gebhart/patrepeval huggingface dataset:
Tissue segmentation of head and neck CT images for treatment planning: A multiatlas approach combined with intensity modeling (2013)

In conclusion, the proposed framework provides in an accurate automatic segmentation of head and neck tissues in CT images for the generation of 3D patient models, which improves reproducibility, and substantially reduces labor involved in therapy planning.
A Novel Method of Immobilizing Antibodies on a Quartz Crystal Microbalance Using Plasma-Polymerized Films for Immunosensors (1996)

A novel method of immobilizing antibodies on quartz crystals for use in immunosensors was developed using an ethylenediamine plasma-polymerized film matrix. The films formed on the quartz crystals are extremely thin and homogeneous, and they incorporate amino groups. Sensors produced using this method are more reproducible from sample to sample and exhibit lower noise and higher sensitivity than sensors made using conventional immobilization methods, e.g., via polyethylenimine and (gamma-aminopropyl)trimethoxysilane. This is, to our knowledge, the first reported application of plasma-polymerized films to quartz crystal microbalance immunosensors. Results on orientation-controlled immobilization of anti-bodies, reusability and calibration tests are also presented.
Janus kinases in immune cell signaling (2009)

The Janus family kinases (Jaks), Jak1, Jak2, Jak3, and Tyk2, form one subgroup of the non-receptor protein tyrosine kinases. They are involved in cell growth, survival, development, and differentiation of a variety of cells but are critically important for immune cells and hematopoietic cells. Data from experimental mice and clinical observations have unraveled multiple signaling events mediated by Jaks in innate and adaptive immunity. Deficiency of Jak3 or Tyk2 results in defined clinical disorders, which are also evident in mouse models. A striking phenotype associated with inactivating Jak3 mutations is severe combined immunodeficiency syndrome, whereas mutation of Tyk2 results in another primary immunodeficiency termed autosomal recessive hyperimmunoglobulin E syndrome. By contrast, complete deletion of Jak1 or Jak2 in the mouse are not compatible with life and, unsurprisingly, do not have counterparts in human disease. However, activating mutations of each of the Jaks are found in association with malignant transformation, the most common being gain-of-function mutations of Jak2 in polycythemia vera and other myeloproliferative disorders. Our existing knowledge on Jak signaling pathways and fundamental work on their biochemical structure and intracellular interactions allow us to develop new strategies for controlling autoimmune diseases or malignancies by developing selective Jak inhibitors, which are now coming into clinical use. Despite the fact that Jaks were discovered only a little more than a decade ago, at the time of writing there are 20 clinical trials underway testing the safety and efficacy of Jak inhibitors.
Human Bocavirus Can Be Cultured in Differentiated Human Airway Epithelial Cells (2009)

In 2005, a human bocavirus was discovered in children with respiratory tract illnesses. Attempts to culture this virus on conventional cell lines has failed thus far. We investigated whether the virus can replicate on pseudostratified human airway epithelium. This cell culture system mimics the human airway environment and facilitates culturing of various respiratory agents. The cells were inoculated with human bocavirus-positive nasopharyngeal washes from children, and virus replication was monitored by measuring apical release of the virus via real-time PCR. Furthermore, we identified different viral mRNAs in the infected cells. All mRNAs were transcribed from a single promoter but varied due to alternative splicing and alternative polyadenylation, similar to what has been described for bovine parvovirus and minute virus of canines, the other two members of the Bocavirus genus. Thus, transcription of human bocavirus displays strong homology to the transcription of the other bocaviruses. In conclusion, we report here for the first time that human bocavirus can be propagated in an in vitro culture system and present a detailed map of the set of mRNAs that are produced by the virus.
Selectfluor: Mechanistic Insight and Applications (2004)

The replacement of hydrogen atoms with fluorine substituents in organic substrates is of great interest in synthetic chemistry because of the strong electronegativity of fluorine and relatively small steric footprint of fluorine atoms. Many sources of nucleophilic fluorine are available for the derivatization of organic molecules under acidic, basic, and neutral conditions. However, electrophilic fluorination has historically required molecular fluorine, whose notorious toxicity and explosive tendencies limit its application in research. The necessity for an electrophilic fluorination reagent that is safe, stable, highly reactive, and amenable to industrial production as an alternative to very hazardous molecular fluorine was the inspiration for the discovery of selectfluor. This reagent is not only one of the most reactive electrophilic fluorinating reagents available, but it is also safe, nontoxic, and easy to handle. In this Review we document the many applications of selectfluor and discuss possible mechanistic pathways for its reaction.
Endogenous Dopamine Amplifies Ischemic Long-Term Potentiation via D1 Receptors (2002)

The present data suggest that endogenous dopamine, via D1 receptors, selectively facilitates the expression of ischemic LTP on the AMPA-mediated component of the EPSPs, while it does not alter the expression of this form of synaptic plasticity on the N-methyl-D-aspartate-mediated component of corticostriatal synaptic potentials. Understanding the cellular and molecular mechanisms of ischemia-triggered excitotoxicity offers hope for the development of specific treatments able to interfere with this pathological process.
A high-speed CMOS image sensor with profile data acquiring function (2005)

We have developed a Profile Imager aimed at high-speed automatic target tracking. The Profile Imager can perform both target tracking within a 512 /spl times/ 512-pixel entire image area and acquisition of partial images simultaneously and independently. Experimental results of capturing 128 /spl times/ 128-pixel partial images of an automobile license plate at 1620 frames/s are presented. In addition, results of integrating 89 partial images demonstrate the capability of the device as a high-speed, high-resolution, high-dynamic-range image tracker. A 0.6-/spl mu/m two-poly three-metal CMOS process is used to implement a 13.0 mm /spl times/ 14.3 mm imager.
Evaluation of a novel CD20-targeted IL-15 immunotherapeutic with potent activity against B cell lymphoma (2014)

Meeting abstracts IL-15 exhibits potent antitumor efficacy in mouse models through its ability to promote proliferation and activation of NK cells and memory CD8+ T cells. Recently, targeting approaches have been developed to direct these activities against tumor cells and minimize potential
A systematic review of the clinical performance of CAD/CAM single-tooth restorations. (2010)

Long-term survival rates for CAD/CAM single-tooth Cerec 1, Cerec 2, and Celay restorations appear to be similar to conventional ones. No clinical studies or randomized clinical trials reporting on other CAD/CAM systems currently used in clinical practice and with follow-up reports of 3 or more years were found at the time of the search.
Single molecular assay of individual ATP turnover by a myosin‐GFP fusion protein expressed in vitro (1997)

Fusion proteins of a truncated mutant of myosin subfragment-1 (S1dC) and green fluorescent protein (GFP) were expressed in vitro by T7 RNA polymerase and rabbit reticulocyte lysate. Single S1dC-GFP fusion proteins were clearly seen and their individual ATP turnovers were directly monitored using low background total internal reflection fluorescence microscopy (LBTIRFM), recently developed by our laboratory. LBTIRFM using GFP as a fluorescent tag allowed us to assay functions of single protein molecules expressed in vitro. Thus, the results suggested that this method may be particularly useful to analyze functions of proteins that cannot be produced in an active form and/or in large quantities in conventional heterologous expression systems.
Some New Fluorinated β-Ketoamines and Their Copper Complexes (1986)

Abstract Synthesis and characterization of some new fluorinated bidentate-monofunctional and tetradentate-bifunctional β-ketoamines and their copper complexes are reported. The spectral data of the free Schiff bases indicate that the site of amine condensation in the unsymmetrical β-diketones is the lesser enolized acyl-oxygen and the ketoamine form is the predominant tautomer. The copper complexes of these ligands have been characterized by elemental analysis and IR spectroscopy.
Targeting of an inducible toxic phenotype in animal cells. (1988)

We have developed a toxic, or suicide, vector whose action is based on the targeted expression of the herpes simplex virus 1 thymidine kinase gene product in cultured cells or transgenic animals. This protein is able to convert nucleoside analogs such as acyclovir and 1-(2-deoxy-2-fluoro-beta-D-arabino-furanosyl)-5-iodouracil (FIAU) to toxic intermediates. The activation of these compounds disrupts cellular DNA replication, leading to rapid cell death. Neither acyclovir, FIAU, nor the herpes thymidine kinase alone is harmful to cells. This approach is simple and should have widespread applicability in studying lineage formation in cultured cells and transgenic animals.
Use of an Induced Fit Receptor Structure in Virtual Screening (2005)

Structured-based drug design has traditionally relied on a single receptor structure as a target for docking and screening studies. However, it has become increasingly clear that in many cases where protein flexibility is an issue, it is critical to accurately model ligand-induced receptor movement in order to obtain high enrichment factors. We present a novel protein-ligand docking method that accounts for both ligand and receptor flexibility and accurately predicts the conformation of protein-ligand binding complexes. This method can generate viable receptor ensembles that can be used in virtual database screens.
Inhibition of Interleukin-22 Attenuates Bacterial Load and Organ Failure during Acute Polymicrobial Sepsis (2007)

Interleukin-22 (IL-22) is a recently discovered proinflammatory cytokine, structurally related to IL-10. Since IL-22 is induced by lipopolysaccharide in vivo, we studied the role of IL-22 in a model of polymicrobial peritonitis. Quantitative real-time reverse transcription-PCR analysis showed marked induction of IL-22 and IL-22 receptor in spleen and kidney during the course of sepsis. The biological activity of IL-22 is modulated by IL-22-binding protein (IL-22BP), which is considered a natural antagonist of IL-22. To further analyze the role of IL-22 during septic peritonitis, mice were treated with recombinant IL-22BP generated as Fcgamma2a fusion protein. IL-22BP-Fc completely blocked IL-22-induced STAT3 activation in hepatocytes in vitro. Treatment of mice with IL-22BP-Fc 4 h before sepsis induction led to enhanced accumulation of neutrophils and mononuclear phagocytes and a reduced bacterial load at the site of infection. In addition, IL-22 blockade led to an enhanced bacterial clearance in liver and kidney and reduced kidney injury. These results imply an important proinflammatory role of IL-22 during septic peritonitis, contributing to bacterial spread and organ failure. IL-22 therefore appears to play an important role in the regulation of inflammatory processes in vivo.
The rluC Gene of Escherichia coli Codes for a Pseudouridine Synthase That Is Solely Responsible for Synthesis of Pseudouridine at Positions 955, 2504, and 2580 in 23 S Ribosomal RNA (1998)

Escherichia coli ribosomal RNA contains 10 pseudouridines, one in the 16 S RNA and nine in the 23 S RNA. Previously, the gene for the synthase responsible for the 16 S RNA pseudouridine was identified and cloned, as was a gene for a synthase that makes a single pseudouridine in 23 S RNA. The yceC open reading frame of E. coli is one of a set of genes homologous to these previously identified ribosomal RNA pseudouridine synthases. In this work, the gene was cloned, overexpressed, and shown to code for a pseudouridine synthase able to react with in vitro transcripts of 23 S ribosomal RNA. Deletion of the gene and analysis of the 23 S RNA from the deletion strain for the presence of pseudouridine at its nine known sites revealed that this synthase is solely responsible in vivo for the synthesis of three of the nine pseudouridine residues, at positions 955, 2504, and 2580. Therefore, this gene has been renamed rluC. Despite the absence of one-third of the normal complement of pseudouridines, there was no change in the exponential growth rate in either LB or M-9 medium at temperatures ranging from 24 to 42 degrees C. From this work and our previous studies, we have now identified three synthases that account for 50% of the pseudouridines in the E. coli ribosome.
Low glass transition temperature fluorocarbon ether bibenzoxazole polymers (1978)

Abstract Fluorocarbon ether bis( o ‐aminophenol) monomers were prepared by a multistep synthetic route based on the copper‐promoted coupling of 4‐iodophenyl acetate with 1,8‐diiodoperfluoro‐3,6‐dioxaoctane, 1,11‐diiodoperfluoro‐3,9‐dioxaundecane, 1,14‐diiodoperfluoro‐5,10‐dimethyl‐3,‐6,9,12‐tetraoxatetradecane, and 1,17‐diiodoperfluoro‐3,6,9,15‐tetraoxaheptadecane. Acetic acidpromoted polycyclocondensations of the monomers with long‐chain fluorocarbon ether‐diimidate esters and ‐dithioimidate esters led to linear fluorocarbon ether‐bibenzoxazole polymers soluble in 1,1,1,3,3,3‐hexafluoroisopropanol and 1,1,2‐trichloro‐1,2,2‐trifluoroethane. Polymer structures were verified by elemental and infrared spectral analysis. The polymers were rubbery gums and could be obtained in the inherent viscosity range of 0.20–0.79 dlg −1 . Selection of monomers governed the glass transition temperatures of the resultant polymers. As expected, the polymers exhibited lower glass transition temperatures with increased fluorocarbon ether content, a minimum value of −58°C being achieved. None of the polymers exhibited crystalline melt temperatures. Based on thermogravimetric analysis data, the thermooxidative stability of the polymers tended to decrease with increased fluorocarbon ether content. Onset of breakdown during thermogravimetric analysis in air occurred in the 350–400°C range. Isothermal aging of the polymers in air indicated good thermooxidative stability at 260°C; only 5% weight loss was recorded after 200 hr.
Kinetic models for astaxanthin production by high cell density mixotrophic culture of the microalga Haematococcus pluvialis (1999)

High cell density cultivation of Haematococcus pluvialis for astaxanthin production was carried out in batch and fed-batch modes in 3.7-L bioreactors with stepwise increased light intensity control mode. A high cell density of 2.65 g x L(-1) (batch culture) or 2.74 g x L(-1) (fed-batch culture) was obtained, and total astaxanthin production in the fed-batch culture (64.36 mg x L(-1)) was about 20.5% higher than in the batch culture (53.43 mg x L(-1)). An unstructured kinetic model to describe the microalga culture system including cell growth, astaxanthin formation, as well as sodium acetate consumption was proposed. Good agreement was found between the model predictions and experimental data. The models demonstrated that the optimal light intensity for mixotrophic growth of H. pluvialis in batch or fed-batch cultures in a 3.7-L bioreactor was 90-360 micromol x m(-2) x s(-1), and that the stepwise increased light intensity mode could be replaced by a constant light intensity mode.
Guided Bone Regeneration Around Endosseous Implants With Anorganic Bovine Bone Mineral. A Randomized Controlled Trial Comparing Bioabsorbable Versus Non‐Resorbable Barriers (2000)

In conclusion, both collagen and ePTFE barriers proved suitable for achieving GBR of osseous defects surrounding dental implants. The results of this study stress the importance of barrier fixation at the time of initial surgery.
Noncontact Thermal and Vibrotactile Display Using Focused Airborne Ultrasound (2020)

Abstract In a typical mid-air haptics system, focused airborne ultrasound provides vibrotactile sensations to localized areas on bare skin. Herein, a method for displaying heat sensations to hands where gloves are worn is proposed. The gloves employed in this study are commercially available gloves with sound absorption characteristics, such as cotton work gloves without any additional devices such as Peltier elements. The method proposed in this study can also provide vibrotactile sensations by changing the ultrasonic irradiation pattern. In this paper, we report basic experimental investigations on the proposed method. By performing thermal measurements, we evaluate the local heat generation on the surfaces of both the glove and the skin by focused airborne ultrasound irradiation. In addition, we performed perceptual experiments, thereby confirming that the proposed method produced both heat and vibrotactile sensations. Furthermore, these sensations were selectively provided to a certain extent by changing the ultrasonic irradiation pattern. These results validate the effectiveness of our method and its feasibility in mid-air haptics applications.
Trap-Assisted Tunneling in Si-InAs Nanowire Heterojunction Tunnel Diodes (2011)

We report on the electrical characterization of one-sided p+-si/n-InAs nanowire heterojunction tunnel diodes to provide insight into the tunnel process occurring in this highly lattice mismatched material system. The lattice mismatch gives rise to dislocations at the interface as confirmed by electron microscopy. Despite this, a negative differential resistance with peak-to-valley current ratios of up to 2.4 at room temperature and with large current densities is observed, attesting to the very abrupt and high-quality interface. The presence of dislocations and other defects that increase the excess current is evident in the first and second derivative of the I–V characteristics as distinct peaks arising from trap-and phonon-assisted tunneling via the corresponding defect levels. We observe this assisted tunneling mainly in the forward direction and at low reverse bias but not at higher reverse biases because the band-to-band generation rates are peaked in the InAs, which is also confirmed by modeling. This indicates that most of the peaks are due to dislocations and defects in the immediate vicinity of the interface. Finally, we also demonstrate that these devices are very sensitive to electrical stress, in particular at room temperature, because of the extremely high electrical fields obtained at the abrupt junction even at low bias. The electrical stress induces additional defect levels in the band gap, which reduce the peak-to-valley current ratios.
Malignant leukemic cell separation by iron colloid immunomagnetic adsorption. (1989)

We describe an immunomagnetic assay applicable to bone marrow purging of leukemic patients before an autologous bone marrow transplantation. An iron colloidal suspension with a CD10 monoclonal antibody (MoAb) against the common acute lymphoblastic leukemia antigen (CALLA) covalently bound to the surface of the particles has been used. NALM-6 cells, a pre-B leukemic cell line expressing the CALLA, were labeled with supravital DNA dye (Hoechst 33342), mixed with peripheral blood, and incubated with the MoAb coated to iron particles. Using this reagent, at a cell concentration of 2000/microliters, a purging effect greater than 3.5 logs is observed with 0.1 mg of coated particles. Three successive rounds of treatment with the same coated particles at the same dose showed approximately the same depletion after each treatment. The recovery of clonogenic myeloid progenitors (granulocyte-macrophage colony-forming units; CFU-GM) is around 75%. No depletion was observed when the iron particles were not attached to the CD10 MoAb, or when they were attached to a MoAb not recognizing CD10+ cells. A comparison with another commercially available magnetic support was also performed in order to evaluate the performance of our assay, which appears simple, efficient, cheap, and capable of handling large volumes of cells in sterile conditions and minimal time.
Direct Observation of Terahertz Surface Modes in Nanometer-Sized Liquid Water Pools (2001)

The far-infrared absorption spectrum of nanometer-sized water pools at the core of AOT micelles exhibits a pronounced resonance which is absent in bulk water. The amplitude and spectral position of this resonance are sensitive to the size of the confined water core. This resonance results from size-dependent modifications in the vibrational density of states, and thus has far-reaching implications for chemical processes which involve water sequestered within small cavities. These data represent the first study of the terahertz dielectric properties of confined liquids.
Nuclear Targeting of Chlorin e6 Enhances Its Photosensitizing Activity (1997)

Although photosensitizers, molecules that produce active oxygen species upon activation by visible light, are being extensively used in photodynamic therapy to treat cancer and other clinical conditions, problems include normal cell and tissue damage and associated side effects, which are attributable in part to the fact that cytotoxic effects are largely restricted to the plasma membrane. We have previously shown that the photosensitizer chlorin e6 has significantly higher photosensitizing activity when present in conjugates containing specific ligands and thus able to be internalized by receptor-expressing cells. In this study we use insulin-containing conjugates to which variants of the simian virus SV40 large tumor antigen nuclear localization signal (NLS) were linked to target chlorin e6 to the nucleus, a hypersensitive site for active oxygen species-induced damage. NLSs were either included as peptides cross-linked to the carrier bovine serum albumin or encoded within the sequence of a beta-galactosidase fusion protein carrier. The results for photosensitization demonstrate clearly for the first time that NLSs increase the photosensitizing activity of chlorin e6, maximally reducing the EC50 by a factor of over 2000-fold. This has wide-reaching implications for achieving efficient cell type-specific photodynamic therapy.
Interaction of Heat Shock Proteins with Peptides and Antigen Presenting Cells: Chaperoning of the Innate and Adaptive Immune Responses (2002)

Heat shock proteins are abundant soluble intracellular proteins, present in all cells. Members of the heat shock protein family bind peptides including antigenic peptides generated within cells. Heat shock proteins also interact with antigen presenting cells through CD91 and other receptors, eliciting a cascade of events including re-presentation of heat shock protein-chaperoned peptides by MHC, translocation of NF kappa B into the nuclei and maturation of dendritic cells. These consequences point to a key role of heat shock proteins in fundamental immunological phenomena such as activation of antigen presenting cells, indirect presentation (or cross-priming), and chaperoning of peptides during antigen presentation. Heat shock proteins appear to have been involved in innate immune responses since the emergence of phagocytes in early multicellular organisms and to have been commandeered for adaptive immune responses with the advent of specificity. These properties of heat shock proteins also allow them to be used for immunotherapy of cancers and infections in novel ways.