gebhart/patrepeval huggingface dataset:
Three-dimensional intact-tissue sequencing of single-cell transcriptional states (2018)

Retrieving high-content gene-expression information while retaining three-dimensional (3D) positional anatomy at cellular resolution has been difficult, limiting integrative understanding of structure and function in complex biological tissues. We developed and applied a technology for 3D intact-tissue RNA sequencing, termed STARmap (spatially-resolved transcript amplicon readout mapping), which integrates hydrogel-tissue chemistry, targeted signal amplification, and in situ sequencing. The capabilities of STARmap were tested by mapping 160 to 1020 genes simultaneously in sections of mouse brain at single-cell resolution with high efficiency, accuracy, and reproducibility. Moving to thick tissue blocks, we observed a molecularly defined gradient distribution of excitatory-neuron subtypes across cubic millimeter-scale volumes (>30,000 cells) and a short-range 3D self-clustering in many inhibitory-neuron subtypes that could be identified and described with 3D STARmap.
Some Effects of Nonuniform Fields on Dielectrics (1958)

Some of the more interesting effects of nonuniform electric fields are described in this report. Experimental and theoretical studies show the effects to be rather striking for particles larger than molecular size. The results show that the effect can be used to produce a fairly efficient pumping action of nonconducting liquids, to cause continuous and easily measureable separations in coarse suspensions, to cause selective precipitation, and to produce mixing. By this means, liquids may be thrown several feet into the air with an electromechanical efficiency of about 25%. A separation factor of at least 2.5 in continuous separatory operation may be produced in a suspension of polyvinyl chloride in carbon tetrachloride-benzene mixture. Suspensions of polar materials in less polar liquids may be either dispersed or precipitated. In one interesting ``demonstration'' type experiment, drops were ``hung'' in mid-air.
Characterization of a novel thioesterase (PtTE) from Phaeodactylum tricornutum (2011)

The Phaeodactylum tricornutum (P. tricornutum) thioesterase PtTE was encoded by a 648 bp open reading frame. The deduced 216 amino acids showed no similarity with plant acyl-acyl carrier protein (ACP) thioesterases and bacterial thioesterases. Southern blot analysis revealed that one copy of PtTE was present in the P. tricornutum genome, and Real-time quantitative PCR showed that PtTE was up-regulated upon nitrogen deprivation. Thioesterase activity of PtTE was established by heterologous expression of PtTE cDNA in Escherichia coli (E. coli) XL1-Blue and K27fadD88, a mutant strain of fatty acid β-oxidation pathway. The substrate specificity of PtTE was determined by fatty acid profile analyses of the culture supernatant and membrane lipid of recombinant strains. Recombinant PtTE in E.coli enhanced total fatty acid content of XL1-Blue by 21%, and also changed the fatty acid compositions of membrane lipid and culture supernatant. These changes were directed predominantly towards C18:0 and C18:1 fatty acids. Overexpression of PtTE alone in P. tricornutum did not alter the fatty acid composition of P. tricornutum, but enhanced total fatty acid content by 72%. This novel thioesterase gene shows its potential in metabolic engineering for enhancing lipid yield of microalgae. This is so far the first report of thioesterase from eukaryotic microalgae.
Experimental Photodynamic Treatment of Canine Bladder (1985)

In urology, important limiting factors in the application of hematoporphyrin derivative and photodynamic therapy appear to be the problems of standardization of dosimetry and the technique of transurethral photoradiation. Experimental photodynamic therapy on canine bladder with normal and altered epithelium was performed using an argon laser as an energy source. A 630 nanometer wavelength of light was delivered through a quartz-optical fiber with either a regular flat end for focal illumination or a bulb-type end which produced an isotropic light pattern. It was demonstrated that normal canine bladder was resistant to photodynamic therapy and that the bulb tip produced whole bladder illumination. With a moderate light dose of 18 to 30 Joules/cm.2 the effect following whole bladder illumination on the bladder was generalized and superficial. This approach appears to be ideal for treating superficial transitional cell carcinoma of the bladder. Additional work is needed in selecting appropriate energy doses.
Bifluorophoric molecules as fluorescent beacons for antibody–antigen binding (2002)

The quenching of fluorescence (up to 98%) by anti-fluorescein antibodies is well documented in the literature. Here we report a system where, instead of quenching, bifluorophoric molecules are designed to increase in fluorescence upon binding by an anti-fluorescein antibody. Bifluorophoric molecules are made of fluorescein (F) linked to tetramethylrhodamine (T) via varying numbers of methylene units, denoted as F-(CH(2))(n)-T. These F-(CH(2))(n)-T conjugates are almost nonfluorescent when free in solution due to intramolecular dimerization and stacking. Upon binding to an anti-fluorescein antibody, however, up to 110-fold increase in fluorescence was observed from the rhodamine moiety. This increase is believed to result from intramolecular dimer dissociation that dequenches the rhodamine fluorescence. Fluorescein fluorescence, on the other hand, remains quenched due to binding and intramolecular resonance energy transfer. Moreover, the excitation wavelength was at the absorption maxima of fluorescein, giving a Stoke's shift of about 90 nm. This system couples directly molecular recognition with a concurrent increase in fluorescence emission, obviating wash and incubation steps required by most assays. It is an important molecular reporter system for developing homogeneous assays.
Measurement of skin color: practical application and theoretical considerations. (1998)

Quantification of erythema and/or pigmentation is important for in vivo assessment of skin reactions to external stimuli such as ultraviolet radiation. Measurement of lesional color is also useful for quantitative evaluation of the efficacy of therapies for skin lesions. Several types of portable optoelectronic instruments have recently become available for these purposes and have been applied to research in dermatology, physiology, pharmacology, and cosmetic science. As color is not a genuine physical quantity but a sensory perception based on color vision, any colorimetric data obtained for the skin should be interpreted carefully. Erythema and melanin indices derived from skin reflectance data should also be evaluated in relation to the optical properties of the skin to avoid misuse. In this article, various methods for quantifying skin color and related parameters are reviewed and the characteristics of each method are discussed theoretically using an optical model of the skin.
Role of B7:CD28/CTLA-4 in the induction of chronic relapsing experimental allergic encephalomyelitis. (1995)

T cell activation requires both Ag/MHC recognition and costimulatory signals. The present studies were designed to test whether the loss of tolerance to myelin basic protein (MBP) requires costimulation by members of the B7 receptor family. CTLA-4Ig, a fusion protein ligand for B7-1 and B7-2, was used to assess the role of B7-mediated costimulation in chronic relapsing experimental allergic encephalomyelitis (EAE) induced by the transfer of MBP specific T cell lines. In adoptively transferred EAE, administering CTLA-4Ig to donor mice or during in vitro activation of MBP specific-T cells resulted in diminution of clinical disease. The presence of CTLA-4Ig during both the immunization and in vitro activation stages was most effective in preventing clinical signs of disease. This diminution in clinical disease was paralleled by a decreased proliferative response and reduced production of IL-2 and IL-4, but not IFN-gamma, after antigenic stimulation of encephalitogenic T cells in vitro. In contrast, CTLA-4Ig treatment of recipient animals after the transfer of MBP-activated T cells affected neither disease course nor severity. These results indicate that additional costimulatory pathways may be involved in established EAE, or that some cells are independent of costimulation or, alternatively, that CTLA-4Ig does not enter brain parenchyma in therapeutic concentrations. Thus, we conclude that costimulation provided by B7 molecules plays a major role in the development of encephalitogenic T cells and in the establishment of chronic relapsing EAE, a prototypic CD4+ T cell-mediated autoimmune disease.
A Rehabilitation Training Programme at the End of Life (2011)

Terminally ill patients face many challenges with regard to increasing physical dependence on others to meet their practical needs. Progressive weakness, profound fatigue and gradual deconditioning make daily tasks increasingly difficult to perform. Rehabilitation techniques do not lie solely within the role of physiotherapists and occupational therapists. They are an integral part of holistic care for patients at the end of life. The promotion of rehabilitation reduces patients’ dependency on nurses, allowing them more time to deliver care to patients who are fully dependent. Rehabilitation techniques also enable patients to regain control, self-esteem and quality of life. This article describes ‘The Rehab Project’, a training programme delivered to ward nurses and healthcare assistants, by physiotherapy and occupational therapy staff, at a hospice in London. By focusing on patient empowerment and independence, the project aimed to ensure a consistent and efficient approach to nursing care provided within the hospice inpatient unit. However, the principles of rehabilitation are pertinent to nurses working in more generalist settings. Conflicts of interest: none
MR Imaging of the Arterial Vessel Wall: Molecular Imaging from Bench to Bedside (2013)

Cardiovascular diseases remain the leading cause of morbidity and mortality in the Western world and developing countries. In clinical practice, in vivo characterization of atherosclerotic lesions causing myocardial infarction, ischemic stroke, and other complications remains challenging. Imaging methods, limited to the assessment luminal stenosis, are the current reference standard for the assessment of clinically significant coronary and carotid artery disease and the guidance of treatment. These techniques do not allow distinction between stable and potentially vulnerable atherosclerotic plaque. Magnetic resonance (MR) imaging is a modality well suited for visualization and characterization of the relatively thin arterial vessel wall, because it allows imaging with high spatial resolution and excellent soft-tissue contrast. In clinical practice, atherosclerotic plaque components of the carotid artery and aorta may be differentiated and characterized by using unenhanced vessel wall MR imaging. Additional information can be gained by using clinically approved nonspecific contrast agents. With the advent of targeted MR contrast agents, which enhance specific molecules or cells, pathologic processes can be visualized at a molecular level with high spatial resolution. In this article, the pathophysiologic changes of the arterial vessel wall underlying the development of atherosclerosis will be first reviewed. Then basic principles and properties of molecular MR imaging contrast agents will be introduced. Additionally, recent advances in preclinical molecular vessel wall imaging will be reviewed. Finally, the clinical feasibility of arterial vessel wall imaging at unenhanced and contrast material-enhanced MR imaging of the aortic, carotid, and coronary vessel wall will be discussed.
Laser-jet delayed trapping: electron-transfer trapping of the photoenol from 2-methylbenzophenone (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLaser-jet delayed trapping: electron-transfer trapping of the photoenol from 2-methylbenzophenoneR. Marshall Wilson, Klaus Hannemann, William R. Heineman, and Jon R. KirchhoffCite this: J. Am. Chem. Soc. 1987, 109, 15, 4743–4745Publication Date (Print):July 1, 1987Publication History Published online1 May 2002Published inissue 1 July 1987https://pubs.acs.org/doi/10.1021/ja00249a060https://doi.org/10.1021/ja00249a060research-articleACS PublicationsRequest reuse permissionsArticle Views194Altmetric-Citations19LEARN 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
A method for correctly setting the rf flip angle (1989)

Currently the accepted method for setting the correct rf power levels to achieve 90 degrees and 180 degrees rf pulses for MR imaging is to peak the echo amplitude of a rf spin-echo sequence. The echo amplitude of this alpha-2 alpha pulse sequence is proportional to sin3 (alpha) and has a relatively broad maximum. Recently another method for setting the rf flip angle by maximizing the ratio of the stimulated echo to the primary echo amplitudes (in a 3 alpha sequence) demonstrated accuracy similar to that of the spin-echo method using a shorter repetition time. We present a new, more sensitive, and more accurate method for setting the correct rf power levels for 90 degrees and 180 degrees rf pulses. In this method, based upon the stimulated echo pulse sequence, we are able to accurately set the rf power to within +/- 0.1 dB by minimizing the signal amplitude of the third spin echo. This null method works for both selective and nonselective rf pulses of flip angle 90 degrees or 180 degrees, allowing the user to accurately adjust the relative amplitudes of the four rf pulse types within a single pulse sequence.
Autoimmunity induced by injection of virus-modified cell membrane antigens in syngeneic mice (1977)

C3H/Bi mice developed autoantibodies after repeated inoculations of isolated membranes from primary tissue cultures of a syngeneic ascites lymphoma in which Newcastle disease virus had grown. This was in addition to the tumor transplantation resistance and cytotoxic antibodies previously demonstrated. The complement-fixing antibodies were completely removed from sera by adsorption with ascites tumor cells but only partially by normal mouse liver powder or C3H/Bi erythrocytes. With continued immunization, antibodies to deoxynucleoprotein and heterophile reagins also appeared. After several months, mice showing these serological reactions died with a wasting disease characterized by loss of lymphoid tissue and scarred, atrophied kidneys. No significant antibody response or autoimmune disease occurred in mice receiving membranes from uninfected syngeneic ascites lymphoma.
Reconfigurable Shuffle Network Design in LDPC Decoders (2006)

Several semi-parallel decoding architectures have been explored by researchers for the quasi-cyclic low density parity check (LDPC) codes. In these architectures, the reconfigurability was seldom studied. In most of the published work, the shuffle network between the log-likelihood ratio (LLR) memory and the check- node units (CNU) is predetermined and optimized for a specific code. However, the most of the modern wireless communication systems typically specify multiple code-rates, codeword lengths and sub-matrix sizes (for the QC-LDPC codes) to provide and guarantee quality-of-service (QoS) over challenging channel conditions. It is therefore desirable to define a reconfigurable decoder architecture that can support different parameters. This paper proposes an adaptive shuffling algorithm for QC-LDPC codes which together with the Benes network provides arbitrary cyclic shift for arbitrary submatrix size smaller than the input size of the Benes network. For the submatrix size larger than the Benes network input size, the proposed algorithm can be extended to obtain the cyclic shift in multiple stages. Compared with the direct implementation of m m-to-1 multiplexers, the proposed algorithm achieves significant savings on area and routing complexity.
Degradation of trichloroethylene by toluene dioxygenase in whole-cell studies with Pseudomonas putida F1 (1988)

Toluene-induced cells of Pseudomonas putida F1 removed trichloroethylene from growth media at a significantly greater initial rate than the methanotroph Methylosinus trichosporium OB3b. With toluene-induced P. putida F1, the initial degradation rate varied linearly with trichloroethylene concentration over the range of 8 to 80 microM (1.05 to 10.5 ppm). At 80 microM (10.5 ppm) trichloroethylene and 30 degrees C, the initial rate was 1.8 nmol/min per mg of total cell protein, but the rate decreased rapidly with time. A series of mutant strains derived from P. putida F1 that are defective in the todC gene, which encodes the oxygenase component of toluene dioxygenase, failed to degrade trichloroethylene and to oxidize indole to indigo. A spontaneous revertant selected from a todC culture regained simultaneously the abilities to oxidize toluene, to form indigo, and to degrade trichloroethylene. The three isomeric dichloroethylenes were degraded by P. putida F1, but tetrachloroethylene, vinyl chloride, and ethylene were not removed from incubation mixtures.
Analysis of the leaf methylomes of parents and their hybrids provides new insight into hybrid vigor in Populus deltoides (2014)

The methylation patterns of the parents both partially and dynamically passed onto their hybrids, and F1 hybrids has a non-additive mathylation level. A multidimensional process is involved in the formation of heterosis.
Evaluation of a real-time PCR assay for detection of Bordetella pertussis and B. parapertussis in clinical samples (2001)

A real-time PCR assay based on the TaqMan technology was developed for the detection of Bordetella pertussis and B. parapertussis in clinical samples. The assay was evaluated with 182 specimens from 153 patients with and without symptoms of pertussis. The analytical sensitivity ranged from 0.1 to 10 cfu for B. pertussis and B. parapertussis, respectively, and diagnostic sensitivity was 94.1% when culture was used as a reference. No sample from a patient without symptoms of pertussis was positive in PCR. Twenty-four of 28 patients who were negative by culture and positive by PCR assay met the CDC clinical case definition for pertussis; the remaining four patients had paroxysms of shorter duration. Intra- and inter-assay variation were <5% and results were available within 4 h.
Privacy Settings in Online Social Networks -- Preferences, Perception, and Reality (2013)

To approach privacy threats stemming from interacting with other users on Online Social Networks (OSN), effective Social Identity Management (SIdM) is a key requirement. SIdM refers to the deliberate and targeted disclosure of personal information to a subset of one's contacts on OSN. Yet, unlike the physical world, SIdM on OSN is compromised by unavailable or insufficient settings as well as by properties of mediated communication (e.g. persistence). In this paper, we employ a novel approach based on the participants' Facebook profiles content to study privacy settings in OSN. Our results indicate a mismatch between perceived, preferred, and actual settings that can be reduced to lack of awareness and control by the user.
Found in Translation (2009)

Abstract The first English translation of Charles Perrault’s French fairy tale, “Bluebeard,” was provided by Robert Samber in 1729. Samber’s edition, entitled Histories, or Tales of past Times...with morals, by M. Perrault, Translated into English was followed by the publishing of a series of reprints, new editions, and bilingual versions throughout the eighteenth century. Moreover, it also strongly impressed itself on the “Bluebeard tradition” that continued to thrive throughout the Victorian period. English translations based on Perrault’s “Bluebeard” remained the norm even after the appearance of Grimm stories from Kinderund Hausmärchen (Grimm 1812–1815, 1819), which were translated (without any “Bluebeard” variant) into English as German Popular Stories in 1823–1826 (Grimm). Perrault’s “Bluebeard” was translated in editions of Mother Goose. In her book on English chapbooks, Margaret Spufford’s very first quotation from a reader includes a testimony to “Bluebeard.”
CUBIC pathology: three-dimensional imaging for pathological diagnosis (2017)

The examination of hematoxylin and eosin (H&E)-stained tissues on glass slides by conventional light microscopy is the foundation for histopathological diagnosis. However, this conventional method has some limitations in x-y axes due to its relatively narrow range of observation area and in z-axis due to its two-dimensionality. In this study, we applied a CUBIC pipeline, which is the most powerful tissue-clearing and three-dimensional (3D)-imaging technique, to clinical pathology. CUBIC was applicable to 3D imaging of both normal and abnormal patient-derived, human lung and lymph node tissues. Notably, the combination of deparaffinization and CUBIC enabled 3D imaging of specimens derived from paraffin-embedded tissue blocks, allowing quantitative evaluation of nuclear and structural atypia of an archival malignant lymphoma tissue. Furthermore, to examine whether CUBIC can be applied to practical use in pathological diagnosis, we performed a histopathological screening of a lymph node metastasis based on CUBIC, which successfully improved the sensitivity in detecting minor metastatic carcinoma nodules in lymph nodes. Collectively, our results indicate that CUBIC significantly contributes to retrospective and prospective clinicopathological diagnosis, which might lead to the establishment of a novel field of medical science based on 3D histopathology.
Targeted Radiotherapy with Gold Nanoparticles: Current Status and Future Perspectives (2014)

Radiation therapy (RT) is the treatment of cancer and other diseases with ionizing radiation. The ultimate goal of RT is to destroy all the disease cells while sparing healthy tissue. Towards this goal, RT has advanced significantly over the past few decades in part due to new technologies including: multileaf collimator-assisted modulation of radiation beams, improved computer-assisted inverse treatment planning, image guidance, robotics with more precision, better motion management strategies, stereotactic treatments and hypofractionation. With recent advances in nanotechnology, targeted RT with gold nanoparticles (GNPs) is actively being investigated as a means to further increase the RT therapeutic ratio. In this review, we summarize the current status of research and development towards the use of GNPs to enhance RT. We highlight the promising emerging modalities for targeted RT with GNPs and the corresponding preclinical evidence supporting such promise towards potential clinical translation. Future prospects and perspectives are discussed.