gebhart/patrepeval huggingface dataset:
Acoustically Detonated Biomolecules for Genetically Encodable Inertial Cavitation (2019)

ABSTRACT Recent advances in molecular engineering and synthetic biology have made it possible for biomolecular and cell-based therapies to provide highly specific disease treatment. However, both the ability to spatially target the action of such therapies, and their range of effects on the target tissue remain limited. Here we show that biomolecules and cells can be engineered to deliver potent mechanical effects at specific locations inside the body under the direction of focused ultrasound. This capability is based on gas vesicles, a unique class of air-filled protein nanostructures derived from buoyant photosynthetic microbes. We show that low-frequency ultrasound can convert these nanoscale biomolecules into micron-scale cavitating bubbles, as demonstrated with acoustic measurements and ultrafast optical microscopy. This allows gas vesicles targeted to cell-surface receptors to serve as remotely detonated cell-killing agents. In addition, it allows cells genetically engineered to express gas vesicles to be triggered with ultrasound to lyse and release therapeutic payloads. We demonstrate these capabilities in vitro , in cellulo , and in vivo . This technology equips biomolecular and cellular therapeutics with unique capabilities for spatiotemporal control and mechanical action.
MC4 receptor antagonists: a potential treatment for cachexia. (2005)

Cachexia (involuntary weight loss) is a devastating syndrome associated with many chronic diseases including cancer, and heart, lung, kidney and liver failure. There are currently no effective treatments capable of reversing the loss of lean body mass that is believed to be a major contributor to morbidity and mortality in these chronic diseases. Recent findings strongly indicate that blockade of central melanocortin signaling through the MC4 receptor subtype attenuates cachexia. This review summarizes the evidence supporting the role of MC4 receptors in cachexia, and highlights the progress achieved in the development of small-molecule MC4 antagonists, which have recently proved to be effective in animal models of cachexia. MC4 antagonists are an attractive therapeutic approach for cachexia that may ameliorate the loss of lean body mass in cachectic patients.
Immune Inhibitory Receptors (2000)

With the detailed description and analysis of several inhibitory receptor systems on lymphoid and myeloid cells, a central paradigm has emerged in which the pairing of activation and inhibition is necessary to initiate, amplify, and then terminate immune responses. In some cases, the activating and inhibitory receptors recognize similar ligands, and the net outcome is determined by the relative strength of these opposing signals. The importance of this modulation is demonstrated by the sometimes fatal autoimmune disorders observed in mice with targeted disruption of inhibitory receptors. The significance of these receptors is further evidenced by the conservation of immunoreceptor tyrosine-based inhibitory motifs during their evolution.
Design and Synthesis of New Circularly Polarized Thermally Activated Delayed Fluorescence Emitters (2016)

This work describes the first thermally activated delayed fluorescence material enabling circularly polarized light emission through chiral perturbation. These new molecular architectures obtained through a scalable one-pot sequential synthetic procedure at room temperature (83% yield) display high quantum yield (up to 74%) and circularly polarized luminescence with an absolute luminescence dissymmetry factor, |glum|, of 1.3 × 10(-3). These chiral molecules have been used as an emissive dopant in an organic light emitting diode exhibiting external quantum efficiency as high as 9.1%.
Large-Scale Isolation of Human Hepatocytes for Therapeutic Application (2005)

During the last decade, hepatocyte transplantation has been suggested as a safe and potentially effective clinical option for the treatment of acute or decompensating chronic liver failure as well as for hereditary liver disease. Currently, one of the major limiting factors for clinical application is the insufficient access to suitable liver cell preparations. In cooperation with the German and Catalane organ procurement organizations, a routine procedure for the isolation of hepatocytes from donor organs rejected for transplantation (n = 117) has been established. The process is performed according to the current EC Guidelines for Good Manufacturing Practice (cGMP) and all corresponding national laws and regulations concerning donor organ and tissue procurement. In about 50% of the cases (n = 58) the three-step perfusion procedure has been completed with an average total cell yield of 5.9 x 10(9) cells per organ, the cell preparations displaying a mean viability of 64%. The mean specific yield was 3.6 x 10(6) total and 2.6 x 10(6) viable cells per gram liver tissue, respectively. Specific cell yields from three infantile donor livers were considerably higher. No correlation between isolation efficiency and cold ischemia time or donor age was found within the adult organ donors. In contrast, organs with a severe steatosis generally did not result in successful cell isolation. Results of sterility and endotoxin determination are also presented. In summary, a standardized and cGMP conform method of hepatocyte isolation from nontransplantable liver organs was established, which reproducibly yields large amounts of hepatocytes suitable for therapeutic application.
Real-Time Continuous Collision Detection Based on Swept Volume and Depth Texture (2006)

We present a novel algorithm to perform continuous collision detection in distributed virtual environment. Our algorithm consists of four stages: (1) generating depth texture of model; (2) computing depth texture of swept volume by model depth texture; (3) mapping depth image of swept volume on a face of bounding box; (4) comparing depth of swept volume with depth of another object to detect collisions. We have implemented the algorithm and the results show that our algorithm is able to perform fast and accurate continuous collision detection and have fixed executing time to suit for real-time applications
Interchangeability between heart rate and photoplethysmography variabilities during sympathetic stimulations (2009)

Photoplethysmography variability (PPGV) is currently considered to be a good surrogate to heart rate variability (HRV) measurements using the time between two pulse waves instead of RR intervals. Nevertheless, the interchangeability between HRV and PPGV has never been evaluated in situations with severe alterations in the autonomic nervous system (ANS). We aimed to identify the conditions for a correct utilization of PPGV in evaluating the consequences of sympathetic stimulations. Nine subjects performed three tests: active orthostatic test, slow walk and moderate and exhaustive cycling exercises in the supine position. Pulse waves at the fingertip and RR intervals were recorded at the same time. We used correlations and the Bland and Altman method to compare and evaluate interchangeability between several HRV indices. Bland and Altman analysis highlighted small discrepancies between PPGV and HRV for all HRV indices in the supine position and for LF(ms)(2), HF(ms)(2), LF(peak) and RMSSD in the upright position. During the slow walk, it was impossible to detect properly PPG peaks. We observed large differences between the two methods during the cycling exercise. In conclusion, PPGV can be used instead of HRV without reserve in the supine position but only for some HRV indices in the upright position and not during slow walk and cycling exercise.
Analogous Telesensing Pathways Regulate Mating and Virulence in Two Opportunistic Human Pathogens (2010)

Telesensing, or probing of the environment by the release of chemical messengers, plays a central role in the sexual programs of microbial organisms. Sex pheromones secreted by mating cells are sensed by potential partner cells and mediate cell-to-cell contact and the subsequent exchange of genetic material. Although the mechanisms used by bacterial and fungal species to promote genetic exchange are distinct, recent studies have uncovered surprising parallels between pheromone signaling in these species. In addition, it is now apparent that pheromone signaling not only controls sexual reproduction and genetic exchange but can also activate expression of potential virulence factors in diverse opportunistic pathogens.
Practical aspects of <i>in situ</i> activation using a conventional medical accelerator for the purpose of perfusion imaging (2001)

We report investigations into the feasibility of generating radioactive oxygen (15O, a positron emitter, with half-life 2.05 min) using a tuned Elekta SL25 accelerator, for the end purpose of imaging tumor perfusion. 15O is produced by the "gamma, neutron," (gamma,n) reaction between high-energy photons and normal oxygen (16O) in the body. As most in vivo 16O is bound in water molecules the 15O radio-marker is produced in proportion to water content in tissue. Imaging the washout of the 15O distribution using sensitive positron-emission-tomography (PET) technology can yield spatial information about blood perfusion in the tissue. The aim of this article was to determine the amount of 15O activity that could be produced by the tuned medical accelerator. A further aim was to model the activation process using Monte Carlo and to investigate ways to optimize the amount of 15O that could be generated. Increased activation was achieved by (i) tuning the beam to give higher-energy electrons incident on the target of the accelerator, (ii) increasing dose rate by removing the conventional filtration in the beam and reducing the source to object distance, and (iii) reducing low-energy photons by means of a carbon block absorber. The activity per-unit-dose produced by the tuned beam was measured by irradiating spheres of water to known doses and placing the spheres in a calibrated coincidence-counting apparatus. Peak energy of the tuned bremsstrahlung beam was estimated at 29 MeV, and generated activity up to 0.24/microCi/cc/3Gy in water. The measured amount of 15O agreed to within 10% of the prediction from the Monte-Carlo-computed spectrum, indicating reasonable ability to model the activation process. The optimal thickness of the carbon absorber was found to be about 25 cm. The insertion of a carbon absorber improved spectral quality for activation purposes but at the cost of reduced dose rate. In conclusion, the viability of generating 15O with an Elekta SL25 has been demonstrated. In conjunction with recent advances in high-sensitivity portable PET imaging devices, real potential exists for imaging in situ activated 15O washout as a surrogate measurement of macroscopic tumor perfusion.
Zonal Regulation of Gene Expression During Liver Regeneration of Urokinase Transgenic Mice (1999)

Liver gene transcription plays a fundamental role in the hepatic reparative response to injury. However, little is known about the functional relationship of gene expression between diseased and regenerative compartments following a liver injury. To address the hypothesis that the control of gene expression and the cellular proliferative response are specific to diseased and regenerative liver compartments independently, we assessed the expression of liver growth modulators, hepatocyte proliferation, and apoptosis in transgenic livers overexpressing the urokinase-type plasminogen activator (uPA). uPA livers have regenerative nodules that are visually distinct from the surrounding diseased compartments. Northern analyses using RNA from microdissected regenerative and diseased compartments showed that, among the known liver growth factors studied, there was a selective increase in the expression of hepatocyte growth factor (HGF) in diseased compartments above the levels seen in regenerative compartments and in livers of nontransgenic littermates. Despite the high level of HGF mRNA in diseased compartments, hepatocyte proliferation was low. In contrast, in regenerative compartments, where HGF mRNA was low, hepatocyte proliferation was abundant. For growth inhibitors, mRNA expression for transforming growth factor beta1 (TGF-beta1), p53, and activin A was increased in diseased compartments, where hepatocytes displayed apoptosis. These findings define a zone-specific regulation of gene expression in injured livers and point to an important role of the diseased microenvironment in the fate of hepatocytes during the regenerative process.
Half-face detector for enhanced performance of flash-eye filter (2013)

Red-eye and flash-eye defects in still photography continue to cause problems for digital imaging devices. New variants of flash-eye defects have appeared as cameras and cameras sub-systems get smaller in size. This paper describes advanced techniques to improve the detection of flash-eye defects using a novel half-face detector. In addition to improving the detection rate, the inherent symmetries of many of the haar-like classifiers used for such a face detector allow compression of the classifier chain providing benefits for resource constrained consumer electronics devices.
3'-C-Branched 2'-deoxy-5-methyluridines: synthesis, enzyme inhibition, and antiviral properties (1992)

A synthesis scheme for 3'-C-methyl-2'-deoxynucleosides and 3'-C-methylidene-2',3'-dideoxy-5-methyluridine has been proposed with 2-deoxyribose as the starting material. Methyl 5-O-benzoyl-2-deoxyribofuranose was oxidized and the mixture of the 3'-keto derivatives was separated into the alpha- and beta-anomers. The beta-keto derivative was converted by reaction with MeMgBr, and after reaction with thymine and subsequent deprotection 1-(3'-C-methyl-2'-alpha-deoxy-alpha-D-threo-pentofuranosyl)thymine and its beta-anomer were obtained. The same reactions with the alpha-keto sugar gave 1-(3'-C-methyl-2'-deoxy-alpha-D-erythro-pentofuranosyl)thymine and its beta-anomer. 1-(5-O-Benzoyl-3'-C-methyl-2'-deoxy-alpha-D-threo-pentofuranosyl)thymine was converted to a mixture of 3'-C-methylidene-2',3'-dideoxy-5-methyluridine and 3'-C-methyl-2',3'-dideoxy-2',3'-didehydro-5-methyluridine, which were separated. The stereoselectivity of the Grignard reagent's attachment to 2-deoxyfuranose 3-ulosides has been ruled by the substitute configuration at Cl. Also, the effect of the hydroxyl or OBz group configuration at C3 on the condensation stereoselectivity of 3-C-methyl-2-deoxyfuranosides with silylated thymine has been studied. The structure of the obtained compounds was proved by 1H NMR UV, 13C NMR, and CD spectroscopy, as well as elemental (C, H, N) analysis. The C2'-endo-C1'-exo conformation, the anti conformation of thymine in relation to the glycosidic bond, and the gauche+conformation in relation to the C4'-C5' bond are characteristic for the 3'-C-methyl-2'-deoxythymidine structure in the crystals. 3'-C-Methyl-2'-deoxythymidine 5'-triphosphate was synthesized and proved to be a competitive inhibitor, with respect to dTTP, of a number of DNA polymerases, including the reverse transcriptases of human immunodeficiency virus type 1 (HIV-1) and avian myeloblastosis virus (AMV). None of the DNA polymerases examined were able to incorporate this compound into the growing DNA chain. In contrast, 3'-C-methylidene-2',3'-dideoxy-5-methyluridine 5'-triphosphate was found to be incorporated at the 3'-end of the DNA chain by HIV-1 reverse transcriptase, albeit with very low efficiency. 3'-C-Methyl-2'-deoxy-5-methyluridine did not suppress HIV-1 replication in MT-4 cells at 500 microM while its 5'-phosphite derivative exhibited modest anti-HIV-1 activity.
Fine-grained Categorization and Dataset Bootstrapping using Deep Metric Learning with Humans in the Loop (2015)

Existing fine-grained visual categorization methods often suffer from three challenges: lack of training data, large number of fine-grained categories, and high intraclass vs. low inter-class variance. In this work we propose a generic iterative framework for fine-grained categorization and dataset bootstrapping that handles these three challenges. Using deep metric learning with humans in the loop, we learn a low dimensional feature embedding with anchor points on manifolds for each category. These anchor points capture intra-class variances and remain discriminative between classes. In each round, images with high confidence scores from our model are sent to humans for labeling. By comparing with exemplar images, labelers mark each candidate image as either a "true positive" or a "false positive". True positives are added into our current dataset and false positives are regarded as "hard negatives" for our metric learning model. Then the model is retrained with an expanded dataset and hard negatives for the next round. To demonstrate the effectiveness of the proposed framework, we bootstrap a fine-grained flower dataset with 620 categories from Instagram images. The proposed deep metric learning scheme is evaluated on both our dataset and the CUB-200-2001 Birds dataset. Experimental evaluations show significant performance gain using dataset bootstrapping and demonstrate state-of-the-art results achieved by the proposed deep metric learning methods.
Learning Deep Representation for Face Alignment with Auxiliary Attributes (2015)

In this study, we show that landmark detection or face alignment task is not a single and independent problem. Instead, its robustness can be greatly improved with auxiliary information. Specifically, we jointly optimize landmark detection together with the recognition of heterogeneous but subtly correlated facial attributes, such as gender, expression, and appearance attributes. This is non-trivial since different attribute inference tasks have different learning difficulties and convergence rates. To address this problem, we formulate a novel tasks-constrained deep model, which not only learns the inter-task correlation but also employs dynamic task coefficients to facilitate the optimization convergence when learning multiple complex tasks. Extensive evaluations show that the proposed task-constrained learning (i) outperforms existing face alignment methods, especially in dealing with faces with severe occlusion and pose variation, and (ii) reduces model complexity drastically compared to the state-of-the-art methods based on cascaded deep model.
Rayleigh scattering of whispering gallery modes of microspheres due to a single dipole scatterer (2009)

An exact solution for the problem of interaction between whispering gallery modes of spherical microresonators and a single dipole is presented. It is predicted that experimentally observed spectral doublets associated with this interaction are a part of a triplet whose third component has yet to be observed. It is also shown that the interaction between the dipole and nonresonant whispering gallery modes results in a renormalization of the dipole's polarizability and experimental manifestations of this effect are discussed.
Selective growth of Ge islands on nanometer-scale patterned SiO2∕Si substrate by molecular beam epitaxy (2006)

The authors studied the selective growth of Ge islands by molecular beam epitaxy on Si(001) covered with nanometer-scale patterned SiO2 mask generated using self-assembled diblock copolymer. Selective growth is made possible by Ge adatoms desorbing from the SiO2 surface as well as diffusing into the exposed Si area. For the Ge coverage of 2nm, multiple islands are observed along the periphery of individual exposed Si areas. At 3.5nm coverage, the coalescence of small islands with significant strain relaxation becomes evident. The ramifications of the multiple islands morphology and their coalescence on potential device applications are discussed.
LASSIE: structure to layout for behavioral synthesis tools (1989)

Behavioral synthesis tools generate a wide range of designs, not all suited to one layout style. Thus there is a need for a flexible framework for mapping behavioral synthesis output onto module generators and layout tools. LASSIE provides this flexible framework and introduces a structural binding step that adapts the output of behavioral synthesis tools to different layout styles. The design process is divided into structural binding, partitioning, placement, and layout generation. Several options are provided at each step, and feedback is provided to the user to allow him to evaluate the results of each step.
Quantifying colocalization by correlation: The Pearson correlation coefficient is superior to the Mander's overlap coefficient (2010)

The Pearson correlation coefficient (PCC) and the Mander's overlap coefficient (MOC) are used to quantify the degree of colocalization between fluorophores. The MOC was introduced to overcome perceived problems with the PCC. The two coefficients are mathematically similar, differing in the use of either the absolute intensities (MOC) or of the deviation from the mean (PCC). A range of correlated datasets, which extend to the limits of the PCC, only evoked a limited response from the MOC. The PCC is unaffected by changes to the offset while the MOC increases when the offset is positive. Both coefficients are independent of gain. The MOC is a confusing hybrid measurement, that combines correlation with a heavily weighted form of co-occurrence, favors high intensity combinations, downplays combinations in which either or both intensities are low and ignores blank pixels. The PCC only measures correlation. A surprising finding was that the addition of a second uncorrelated population can substantially increase the measured correlation, demonstrating the importance of excluding background pixels. Overall, since the MOC is unresponsive to substantial changes in the data and is hard to interpret, it is neither an alternative to nor a useful substitute for the PCC. The MOC is not suitable for making measurements of colocalization either by correlation or co-occurrence.
Evidence for redox forms of the <i>Aequorea</i> green fluorescent protein (1994)

Highly purified recombinant Aequorea green fluorescent protein is able to undergo a reversible oxidation-reduction reaction in the presence of molecular oxygen. In the oxidized form in near UV light, the protein is highly fluorescent, but when reduced with sodium dithionite, it becomes completely non-fluorescent. On exposure to molecular oxygen the reduced, non-fluorescent protein reverts to its original fluorescent state.
Limited heterogeneity of T cell receptor BV usage in aplastic anemia (2001)

Immune mediation of aplastic anemia (AA) has been inferred from clinical responsiveness to immunosuppressive therapies and a large body of circumstantial laboratory evidence. However, neither the immune response nor the nature of the antigens recognized has been well characterized. We established a large number of CD4 and CD8 T cell clones from a patient with AA and analyzed their T cell receptor (TCR) usage. Most CD4 clones displayed BV5, whereas most CD8 clones displayed BV13. We found sequence identity for complementarity determining region 3 (CDR3) among a majority of CD4 clones; the same sequence was present in marrow lymphocytes from four other patients with AA but was not detected in controls. The dominant CD4 clone showed a Th1 secretion pattern, lysed autologous CD34 cells, and inhibited their hematopoietic colony formation. In three of four patients, successful immunosuppressive treatment led to marked decrease in clones bearing the dominant CDR3 BV5 sequence. These results suggest surprisingly limited heterogeneity of the T cell repertoire in an individual patient and similarity at the molecular level of the likely pathological lymphocyte response among multiple patients with AA, consistent with recognition of limited numbers of antigens shared by individuals with the same HLA type in this disease.
Seed dormancy (1997)

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