gebhart/patrepeval huggingface dataset:
A Simple Device for Concentration of Parasite Eggs, Larvae, and Protozoa (1978)

Zierdt, Willadene S.: A simple device for concentration of parasite eggs, larvae, and protozoa. Am J Clin Pathol 70: 89–93, 1978. A device for the concentration of parasite eggs, larvae and protozoa from a 1 gram fecal sample is described. It consists of separable upper chamber and lower 15 ml conical centrifuge tube connected by a midpiece which incorporates a filter of stainless steel mesh. A small plastic tube for air venting passes through the filter. Emulsification of the sample is done in the upper chamber by shaking with 10% formalin, glass beads, and Triton X-100. The emulsified sample is then filtered into the lower chamber. Ether is added through the upper chamber to wash remaining eggs and larvae into the lower chamber, which is then capped, shaken, and centrifuged. Following centrifugation, the top plug of debris is removed and the tube is drained and swabbed clean, leaving a small, packed sediment, containing the parasite eggs and larvae. The device yielded as much as 300 times the egg yield of the direct wet mount and was comparable to standard concentration methods. The increased separation of eggs and larvae in this device is probably due to the physical characteristics that are imparted to the fecal solids during shaking with ether, glass beads, and Triton, and passage through the wire gauze.
High-quality pyrographite films (1986)

High-temperature heat treatment of a heat-resistant, condensation polymer poly ( ρ-phenylene-1,3,4-oxadiazole) yielded a large-area, flexible film composed of highly oriented and nearly ideal graphite crystallites. The graphitic behavior was exemplified by both the (002) lattice spacing of 3.354 Å and extremely small full width at half-maximum intensity of the (002) reflection, 0.16–0.17°, for the films heat treated above 2800 °C.
Fuel Reformation: Microchannel Reactor Design (2005)

Fuel processing extracts hydrogen from conventional vehicle fuel and allows fuel cell powered vehicles to use the existing petroleum fuel infrastructure. Kilowatt scale microchannel steam reforming, water-gas shift, and preferential oxidation reactors are being developed to meet DOE-required system performance metrics. MicroChannel design effectively supplies heat to the highly endothermic steam reforming reactor to maintain high conversions, controls the temperature profile for the exothermic water gas shift reactor, which optimizes the overall reaction conversion, and removes heat to prevent unwanted hydrogen oxidation in the preferential oxidation reactor. The reactors combined with microchannel heat exchangers, when scaled to a full sized 50 kWe automotive system, will be less than 21 L in volume and 52 kg in weight.
State of the Art in Holographic Displays: A Survey (2010)

True-3D imaging and display systems are based on physical duplication of light distribution. Holography is a true-3D technique. There are significant developments in electro-holographic displays in recent years. Liquid crystal, liquid crystal on silicon, optically addressed, mirror-based, holographic polymer-dispersed, and acousto-optic devices are used as holographic displays. There are complete electro-holographic display systems and some of them are already commercialized.
DNA hybridization technique to detect Shigella species and enteroinvasive escherichia coli (1984)

A DNA hybridization method for the detection of Shigella species and enteroinvasive Escherichia coli is described. It is based upon the high degree of homology shared by the virulence plasmids present in all pathogenic strains. After 32P labeling, a 17-kilobase EcoRI restriction fragment of a virulence plasmid belonging to Shigella flexneri serotype 5 was used as a probe to detect Shigella species and enteroinvasive E. coli in isolated colonies. This method proved highly specific as well as sensitive and should be particularly useful for the characterization of atypical isolates and for large-scale epidemiological studies in endemic areas.
A New Multi-Static System for Microwave Breast Cancer Imaging: Preliminary Design (2018)

Experimental microwave imaging systems for breast cancer diagnosis typically employ multi-static antenna configurations. In such systems, large number of antennas, which are positioned around breast at fixed locations, are driven by N-port microwave switching matrix or a N-port vector network analyzer. In either case, multi-static scattering parameters measurements required for breast imaging can be completed very rapidly due to electronic switching between ports. This rapidness is in fact very advantageous from patient perspective. In this work, we investigate design consideration for a cylindrical microwave breast scanner and present a preliminary design that uses low-cost and low-loss dielectric materials for impedance matching between the breast and the antennas.
Comparison of a new dental trauma splint device (TTS) with three commonly used splinting techniques (2001)

Splinting is the standard of care for stabilization of replanted or repositioned permanent teeth following trauma. The present experimental study compared four dental trauma splints in 10 volunteers. The evaluated splints included a wire-composite splint (WCS), a button-bracket splint (BS), a resin splint (RS), and a new device (TTS=Titanium Trauma Splint) specifically developed for splinting traumatized teeth. All splints were bonded to the labial surfaces of the maxillary lateral and central incisors. Splints were left in place for 1 week. After splint removal, the next splint was placed after a 1-week rest period. The sequence of splint application was randomized for each individual. The following parameters were assessed: tooth mobility with horizontal and vertical Periotest values (PTV) before and after splint application and splint removal, respectively; probing depths, plaque and bleeding on probing indices before splint application and removal, and chair time needed for splint application and removal. After splint application, horizontal PTV were significantly lower in central incisors for BS compared to TTS (P=0.04), and for RS compared to TTS (P=0.005) and to WCS (P=0.006). Reduction of lateral tooth mobility (=splint effect) expressed by the difference between horizontal pre- and postoperative PTV was significantly greater in RS compared to TTS and WCS (P<0.05) for central as well as for lateral incisors. However, changes of vertical tooth mobility were not significant across the splinting techniques. Periodontal parameters remained unchanged, reflecting the excellent oral hygiene by the study subjects. The chair time needed for splint application was significantly shorter for TTS (P<0.01). In conclusion, all tested splints appeared to maintain physiologic vertical and horizontal tooth mobility. However, the latter was critically reduced in RS splints.
Possibility of an integrated transmission electron microscope: enabling complex in-situ experiments (2021)

Abstract Multimodal in-situ experiments are the wave of the future, as this approach will permit multispectral data collection and analysis during real-time nanoscale observation. In contrast, the evolution of technique development in the electron microscopy field has generally trended toward specialization and subsequent bifurcation into more and more niche instruments, creating a challenge for reintegration and backward compatibility for in-situ experiments on state-of-the-art microscopes. We do not believe this to be a requirement in the field; therefore, we propose an adaptive instrument that is designed to allow nearly simultaneous collection of data from aberration-corrected transmission electron microscopy (TEM), probe-corrected scanning transmission electron microscopy, ultrafast TEM, and dynamic TEM with a flexible in-situ testing chamber, where the entire instrument can be modified as future technologies are developed. The value would be to obtain a holistic understanding of the underlying physics and chemistry of the process-structure–property relationships in materials exposed to controlled extreme environments. Such a tool would permit the ability to explore, in-situ, the active reaction mechanisms in a controlled manner emulating those of real-world applications with nanometer and nanosecond resolution. If such a powerful tool is developed, it has the potential to revolutionize our materials understanding of nanoscale mechanisms and transients. Graphical Abstract
Vaccine Potentials of an Intrinsically Unstructured Fragment Derived from the Blood Stage-Associated <i>Plasmodium falciparum</i> Protein PFF0165c (2009)

We have identified new malaria vaccine candidates through the combination of bioinformatics prediction of stable protein domains in the Plasmodium falciparum genome, chemical synthesis of polypeptides, in vitro biological functional assays, and association of an antigen-specific antibody response with protection against clinical malaria. Within the predicted open reading frame of P. falciparum hypothetical protein PFF0165c, several segments with low hydrophobic amino acid content, which are likely to be intrinsically unstructured, were identified. The synthetic peptide corresponding to one such segment (P27A) was well recognized by sera and peripheral blood mononuclear cells of adults living in different regions where malaria is endemic. High antibody titers were induced in different strains of mice and in rabbits immunized with the polypeptide formulated with different adjuvants. These antibodies recognized native epitopes in P. falciparum-infected erythrocytes, formed distinct bands in Western blots, and were inhibitory in an in vitro antibody-dependent cellular inhibition parasite-growth assay. The immunological properties of P27A, together with its low polymorphism and association with clinical protection from malaria in humans, warrant its further development as a malaria vaccine candidate.
Polarisation- and pattern-independent optical FSK heterodyne system using data-induced polarisation switching (1990)

Data-induced polarisation switching is a simple yet powerful technique to solve the polarisation problem in optical FSK heterodyne systems. We achieve a polarisation- and patternindependent sensitivity of −53.5 dBm for a 140Mbit/s FSK receiver. The response time to polarisation changes is estimated as 100 ns.
Test time of multiplier/accumulator based output response analyzer in built-in analog functional testing (2009)

A Built-In Self-Test (BIST) approach has been proposed for functionality measurements of analog circuitry in mixed-signal systems. The BIST circuitry consists of a direct digital synthesizer (DDS) based test pattern generator (TPG) and multiplier/accumulator (MAC) based output response analyzer (ORA). In this paper we investigate and discuss the test time required by the ORA for analog measurements such as frequency response and 3rd order intercept point (IP3). We show that the test time can be greatly shortened if the ORA accumulation can be stopped at the right point. Three simple digital circuits are also proposed for such a purpose and their performance is simulated to show how the efficiency of the test time is improved.
Biochemical and Functional Antigenic Mimicry by a Polyclonal Anti-ldiotypic Antibody for Chlamydial Exoglycolipid Antigen (1997)

A vaccine developed by using a genus-specific antigen (Ag) of Chlamydia trachomatis would elicit a wide range of protection against various chlamydial infections. We have produced an anti-idiotypic antibody (Ab2) in guinea pigs which, in rabbits, mimics the immunogenicity of a genus-specific exoglycolipid Ag (GLXA) of C trachomatis. Furthermore, the Ab2 fulfills the functional criteria of an 'internal image' of the nominal Ag: it inhibits the binding of the idiotypic (Id) monoclonal Ab (mAb1) to GLXA, and it induces in rabbits anti-anti-Id antibody (Ab3) which recognizes both the affinity-purified nominal Ag GLXA and whole organisms. Moreover, Ab3 induced by immunization of rabbits with guinea pig Ab2 neutralizes infectious heterologous chlamydiae and prevents in vitro and in vivo infection. Taken together, these results demonstrate functional and biochemical mimicry of the Ab2 for the chlamydial GLXA and suggest that anti-idiotypic Ab to GLXA is a potential candidate vaccine against chlamydia-related diseases.
Expression rewriting for optimizing secure computation (2013)

In theory secure computation offers a solution for privacy in many collaborative applications. However, in practice poor efficiency of the protocols prevents their use. Hand-crafted protocols are more efficient than those implemented in compilers, but they require significantly more development effort in programming and verification. Recently, Kerschbaum introduced an automatic compiler optimization technique for secure computations that can make compilers as efficient as hand-crafted protocols. This optimization relies on the structure of the secure computation program. The programmer has to implement the program in such a way, such that the optimization can yield the optimal performance. In this paper we present an algorithm that rewrites the program -- most notably its expressions -- optimizing their efficiency in secure computation protocols. We give a heuristic for whole-program optimization and show the resulting performance gains using examples from the literature.
Abstract 2914: Creation of a novel biochemical and biophysical assay suite to enable the identification of inhibitors targeting inactive kinases (2012)

Abstract We have recently reported the implementation of a structural biology-based drug design platform for the identification of protein kinase inhibitors which utilize hydrophobic clusters to stabilize the inactive state of a kinase. These clusters are not formed in active kinases and result in the conversion of the ATP binding cleft into a non-polar environment which is sterically and electrostatically incompatible with ATP binding. We have industrialized this approach, designated the ArQule Kinase Inhibitor Platform (AKIPTM), and synthesized a library of more than 15,000 small molecules through the application of an in silico guided process. This has allowed us to rapidly generate leads to a variety of kinases, including receptor tyrosine kinases, non-receptor tyrosine kinases, and serine-threonine kinases. By virtue of their unique binding modes, many of these inhibitors would not be identified in standard assays using highly activated kinases. We have therefore deliberately re-engineered standard biochemical kinase assays using unphosphorylated inactive kinases to aid in the optimization of these inhibitors. In addition to these biochemical assays, we have also implemented a variety of well-established technologies not commonly used early in the hit generation process, including a thermal shift assay (TSA), affinity mass spectrometry, endogenous tryptophan fluorescence detection, an ATP-exclusion assay using a non-hydrolyzable ATP analogue, classical kinetic analysis to assess ATP-dependence and mechanism-of-inhibition, X-ray crystallography, and finally, cross-competition experiments with known inhibitors. Using the cumulative knowledge gained from these technologies throughout the hit generation, hit-to-lead, and lead optimization stages has enabled us to make informed decisions and resulted in identification of many potent ATP-independent inhibitors. The AKIP technology to date has produced at least one clinical candidate, ARQ 092, which potently inhibits AKT with a high degree of selectivity amongst the human kinome. Further examples of the application of these various technologies will be provided for a diverse range of kinases, including c-Met, FGFR, Ack, and TNIK. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2914. doi:1538-7445.AM2012-2914
Synthesis and Properties of Cross-Linked Polyamide Aerogels (2014)

We report our ongoing research on polyamide aerogels made by step growth polymerization using a combination of terephthaloyl chloride, isophthaloyl chloride and m-phenylenediamine. Crosslinking of the amine capped polymer chains with 1,3,5-benzenetricarbonyl trichloride causes gelation in as little as two to five minutes. Removing the reaction solvent is accomplished through solvent exchange, followed by drying using supercritical CO2 extraction to give colorless aerogels with densities ranging from 0.07 to 0.33 grams per cubic centimeter and surface areas as high as 440 square meters per gram. Statistical experimental design methodology has been utilized to investigate dependence of properties of these aerogels, such as density, compressive modulus, and surface area, on changes in fabrication parameters including formulated number of amide oligomer repeat units (n-value), acid chloride (meta, para or combination), and solids concentration of solution used for gelation. For example, the density of these materials was found to be dependent on the acid chloride type and the solids concentration, but n was not a significant variable. However, surface area was significantly influenced by all three parameters. The polyamide aerogels represent a potential cost savings over previously reported polyimide aerogels, since monomers are all inexpensive and commercially available. Surface area and density were both highest when 100 terephthaloyl chloride was used but a combination of 5 solid concentration, 100 terephthaloyl chloride and n of 20 gave the best combination of properties.
Probing the growth and mechanical properties of Bacillus subtilis biofilms through genetic mutation strategies (2022)

Bacterial communities form biofilms on various surfaces by synthesizing a cohesive and protective extracellular matrix, and these biofilms protect microorganisms against harsh environmental conditions. <i>Bacillus subtilis</i> is a widely used experimental species, and its biofilms are used as representative models of beneficial biofilms. Specifically, <i>B. subtilis</i> biofilms are known to be rich in extracellular polymeric substances (EPS) and other biopolymers such as DNA and proteins like the amyloid protein TasA and the hydrophobic protein BslA. These materials, which form an interconnected, cohesive, three-dimensional polymer network, provide the mechanical stability of biofilms and mediate their adherence to surfaces among other functional contributions. Here, we explored how genetically-encoded components specifically contribute to regulate the growth status, mechanical properties, and antibiotic resistance of <i>B. subtilis</i> biofilms, thereby establishing a solid empirical basis for understanding how various genetic engineering efforts are likely to affect the structure and function of biofilms. We noted discrete contributions to biofilm morphology, mechanical properties, and survival from major biofilm components such as EPS, TasA and BslA. For example, EPS plays an important role in maintaining the stability of the mechanical properties and the antibiotic resistance of biofilms, whereas BslA has a significant impact on the resolution that can be obtained for printing applications. This work provides a deeper understanding of the internal interactions of biofilm components through systematic genetic manipulations. It thus not only broadens the application prospects of beneficial biofilms, but also serves as the basis of future strategies for targeting and effectively removing harmful biofilms.
Total Synthesis of Shishijimicin A (2015)

The total synthesis of the rare but extremely potent antitumor agent shishijimicin A has been achieved via a convergent strategy involving carboline disaccharide 3 and hydroxy enediyne thioacetate 4.
Ferumoxytol-based Dual-modality Imaging Probe for Detection of Stem Cell Transplant Rejection (2018)

<b>Purpose:</b> Stem cell transplants are an effective approach to repair large bone defects. However, comprehensive techniques to monitor the fate of transplanted stem cells <i>in vivo</i> are lacking. Such strategies would enable corrective interventions at an early stage and greatly benefit the development of more successful tissue regeneration approaches. In this study, we designed and synthesized a dual-modality imaging probe (Feru-AFC) that can simultaneously localize transplanted stem cells and diagnose immune rejection-induced apoptosis at an early stage <i>in vivo</i>. <b>Methods:</b> We used a customized caspase-3 cleavable peptide-dye conjugate to modify the surface of clinically approved ferumoxytol nanoparticles (NPs) to generate the dual-modality imaging probe with fluorescence "light-up" feature. We labeled both mouse mesenchymal stem cells (mMSCs, matched) and pig mesenchymal stem cells (pMSCs, mismatched) with the probe and transplanted the labeled cells with biocompatible scaffold at the calvarial defects in mice. We then employed intravital microscopy (IVM) and magnetic resonance imaging (MRI) to investigate the localization, engraftment, and viability of matched and mismatched stem cells, followed by histological analyses to evaluate the results obtained from <i>in vivo</i> studies. <b>Results:</b> The Feru-AFC NPs showed good cellular uptake efficiency in the presence of lipofectin without cytotoxicity to mMSCs and pMSCs. The fluorescence of Feru-AFC NPs was turned on inside apoptotic cells due to the cleavage of peptide by activated caspase-3 and subsequent release of fluorescence dye molecules. Upon transplantation at the calvarial defects in mice, the intense fluorescence from the cleaved Feru-AFC NPs in apoptotic pMSCs was observed with a concomitant decrease in the overall cell number from days 1 to 6. In contrast, the Feru-AFC NP-treated mMSCs exhibited minimum fluorescence and the cell number also remained similar. Furthermore, <i>in vivo</i> MRI of the Feru-AFC NP-treated mMSC and pMSCs transplants could clearly indicate the localization of matched and mismatched cells, respectively. <b>Conclusions:</b> We successfully developed a dual-modality imaging probe for evaluation of the localization and viability of transplanted stem cells in mouse calvarial defects. Using ferumoxytol NPs as the platform, our Feru-AFC NPs are superparamagnetic and display a fluorescence "light-up" signature upon exposure to activated caspase-3. The results show that the probe is a promising tool for long-term stem cell tracking through MRI and early diagnosis of immune rejection-induced apoptosis through longitudinal fluorescence imaging.
Proteasome inhibitors as therapeutics (2005)

The ubiquitin–proteasome pathway is a principle intracellular mechanism for controlled protein degradation and has recently emerged as an attractive target for anticancer therapies, because of the pleiotropic cell-cycle regulators and modulators of apoptosis that are controlled by proteasome function. In this chapter, we review the current state of the field of proteasome inhibitors and their prototypic member, bortezomib, which was recently approved by the U.S. Food and Drug Administration for the treatment of advanced multiple myeloma. Particular emphasis is placed on the pre-clinical research data that became the basis for eventual clinical applications of proteasome inhibitors, an overview of the clinical development of this exciting drug class in multiple myeloma, and a appraisal of possible uses in other haematological malignancies, such non-Hodgkin's lymphomas.