gebhart/patrepeval huggingface dataset:
A Study on Different Types of Fiber Coils for Fiber Optic Current Sensors (2014)

We consider an interferometric fiber optic current sensor with a fiber coil operated in reflection and compare three different techniques to prepare the coil: thermally annealed coils, stress-free packaging of a bare low birefringent fiber in a fused silica capillary, and coils from highly birefringent spun fiber. In particular we theoretically and experimentally investigate how the fiber retarder that generates the near left and right circular light waves in the sensing fiber must be prepared for temperature compensation of the Faraday effect in the three cases. All three methods can achieve accuracy within ±<0.2% over an extended temperature range but they considerably differ in their practical challenges.
Prediction of the true IOL position (2017)

Accurate relationships to determine the true postoperative IOL position were obtained. In addition to axial length and corneal radius, which are required for the IOL power calculation as such, they require measurement of preoperative anterior chamber depth only.
5-Allyl-9-oxobenzomorphans. 3. Potent narcotic antagonists and analgesics-antagonists in the series of substituted 2',9.beta.-dihydroxy-6,7-benzomorphans (1977)

5-Allyl-2'-methoxy-2-methyl-9-oxo-6,7-benzomorphan methiodide (1) has been converted in a selective two-step process to the corresponding 9beta-hydroxy intermediates 4 and 6, which in turn were transformed via modified von Braun demethylation-acylation to the amides 11 and 21, respectively. These were reduced and demethylated to give a series of 5-allyl-2',9beta-dihydroxy-2-substituted 6,7-benzomorphans 13 and 23, some of which have been found to be highly potent narcotic antagonists and/or analgesics. The resolution of the most interesting compounds (23a and 23b) and pharmacological properties of the optical isomers are also described. Reduction of the double bond in 13 and 23 to give 14 and 24, with one exception, did not appreciably alter pharmacological profiles, while cyclization to the tetrahydrofuranobenzomorphans 25 substantially reduced the level of activities.
Improved Synthesis of Chiral Pyrrolidine Inhibitors and Their Binding Properties to Neuronal Nitric Oxide Synthase (2011)

We report an efficient synthetic route to chiral pyrrolidine inhibitors of neuronal nitric oxide synthase (nNOS) and crystal structures of the inhibitors bound to nNOS and to endothelial NOS. The new route enables versatile structure-activity relationship studies on the pyrrolidine-based scaffold, which can be beneficial for further development of nNOS inhibitors. The X-ray crystal structures of five new fluorine-containing inhibitors bound to nNOS provide insights into the effect of the fluorine atoms on binding.
Formation of multimers of bacterial collagens through introduction of specific sites for oxidative crosslinking (2016)

A range of non-animal collagens has been described, derived from bacterial species, which form stable triple-helical structures without the need for secondary modification to include hydroxyproline in the sequence. The non-animal collagens studied to date are typically smaller than animal interstitial collagens, around one quarter the length and do not pack into large fibrillar aggregates like those that are formed by the major animal interstitial collagens. A consequence of this for biomedical products is that fabricated items, such as collagen sponges, are not as mechanically and dimensionally stable as those of animal collagens. In the present study, we examined the production of larger, polymeric forms of non-animal collagens through introduction of tyrosine and cysteine residues that can form selective crosslinks through oxidation. These modifications allow the formation of larger aggregates of the non-animal collagens. When Tyr residues were incorporated, gels were obtained. And with Cys soluble aggregates were formed. These materials can be formed into sponges that are more stable than those formed without these modifications. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 2369-2376, 2016.
Cell Sheet-Based Myocardial Tissue Engineering: New Hope for Damaged Heart Rescue (2009)

Regenerative therapy has currently emerged as one of the most promising treatments for the patients suffering from severe heart failure. Several cell therapies by direct injection have been already clinically performed. However, significant cell loss due to physical strain, primary hypoxia or cell wash-out has become problematic. To overcome this obstacle, tissue engineered myocardial patch transplantation has been examined as the second generation cell therapy. Furthermore several research groups have challenged to engineer pulsatile myocardial tissues/organs using beating cardiomyocytes. Among several tissue engineering technologies, we have developed cell sheet-based tissue engineering, which utilize two-dimensional (2-D) cell sheets harvested from temperature-responsive culture surfaces and create three-dimensional (3-D) tissues by stacking cell sheets without generally utilized scaffolds. Several types of cell sheet-based patches have improved damaged heart function in rat, canine and pig models. Stacked cardiomyocyte sheets simultaneously beat in macroscopic view both in vitro and in vivo and revealed characteristic structures of native heart tissue. As a possible solution for scaling up, multi-step transplantation of triple-layer cell sheets was performed and finally, 10-time transplantations have realized about 1 mm-thick functional myocardial tissue. As further advanced therapy, functional myocardial tubes have been also engineered by wrapping cell sheets. Cell sheet-based tissue engineering should have enormous potential in myocardial tissue regenerative medicine and rescue many patients suffering severe heart failure.
Anterior chamber angle classification using multiscale histograms of oriented gradients for glaucoma subtype identification (2012)

Glaucoma subtype can be identified according to the configuration of the anterior chamber angle(ACA). In this paper, we present an ACA classification approach based on histograms of oriented gradients at multiple scales. In digital optical coherence tomography (OCT) photographs, our method automatically localizes the ACA, and extracts histograms of oriented gradients (HOG) features from this region to classify the angle as an open angle (OA) or an angle-closure(AC). This proposed method has three major features that differs from existing methods. First, the ACA localization from OCT images is fully automated and efficient for different ACA configurations. Second, the ACA is directly classified as OA/AC by using multiscale HOG visual features only, which is different from previous ACA assessment approaches that on clinical features. Third, it demonstrates that visual features with higher dimensions outperform low dimensional clinical features in terms of angle closure classification accuracy. Testing was performed on a large clinical dataset, comprising of 2048 images. The proposed method achieves a 0.835±0.068 AUC value and 75.8% ± 6.4% balanced accuracy at a 85% specificity, which outperforms existing ACA classification approaches based on clinical features.
Photomechanical mechanism and structure-property considerations in the generation of photomechanical work in glassy, azobenzene liquid crystal polymer networks (2011)

Azobenzene-functionalized polymeric materials have proven capable of shape adaptive responses when irradiated with light. This work focuses on isolating the fundamental differences between the photogenerated mechanical output of glassy, polydomain azobenzene liquid crystal polymer networks (azo-LCN) upon exposure to either UV and blue-green irradiation. Profound differences in the fundamental photochemical mechanism are identified through spectroscopic examination of representative materials before and after irradiation with UV or blue-green light. The photomechanical response is further elucidated in structure-property examination to ascertain the role of crosslink density, azobenzene concentration, and azobenzene connectivity (crosslinked or pendant) on the photomechanical output.
Semantic TagPrint - Tagging and Indexing Content for Semantic Search and Content Management (2010)

Existing search and content management technology is facing a challenge of locating desired content with the exponentially growing volume of documents. An approach for mitigating this issue is to make use of user-generated tags. However, the improvements are limited because tags are (1) free from context and form, (2) user generated, (3) used for purposes other than description, and (4) often ambiguous. Since tagging is a voluntary action, some documents are not tagged at all. Furthermore, the interpretation of the tags associated with tagged documents also remains a challenge. To overcome these challenges, semantic web resources and technologies can be utilized to automatically generate semantic tags. Semantic tags not only reflect document content more accurately, they also enable better search results. Ontology coverage, ontology mapping and weighting significant ontological entities within a context are key challenges in semantic tagging systems. To address these challenges, this paper presents a semantic tagging system - Semantic TagPrint - to map a text document to semantic tags defined as entities in an ontology. Semantic TagPrint uses a linear time lexical chaining Word Sense Disambiguation (WSD) algorithm for real time concept mapping. In addition, it utilizes statistical metrics and ontological features of the ontology for weighting and recommending the semantic tags. A comparative evaluation shows that our mapping algorithm is fairly accurate and our tag recommendation algorithm performs better than other systems and algorithms.
Conservation of the 2,4-diacetylphloroglucinol biosynthesis locus among fluorescent Pseudomonas strains from diverse geographic locations (1996)

The broad-spectrum antibiotic 2,4-diacetylphloroglucinol (PHL) is a major determinant in the biological control of a range of plant pathogens by many fluorescent Pseudomonas spp. A 4.8-kb chromosomal DNA region from Pseudomonas fluorescens Q2-87, carrying PHL biosynthetic genes, was used as a probe to determine if the PHL biosynthetic locus is conserved within PHL-producing Pseudomonas strains of worldwide origin. The phl gene probe hybridized with the genomic DNA of all 45 PHL-producing Pseudomonas strains tested, including well-characterized biocontrol strains from the United States and Europe and strains isolated from disease-suppressive soils from Switzerland, Washington, Italy, and Ghana. The PHL producers displayed considerable phenotypic and genotypic diversity. Two phenotypically distinct groups were detected. The first produced PHL, pyoluteorin, and hydrogen cyanide and consisted of 13 strains from almost all locations sampled in the United States, Europe, and Africa. The second produced only PHL and HCN and consisted of 32 strains from the U.S. and European soils. Analysis of restriction patterns of genomic DNA obtained after hybridization with the phl gene probe and cluster analysis of restriction patterns of amplified DNA coding for 16S rRNA (ARDRA) and randomly amplified polymorphic DNA (RAPD) markers indicated that the strains that produced both PHL and pyoluteorin were genetically highly similar. In contrast, there was more diversity at the genotypic level in the strains that produced PHL but not pyoluteorin. ARDRA analysis of these strains indicated two clusters which, on the basis of RAPD analysis, split into several subgroups with additional polymorphisms. In general, the occurrence of phenotypically and genotypically similar groups of PHL producers did not correlate with the geographic origin of the isolates, and highly similar strains could be isolated from diverse locations worldwide.
Bioanalytical Assay Development and Validation for the Pharmacokinetic Study of GMC1, a Novel FKBP52 Co-chaperone Inhibitor for Castration Resistant Prostate Cancer (2020)

Pharmacokinetic evaluation of GMC1 revealed that the molecule has a biexponential disposition in rats, is distributed rapidly and extensively, has a long elimination half-life, and appears to be eliminated primarily by first order kinetics.
Applying Ionic Liquids for Controlled Processing of Polymer Materials (2005)

This perspective examines the potential, highlighting some examples from our on-going research program, to evaluate and apply ionic liquids as advanced functional solvents for dissolving and processing polymers in order to prepare active materials and composites for sensor and smart materials applications integrating complexants or colorimetric and biological receptors into biorenewable, biocompatable substrate matrices.
Synthesis and characterization of cryogenic adhesives based on epoxy‐modified polyurethane resin systems (1994)

Abstract Polyurethane adhesives containing the polyether backbone exhibit a good joint strength in cryogenic environments. In practice, many of the commercially available polyurethane adhesive systems contain free or chemically blocked isocyanates which have some limitations. This study presents the synthesis and characterization of a modified polyurethane type adhesive. Glycidol was used to convert the isocyanate‐terminated polyurethane prepolymer to glycidylterminated polyurethane prepolymer. A series of glycidyl‐terminated polyurethanes, based on polyoxypropylene glycol (PPG) soft segments having different molecular weights, were synthesized and their adhesive properties on aluminium were evaluated. The effect of the soft segment length on adhesion was examined. The adhesive properties at room temperature and cryogenic temperature are in line with the phenomenon observed in dynamical mechanical analysis (DMA) and in the phase separation behavior of the polyurethanes. Differential scaning calorimetry (DSC) was used to assess the phase separation content. An improvement in the adhesive strengths at room temperature is achieved by adding epoxy resins to the glycidyl‐terminated polyurethane resins.
High-dose radiation with bone marrow transfer prevents neurodegeneration in an inherited glaucoma (2005)

Here, we show that high-dose gamma-irradiation accompanied with syngeneic bone marrow transfer can confer complete protection against glaucoma in a mouse model. Because bone marrow genotype was unaltered by this procedure, it was not the causative agent. The neuroprotection is robust and highly reproducible. Glaucoma-prone DBA/2J mice received a single treatment at 5-8 weeks of age and were protected from glaucomatous retinal ganglion cell degeneration out to 14 months of age (oldest assessed). By 12-14 months, retinal ganglion cell degeneration is usually very severe and essentially complete in the majority of untreated DBA/2J mice. To assess reproducibility, three groups of mice were treated at different times, and the results were essentially the same each time. Considering all experiments, the vast majority of treated mice had no detectable glaucomatous neurodegeneration. A beneficial effect of treatment including high-dose radiation is unprecedented, and we are not aware of any other neuroprotective effects this substantial. Because of the robust protective effect, this treatment offers another tool for studying mechanisms of neuroprotection.
Development of a high-throughput assay for measuring lipase activity using natural triacylglycerols coated on microtiter plates (2013)

We have designed a convenient, specific, sensitive and continuous lipase assay based on the use of natural triacylglycerols (TAGs) from the Aleurites fordii seed oil which contains α-eleostearic acid (9,11,13,cis,trans,trans-octadecatrienoic acid) and which was coated in the wells of microtiter plates. The coated TAG film cannot be desorbed by the various buffers used during the lipase assay. Upon lipase action, α-eleostearic acid is liberated and desorbed from the interface and then solubilized into the micellar phase. Consequently, the UV absorbance of the α-eleostearic acid is considerably enhanced due to the transformation from an adsorbed to a water soluble state. The lipase activity can be measured continuously by recording the variations with time of the UV absorption spectra. The rate of lipolysis was monitored by measuring the increase of OD at 272 nm, which was found to be linear with time and directly proportional to the amount of added lipase. This microtiter plate lipase assay, based on coated TAGs, presents various advantages as compared to the classical systems: (i) coated TAGs on the microtiter plates could be stored for a long-time at 4 °C, (ii) higher sensitivity in lipase detection, (iii) good reproducibility, and (iv) increase of signal to noise ratio due to high UV absorption after transfer of α-eleostearic acid from an adsorbed to a soluble state. Low concentrations, down to 1 pg mL(-1) of pure Thermomyces lanuginosus or human pancreatic lipase, could be detected under standard assay conditions. The detection sensitivity of this coated method is around 1000 times higher as compared to those obtained with the classical emulsified systems. This continuous high throughput lipase assay could be used to screen new lipases and/or lipase inhibitors present in various biological samples.
Poly(vinyl chloride)–polyol (AB)<sub>x</sub> block copolymers: Synthesis, characterization, and mechanical properties (1981)

Abstract Poly(vinyl chloride)–polyol (AB) x block copolymers have been prepared by the condensation polymerization of low‐molecular‐weight hydroxy‐terminated poly(vinyl chlorides) (PVC) and diisocyanate‐capped polyester and polyether diols. The difunctional poly(vinyl chlorides) were synthesized by ozonization of commercial resin followed by metal hydride reduction. The (AB) x block copolymers, which contained 3000 or 4300 molecular weight PVC block sizes and 1000–2000 molecular weight polyol segments, had a wide range of mechanical properties, depending on overall polymer structure. Tensile strengths ranged from 7.8 to 31.5 MPa, elongations from 125% to 610% and torsional stiffness temperatures ( T f ) from 25°C to −22°C.
Liposome immunosensing devices for environmental contaminant screening (1995)

Single-use strip assays using immunomigration and immunoabsorption formats have been developed for the extra-laboratory determination of environmental contaminants. Dye-loaded liposomes are used as the amplification strategy in these immunoassays. Details of the assay performance and liposome characteristics are given.
Transient stabilization, rather than inhibition, of MYC amplifies extrinsic apoptosis and therapeutic responses in refractory B-cell lymphoma (2019)

Therapeutic targeting of initiating oncogenes is the mainstay of precision medicine. Considerable efforts have been expended toward silencing MYC, which drives many human cancers including Burkitt lymphomas (BL). Yet, the effects of MYC silencing on standard-of-care therapies are poorly understood. Here we found that inhibition of MYC transcription renders B-lymphoblastoid cells refractory to chemotherapeutic agents. This suggested that in the context of chemotherapy, stabilization of Myc protein could be more beneficial than its inactivation. We tested this hypothesis by pharmacologically inhibiting glycogen synthase kinase 3β (GSK-3β), which normally targets Myc for proteasomal degradation. We discovered that chemorefractory BL cell lines responded better to doxorubicin and other anti-cancer drugs when Myc was transiently stabilized. In vivo, GSK3 inhibitors (GSK3i) enhanced doxorubicin-induced apoptosis in BL patient-derived xenografts (BL-PDX), as well as in murine MYC-driven lymphoma allografts. This enhancement was accompanied by and required deregulation of several key genes acting in the extrinsic, death-receptor-mediated apoptotic pathway. Consistent with this mechanism of action, GSK3i also facilitated lymphoma cell killing by a death ligand TRAIL and by a death receptor agonist mapatumumab. Thus, GSK3i synergizes with both standard chemotherapeutics and direct engagers of death receptors and could improve outcomes in patients with refractory lymphomas.
An overview of cochlear implant electrode array designs (2017)

Cochlear implant electrode arrays are designed with specific characteristics that allow for the preservation of intra-cochlear structures during the insertion process, as well as during explantation. Straight lateral wall (LW) electrode arrays and pre-curved modiolar hugging (MH) electrode arrays are the two types that are commercially available. Although there is a third type of electrode array called the mid-scala (MS), which is positioned in the middle of the scala tympani (ST), and is usually considered as an MH type of electrode. Different lengths of straight LW electrode arrays are currently available which allow for insertion across a range of different sized cochleae; however, due to manufacturing limitations, pre-curved MH electrodes are generally only available to cover the basal turn of the cochlea, while the spiral ganglion cells are distributed in the Rosenthal's canal that extends into 1.75 turns of the cochlea. Both straight LW and pre-curved MH electrodes can cause a certain degree of intra-cochlear trauma, but pre-curved MH electrodes tend to deviate into the scala vestibuli from the scala tympani more often than the straight LW electrodes, resulting in damage to the osseous spiral lamina/spiral ligament which could initiate new bone formation and eventually affect the cochlear implant users' hearing performance. Structural damage to the cochlea could also affect the vestibular function. With pre-curved MH electrodes, higher degrees of trauma are related to the fixed curling geometry of the electrode in relation to the variable coiling pattern of individual cochleae, the orientation of the electrode contacts in relation to the modiolus wall, and how effectively the stylet was handled by the surgeon during the procedure. Wire management, metal density, and the shore hardness of the silicone elastomer all contribute to the stiffness/flexibility of the electrode. It is important to acknowledge the impact of bringing the stimulating contacts closer to the modiolus wall with an MH electrode type in terms of the resultant damage to intra-cochlear structures. The presence of malformed cochleae should be identified and appropriate electrodes should be chosen for each specific cochlea, irrespective of the cochlear implant brand. In order to utilize drug therapy, the cochlea should be free from any trauma.
A human gastric carcinoma contains a single mutated and an amplified normal allele of the Ki-<i>ras</i>oncogene (1986)

The DNA from various human tumors and tumor cell lines was screened for the presence of mutated ras oncogenes with synthetic oligonucleotide probes, as well as with the NIH/3T3 cell transfection assay. Among the various mutations found we discovered two novel Ki-ras mutations in codon 12: gly to ala and gly to ser. A gastric carcinoma was found to possess a single mutated Ki-ras allele (gly-12 to ser), as well as a 30-50 fold amplified normal allele. This implies that two activating steps must have occurred in this malignancy.