gebhart/patrepeval huggingface dataset:
Overcoming the distortion problem in image-enhanced fluoroscopy (2003)

In this paper, we examine the problem of image distortion influoroscopy, in particular its effect applications in image-guided surgery that make use of tracking and calibration techniques to relate a point in physical space in the operating room (OR)to the corresponding pointin an intraoperative fluoroscopic image. We call such applications <i>image-enhanced fluoroscopy</i>. In order to derive the relationship between physical space and a fluoroscopic image, two sets of parameters must be known. The first set describes the pose of the fluoroscope at the time when the image was taken; these parameters are usually estimated by rigidly attaching a device to the fluoroscope that is able to be tracked by either an optical or magnetic tracking system present in the OR. The second set of parameters describes the projection model of the fluoroscope itself: this set includes focal length and X-ray source position relative to the image intensifier. In the case that we examine here, these values are estimated using a set of BBs of known geometry placed between the X-ray source and the image intensifier. Because the image intensifier is not perfectly planar, and also because of ambient magnetic fields, the image displayed by the fluoroscope does not match that predicted by a linear projection model. Using the known geometry of the BBs appearing in the image, we may attempt to recover the image that would be given by a linear projection. We call this process <i>dewarping</i>. In this paper, we address the question of the optimal dewarp function. Although a fifth-order polynomial is commonly used, we show that a third-order polynomial is superior. We use real fluoroscope images to demonstrate the potential dangers of using too high a polynomial order for the dewarping process.
Conformational Switching by Asparagine-Linked Glycosylation (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTConformational Switching by Asparagine-Linked GlycosylationSarah E. O'Connor and Barbara ImperialiView Author Information Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California 91125 Cite this: J. Am. Chem. Soc. 1997, 119, 9, 2295–2296Publication Date (Web):March 5, 1997Publication History Received1 October 1996Published online5 March 1997Published inissue 1 March 1997https://pubs.acs.org/doi/10.1021/ja963435ohttps://doi.org/10.1021/ja963435orapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views420Altmetric-Citations68LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Amides,Chemical structure,Conformation,Peptides and proteins,Post-translational modification Get e-Alerts
Column Interconnects: A Path Forward for Embedded Cooling of High Power 3D Chip Stacks (2018)

In this paper we present a novel approach to addressing the challenges of integrating embedded cooling into 3D chip stacks with multiple large high power die layers. 3D chip stacks require the integration of through silicon vias (TSVs) in the active device die layers, with demonstrated reliable production capable processes limiting the height of such vias (and thus the active device die thickness) to approximately 50 micrometers for integrated copper vias, creating constraints on channel height. Limited channel height capability constrains the power which can be transferred to the coolant at reasonable coolant pressure drops. An ideal solution to integrating embedded cooling into a stack of large high power dies would allow higher channel height and require no additional processing of the active dies. In this work we describe and provide initial experimental results for an approach that meets this ideal. In this approach a separate interconnect/channel defining structure is created utilizing a die thinned to a thickness compatible with TSV processes that do not require active device integration. Reliable TSV heights of 100 micrometers or more are obtainable when integration with fine wiring or active devices is not required on either end of the TSV. The thinned die is attached to a handler wafer utilizing a blanket adhesive process. TSV structures along with endpoint metallurgies (pads, solder bumps, etc) are created in the thinned die either before or after thinning and handler attach, depending on the exact TSV and endpoint metallurgy processes chosen. Pillar and/or channel wall structures are lithographically laid out to incorporate the TSVs. The die area outside these pillar/wall structures is completely etched away with a Deep Reactive Ion Etch (RIE) process, leaving an array of fully separated pillar/wall structures attached to the handler wafer. This wafer may, if desired, then be diced into active-die sized arrays. These structures are now attached to receiving pads/solder bumps on one active die or wafer. The handler wafer/die is then released from the structures, leaving them standing attached to the active die or wafer. Finally a second active die or wafer is attached to the other end of the structures, creating coolant channels with embedded TSVs. The process can be repeated with an arbitrary number of active die/interconnect array pairs. The initial experimental work presented here demonstrates this process without integrated TSV's, showing that it is possible to create such structures, attach them to a die, release the handler, and attach a die to the other end of the structures thus creating coolant channels or cavities. This approach and initial demonstration show the potential for reliable high power 3D integration of embedded cooling using active dies incorporating demonstrated TSV processes.
An Engineered Protease that Cleaves Specifically after Sulfated Tyrosine (2008)

Picky eater: The bacterial protease OmpT has been engineered to cleave after sulfotyrosine residues in peptide substrates but not after phosphotyrosine (see scheme). A selection/counterselection screen was used to identify OmpT variants with the desired specificity and high levels of overall catalytic activity. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z800736_s.pdf or from the author. 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.
Axonal Transport of Dopamine‐containing Vesicles Labelled In Vivo with [3H] Reserpine (1993)

Axonal transport of the vesicular monoamine transporter was assayed in the rat brain by in vivo binding of the specific ligand [3H]reserpine. Because of the marked localization of reserpine binding sites in dopaminergic cell bodies and nerve terminals, the dopaminergic nigrostriatal pathway was chosen for the study of the axonal transport of the monoamine carrier present in the membrane of synaptic vesicles. When labelled reserpine was injected into the substantia nigra, a delayed accumulation of radioactivity in the ipsilateral striatum was observed approximately 4 h after the injection. Similarly, injection into the right striatum was followed by a substantial accumulation of radioactivity in the ipsilateral substantia nigra, which was prevented by peripheral injection of unlabelled reserpine or tetrabenazine. This process was rapid and dependent on microtubules. In senescent rats, the amount of retrogradely transported [3H]reserpine was significantly reduced. These results demonstrate that labelled reserpine may be used to monitor in vivo fast axonal transport in central neurons.
Association of Whole-Genome and NETRIN1 Signaling Pathway–Derived Polygenic Risk Scores for Major Depressive Disorder and White Matter Microstructure in the UK Biobank (2018)

Our findings indicate that variation in the NETRIN1 signaling pathway may confer risk for major depressive disorder through effects on a number of white matter tracts.
Targeted Proteomic Quantitation of the Absolute Expression and Turnover of Cystic Fibrosis Transmembrane Conductance Regulator in the Apical Plasma Membrane (2020)

Deficient chloride transport through cystic fibrosis (CF) transmembrane conductance regulator (CFTR) causes lethal complications in CF patients. CF is the most common autosomal recessive genetic disease, which is caused by mutations in the CFTR gene; thus, CFTR mutants can serve as primary targets for drugs to modulate and rescue the ion channel’s function. The first step of drug modulation is to increase the expression of CFTR in the apical plasma membrane (PM); thus, accurate measurement of CFTR in the PM is desired. This work reports a tandem enrichment strategy to prepare PM CFTR and uses a stable isotope labeled CFTR sample as the quantitation reference to measure the absolute amount of apical PM expression of CFTR in CFBE 41o- cells. It was found that CFBE 41o- cells expressing wild-type CFTR (wtCFTR), when cultured on plates, had 2.9 ng of the protein in the apical PM per million cells; this represented 10% of the total CFTR found in the cells. When these cells were polarized on filters, the apical PM expression of CFTR increased to 14%. Turnover of CFTR in the apical PM of baby hamster kidney cells overexpressing wtCFTR (BHK-wtCFTR) was also quantified by targeted proteomics based on multiple reaction monitoring mass spectrometry; wtCFTR had a half-life of 29.0 ± 2.5 h in the apical PM. This represents the first direct measurement of CFTR turnover using stable isotopes. The absolute quantitation and turnover measurements of CFTR in the apical PM can significantly facilitate understanding the disease mechanism of CF and thus the development of new disease-modifying drugs. Absolute CFTR quantitation allows for direct result comparisons among analyses, analysts, and laboratories and will greatly amplify the overall outcome of CF research and therapy.
Kinetics of Absorbed Chromophore Exchange on Metal Oxide Electrodes (2003)

Exchange experiments utilizing Ru(bpy)2(4,4‘-(CO2H)2bpy)2+ and Os(bpy)2(4,4‘-(CO2H)2bpy)2+ (4,4‘-(CO2H)2bpy is 4,4‘-dicarboxy-2,2‘-bipyridine) provide evidence for a distribution of binding sites on ITO electrodes by electrochemical monitoring and on optically transparent, nanoparticle TiO2 films by optical monitoring. Using the Albery model of dispersed kinetics for the analysis of exchange, the results are consistent with dissociative loss from the surface with k1 = 0.1 s-1 for the dissociative step in CH3CN on ITO. Equilibrium binding data after exchange suggest that a site or distribution of sites is also present that undergoes exchange on a very slow time scale. Complete exchange takes place in EtOH, and the rate is greatly enhanced compared to that in CH3CN, suggesting that EtOH labilizes the surface to exchange. On TiO2 the time scale for exchange is far longer than that on ITO, and in CH3CN it scales with film thickness.
Competition studies in horse spleen ferritin probed by a kinetically inert inhibitor, (Cr(TREN)(H 2 O)(OH)) 2+ , and a highly luminescent (2003)

The ability of ferritin as an Fe(II) detoxifier and Fe(III) storage protein is limited by its ability to recognize and incorporate Fe(II), which is then oxidized and mineralized at internal protein sites. The Cr(III) amine complex (Cr(N(CH2CH2NH2)3(H2O)(OH)) 2+ (abbreviated as Cr(TREN)) is a kinetically inert inhibi- tor of iron incorporation and mineralization in ferritin. Unlike other inhibitors, Cr(TREN) can only exchange its two aqua/hydroxy ligands. Competition studies be- tween Cr(TREN) and Tb(III) binding have been per- formed in horse spleen ferritin (HoSF) to probe uptake of Fe(II). From these studies, we propose that Cr(TREN) inhibits Fe(II) uptake by obstructing the routes of metal uptake and by disrupting the early rec- ognition events at the protein surface that precede metal ion uptake. Using an improved luminescence approach to quantify Tb(III) binding to the protein, we demon- strate that Tb(III) cannot interfere with Cr(TREN) binding to ferritin, but that Cr(TREN) dramatically inhibits Tb(III) binding. We show that bound Tb(III) serves as a reliable reporter for Cr(TREN) binding, as the latter efficiently quenches the Tb(III) luminescence via inter-ion energy transfer. Two types of Cr(TREN) binding sites were successfully distinguished from these competition experiments. A common Tb(III)/Cr(TREN) site was identified with stoichiometry of � 0.6 equiva- lents of metal cation per ferritin subunit. We propose that the sites along the three-fold channels and the ferroxidase sites are common binding sites for Tb(III) and Cr(TREN). The remaining Cr(TREN) (2.4 equiva- lents of metal ions/subunit) does not compete with Tb(III) but rather blocks Tb(III) access into the cavity and decreases the protein's affinity for Tb(III). Electronic supplementary material is available if you ac- cess this article at http://dx.doi.org/10.1007/s00775-002- 0409-4. On that page (frame on the left side), a link takes you directly to the supplementary material.
In‐vivo quality assurance of dynamic tumor tracking (DTT) for liver SABR using EPID images (2023)

Marker-based DTT uncertainty can be evaluated in-vivo on a field-by-field basis using EPID images. This information can contribute to PTV margin calculations for DTT.
Novel Ion-Implanted VCSEL Structures (1999)

We describe the design and performance of VCSEL’s which have low thresholds and high quantum efficiency for practicality, are made with only photolithographically defined features for reproducibility, and easily integrate with electronic circuitry for usefulness.
Measurement of Angular and CP Asymmetries in D0→π+π−μ+μ− and D0→K+K−μ+μ− Decays (2018)

The first measurements of the forward-backward asymmetry of the dimuon pair (A_{FB}), the triple-product asymmetry (A_{2ϕ}), and the charge-parity-conjugation asymmetry (A_{CP}), in D^{0}→π^{+}π^{-}μ^{+}μ^{-} and D^{0}→K^{+}K^{-}μ^{+}μ^{-} decays are reported. They are performed using data from proton-proton collisions collected with the LHCb experiment from 2011 to 2016, corresponding to a total integrated luminosity of 5 fb^{-1}. The asymmetries are measured to be A_{FB}(D^{0}→π^{+}π^{-}μ^{+}μ^{-})=(3.3±3.7±0.6)%, A_{2ϕ}(D^{0}→π^{+}π^{-}μ^{+}μ^{-})=(-0.6±3.7±0.6)%, A_{CP}(D^{0}→π^{+}π^{-}μ^{+}μ^{-})=(4.9±3.8±0.7)%, A_{FB}(D^{0}→K^{+}K^{-}μ^{+}μ^{-})=(0±11±2)%, A_{2ϕ}(D^{0}→K^{+}K^{-}μ^{+}μ^{-})=(9±11±1)%, A_{CP}(D^{0}→K^{+}K^{-}μ^{+}μ^{-})=(0±11±2)%, where the first uncertainty is statistical and the second systematic. The asymmetries are also measured as a function of the dimuon invariant mass. The results are consistent with the standard model predictions.
Capacitance of thin Ferroelectric films obtained with different methods (2008)

Thin film Ferroelectric capacitance can be obtained with two methods. Capacitance obtained by the derivative of its hysteresis loop is related to large applied signal. Capacitance measured directly with small applied alternate current signal together with slow changing dc bias is related to small signal circuit analysis. This paper investigated the relationship between the two types of capacitance. Measurements show that C-V curves obtained with the first method have much sharper peaks and higher peak values. A model, which divides the polarization of Pb (Zr, Ti) O3 (PZT) into linear polarization and switching polarization, was utilized to analyze the mechanism.
Green Well Stimulation Fluids for Enhanced Oil Recovery from Tight Sand Formations: Field Wide 70+ Wells Study Over 4 Years (2021)

Abstract Legacy oil production from Appalachian basin has been in a decline mode since 2013. With more than 80% of wells producing less than 15 bbl/day, there is a growing interest in economically and environmentally viable options for well stimulation treatments. Analysis of formation mineralogy and reservoir fluids along with history of well interventions indicated formation damage in many wells due precipitation of organics and a change in wettability being partially responsible for production decline rates in excess of forecasts. The development and properties of a novel cost-effective biosurfactant based well-stimulation fluid are described here along lessons learned from several field trials in wells completed in the Upper Devonian Bradford Group. This group of 74 wells, completed in siltstone and sandstone reservoirs were presenting more than 12 well failures annually across the field, which was attributed to the accumulation of organic deposits in the tubulars. Based on these cases, batch stimulation treatments using a novel fluid comprising biosurfactants were proposed and implemented field wide. The treatments effectively removed organic deposits, changed formation wettability from oil to water wet and resulted in a sustained oil production increase. Well failures were significantly reduced as a result of this program and the group of 74 wells did not have a paraffin-related well failure for 18 months. Results from this program demonstrates the efficiency of the green well stimulation fluids in mitigating formation damage, reducing organics deposition and in increasing oil production as a promising method to stimulate tight formations.
Resolution of Mesenteric Panniculitis in a Patient With Vibrio cholerae: A Case Report (2014)

Introduction: Mesenteric panniculitis (MP) has been defined as a “misty” or “hazy” mesentery and/or an unexplained mesenteric mass, and is an uncommon finding on computerized tomographic (CT) scanning. A variety of conditions are associated with this finding, including abdominal trauma, lymphoma, solid tumors, and autoimmune diseases. To our knowledge, we report the first case of acute Vibrio cholerae infection and CT changes consistent with MP. A 78-year-old Indian male returned from a trip to India with symptoms of nausea, vomiting, abdominal pain, and watery diarrhea. He was afebrile. The patient chose food carefully and only drank boiled water in India. His symptoms began on the flight back to the U.S., and he had an episode of syncope requiring hospital admission. Physical examination revealed dry mucus membranes and mid-abdominal tenderness. His stool tested positive twice for pan-susceptible Vibrio cholerae with moderate Charcot-Leyden crystals and moderate leukocytes. Initial CT revealed prominent lymph nodes and a hazy mesentery consistent with MP (Figure 1). The patient was treated with ondansetron, metoclopramide, and intravenous fluids. He was subsequently treated with ciprofloxacin and metronidazole for 10 days, yet his abdominal pain persisted for 1 month and diarrhea was present for 2 months. Follow-up CT 8 months after initial presentation indicated complete resolution of MP (Figure 1). This is the first case report of mesenteric lymphadenopathy, and MP associated with a human Vibrio cholerae infection. In animal studies, inoculation with Vibrio cholerae produced a systemic immune response characterized by antibody formation preceding mesenteric lymphadenopathy. It may be inferred that mesenteric involvement associated with Vibrio cholerae infection is a reactive phenomenon. In the setting of Vibrio cholerae, the finding of MP appears to be a reactive inflammatory disorder of the mesentery that is immunologically mediated. In our patient, the mesenteric process caused prolonged symptoms that ultimately resolved after antibiotic treatment.Figure 1: Initial CT with MP (top left, arrows) and mesenteric lymph nodes (top right, arrows). Follow-up CT with resolution of MP and regression of the mesenteric mass and mesenteric lymph nodes (bottom left and right).
Two Distinct Routes to Oral Cancer Differing in Genome Instability and Risk for Cervical Node Metastasis (2011)

Two subtypes of oral lesions indicative of at least two pathways for oral cancer development were distinguished that differ in chromosomal instability and risk for metastasis, suggesting that +3q,-8p, +8q, and +20 constitute a biomarker with clinical utility for identifying patients at risk for metastasis. Moreover, although increased numbers of genomic alterations can be harbingers of progression to cancer, dysplastic lesions lacking copy number changes cannot be considered benign as they are potential precursors to non-3q8pq20 locally invasive, yet not metastatic oral SCC.
Drug repurposing screens reveal cell-type-specific entry pathways and FDA-approved drugs active against SARS-Cov-2 (2021)

There is an urgent need for antivirals to treat the newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To identify new candidates, we screen a repurposing library of ∼3,000 drugs. Screening in Vero cells finds few antivirals, while screening in human Huh7.5 cells validates 23 diverse antiviral drugs. Extending our studies to lung epithelial cells, we find that there are major differences in drug sensitivity and entry pathways used by SARS-CoV-2 in these cells. Entry in lung epithelial Calu-3 cells is pH independent and requires TMPRSS2, while entry in Vero and Huh7.5 cells requires low pH and triggering by acid-dependent endosomal proteases. Moreover, we find nine drugs are antiviral in respiratory cells, seven of which have been used in humans, and three are US Food and Drug Administration (FDA) approved, including cyclosporine. We find that the antiviral activity of cyclosporine is targeting Cyclophilin rather than calcineurin, revealing essential host targets that have the potential for rapid clinical implementation.
Effect of Human Conductivity Distributions during Magnetic Nanoparticles Hyperthermia (2021)

This paper investigates electromagnetic field interaction with human tissue during magnetic nano-particles hyperthermia (MNPH). Namely, the specific absorption rates (SARs) are computed and presented across different tissues in the body with different coil configurations for deep seated cancers, such as pancreatic cancers. Special attention is given to the coil placement in front and at the back of the human model centered at the pancreas. The studies have showed that the from coil produces less unwanted eddy currents in the normal tissues than back coil.