1.0 to 10.6. E3 is nonessential for adenovirus replication in cultured cells, and E1 is nonessential when the virus is propagated in 293 cells which constitutively express the E1 gene products. The resulting new virus, dlE1,3 is about 5.5 kb shorter than wild-type Ad5 and therefore should be able to accept up to 7.5 kb in foreign DNA. To test the usefulness of this vector, the herpes simplex virus type 1 (HSV-1) thymidine kinase gene (tk) along with its regulatory sequences was inserted into the unique XbaI site of dlE1,3 (at map position 78.5/84.7). The resulting recombinant virus, Adtk, expressed the HSV tk at a low level (as compared with HSV-1) in infected cells; however, tk expression was markedly enhanced when Adtk-infected cells were superinfected with a tk- mutant of HSV. Furthermore, the Adtk virus efficiently transformed tk- mouse cells (line LTA) to the tk+ phenotype. At a low efficiency, it was also possible to transform tk- human cells (line 143), and tk+ transformants of both mouse and human origin have been established as permanent lines.
Nucleosides. XIII. Synthesis of 3'-Amino-3'-deoxy-arabinosyl-uracil via 2',3'-Epoxy-lyxosyl Nucleosides1-3 (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNucleosides. XIII. Synthesis of 3'-Amino-3'-deoxy-arabinosyl-uracil via 2',3'-Epoxy-lyxosyl Nucleosides1-3JOHN F. CODINGTON, RONALD FECHER, and JACK J. FOXCite this: J. Org. Chem. 1962, 27, 1, 163–167Publication Date (Print):January 1, 1962Publication History Published online1 May 2002Published inissue 1 January 1962https://pubs.acs.org/doi/10.1021/jo01048a040https://doi.org/10.1021/jo01048a040research-articleACS PublicationsRequest reuse permissionsArticle Views225Altmetric-Citations40LEARN 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-Alertsclose Get e-Alerts
Location inference using microblog messages (2012)

In order to sense and analyze disaster information from social media, microblogs as sources of social data have recently attracted attention. In this paper, we attempt to discover geolocation information from microblog messages to assess disasters. Since microblog services are more timely compared to other social media, understanding the geolocation information of each microblog message is useful for quickly responding to a sudden disasters. Some microblog services provide a function for adding geolocation information to messages from mobile device equipped with GPS detectors. However, few users use this function, so most messages do not have geolocation information. Therefore, we attempt to discover the location where a message was generated by using its textual content. The proposed method learns associations between a location and its relevant keywords from past messages, and guesses where a new message came from.
Revisiting the role of IL‐2 in autoimmunity (2010)

IL-2 was discovered as a T-cell growth factor that promoted T-cell-dependent immune responses; however, more recent studies suggest that the essential role of IL-2 is to maintain functional Treg and thus control immune responses. These results are leading to new ideas about the potential of IL-2 as a therapeutic strategy in autoimmune diseases. In this issue of the European Journal of Immunology, a study further examines the role of IL-2 in immune regulation and shows for the first time that IL-2 complexes can ameliorate autoantibody-mediated autoimmunity. This commentary examines the current findings in relation to what we already know about IL-2 complexes.
Parametric Analysis of Cross-Frame Layout on Distortion-Induced Fatigue in Skewed Steel Bridges (2012)

The effects of skew angle, cross-frame spacing, cross-frame layout, cross-frame stiffness, and load placement on the potential for distortion-induced fatigue damage in steel bridges was investigated by performing a suite of more than 1,000 analysis jobs of high-resolution three-dimensional finite-element models. Susceptibility to fatigue damage was quantified in terms of computed stress demand in the web gap region of the girders. Bridge configurations with three different cross-frame layouts were evaluated, including configurations with cross-frames placed parallel to skew angle (skewed-parallel) and perpendicular to the girder line, both staggered (skewed-staggered) and unstaggered (skewed-unstaggered). Skew angles of configurations evaluated ranged between 0 and 50°, and cross-frame spacing ranged from 2.29 to 9.14 m (7.50 to 30.0 ft). Influence and envelope surfaces were constructed to show the relationship between load placement, location of the maximum web gap stress, and the magnitude of the maximum web gap stress. It was found that maximum web gap stress always occurred when loads were positioned directly above the intersection of a cross-frame and girder web. The parametric study showed that cross-frame stiffness and spacing had a significant effect on the susceptibility to distortion-induced fatigue damage; greater cross-frame stiffness resulted in higher web gap stresses, and increased cross-frame spacing resulted in increased web gap stresses. It was also found that the bridge configuration was key to determining the location of the web gaps where damage is most likely to occur. In skewed-parallel and skewed-unstaggered layouts, maximum web gap stresses were identified in top web gaps, whereas in skewed-staggered configurations, maximum stresses occurred in bottom web gaps. It was found that in configurations with staggered cross-frames, maximum web gap stresses tended to occur in regions of support, where cross-frames are often placed back-to-back along the skewed alignment.
Gene complementation using myoblast transfer into fetal muscle. (1994)

Gene complementation by myoblast transfer into neonatal or adult muscle has been proposed as a therapy for primary myopathies as well as to augment non-muscle gene products that may be diminished in the adult circulation. This paper describes a technique whereby myoblasts have been injected into limb muscles of normal and dystrophin-deficient (mdx) fetal mice (during the period of active myotube formation and prior to the development of the host's immune competence) without significantly interfering with fetal viability or further maturation. More mosaic myofibers (myofibers containing both host- and donor-derived myonuclei) appear to result from these transfers than have been reported following myoblast transfer into neonatal muscle or adult muscle. The small size of the fetal hosts' muscles and the lack of well-defined connective tissue septa facilitate migration of donor myoblasts into muscle groups distal to the injection site. The use of donor myoblasts derived from a tetraploid variant of a mouse myogenic cell line (MM14) provides a convenient and permanent cytological marker for the recognition of donor myoblasts and donor-derived myonuclei. When MM14 myoblasts are injected into mdx fetuses, whose muscles lack dystrophin, mosaic myofibers contain sufficient dystrophin to be visualized with routine immunohistochemical techniques. The myoblast transfer system, using fetal hosts, described in this study will facilitate the evaluation of myoblasts as vectors to overcome genetic deficiencies that may be manifested during fetal development.
Eukaryotic transcription factors: paradigms of protein intrinsic disorder (2017)

Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains targeting specific <i>cis</i>-acting elements in genes, and by the significant lack of fixed tertiary structure in their extensive intrinsically disordered regions. Recent research in protein intrinsic disorder (ID) has changed our understanding of transcriptional activation domains from 'negative noodles' to ID regions with function-related, short sequence motifs and molecular recognition features with structural propensities. This review focuses on molecular aspects of TFs, which represent paradigms of ID-related features. Through specific examples, we review how the ID-associated flexibility of TFs enables them to participate in large interactomes, how they use only a few hydrophobic residues, short sequence motifs, prestructured motifs, and coupled folding and binding for their interactions with co-activators, and how their accessibility to post-translational modification affects their interactions. It is furthermore emphasized how classic biochemical concepts like allostery, conformational selection, induced fit, and feedback regulation are undergoing a revival with the appreciation of ID. The review also describes the most recent advances based on computational simulations of ID-based interaction mechanisms and structural analysis of ID in the context of full-length TFs and suggests future directions for research in TF ID.
Attention-Based Natural Language Person Retrieval (2017)

Following the recent progress in image classification and captioning using deep learning, we develop a novel natural language person retrieval system based on an attention mechanism. More specifically, given the description of a person, the goal is to localize the person in an image. To this end, we first construct a benchmark dataset for natural language person retrieval. To do so, we generate bounding boxes for persons in a public image dataset from the segmentation masks, which are then annotated with descriptions and attributes using the Amazon Mechanical Turk. We then adopt a region proposal network in Faster R-CNN as a candidate region generator. The cropped images based on the region proposals as well as the whole images with attention weights are fed into Convolutional Neural Networks for visual feature extraction, while the natural language expression and attributes are input to Bidirectional Long Short- Term Memory (BLSTM) models for text feature extraction. The visual and text features are integrated to score region proposals, and the one with the highest score is retrieved as the output of our system. The experimental results show significant improvement over the state-of-the-art method for generic object retrieval and this line of research promises to benefit search in surveillance video footage.
NHE3 Regulatory Factor 1 (NHERF1) Modulates Intestinal Sodium-dependent Phosphate Transporter (NaPi-2b) Expression in Apical Microvilli (2012)

P(i) uptake in the small intestine occurs predominantly through the NaPi-2b (SLC34a2) co-transporter. NaPi-2b is regulated by changes in dietary P(i) but the mechanisms underlying this regulation are largely undetermined. Sequence analyses show NaPi-2b has a PDZ binding motif at its C terminus. Immunofluorescence imaging shows NaPi-2b and two PDZ domain containing proteins, NHERF1 and PDZK1, are expressed in the apical microvillar domain of rat small intestine enterocytes. Co-immunoprecipitation studies in rat enterocytes show that NHERF1 associates with NaPi-2b but not PDZK1. In HEK co-expression studies, GFP-NaPi-2b co-precipitates with FLAG-NHERF1. This interaction is markedly diminished when the C-terminal four amino acids are truncated from NaPi-2b. FLIM-FRET analyses using tagged proteins in CACO-2(BBE) cells show a distinct phasor shift between NaPi-2b and NHERF1 but not between NaPi-2b and the PDZK1 pair. This shift demonstrates that NaPi-2b and NHERF1 reside within 10 nm of each other. NHERF1(-/-) mice, but not PDZK1(-/-) mice, had a diminished adaptation of NaPi-2b expression in response to a low P(i) diet. Together these studies demonstrate that NHERF1 associates with NaPi-2b in enterocytes and regulates NaPi-2b adaptation.
Induction and Measurement of Cytotoxic T Lymphocyte Activity (2018)

Abstract Cytotoxic T cells (CTLs) are important immune effector cells in the adaptive immune response. It has been well documented that CTLs are important in host immune responses to viral and bacterial intracellular pathogens, tumors, and transplanted tissues. The properties of CTLs have been studied extensively in murine models, and their roles validated in the human setting. Frequently, the presence of these cells correlates well with protective immunity, so the ability to readily measure the activity of these cells is an important immunological measurement. In this unit, several assays are described that are commonly utilized to induce CTLs and to measure CTL activity both in vitro and in vivo . These assays are adaptable to many experimental and/or disease models, and in the case of the in vitro assays can be applied to measure CTL activity in human samples. © 2018 by John Wiley &amp; Sons, Inc.
High Conductivity La2-xSrxCu1-y(Mg, Al)yO4 Solid State Metal Oxide Gas Sensors with the K2NiF4 Structure (2006)

Materials of the K2NiF4 structure type have been identified as new highly conducting conductometric gas sensors. The materials of interest are based on substituted La2CuO4, a known superconducting material at low temperatures. La2CuO4 has been substituted with Sr for La and with Al or Mg for Cu, and sensitivity was demonstrated toward CO, NH3, and NO2 gases at temperatures in the range 300−600 °C. The level and type of substitution can be adjusted to enhance selectivity and minimize humidity interference. As a result of the relatively high conductivity of these sensor materials there is great potential for miniaturization of devices for use in small area applications. Uncomplicated electrode requirements also mean a simplification of the manufacturing of these new devices.
Improved Training Speed, Accuracy, and Data Utilization Through Loss Function Optimization (2020)

As the complexity of neural network models has grown, it has become increasingly important to optimize their design automatically through metalearning. Methods for discovering hyperparameters, topologies, and learning rate schedules have lead to significant increases in performance. This paper shows that loss functions can be optimized with metalearning as well, and result in similar improvements. The method, Genetic Lossfunction Optimization (GLO), discovers loss functions de novo, and optimizes them for a target task. Leveraging techniques from genetic programming, GLO builds loss functions hierarchically from a set of operators and leaf nodes. These functions are repeatedly recombined and mutated to find an optimal structure, and then a covariance-matrix adaptation evolutionary strategy (CMA-ES) is used to find optimal coefficients. Networks trained with GLO loss functions are found to outperform the standard cross-entropy loss on standard image classification tasks. Training with these new loss functions requires fewer steps, results in lower test error, and allows for smaller datasets to be used. Loss function optimization thus provides a new dimension of metalearning, and constitutes an important step towards AutoML.
Motion segmentation based on factorization method and discriminant criterion (1999)

A motion segmentation algorithm based on factorization method and discriminant criterion is proposed. This method uses a feature with the most useful similarities for grouping, selected using motion information calculated by factorization method and discriminant criterion. A group is extracted based on discriminant analysis for the selected feature's similarities. The same procedure is applied recursively to the remaining features to extract other groups. This grouping is robust against noise and outliers because features with no useful information are automatically rejected. Numerical computation is simple and stable. No prior knowledge is needed on the number of objects. Experimental results are shown for synthetic data and real image sequences.
Treatment of Mice with the Neutrophil-Depleting Antibody RB6-8C5 Results in Early Development of Experimental Lyme Arthritis via the Recruitment of Gr-1 − Polymorphonuclear Leukocyte-Like Cells (2004)

Recently, we demonstrated that blocking the entry of neutrophils into Borrelia burgdorferi-infected joints in mice deficient in the chemokine receptor CXCR2 prevented the development of experimental Lyme arthritis. Neutrophils were marginalized in blood vessels at the site of infection but could not enter the joint tissue. In the present study, we treated both genetically arthritis-resistant DBA/2J (DBA) and arthritis-susceptible C3H/HeJ (C3H) mice with the neutrophil-depleting monoclonal antibody RB6-8C5 (RB6) to determine the effect on arthritis development. Surprisingly, both DBA and C3H mice treated with RB6 developed arthritis at 1 week postinfection, approximately 1 week earlier than the control-treated C3H mice. The early development of arthritis in the RB6-treated mice was accompanied by an influx into the joints of cells with ring-shaped polymorphonuclear leukocyte (PMN) cell morphology that were negative for the Gr-1 neutrophil maturation marker. RB6 treatment of mice also resulted in increased numbers of B. burgdorferi cells in the joints at 7 days postinfection and earlier expression of the chemokines KC and monocyte chemoattractant protein 1 in the joints compared to control-treated animals. Together, these results suggest that recruitment of neutrophils or PMN-like cells into an infected joint is a key requirement for Lyme arthritis development and that altered recruitment of these cells into the joints of arthritis-resistant mice can exacerbate the development of pathology.
Late First-Trimester Invasive Prenatal Diagnosis: Results of an International Randomized Trial (2004)

I
Mesoporous Platinum Films from Lyotropic Liquid Crystalline Phases (1997)

The lyotropic liquid crystalline phases of surfactants exhibit a rich polymorphism of structures that have long-range periodicities and whose characteristic repeat distances range from 2 to 15 nanometers. The electrochemical reduction of platinum salts confined to the aqueous environments of these phases leads to the deposition of platinum films that have a well-defined long-ranged porous nanostructure and high specific surface areas. These results suggest that the use of liquid crystalline plating solutions could be a versatile way to create mesoporous electrodes for batteries, fuel cells, electrochemical capacitors, and sensors.
Electron-energy-loss spectra and the structural stability of nickel oxide:  An LSDA+U study (1998)

We demonstrate how by taking better account of electron correlations in the $3d$ shell of metal ions in nickel oxide it is possible to improve the description of both electron energy loss spectra and parameters characterizing the structural stability of the material compared with local spin density functional theory.
MR-based technology for in vivo detection, characterization, and quantification of pathology of relapsing-remitting multiple sclerosis. (2002)

In relapsing-remitting (RR) multiple sclerosis (MS), conventional magnetic resonance (MR) imaging (MRI) has proved to be a valuable tool to assess the lesion burden and activity over time. However, conventional MRI cannot characterize and quantify the tissue damage within and outside such lesions and only can provide some gross measures reflecting the presence of irreversible tissue damage, such as the load of T1 "black holes" and the severity of brain or cord atrophy. Other MR-based techniques, including cell-specific imaging, magnetization transfer (MT) MRI (MT-MRI), diffusion-weighted (DW) MRI (DW-MRI), proton magnetic resonance spectroscopy (1H-MRS), and functional MRI (fMRI), have the potential to overcome this limitation and, consequently, to provide additional information about the nature and the extent of MS tissue damage, which would inevitably remain undetected when only a conventional MRI is obtained. Cell-specific imaging should result in a better definition of the cellular mechanisms associated with MS inflammation. Metrics derived from MT- and DW-MRI can quantify the structural changes occurring within and outside lesions visible on conventional MRI scans. 1H-MRS could add information on the biochemical nature of such changes. fMRI is a promising technique to assess the mechanisms of cortical reorganization, which may limit the consequences of an MS-related injury. The application of these MR techniques to the study of RRMS is likely to provide useful insights into the pathophysiology of this disease and to improve our ability to assess the efficacy of experimental treatments.
A general purpose RNA-cleaving DNA enzyme (1997)

An in vitro selection procedure was used to develop a DNA enzyme that can be made to cleave almost any targeted RNA substrate under simulated physiological conditions. The enzyme is comprised of a catalytic domain of 15 deoxynucleotides, flanked by two substrate-recognition domains of seven to eight deoxynucleotides each. The RNA substrate is bound through Watson-Crick base pairing and is cleaved at a particular phosphodiester located between an unpaired purine and a paired pyrimidine residue. Despite its small size, the DNA enzyme has a catalytic efficiency (kcat/Km) of approximately 10(9) M-1.min-1 under multiple turnover conditions, exceeding that of any other known nucleic acid enzyme. Its activity is dependent on the presence of Mg2+ ion. By changing the sequence of the substrate-recognition domains, the DNA enzyme can be made to target different RNA substrates. In this study, for example, it was directed to cleave synthetic RNAs corresponding to the start codon region of HIV-1 gag/pol, env, vpr, tat, and nef mRNAs.
Layered Structures Constructed from New Linkages of Ge7(O,OH,F)19 Clusters. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.