gebhart/patrepeval huggingface dataset:
Nonspherical Colloidosomes with Multiple Compartments from Double Emulsions (2009)

Nonspherical colloidosomes with multiple compartments are generated using water-in-oil-in-water double emulsions with controlled morphology as templates (see image). Double emulsions are prepared using a glass capillary microfluidic device that provides a precise means to control the number of internal aqueous droplets and the volume ratio of oil and aqueous phases. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Consequences of knocking out BMP signaling in the mouse (2002)

During the past two decades, a significant amount of data has been accumulated revealing the intriguing functions of bone morphogenetic proteins (BMPs) in all aspects of embryonic development and organogenesis. Numerous genes encoding BMPs, BMP receptors, and their downstream signal transducers have been mutated in the mouse through targeted mutagenesis. This review focuses on what is known about the role of BMP signaling in gastrulation, mesoderm formation, left-right asymmetry, neural patterning, skeletal and limb development, organogenesis, and gametogenesis as revealed by BMP-signaling mutants.
A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model (2005)

Advances in DNA sequencing and the increasing number of sequences available in databases have greatly enhanced the bacterial identification process. Several species within the genus Mycobacterium cause serious human and animal diseases. In order to assess their relative positions in the evolutionary process, four gene fragments, from the 16S rRNA (564 bp), hsp65 (420 bp), rpoB (396 bp) and sod (408 bp) genes, were sequenced from 97 strains, including all available type strains of the genus Mycobacterium. The results demonstrate that, in this case, the concatenation of different genes allows significant increases in the power of discrimination and the robustness of the phylogenetic tree. The sequential and/or combined use of sequences of several genes makes it possible to refine the phylogenetic approach and provides a molecular basis for accurate species identification.
Rationally engineered Cas9 nucleases with improved specificity (2015)

The RNA-guided endonuclease Cas9 is a versatile genome-editing tool with a broad range of applications from therapeutics to functional annotation of genes. Cas9 creates double-strand breaks (DSBs) at targeted genomic loci complementary to a short RNA guide. However, Cas9 can cleave off-target sites that are not fully complementary to the guide, which poses a major challenge for genome editing. Here, we use structure-guided protein engineering to improve the specificity of Streptococcus pyogenes Cas9 (SpCas9). Using targeted deep sequencing and unbiased whole-genome off-target analysis to assess Cas9-mediated DNA cleavage in human cells, we demonstrate that “enhanced specificity” SpCas9 (eSpCas9) variants reduce off-target effects and maintain robust on-target cleavage. Thus, eSpCas9 could be broadly useful for genome-editing applications requiring a high level of specificity.
Automatic Face Reenactment (2014)

We propose an image-based, facial reenactment system that replaces the face of an actor in an existing target video with the face of a user from a source video, while preserving the original target performance. Our system is fully automatic and does not require a database of source expressions. Instead, it is able to produce convincing reenactment results from a short source video captured with an off-the-shelf camera, such as a webcam, where the user performs arbitrary facial gestures. Our reenactment pipeline is conceived as part image retrieval and part face transfer: The image retrieval is based on temporal clustering of target frames and a novel image matching metric that combines appearance and motion to select candidate frames from the source video, while the face transfer uses a 2D warping strategy that preserves the user's identity. Our system excels in simplicity as it does not rely on a 3D face model, it is robust under head motion and does not require the source and target performance to be similar. We show convincing reenactment results for videos that we recorded ourselves and for low-quality footage taken from the Internet.
A frame-work for live multicast of video streams over the Internet (2002)

This paper presents a frame-work for live multicast of video streams over the Internet. The overall system combines a scalable video compression algorithm, a cheap software only real-time video encoder and decoder, and a network unit. The scalable compression algorithm produces an embedded bit-stream to support decoders with various spatial and temporal resolutions. Bandwidth scalability with a dynamic range from a few Kbps to several Mbps is provided. The subjective quality of compressed frames improves significantly by the use of perceptual distortion measures. For cheap software only encoding and decoding we use hierarchical table-lookup vector quantization. Multiple multicast groups are used for the delivery of the scalable streams over the Internet.
EPO Promotes Bone Repair through Enhanced Cartilaginous Callus Formation and Angiogenesis (2014)

Erythropoietin (EPO)/erythropoietin receptor (EPOR) signaling is involved in the development and regeneration of several non-hematopoietic tissues including the skeleton. EPO is identified as a downstream target of the hypoxia inducible factor-α (HIF-α) pathway. It is shown that EPO exerts a positive role in bone repair, however, the underlying cellular and molecular mechanisms remain unclear. In the present study we show that EPO and EPOR are expressed in the proliferating, pre-hypertrophic and hypertrophic zone of the developing mouse growth plates as well as in the cartilaginous callus of the healing bone. The proliferation rate of chondrocytes is increased under EPO treatment, while this effect is decreased following siRNA mediated knockdown of EPOR in chondrocytes. EPO treatment increases biosynthesis of proteoglycan, accompanied by up-regulation of chondrogenic marker genes including SOX9, SOX5, SOX6, collagen type 2, and aggrecan. The effects are inhibited by knockdown of EPOR. Blockage of the endogenous EPO in chondrocytes also impaired the chondrogenic differentiation. In addition, EPO promotes metatarsal endothelial sprouting in vitro. This coincides with the in vivo data that local delivery of EPO increases vascularity at the mid-stage of bone healing (day 14). In a mouse femoral fracture model, EPO promotes cartilaginous callus formation at days 7 and 14, and enhances bone healing at day 28 indexed by improved X-ray score and micro-CT analysis of microstructure of new bone regenerates, which results in improved biomechanical properties. Our results indicate that EPO enhances chondrogenic and angiogenic responses during bone repair. EPO's function on chondrocyte proliferation and differentiation is at least partially mediated by its receptor EPOR. EPO may serve as a therapeutic agent to facilitate skeletal regeneration.
Distinguishing excitotoxic from apoptotic neurodegeneration in the developing rat brain (1999)

Much confusion has arisen recently over the question of whether excitotoxic neuronal degeneration can be considered an apoptotic phenomenon. Here, we addressed this question by using ultrastructural methods and DNA fragmentation analysis to compare a prototypic apoptotic in vivo central nervous system cell death process (physiologic cell death in the developing rat brain) with several central nervous system cell death processes in the in vivo infant rat brain that are generally considered excitotoxic (degeneration of hypothalamic neurons after subcutaneous administration of glutamate and acute neurodegeneration induced by hypoxia/ischemia or by concussive head trauma). We found by ultrastructural analysis that glutamate induces neurodegenerative changes in the hypothalamus that are identical to acute changes induced in the infant rat brain by either hypoxia/ischemia or head trauma, and that these changes are fundamentally different both in type and sequence from those associated with physiologic cell death (apoptosis). In addition, we show by ultrastructural analysis that concussive head trauma induces both excitotoxic and apoptotic neurodegeneration, the excitotoxic degeneration being very acute and localized to the impact site, and the apoptotic degeneration being delayed and occurring in regions distant from the impact site. Thus, in the head trauma model, excitotoxic and apoptotic degeneration can be distinguished not only by ultrastructural criteria but by their temporal and spatial patterns of expression. Whereas ultrastructural analysis provided an unambiguous means of distinguishing between excitotoxic and apoptotic neurodegeneration in each example analysed in this study, DNA fragmentation analysis (TUNEL staining or gel electrophoresis) was of no value because these tests were positive for both processes.
A constraint-based approach to rigid body dynamics for virtual reality applications (1998)

The GALILEO-system is a developmental state-of-the-art rigid body simulation tool with a strong bias to the simulation of unilateral contacts for virtual reality applications.
Sulfonation with Inversion by Mitsunobu Reaction:  An Improvement on the Original Conditions (1996)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTSulfonation with Inversion by Mitsunobu Reaction: An Improvement on the Original ConditionsNeal G. Anderson, David A. Lust, Kay A. Colapret, James H. Simpson, Mary F. Malley, and Jack Z. GougoutasView Author Information Chemical Process Technology, Pharmaceutical Research Institute, Bristol-Myers Squibb Co., P.O. Box 191, New Brunswick New Jersey 08903-0191, and Department of Solid State Chemistry, Pharmaceutical Research Institute, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton New Jersey 08543-4000 Cite this: J. Org. Chem. 1996, 61, 22, 7955–7958Publication Date (Web):November 1, 1996Publication History Received23 May 1996Published online1 November 1996Published inissue 1 January 1996https://doi.org/10.1021/jo9609539Copyright © 1996 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views2980Altmetric-Citations51LEARN 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 InReddit Read OnlinePDF (169 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Byproducts,Reaction products,Salts,Substituents,Zinc Get e-Alerts
Synthesis of Furan Derivatives. XV. 5-Nitrofuryl Polyene Aldehydes (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of Furan Derivatives. XV. 5-Nitrofuryl Polyene AldehydesHaruo Saikachi and Haru OgawaCite this: J. Am. Chem. Soc. 1958, 80, 14, 3642–3645Publication Date (Print):July 1, 1958Publication History Published online1 May 2002Published inissue 1 July 1958https://pubs.acs.org/doi/10.1021/ja01547a043https://doi.org/10.1021/ja01547a043research-articleACS PublicationsRequest reuse permissionsArticle Views203Altmetric-Citations16LEARN 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
Systemic inflammation and decline in lung function in a general population: a prospective study (2007)

Although serum CRP levels are inversely associated with lung function in cross-sectional studies, there was no effect of a marker of systemic inflammation on decline in lung function over 9 years.
Substrate specificity studies of Flavobacterium chondroitinase C and heparitinases towards the glycosaminoglycan–protein linkage region (1999)

Bacterial chondroitinases and heparitinases are potentially useful tools for structural studies of chondroitin sulfate and heparin/heparan sulfate. Substrate specificities of Flavobacterium chondroitinase C, as well as heparitinases I and II, towards the glycosaminoglycan-protein linkage region -HexA-HexNAc-GlcA-Gal-Gal-Xyl-Ser (where HexA represents glucuronic acid or iduronic acid and HexNAc represents N-acetylgalactosamine or N-acetylglucosamine) were investigated using various structurally defined oligosaccharides or oligosaccharide-serines derived from the linkage region. In the case of oligosaccharide-serines, they were labeled with a chromophore dimethylaminoazobenzenesulfonyl chloride (DABS-Cl), which stably reacted with the amino group of the serine residue and rendered high absorbance for microanalysis. Chondroitinase C cleaved the GalNAc bond of the pentasaccharides or hexasaccharides derived from the linkage region of chondroitin sulfate chains and tolerated sulfation of the C-4 or C-6 of the GalNAc residue and C-6 of the Gal residues, as well as 2-O-phosphorylation of the Xyl residue. In contrast, it did not act on the GalNAc-GlcA linkage when attached to a 4-O-sulfated Gal residue. Heparitinase I cleaved the innermost glucosaminidic bond of the linkage region oligosaccharide-serines of heparin/heparan sulfate irrespective of substitution by uronic acid, whereas heparitinase II acted only on the glucosaminidic linkages of the repeating disaccharide region, but not on the innermost glucosaminidic linkage. These defined specificities of chondroitinase C, as well as heparitinases I and II, will be useful for preparation and structural analysis of the linkage oligosaccharides.
Technical Considerations for Dominant Frequency Analysis (2007)

Various factors affect DF analysis. Proper interpretation of DF analysis requires careful evaluation of the AF signals and robust processing techniques.
Complete genome sequence of Dyadobacter fermentans type strain (NS114T) (2009)

Dyadobacter fermentans (Chelius and Triplett, 2000) is the type species of the genus Dyadobacter. It is of phylogenetic interest because of its location in the Cytophagaceae, a very diverse family within the order 'Sphingobacteriales'. D. fermentans has a mainly respiratory metabolism, stains Gram-negative, is non-motile and oxidase and catalase positive. It is characterized by the production of cell filaments in aging cultures, a flexirubin-like pigment and its ability to ferment glucose, which is almost unique in the aerobically living members of this taxonomically difficult family. Here we describe the features of this organism, together with the complete genome sequence, and its annotation. This is the first complete genome sequence of the sphingobacterial genus Dyadobacter, and this 6,967,790 bp long single replicon genome with its 5804 protein-coding and 50 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
SYMPATHETIC AND SENSORY NEURAL ELEMENTS IN THE TENDON OF THE LONG HEAD OF THE BICEPS (2005)

Background: Although the tendon of the long head of the biceps is a well-known source of shoulder pain, the pathophysiological basis of this pain has yet to be explained. The aim of this study was to detect and characterize any nervous element of the tendon and to determine a possible explanation for pain originating from this structure. Methods: The nature of the neuronal innervation of the tendon of the long head of the biceps was studied immunohistochemically, in four tendons from different human cadavers, with use of neurofilament antibody 2H3, neurofilament-like antibody 3A10, calcitonin gene-related peptide, substance P, and tyrosine hydroxylase. Results: A large neuronal network, asymmetrically distributed along the length of the tendon with a higher degree of innervation at the tendon origin, was identified by the neurofilament and neurofilament-like antibodies 2H3 and 3A10. This innervation was found to be positive for calcitonin gene-related peptide and substance P, suggesting the presence of thinly myelinated or unmyelinated sensory neurons. It was also positive for tyrosine hydroxylase, suggesting a post-ganglionic sympathetic origin. Conclusions and Clinical Relevance: These findings demonstrate that the tendon of the long head of the biceps is innervated by a network of sensory sympathetic fibers, which may play a role in the pathogenesis of shoulder pain.
The immune system and cancer evasion strategies: therapeutic concepts (2016)

The complicated interplay between cancer and the host immune system has been studied for decades. New insights into the human immune system as well as the mechanisms by which tumours evade immune control have led to the new and innovative therapeutic strategies that are considered amongst the medical breakthroughs of the last few years. Here, we will review the current understanding of cancer immunology in general, including immune surveillance and immunoediting, with a detailed look at immune cells (T cells, B cells, natural killer cells, macrophages and dendritic cells), immune checkpoints and regulators, sialic acid-binding immunoglobulin-like lectins (Siglecs) and other mechanisms. We will also present examples of new immune therapies able to reverse immune evasion strategies of tumour cells. Finally, we will focus on therapies that are already used in daily oncological practice such as the blockade of immune checkpoints cytotoxic T-lymphocyte antigen 4 (CTLA-4) and programmed death-1 (PD-1) in patients with metastatic melanoma or advanced lung cancer, or therapies currently being tested in clinical trials such as adoptive T-cell transfer.
Alternans and spiral breakup in a human ventricular tissue model (2006)

Ventricular fibrillation (VF) is one of the main causes of death in the Western world. According to one hypothesis, the chaotic excitation dynamics during VF are the result of dynamical instabilities in action potential duration (APD) the occurrence of which requires that the slope of the APD restitution curve exceeds 1. Other factors such as electrotonic coupling and cardiac memory also determine whether these instabilities can develop. In this paper we study the conditions for alternans and spiral breakup in human cardiac tissue. Therefore, we develop a new version of our human ventricular cell model, which is based on recent experimental measurements of human APD restitution and includes a more extensive description of intracellular calcium dynamics. We apply this model to study the conditions for electrical instability in single cells, for reentrant waves in a ring of cells, and for reentry in two-dimensional sheets of ventricular tissue. We show that an important determinant for the onset of instability is the recovery dynamics of the fast sodium current. Slower sodium current recovery leads to longer periods of spiral wave rotation and more gradual conduction velocity restitution, both of which suppress restitution-mediated instability. As a result, maximum restitution slopes considerably exceeding 1 (up to 1.5) may be necessary for electrical instability to occur. Although slopes necessary for the onset of instabilities found in our study exceed 1, they are within the range of experimentally measured slopes. Therefore, we conclude that steep APD restitution-mediated instability is a potential mechanism for VF in the human heart.
Compute-and-Forward: Harnessing Interference Through Structured Codes (2011)

Interference is usually viewed as an obstacle to communication in wireless networks. This paper proposes a new strategy, compute-and-forward, that exploits interference to obtain significantly higher rates between users in a network. The key idea is that relays should decode linear functions of transmitted messages according to their observed channel coefficients rather than ignoring the interference as noise. After decoding these linear equations, the relays simply send them towards the destinations, which given enough equations, can recover their desired messages. The underlying codes are based on nested lattices whose algebraic structure ensures that integer combinations of codewords can be decoded reliably. Encoders map messages from a finite field to a lattice and decoders recover equations of lattice points which are then mapped back to equations over the finite field. This scheme is applicable even if the transmitters lack channel state information.
Abnormally enhanced thermoelectric transport properties of SWNT/PANI hybrid films by the strengthened PANI molecular ordering (2014)

Single-walled carbon nanotube (SWNT)/polyaniline (PANI) hybrid films were prepared by casting the suspension containing well-dispersed SWNTs and CSA-doped PANI. The electrical conductivity of the SWNT/PANI film at first increased with the increasing SWNT content and then decreased at high SWNT content, whereas the Seebeck coefficient increased monotonically in the present SWNT content range. Moreover, the electrical conductivity values of the SWNT/PANI composites were much higher than the values calculated based on the series-connected two-component mixture model, whereas the dependence of the Seebeck coefficient on the SWNT content fitted well with the mixture model. Thermal conductivities increased with the SWNT content, but the rate of increase was much lower than the values estimated using the mixture model. The maximum values of electrical conductivity and Seebeck coefficient of hybrid films were up to 769 S cm−1 and 65 μV K−1. Consequently, the maximum thermoelectric power factor and ZT value at room temperature reached 176 μW m−1 K−2 and 0.12, respectively. The optimal TE property of the SWNT/PANI hybrid film was remarkably higher than those of either individual component of the composite, and exhibits the highest values for inorganic–organic composite materials reported so far. XRD and Raman analyses revealed that the PANI molecules in the composite film had a more expanded conformation, and were more orderly arranged compared with both pure PANI bulk and pure PANI film. The abnormally enhanced thermoelectric performance is attributed to the highly ordered PANI interface layer on the SWNT surface, which formed by the synergetic effect of chain expansion by the chemical interactions between PANI and the solvent and chain-ordering due to the π–π conjugation between PANI and CNTs.