gebhart/patrepeval huggingface dataset:
Automated matching and segmentation of lymphoma on serial CT examinations (2006)

In patients with lymphoma, identification and quantification of the tumor extent on serial CT examinations is critical for assessing tumor response to therapy. In this paper, we present a computer method to automatically match and segment lymphomas in follow-up CT images. The method requires that target lymph nodes in baseline CT images be known. A fast, approximate alignment technique along the x, y, and axial directions is developed to provide a good initial condition for the subsequent fast free form deformation (FFD) registration of the baseline and the follow-up images. As a result of the registration, the deformed lymph node contours from the baseline images are used to automatically determine internal and external markers for the marker-controlled watershed segmentation performed in the follow-up images. We applied this automated registration and segmentation method retrospectively to 29 lymph nodes in 9 lymphoma patients treated in a clinical trial at our cancer center. A radiologist independently delineated all lymph nodes on all slices in the follow-up images and his manual contours served as the "gold standard" for evaluation of the method. Preliminary results showed that 26/29 (89.7%) lymph nodes were correctly matched; i.e., there was a geometrical overlap between the deformed lymph node from the baseline and its corresponding mass in the follow-up images. Of the matched 26 lymph nodes, 22 (84.6%) were successfully segmented; for these 22 lymph nodes, several metrics were calculated to quantify the method's performance. Among them, the average distance and the Hausdorff distance between the contours generated by the computer and those generated by the radiologist were 0.9 mm (stdev. 0.4 mm) and 3.9 mm (stdev. 2.1 mm), respectively.
Evaluation of Ultrasound-Based Sensor to Monitor Respiratory and Nonrespiratory Movement and Timing in Infants (2015)

It is feasible to use the sensor as trigger for synchronizing mechanical ventilators to spontaneous breathing, to quantify overall movement, to determine sleep state, to detect seizures, and to document the amount and effects of caretaker activity in infants.
Advances In Surface Magnetic Field Measurement Technique For Detection And Sizing of Surface-Breaking Cracks In Offshore Structures (1994)

In detecting and sizing cracks in metal structures, the two common techniques of eddy-current and potential-drop, suffer from a number of problems which may not be acceptable in offshore environments. This paper describes recent advances in the surface magnetic field measurement (SMFM) technique as an alternative method for integrity evaluation of offshore metal structures.
A Simple Assay Method for Erythropoietin<i>In Vitro</i> (1983)

A simple in vitro assay method for erythropoietin, a plasma glycoprotein which stimulates erythroid differentiation, has been developed. In this method, a liver cell suspension from 13-day mouse fetus was planted in the wells of a flat-bottomed 96-well microtiter plate and incubated for culturing. The formation of erythroid colonies, which were identified with benzidine staining, was dependent on added erythropoietin. Since this method is inexpensive, sensitive, simple, and only requires a small sample, it could be adopted for assaying the erythropoietin levels in blood, urine, and other materials.
Analysis ofN-acetylated hexosamine monosaccharides by ferrocenyl boronation and tandem electrospray ionization mass spectrometry (2000)

A tandem electrospray mass spectrometric (MS(n)) technique for the analysis of N-acetylated hexose carbohydrates using ferrocene boronate (F(c)Bor) derivatization was developed. The biologically important N-acetyl hexosamines can be readily distinguished utilizing this technique. The analysis is made possible by utilizing the inherent electrochemical properties of the electrospray device to produce oxidized, pre-formed single-electron ferrocenyl ions in a non-aqueous solvent system. The electrospray device was modified using a custom built cell consisting of concentric stainless steel tubes, which produced an enhanced signal for the molecular ion of each analyte species. The MS(2) spectra derived from isomeric populations of ferrocenyl boronic esters of these carbohydrates when generated under the same conditions possessed features unique to each sugar allowing easy differentiation between a number of N-acetyl hexosamine isomers.
3D object recognition using single exposure on-line digital holography (2006)

On-line phase shifting digital holography requires recording of multiple holograms. In this paper, we describe a real time 3-D object recognition system using single exposure on-line digital holography. In contrast to 3-D object recognition employing conventional phase shifting scheme which requires multiple exposures, this method requires only one single digital hologram to be synthesized and used to recognize 3-D objects. A benefit of the proposed 3-D recognition method is enhanced practicality of digital holography for 3-D recognition in terms of its simplicity and more robustness to external scene parameters such as moving targets and environmental noise factors. We show experimentally, that the single exposure on-line digital holography based 3-D object recognition method is capable of providing 3-D object recognition. The experimental results are compared with that of the on-line phase shifting digital holographic based 3D recognition.
ChemInform Abstract: Synthesis of Pentathymidylate Using a 4‐Monomethoxytritylthio (MMTrS) Group as a 5′‐Hydroxyl Protecting Group: Toward Oligonucleotide Synthesis Without Acid Treatment. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Preparation of Trifluoromethylphenyl Magnesium Halides in the Presence of LiCl and Synthesis of 2′-Trifluoromethyl-Aromatic Ketones (2016)

The effect of LiCl-promoted insertion of magnesium turnings into halogenated-trifluoromethylbenzenes for Grignard reagent synthesis was investigated. In the presence of less than 1.0 equiv of LiCl, chloro(trifluoromethyl)benzene Grignard reagents were easily generated. The 2-trifluoromethylphenyl magnesium chloride Grignard reagent was obtained in high yield and 2′-trifluoromethyl-substituted aromatic ketone was synthesized through reaction of the obtained Grignard reagent with a carboxylic anhydride in an 83% yield.
Prodrugs of bisthiazolium salts are orally potent antimalarials (2004)

We created neutral antimalarial prodrugs that deliver bisthiazolium compounds with antimalarial activity in the nanomolar range. These drugs primarily affect early intraerythrocytic stages through rapid, nonreversible cytotoxicity. The compounds are suitable for both parenteral and oral use and plasma promotes rapid conversion of the prodrug into the drug. We demonstrate that very low doses offer protection in a murine model of malaria. The drugs show great potential for curing high parasitemia with short-course treatments. Oral administration of the TE3 prodrug completely cures Plasmodium cynomolgi infection in rhesus monkeys. The drugs specifically accumulate inside infected erythrocytes, block phosphatidylcholine biosynthesis, and interact with hemozoin. To our knowledge, this class of compounds represents one of the most potent antimalarials tested to date. These unique properties signal a promising future for this class of antimalarial.
Synthesis of Cryptophycin 52 Using the Sharpless Asymmetric Dihydroxylation:  Diol to Epoxide Transformation Optimized for a Base-Sensitive Substrate (2000)

A synthesis of cryptophycin 52 (2) is reported using a Sharpless asymmetric dihydroxylation (AD) strategy to install the epoxide moiety. The high stereoselectivity of the AD reaction that allows for an efficient means of preparing the epoxide is in contrast to the standard direct epoxidation of cryptophycin substrates, which proceeds with poor diastereoselectivity. Methodology for conversion of the diol AD product to the requisite epoxide is disclosed. The transformation has been optimized to proceed in high yield in the presence of base sensitive functionality.
Chemical inhibition of FBXO7 reduces inflammation and confers neuroprotection by stabilizing the mitochondrial kinase PINK1 (2020)

Mitochondrial quality control is mediated by the PTEN-induced kinase 1 (PINK1), a cytoprotective protein that is dysregulated in inflammatory lung injury and neurodegenerative diseases. Here, we show that a ubiquitin E3 ligase receptor component, FBXO7, targets PINK1 for its cellular disposal. FBXO7, by mediating PINK1 ubiquitylation and degradation, was sufficient to induce mitochondrial injury and inflammation in experimental pneumonia. A computational simulation-based screen led to the identification of a small molecule, BC1464, which abrogated FBXO7 and PINK1 association, leading to increased cellular PINK1 concentrations and activities, and limiting mitochondrial damage. BC1464 exerted antiinflammatory activity in human tissue explants and murine lung inflammation models. Furthermore, BC1464 conferred neuroprotection in primary cortical neurons, human neuroblastoma cells, and patient-derived cells in several culture models of Parkinson's disease. The data highlight a unique opportunity to use small molecule antagonists that disrupt PINK1 interaction with the ubiquitin apparatus to enhance mitochondrial quality, limit inflammatory injury, and maintain neuronal viability.
Iterated neighbor-embeddings for image super-resolution (2014)

We propose an exemplar-based super-resolution algorithm based on sparsity constrained neighbor-embeddings of local image patches. We extract exemplar patch pairs from as little as the given low-resolution image, and we rely on local geometric similarities of low-and high-resolution patch spaces. While sparsely coding the local geometry with a greedy patch selection method, we refine our solution by iteratively updating the obtained high-resolution image. We finally apply an adaptive back-projection to ensure the global consistency. Our experimental results indicate promising performance on synthesizing natural looking textures and sharp edges when compared to other super-resolution methods from the literature.
A <i>Drosophila</i> model of closed head traumatic brain injury (2013)

Traumatic brain injury (TBI) is a substantial health issue worldwide, yet the mechanisms responsible for its complex spectrum of pathologies remains largely unknown. To investigate the mechanisms underlying TBI pathologies, we developed a model of TBI in Drosophila melanogaster. The model allows us to take advantage of the wealth of experimental tools available in flies. Closed head TBI was inflicted with a mechanical device that subjects flies to rapid acceleration and deceleration. Similar to humans with TBI, flies with TBI exhibited temporary incapacitation, ataxia, activation of the innate immune response, neurodegeneration, and death. Our data indicate that TBI results in death shortly after a primary injury only if the injury exceeds a certain threshold and that age and genetic background, but not sex, substantially affect this threshold. Furthermore, this threshold also appears to be dependent on the same cellular and molecular mechanisms that control normal longevity. This study demonstrates the potential of flies for providing key insights into human TBI that may ultimately provide unique opportunities for therapeutic intervention.
Total Synthesis of the Potent Antitumor Macrolides Pladienolide B and D (2007)

Getting cross: The total syntheses of two pladienolides (see picture), which have prominent antitumor activity based on a unique mechanism of action, have been accomplished, and their absolute configurations were verified. The 12-membered aliphatic macrolide structure was formed by ring-closing metathesis, and the side-chain moiety was coupled to the macrolide by Julia–Kocienski olefination or cross-metathesis. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z604997_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.
Longitudinal monitoring of patient limb loading throughout ankle fracture rehabilitation using an insole load monitoring system: a case series (2017)

Background: The purpose of this prospective, direct observational study was to evaluate limb loading in lower extremity orthopaedic trauma patients using a novel insole sensor, the Ambulatory Tibial Load Analysis System (ATLAS). Methods: Three patients from a level I trauma center, one with a trimalleolar ankle fracture, one with a distal, spiral fracture of the tibia and fibula at the same level, and one with a bimalleolar ankle fracture were observed using an insole load monitoring system to record their weight bearing during standard of care rehabilitation. No clinical decisions were made based on the limb loading data. The primary study measures were limb-loading data provided by the ATLAS and patient reported physical function as measured by the PROMIS Physical Function Computer Adapted Test. Results: The ATLAS provided 8-12 wk of continuous limb loading data, with raw loading data, duration of insole sensor and CAM walker wear, daily step count, median load per day, and periods of static and dynamic loading for three patients with varying ankle fractures. Conclusions: The findings of this case study support the use of the ATLAS sensor in evaluation of limb loading in patients with lower extremity fracture. The data suggest that the current weight bearing prescription may not be sufficient for all patients and that personalized protocols are warranted.
Dopaminergic (4aR,10bS)-cis- and (4aS,10bS)-trans-octahydrobenzo[F]quinolines have similar pharmacophores. (1995)

The structures and absolute configurations of two N-phenethyl substituted cis- and trans-octahydrobenzo[f]quinolines were determined by X-ray crystallography. The absolute configurations of the enantiomers that have high affinity for dopaminergic receptors were found to be (4aR,10bS) and (4aS,10bS) for the (-)-cis- and (-)-trans-8,9-dihydroxy substituted compounds. This is consistent with previous results for a dopamine agonist pharmacophore. MM2-87 calculations for a cis isomer, which has two alternative chair conformations of the piperidine ring, indicated that the preferred conformer is the same as that observed in the crystal structure. Superposition of the more active cis and trans enantiomers showed that the three dimensional orientations of the phenyl ring and the ammonium group are similar in the two geometrical isomers. The cis isomer, however, has steric bulk out of the plane of the molecule and this appears to result in a loss of agonist efficacy. The addition of the N-phenethyl group to the 7-OH and 7,8-diOH cis compounds, however, appears to be sufficient to restore high affinity for dopaminergic receptors unlike previously synthesized cis compounds. These cis compounds, however, appear to be mixed agonist/antagonists or antagonists on functional assays of dopaminergic activity.
The AcbC Protein from Actinoplanes Species Is a C7-cyclitol Synthase Related to 3-Dehydroquinate Synthases and Is Involved in the Biosynthesis of the α-Glucosidase Inhibitor Acarbose (1999)

The putative biosynthetic gene cluster for the alpha-glucosidase inhibitor acarbose was identified in the producer Actinoplanes sp. 50/110 by cloning a DNA segment containing the conserved gene for dTDP-D-glucose 4,6-dehydratase, acbB. The two flanking genes were acbA (dTDP-D-glucose synthase) and acbC, encoding a protein with significant similarity to 3-dehydroquinate synthases (AroB proteins). The acbC gene was overexpressed heterologously in Streptomyces lividans 66, and the product was shown to be a C7-cyclitol synthase using sedo-heptulose 7-phosphate, but not ido-heptulose 7-phosphate, as its substrate. The cyclization product, 2-epi-5-epi-valiolone ((2S,3S,4S,5R)-5-(hydroxymethyl)cyclohexanon-2,3,4,5-tetrol), is a precursor of the valienamine moiety of acarbose. A possible five-step reaction mechanism is proposed for the cyclization reaction catalyzed by AcbC based on the recent analysis of the three-dimensional structure of a eukaryotic 3-dehydroquinate synthase domain (Carpenter, E. P., Hawkins, A. R., Frost, J. W., and Brown, K. A. (1998) Nature 394, 299-302).
Differentiation of bacterial versus viral otitis media using a combined Raman scattering spectroscopy and low coherence interferometry probe (Conference Presentation) (2016)

Otitis media (OM) is a highly prevalent disease that can be caused by either a bacterial or viral infection. Because antibiotics are only effective against bacterial infections, blind use of antibiotics without definitive knowledge of the infectious agent, though commonly practiced, can lead to the problems of potential harmful side effects, wasteful misuse of medical resources, and the development of antimicrobial resistance. In this work, we investigate the feasibility of using a combined Raman scattering spectroscopy and low coherence interferometry (LCI) device to differentiate OM infections caused by viruses and bacteria and improve our diagnostic ability of OM. Raman spectroscopy, an established tool for molecular analysis of biological tissue, has been shown capable of identifying different bacterial species, although mostly based on fixed or dried sample cultures. LCI has been demonstrated recently as a promising tool for determining tympanic membrane (TM) thickness and the presence and thickness of middle-ear biofilm located behind the TM. We have developed a fiber-based ear insert that incorporates spatially-aligned Raman and LCI probes for point-of-care diagnosis of OM. As shown in human studies, the Raman probe provides molecular signatures of bacterial- and viral-infected OM and normal middle-ear cavities, and LCI helps to identify depth-resolved structural information as well as guide and monitor positioning of the Raman spectroscopy beam for relatively longer signal acquisition time. Differentiation of OM infections is determined by correlating in vivo Raman data collected from human subjects with the Raman features of different bacterial and viral species obtained from cultured samples.
Spectrally encoded machine vision using trainable materials (2021)

Using deep learning-based training of diffractive layers we designed single-pixel machine vision systems to all-optically classify images by maximizing the output power of the wavelength corresponding to the correct data-class. We experimentally validated our diffractive designs using a plasmonic nanoantenna-based time-domain spectroscopy setup and 3D-printed diffractive layers to successfully classify the images of handwritten-digits using a single-pixel and snap-shot illumination. Furthermore, we trained a shallow electronic neural network as a decoder to reconstruct the images of the input objects, solely from the power detected at ten distinct wavelengths, also demonstrating the success of this platform as a task-specific, single-pixel imager.
Potential Application of Fabricated Sulfide-Based Scintillation Materials for Radiation Detection (2010)

In our laboratories, we have produced ZnS(Ag)/6Li sol-gel scintillation materials which produce an excellent light output with an alpha radiation (compared to commercial high temperature lithiated glass; KG-2 and a plastic scintillator; BC-400). However, when tested with a neutron radiation, the opacity of the ZnS(Ag)/6Li sol-gel scintillation materials, which were composed of a homogeneous micron-sized ZnS(Ag), prevented a clear neutron energy peak formation, thus making it difficult to set a threshold for neutron-gamma discrimination. In an effort to increase the transparency of the scintillation materials and to develop new technologies to fabricate sulfide-based scintillation materials for neutron detection, we turned to the methods of a chemical bath deposition (CBD) and a nano-particle synthesis for possible solutions.
Novel postexposure bake simulator: First results (1995)

We have designed and implemented a simulator that models the physics of the chemically amplified photoresist process postexposure bake (PEB) step, based on a general mathematical formulation. The photoacid loss due to kinetic reaction and the photoacid diffusion are simulated using experimentally determined model parameters. The PEB simulator, which can be used in conjunction with any lithographic image modeling software, has been integrated into the CXrL ToolSet, a comprehensive modeling system for x-ray lithography. The PEB simulator converts the deposited dose into an initial concentration of photoacid, and then computes its evolution and the corresponding evolution of the protected sites, for a given bake time and temperature. System dynamics are defined by coupled partial differential equations containing acid loss and diffusion terms. As the two phenomena take place at the same time during PEB, the numerical algorithm does not separate the terms in the calculation. An alternating direction implicit and explicit numerical differentiation technique for solving a multidimensional partial differential equation in x and z has been employed, resulting in a system which reduces computational complexity without loss of accuracy or speed. Linewidth can be extracted from the final profile of the protected sites, or, alternatively, the concentration of the protected sites can be converted into a dissolution rate and fed to other dissolution modeling tools to generate a developed resist profile. Process latitude simulations can be performed to study linewidth variation with respect to dose, gap or focus, bake temperature, and time. An initial evaluation has been performed by comparing simulation results with data from an x-ray lithography experimental study.
Protection of high voltage power and programming pins (1997)

Electrostatic discharge (ESD) protection of an inte- grated circuit's (IC's) high voltage power pins is achieved without damage to thin oxides by dividing the steady-state voltage and arranging weak forward bias of the diodes of a cantilever clamp. Also, programming pins are protected by cantilever clamps of various kinds, including some which turn on when breakdown is detected and turn off after is powered up.