gebhart/patrepeval huggingface dataset:
A computer vision based machine for automated packaging of photonics components (2002)

Three low-cost machines were designed and built under an ARPA-funded project to perform sub-micron alignments and attachments of single-mode fibers to different OE devices. These Automated Fiber Pigtailing Machines (AFPMs) are compatible with a manufacturing environment and have a modular design for standardization of parts and machine vision for maximum flexibility. The vision system greatly reduces mechanical fixturing constraints by requiring the critical components to be positioned only within the 1 mm field of view of the camera. Object-recognition algorithms allow the AFPM to quickly determine the initial locations of the OE device and the fiber and to position the fiber with sufficient accuracy for fine alignment via optical throughput maximization.
Advances in surface-enhanced fluorescence (2004)

We report recent achievements in metal-enhanced fluorescence. Several fluorophore systems have been studied on metal particle-coated surface and in colloid suspensions. In particular, we describe a distance dependent enhancement on silver island films (SIFs), release of self-quenching of fluorescence near silver particles, and the applications of fluorescence enhancement near metalized surfaces to bioassays. We discuss a number of methods for various shpae silver particle deposition on surfaces.
An Effective Strategy for Stabilizing Minimal Coiled Coil Mimetics (2015)

Coiled coils are a major motif in proteins and orchestrate multimerization of various complexes important for biological processes. Inhibition of coiled coil-mediated interactions has significant biomedical potential. However, general approaches that afford short peptides with defined coiled coil conformation remain elusive. We evaluated several strategies to stabilize minimal helical bundles, with the dimer motif as the initial focus. A stable dimeric scaffold was realized in a synthetic sequence by replacing an interhelical ionic bond with a covalent bond. Application of this strategy to a more challenging native protein-protein interaction (PPI) suggested that an additional constraint, a disulfide bond at the internal a/d' position along with a linker at the e/e' position, is required for enhanced conformational stability. We anticipate the coiled coil stabilization methodology described herein to yield new classes of modulators for PPIs.
Recent Developments in the Osmium‐Catalyzed Dihydroxylation of Olefins (2004)

This chapter contains sections titled: Introduction Environmentally Friendly Terminal Oxidants Hydrogen Peroxide Hypochlorite Oxygen or Air Supported Osmium Catalyst Ionic Liquids References
Low-cost detection of norovirus using paper-based cell-free systems and synbody-based viral enrichment (2018)

Noroviruses are a primary cause of gastroenteritis and foodborne illness with cases that affect millions of people worldwide each year. Inexpensive tests for norovirus that do not require sophisticated laboratory equipment are important tools for ensuring that patients receive timely treatment and for containing outbreaks. Herein, we demonstrate a low-cost colorimetric assay that detects norovirus from clinical samples by combining paper-based cell-free transcription-translation systems, isothermal amplification and virus enrichment by synbodies. Using isothermal amplification and cell-free RNA sensing with toehold switches, we demonstrate that the assay enables detection of norovirus GII.4 Sydney from stool down to concentrations of 270 aM in reactions that can be directly read by eye. Furthermore, norovirus-binding synbodies and magnetic beads are used to concentrate the virus and provide a 1000-fold increase in assay sensitivity extending its detection limit to 270 zM. These results demonstrate the utility of paper-based cell-free diagnostic systems for identification of foodborne pathogens and provide a versatile diagnostic assay that can be applied to the concentration, amplification and detection of a broad range of infectious agents.
Nonlinear optical fibers with increased SBS thresholds (2006)

Novel profile designs are used to suppress stimulated Brillouin scattering in nonlinear fibers. The measured SBS thresholds of prototype fibers are 3 to 6 dB higher than those of conventional nonlinear fibers.
Analysis of gene expression profiles of multiple skin diseases identifies a conserved signature of disrupted homeostasis (2018)

Triggers of skin disease pathogenesis vary, but events associated with the elicitation of a lesion share many features in common. Our objective was to examine gene expression patterns in skin disease to develop a molecular signature of disruption of cutaneous homeostasis. Gene expression data from common inflammatory skin diseases (eg psoriasis, atopic dermatitis, seborrhoeic dermatitis and acne) and a novel statistical algorithm were used to define a unifying molecular signature referred to as the "unhealthy skin signature" (USS). Using a pattern-matching algorithm, analysis of public data repositories revealed that the USS is found in diverse epithelial diseases. Studies of milder disruptions of epidermal homeostasis have also shown that these conditions converge, to varying degrees, on the USS and that the degree of convergence is related directly to the severity of homeostatic disruption. The USS contains genes that had no prior published association with skin, but that play important roles in many different disease processes, supporting the importance of the USS to homeostasis. Finally, we show through pattern matching that the USS can be used to discover new potential dermatologic therapeutics. The USS provides a new means to further interrogate epithelial homeostasis and potentially develop novel therapeutics with efficacy across a spectrum of skin conditions.
1,5-Benzoxathiepin derivatives. II. Synthesis and serotonin S2-receptor-blocking activity of aminoalkyl-substituted 3,4-dihydro-2H-1,5-benzoxathiepin-3-ols and related compounds. (1987)

Novel 1, 5-benzoxathiepin derivatives, 3, 4-dihydro-2H-1, 5-benzoxathiepin-3-ols with an aminoalkyl group at the 2-, 3- or 4-position, were synthesized and evaluated for serotonin S2-receptor-blocking activity and adrenergic α1-receptor-blocking activity. Methyl 4-aminoalky1-3-hydroxy-3, 4-dihydro-2H-1, 5-benzoxathiepin-4-carboxylates showed significant S2-receptor-block-ing activities. Structure-activity relationships (including the results of a conformational study and skeletal modifications) were examined. In the series of 1, 5-benzoxathiepin, 1-benzoxepin and 1-benzothiepin derivatives, methyl cis-3-hydroxy-7-methoxy-4- [3- (4-phenyl -1-piperazinyl) propyl] -3, 4-dihydro-2H-1, 5-benzoxathiepin-4-carboxylatehydrochloride (CV-5197) showed the most potent and the most selective S2-receptor-blocking activity in the binding profile, and was chosen as a candidate for further pharmacological evaluation.
An Optoacoustic Technique for Measuring the Optical Absorption Coefficient in Solids. (1975)

An investigation was made of an optoacoustic technique for determining the optical absorption coefficients in solids. A train of laser pulses was passed through the solid, and the amplitude of the acoustic wave generated by the absorbed radiation was measured by a piezoelectric transducer attached directly to the sample. It was shown theoretically and experimentally that the output voltage from the transducer was proportional to the absorbed energy. The generated voltage per unit of absorbed energy was established by measuring the output voltage at a laser wavelength of known absorption coefficient. This value was then used as a reference to determine the abosrption coefficient at other laser wavelengths. Measurements were made on various glasses and potential window materials. Absorption coefficients in the 10 to the -5th power/cm range were measurable with laser input powers of only a few hundred mW. The sensitivity of the technique was limited by the voltage generated by radiation scattered onto the transducer. (Author)
Inorganic Polyhedral Metallacarborane Inhibitors of HIV Protease: A New Approach to Overcoming Antiviral Resistance (2008)

HIV protease (PR) is a prime target for rational anti-HIV drug design. We have previously identified icosahedral metallacarboranes as a novel class of nonpeptidic protease inhibitors. Now we show that substituted metallacarboranes are potent and specific competitive inhibitors of drug-resistant HIV PRs prepared either by site-directed mutagenesis or cloned from HIV-positive patients. Molecular modeling explains the inhibition profile of metallacarboranes by their unconventional binding mode.
Winding Layout Considerations for an Integrated Generator–Rectifier System (2021)

An integrated generator–rectifier system is a promising architecture to harvest energy in offshore wind turbines. The system processes the majority of the incoming power using reliable, efficient, and inexpensive passive diodes operating at the generator line frequency. Elimination of capacitors at the diode rectifiers’ output by appropriately phase shifting the voltages of a multiport generator further improves the reliability of the overall architecture. This article creates a generalized framework to evaluate the interactions among different generator ports, diode-bridge rectifiers, and the active rectifier that is used to control the power flow. The framework enables quantifying the effect of integration on the dc bus power ripple and power imbalance among different generator ports. An exemplary winding layout is proposed that ensures theoretically zero interaction between the passive ports, although all the ports are mounted on a magnetic structure. A 10-MW integrated generator–rectifier design and simulation proves the accuracy of the framework using coupled circuit and finite-element simulation. Finally, a laboratory prototype shows the realization of the winding layout. The proposed inductance-matrix-based framework can be used to evaluate other winding layouts to estimate the effect of magnetic coupling on the performance of the system.
Iridium‐Catalyzed Stereoselective Allylic Alkylation Reactions with Crotyl Chloride (2016)

The development of the first enantio-, diastereo-, and regioselective iridium-catalyzed allylic alkylation reaction of prochiral enolates to form an all-carbon quaternary stereogenic center with an aliphatic-substituted allylic electrophile is disclosed. The reaction proceeds with good to excellent selectivity with a range of substituted tetralone-derived nucleophiles furnishing products bearing a newly formed vicinal tertiary and all-carbon quaternary stereodyad. The utility of this protocol is further demonstrated via a number of synthetically diverse product transformations.
Structural Requirements for the Activation of the Human Growth Hormone Secretagogue Receptor by Peptide and Nonpeptide Secretagogues (1998)

Antibodies raised against an intracellular and extracellular domain of the GH secretagogue receptor (GHS-R) confirmed that its topological orientation in the lipid bilayer is as predicted for G protein-coupled receptors with seven transmembrane domains. A strategy for mapping the agonist-binding site of the human GHS-R was conceived based on our understanding of ligand binding in biogenic amine and peptide hormone G protein-coupled receptors. Using site-directed mutagenesis and molecular modeling, we classified GHS peptide and nonpeptide agonist binding in the context of its receptor environment. All peptide and nonpeptide ligand classes shared a common binding domain in transmembrane (TM) region 3 of the GHS-R. This finding was based on TM-3 mutation E124Q, which eliminated the counter-ion to the shared basic N+ group of all GHSs and resulted in a nonfunctional receptor. Restoration of function for the E124Q mutant was achieved by a complementary change in the MK-0677 ligand through modification of its amine side-chain to the corresponding alcohol. Contacts in other TM domains [TM-2 (D99N), TM-5 (M213K, S117A), TM-6 (H280F), and extracellular loop 1 (C116A)] of the receptor revealed specificity for the different peptide, benzolactam, and spiroindolane GHSs. GHS-R agonism, therefore, does not require identical disposition of all agonist classes at the ligand-binding site. Our results support the hypothesis that the ligand-binding pocket in the GHS-R is spatially disposed similarly to the well characterized catechol-binding site in the beta2-adrenergic receptor.
Isolation and characterization of equine amniotic membrane-derived mesenchymal stem cells (2013)

Recent studies have shown that mesenchymal stem cells (MSCs) are able to differentiate into multi-lineage cells such as adipocytes, chondroblasts, and osteoblasts. Amniotic membrane from whole placenta is a good source of stem cells in humans. This membrane can potentially be used for wound healing and corneal surface reconstruction. Moreover, it can be easily obtained after delivery and is usually discarded as classified waste. In the present study, we successfully isolated and characterized equine amniotic membrane-derived mesenchymal stem cells (eAM-MSCs) that were cultured and maintained in low glucose Dulbecco's modified Eagle's medium. The proliferation of eAM-MSCs was measured based on the cumulative population doubling level (CPDL). Immunophenotyping of eAM-MSCs by flow cytometry showed that the major population was of mesenchymal origin. To confirm differentiation potential, a multi-lineage differentiation assay was conducted. We found that under appropriate conditions, eAM-MSCs are capable of multi-lineage differentiation. Our results indicated that eAM-MSCs may be a good source of stem cells, making them potentially useful for veterinary regenerative medicine and cell-based therapy.
Expansion microscopy: enabling single cell analysis in intact biological systems (2018)

There is a need for single cell analysis methods that enable the identification and localization of different kinds of biomolecules throughout cells and intact tissues, thereby allowing characterization and classification of individual cells and their relationships to each other within intact systems. Expansion microscopy (ExM) is a technology that physically magnifies tissues in an isotropic way, thereby achieving super-resolution microscopy on diffraction-limited microscopes, enabling rapid image acquisition and large field of view. As a result, ExM is well-positioned to integrate molecular content and cellular morphology, with the spatial precision sufficient to resolve individual biological building blocks, and the scale and accessibility required to deploy over extended 3-D objects like tissues and organs.
A missense mutation in the bovine <i>SLC35A3</i> gene, encoding a UDP-<i>N</i>-acetylglucosamine transporter, causes complex vertebral malformation (2005)

The extensive use of a limited number of elite bulls in cattle breeding can lead to rapid spread of recessively inherited disorders. A recent example is the globally distributed syndrome Complex Vertebral Malformation (CVM), which is characterized by misshapen and fused vertebrae around the cervico-thoracic junction. Here, we show that CVM is caused by a mutation in the Golgi-resident nucleotide-sugar transporter encoded by SLC35A3. Thus, the disease showed complete cosegregation with the mutation in a homozygous state, and proteome patterns indicated abnormal protein glycosylation in tissues of affected animals. In addition, a yeast mutant that is deficient in the transport of UDP-N-acetylglucosamine into its Golgi lumen can be rescued by the wild-type SLC35A3 gene, but not by the mutated gene. These results provide the first demonstration of a genetic disorder associated with a defective SLC35A3 gene, and reveal a new mechanism for malformation of the vertebral column caused by abnormal nucleotide-sugar transport into the Golgi apparatus.
Identification of Strain-Specific Nucleotide Sequences in the RA 27/3 Rubella Virus Vaccine (1993)

A polymerase chain reaction-based protocol was developed for determination of the sequence of 1300 nucleotides in the E1 coding region of the genomes of multiple strains of rubella virus. From a collection of sequences of 9 independent strains and isolates, characteristic nucleotides were identified that distinguished the RA 27/3 strain, which is the currently used attenuated vaccine strain. These characteristic nucleotides were maintained in virus recovered from recent vaccinees. Both the assay and the knowledge of these characteristic nucleotides should be of use in determining the origin of virus isolated from individuals who have suspected vaccine-associated complications. The nucleotide sequences of the independent rubella virus strains differed by 0.7%-3.6%. Phylogenetic tree analysis of the sequences indicated the existence of at least three distinct genetic lineages.
Anticancer activity of chicken cathelicidin peptides against different types of cancer (2021)

Abstract This study served as the pioneer in studying the anti-cancer role of chicken cathelicidin peptides. Chicken cathelicidins were used as anticancer agent against the breast cancer cell line (MCF-7) and human colon cancer cell line (HCT116). An in vivo investigation was also achieved to evaluate the role of chicken cathelicidin in Ehrlich ascites cell (EAC) suppression as a tumor model after subcutaneous implantation in mice. In addition, the mechanism of action of the interaction of cationic peptides with breast cancer cell line MCF-7 was also investigated. It was found during the study that exposure of cell lines to higher concentration of chicken cathelicidin for 72 h reduced cell lines growth rate by 90%-95%. These peptides demonstrated down-regulation of (cyclin A1 and cyclin D genes) which are essential for G1/S phase transient and S/G2 phase and consequently causes “prometaphase arrest” ultimately leading to death of MCF-7 cells. The study showed two- and three-times higher expression of the caspase-3, and − 7 genes respectively in MCF-7 cells treated with chicken peptides (especially cathelicidin-2 and − 3) relative to untreated cells which encouraged pro-apoptotic pathway, autophagy, and augmentation of the anti-proliferative activity. Our data showed that chicken ( CATH-1 ) enhance releasing of TNFα, INF-γ and upregulation of granzyme K in treated mice groups, in parallel, the tumor size and volume was reduced in the treated EAC-bearing groups after cathelicidin administration compared to untreated EAC-bearing group. Additionally, animals received high dose of cathelicidin-1 (40 µg/ml) displayed an apical survival rate compared to untreated carcinoma control and animals which received low dose of cathelicidin (10 and 20 µg/ml). Tumor of mice groups treated with chicken cathelicidin displayed high area of necrosis compared to untreated EAC-bearing mice. Based on histological analysis and immunohistochemical staining revealed that the tumor section in Ehrlich solid tumor exhibited a strong Bcl2 expression in untreated control compared to mice treated with 10 & 20 µg/ml of cathelicidin. Interestingly, low expression of Bcl2 were observed in mice taken 40 µg/ml of CATH-1. This study drive intention in treatment of cancer through the efficacy of anticancer efficacy of chicken cathelicidin peptides.
Gout‐Causing Q141K Mutation in ABCG2 Leads to Defective Nucleotide‐Binding Domain Function (2015)

ABCG2 is a secretory efflux uric acid transporter of the kidney proximal tubule and gut that plays a key role in uric acid excretion. Genetic defect in ABCG2 leads to significant increases in serum urate levels (SUA) causing hyperuricemia and gout. A single common variant, Q141K, is responsible for the majority of ABCG2 associated gout risk. The Q141K mutation is a loss of function mutation associated with a severe reduction in protein abundance and transport function. Previously we hypothesized the Q141K mutation leads to instability in the nucleotide‐binding domain and here we present the specific molecular mechanism of the defect and a proof of concept of its correction using small molecules. We found using a ABCG2 structural model and targeted amino acid substitutions that the Q141K mutations leads to a localized disruption in packing that affects abundance and can be partially rescued with a secondary substitution at H155A. However the use of the signature motif suppressor mutation, G188E, provides full rescue of the Q141K abundance by stabilizing the NBD dimer sandwich, a finding consistent with a Q141K defect in NBD dimer formation. Finally we show that a small molecule, VRT‐325, known to bind directly to the NBD of ABC transporters can rescue both abundance and function of Q141K ABCG2.
Preparation and recording characteristics of Co-γFe2O3 high density magnetic recording media (1997)

We have investigated the preparation process and the recording characteristics of Co-γFe2O3 perpendicular magnetic recording media obtained by annealing the sputtered CoO-Fe3O4 films on the sputtered NiO underlayer. The NiO and CoO-Fe3O4 films were deposited at the rate of 520 nm/min and 130 nm/min, respectively. by DC magnetron sputtering. Moderately <100>-oriented Co-γFe2O3 media with intermediate perpendicular anisotropy ( Ku ≒ 6.0×105 erg/cm3 ) were prepared with a wide range of oxygen partial pressure used in deposition of NiO and CoO-Fe3O4 films. These media showed a superior high density recording performance which was comparable to that of highly <100>-oriented Co-γFe2O3 media with large perpendicular anisotropy.
Imaging feedback of histotripsy treatments using ultrasound shear wave elastography (2012)

Histotripsy is a cavitation-based ultrasound therapy that mechanically fractionates soft solid tissues into fluid-like homogenates. This paper investigates the feasibility of imaging the tissue elasticity change during the histotripsy process as a tool to provide feedback for the treatments. The treatments were performed on agar tissue phantoms and ex vivo kidneys using 3-cycle ultrasound pulses delivered by a 750-kHz therapeutic array at peak negative/positive pressure of 17/108 MPa and a repetition rate of 50 Hz. Lesions with different degrees of damage were created with increasing numbers of therapy pulses from 0 to 2000 pulses per treatment location. The elasticity of the lesions was measured with ultrasound shear wave elastography, in which a quasi-planar shear wave was induced by acoustic radiation force generated by the therapeutic array, and tracked with ultrasound imaging at 3000 frames per second. Based on the shear wave velocity calculated from the sequentially captured frames, the Young's modulus was reconstructed. Results showed that the lesions were more easily identified on the shear wave velocity images than on B-mode images. As the number of therapy pulses increased from 0 to 2000 pulses/location, the Young's modulus decreased exponentially from 22.1 ± 2.7 to 2.1 ± 1.1 kPa in the tissue phantoms (R2 = 0.99, N = 9 each), and from 33.0 ± 7.1 to 4.0 ± 2.5 kPa in the ex vivo kidneys (R2 = 0.99, N = 8 each). Correspondingly, the tissues transformed from completely intact to completely fractionated as examined via histology. A good correlation existed between the lesions' Young's modulus and the degree of tissue fractionation as examined with the percentage of remaining structurally intact cell nuclei (R2 = 0.91, N = 8 each). These results indicate that lesions produced by histotripsy can be detected with high sensitivity using shear wave elastography. Because the decrease in the tissue elasticity corresponded well with the morphological and histological change, this study provides a basis for predicting the local treatment outcomes from tissue elasticity change.
Study of the read function for bloch line memories (1990)

In Bloch Line memories understanding of the reading process is fundamental for the operation of the memory. The principle of this function is to discriminate parallel and antiparallel domain walls by chopping at different currents. Many parameters can influence this scheme, namely quasistatic or dynamic conditions, material characteristics, actual wall structure before and during chopping. The goal of this paper is to present a systematic study of these factors in order to give indications for practical devices.