gebhart/patrepeval huggingface dataset:
Functional annotation of human long noncoding RNAs via molecular phenotyping (2020)

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for <i>ZNF213-AS1</i> and <i>lnc-KHDC3L-2</i>.
<title>Mapping of imbedded contaminants in transparent material by optical scatter</title> (1991)

The paper reviews the design of an instrument designed to detect and map internal defects found in PMMA plastic. The material is used to manufacture intraocular lenses and must be free of defects larger than about 20 micrometers for a variety of safety, manufacturing and cosmetic reasons. The instrument detects scatter from a diode with a CCD array camera to map defect location. This information is used to avoid manufacturing lenses that will eventually be rejected.
Expression of Enzymes Involved in Estrogen Metabolism in Human Prostate (2006)

There is evidence that estrogens can directly modulate human prostate cell activity. It has also been shown that cultured human prostate cancer LNCaPcan synthesize the active estrogen estradiol (E2). To elucidate the metabolism of estrogens in the human prostate, we have studied the expression of enzymes involved in the formation and inactivation of estrogens at the cellular level. 17β-Hydroxysteroid dehydrogenase (17β-HSD) types 1, 2, 4, 7, and 12, as well as aromatase mRNA and protein expressions, were studied in benign prostatic hyperplasia (BPH) specimens using in situ hybridization and immunohistochemistry. For 17β-HSD type 4, only in situ hybridization studies were performed. Identical results were obtained with in situ hybridization and immunohistochemistry. All the enzymes studied were shown to be expressed in both epithelial and stromal cells, with the exception of 17β-HSD types 4 and 7, which were detected only in the epithelial cells. On the basis of our previous results, showing that 3β-HSD and 17β-HSD type 5 are expressed in human prostate, and of the present data, it can be concluded that the human prostate expresses all the enzymes involved in the conversion of circulating dehydroepiandrosterone (DHEA) to E2. The local biosynthesis of E2 might be involved in the development and/or progression of prostate pathology such as BPH and prostate cancer through modulation of estrogen receptors, which are also expressed in epithelial and stromal cells. (J Histochem Cytochem 54:911-921, 2006)
Computational Modeling of Grain Growth in Self-Reinforced Silicon Nitride. (1999)

A model is proposed for studying grain growth in silicon nitride by computer simulation. The simulation is based on the Monte Carlo method and uses the Potts model with additional features peculiar to silicon nitride ceramics, such as anisotropy of grain boundary energies and the presence of liquid phase. The simulation successfully produced self-reinforced microstructures. It was found that the self-reinforcement phenomenon occurred only within a particular range of liquid phase fractions. The influence of anisotropy in interface energy on inhomogeneous grain growth was also examined. When interface energies are isotropic, the microstructure was essentially homogeneous. The results of these simulations suggest that anisotropy in interface energy and the presence of an appropriate amount of liquid phase are two important factors controlling the self-reinforcement process in silicon nitride materials.
Energy transfer between shallow centers and rare-earth ion cores:Er3+ion in silicon (2000)

Two-color optical spectroscopy is used to directly manipulate shallow levels available in Si:Er samples of different parameters. It is observed that the excitation energy provided by a laser operating in the visible can be temporarily stored by trapping photogenerated carriers at shallow centers available in the material. Subsequently, this energy can be transferred to the $4f$-electron core of the ${\mathrm{Er}}^{3+}$ ion in a trap ionization process induced by a mid-infrared pulse from a free-electron laser. In that way, Er-related luminescence at $1.5 \ensuremath{\mu}\mathrm{m}$ can be generated by an infrared pulse applied within several milliseconds after the band-to-band excitation pulse. By scanning the wavelength of the free-electron laser, ionization spectra of the shallow centers participating in the energy transfer are obtained, allowing for their identification. On that basis, the involvement of thermal donors is suggested. The results demonstrate that excitation of Er ions in Si is a multichannel energy transfer process where shallow centers play an important role.
The Reaction of Vinyl Monomers with “Trapped Free Radicals” (1981)

Abstract Previous attempts to prepare copolymers by the reaction of vinyl monomers, such as styrene, with “trapped free radicals” such as acrylonitrile macroradicles has been unsuccessful because of the large differences in solubility parameters between the liquid and the solid. However, acrylonitrile will react with styrene macroradicals in the absence of oxygen, and yield block copolymers. Block copolymers may be produced from other vinyl monomers and other macroradicals when the difference in the solubility parameter of the monomer and macroradicals is less than 3.2H.
TOPICAL CO-DELIVERY OF INDOMETHACIN AND NIGELLA SATIVA L. ESSENTIAL OIL IN POLY- -CAPROLACTONE NANOPARTICLES: IN VIVO STUDY OF ANTI-INFLAMMATORY ACTIVITY. (2018)

Indomethacin is a potent, nonselective Non-steroidal Anti-inflammatory Drug (NSAID) but its low water-solubility precludes its use as topical dosage form. As with other NSAIDs, the systemic delivery is
AlN Contour-Mode Vibrating RF MEMS for Next Generation Wireless Communications (2006)

AlN contour-mode vibrating RF MEMS resonator technology is described as capable of low-loss filtering and frequency synthesis for next generation wireless devices. Contour-mode piezoelectric resonators can span frequencies from 10 MHz up to few GHz on the same silicon chip offering high quality factors in air (1,000-4,000) and low motional resistance (25-700 Omega). Low loss (<- 1.5 dB) electrically and mechanically coupled filters and low phase noise oscillators can be easily implemented using this resonator technology. Low power transceiver architectures based on frequency hopping, multi-band filtering and direct frequency synthesis are presented as next generation wireless solutions that will be enabled by this new class of AlN contour-mode resonators
Mobility Improvement in N-Type Organic FET with Hetero-Layered Structure (2009)

The field-effect mobility in n-type fullerene field-effect transistors was improved by the hetero-layered structure including the interfacial layer of organic semiconductor between the insulator and channel semiconductor. Various types of hole transporting material were employed for the interfacial layer. The device showed high electron mobility exceeding 1 cm2/Vs that was better than that for the substrates with conventional surface treatments, for example, hexamethyldisilazane (HMDS) and octadecyltrichlorosilane (OTS). These results suggest that the electron-donating character of the hole transporting materials leads to filling the electron traps at the insulator interface.
Multi-stoichiometric quasi-two-dimensional WnO3n−1 tungsten oxides (2020)

Quasi-two-dimensional tungsten oxide structures, which nucleate by epitaxial growth on W19O55 nanowires (NW) and grow as thin platelets, were identified. Both the nanowires and the platelets accommodate oxygen deficiency by the formation of crystallographic shear planes. Stoichiometric phases, W18O53 (WO2.944), W17O50 (WO2.941), W16O47 (WO2.938), W15O44 (WO2.933), W14O41 (WO2.929), W10O29 (WO2.9), and W9O26 (WO2.889), syntactically grow inside a single platelet. These layered crystals show a new kind of polycrystallinity, where crystallographic shear planes accommodate oxygen deficiency and at the same time stabilize this multi-stoichiometric structure.
Hybrid Adeno-Associated Virus Bearing Nonhomologous Inverted Terminal Repeats Enhances Dual-Vector Reconstruction of Minigenes In Vivo (2007)

We have previously demonstrated that hybrid adeno-associated viral (AAV) vectors bearing nonhomologous inverted terminal repeats (ITRs) enhance directional intermolecular recombination and the efficiency of dual-AAV vector trans-splicing in cultured cells. Using hybrid-ITR vectors carrying two exons of a lacZ minigene, we demonstrate that this dual-vector approach also mediates higher levels (3- to 6-fold) of gene reconstitution in mouse skeletal muscle, liver, and heart. Inhibition of the proteasome by systemic administration of Doxil (Food and Drug Administration-approved lipid-formulated doxorubicin) further enhanced dual-vector trans-splicing 6- to 12-fold in two mouse strains. Hence, using hybrid-ITR AAV vectors in combination with proteasome modulation enhanced dual-vector delivery of a transgene approximately 36-fold over the current dual-vector trans-splicing approaches. These data provide in vivo evidence that ITR sequence-dependent homologous recombination, rather than nonhomologous end joining, is the predominant mechanism for AAV genome heterodimerization. Hence, enhanced directional recombination provided by hybrid-ITR vectors may be a useful in vivo strategy for improving dual-vector delivery of transgenes larger than the AAV packaging limit.
Patient and family experience in pediatric spine surgery: a social media analysis (2022)

Abstract There is little data on patient and caregiver perceptions of spine surgery in children and youth. This study aims to characterize the personal experiences of patients, caregivers, and family members surrounding pediatric spine surgery through a qualitative and quantitative social media analysis. The Twitter application programming interface was searched for keywords related to pediatric spine surgery from inception to March 2022. Relevant tweets and accounts were extracted and subsequently classified using thematic labels. Tweet metadata was collected to measure user engagement via multivariable regression. Sentiment analysis using Natural Language Processing was performed on all tweets with a focus on tweets discussing the personal experiences of patients and caregivers. 2424 tweets from 1847 individual accounts were retrieved for analysis. Patients and caregivers represented 1459 (79.0%) of all accounts. Posts discussed the personal experiences of patients and caregivers in 83.5% of tweets. Pediatric spine surgery research was discussed in a few posts (n=90, 3.7%). Within the personal experience category, 975 (48.17%) tweets were positive, 516 (25.49%) were negative, and 533 (26.34%) were neutral. Presence of a tag (beta: -6.1, 95% CI -9.7 to -2.5) and baseline follower count (beta&lt;0.001, 95% CI &lt;0.001 to &lt;0.001) significantly affected tweet engagement negatively and positively, respectively. Patients and caregivers actively discuss topics related to pediatric spine surgery on Twitter. Posts discussing personal experience are most prevalent, while posts on research are scarce, unlike previous social media studies. Pediatric spine surgeons can leverage this dialogue to better understand the worries and needs of patients and their families.
Interdigitated annular CMUT arrays for ultrasound assisted delivery of fluorescent contrast agents (2011)

Detection of early stage cancer is critical to successful treatment. Molecular imaging contrast agents offer great promise for early stage cancer detection. For improved image quality and diagnostics there is a need to improve the delivery, activation, and uptake of molecular imaging contrast agents. Low intensity focused ultrasound is one option to improve the delivery of molecular imaging agents. Here we investigate a circularly symmetric interdigitated capacitive micromachined ultrasonic transducer for improved delivery of fluorescent contrast agents to be imaged by a miniature dual axis confocal microscope. In order to apply ultrasound energy in the field of view of the optical microscope interface waves must be exploited. The device clearly focuses the ultrasound energy on the surface and at the center of the device. Overlapping the field of view of the optical microscope is required for improved in vivo imaging. Reasonable intensities of about 145 mW/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> have been demonstrated for enhanced delivery of the contrast agents.
Chemistry of polynuclear metal complexes with bridging carbene or carbyne ligands. Part 87. Docosahedral carbaborane(alkylidyne)tungsten complexes as reagents for the synthesis of compounds with heteronuclear metal–metal bonds: crystal structures of [NEt4][W(CC6H6Me2-2,6)(CO)2(η6-C2B10H10Me2)] and [NEt4][WFe(µ-CC6H3Me2-2,6)(CO)4(η6-C2B10H10Me2)] (1989)

Addition of thf (tetrahydrofuran) solutions of the salt Na2[C2B10H10Me2] to thf solutions of the compounds [W(CR)Cl(CO)2L2](R = C6H4Me-4 or C6H3Me2-2,6; L = pyridine or 4-methylpyridine), in the presence of [NEt4]Cl, affords the complexes [NEt4][W(CR)(CO)2(η6-C2B10H10Me2)] in good yield. An X-ray diffraction study on the product with R = C6H3Me2-2,6 reveals that the tungsten atom is ligated by two CO groups, the alkylidyne fragment [WC 1.84(1)Å], and the carbaborane cage. The open face of the latter is η6-co-ordinated to the tungsten but is decidedly non-planar. The requirement of a six-atom [graphic omitted] ring above a pentagonal belt of five boron atoms results in two faces in the cage distorting from a triangular to an essentially square arrangement. Variable-temperature n.m.r. studies showed that in solution the anions undergo a dynamic exchange process. Treatment of the salts [NEt4][W(CR)(CO)2(η6-C2B10H10Me2)] with the reagents [AuCl(PPh3)] and [Rh(cod)(PPh3)2][PF6](cod = cyclo-octa-1,5-diene) yields the dimetal compounds [WAu(µ-CR)(CO)2(PPh3)(η6-C2B10H10Me2)] and [WRh(µ-CR)(CO)2(PPh3)2(η6-C2B10H10Me2)], respectively. The tungsten–gold species, and the compound [WRh(µ-CC6H4Me-4)(CO)2(PPh3)2(η6-C2B10H10Me2)], are formed as mixtures of two isomers. The reaction between [NEt4][W(CC6H4Me-4)(CO)2(η6-C2B10H10Me2)] and [Fe2(CO)9] affords the trimetallic complex [NEt4][WFe2(µ3-CC6H4Me-4)(µ-σ:σ′:η6-C2B10H8Me2)(CO)8]. In the latter, the carbaborane fragment has slipped over the WFe2 triangle so that two boron atoms in the face of the cage form σ bonds with the iron atoms. The p-tolylmethylidyne group caps the other side of the metal triangle. In contrast, the reaction between the compounds [NEt4][W(CC6H3Me2-2,6)(CO)2(η6-C2B10H10Me2)] and [Fe2(CO)9] in thf gives the novel bimetallic complex [NEt4][WFe(µ-CC6H3Me2-2,6)(CO)4(η6-C2B10H10Me2)], the structure of which has been established by an X-ray diffraction study. In the anion a very short W–Fe bond [2.512(2)Å] is bridged by the xylylmethylidyne ligand [µ-C–W 2.02(1), µ-C–Fe 1.82(1)Å]. Both metal centres carry two terminally bound CO groups. As expected, the tungsten atom is ligated by the six atoms in the open face of the carbaborane cage, but the latter also bridges the W–Fe linkage via an exopolyhedral B–H⇀Fe three-centre two-electron bond. The n.m.r. data (1H, 13C-{1H}, 11B-{1H}, and 31P-{1H}) for the new compounds are reported, and where appropriate are discussed.
Fabrication of highly stacked quantum dot laser (2009)

We fabricated broad-area laser diodes containing highly stacked InAs quantum dots (QDs) using the strain-compensation technique; these diodes showed laser emission at 1529 nm in pulsed mode with a threshold current of 517.5 mA.
Characteristic intra- and interunit interactions of Kr atoms adsorbed on theSi(111)−7×7surface (2003)

Adsorption of Kr atoms on the $\mathrm{Si}(111)\ensuremath{-}7\ifmmode\times\else\texttimes\fi{}7$ surface at 8 K was studied by scanning tunneling microscopy. Despite similar electronic structures of noble gas atoms, the observed site-dependent adsorbed Kr structures and their formation processes were different from those of Xe atoms. In comparison with the results of simulation, the existence of the characteristic intraunit and interunit interactions between Kr atoms was confirmed.
Rapid identification of a sparse impulse response using an adaptive algorithm in the Haar domain (2003)

This paper proposes a fast convergence adaptive algorithm for identifying a sparse impulse response that is rich in spectral content. A sparse impulse response is referred here as a discrete time impulse response that has a large number of zero or near zero coefficients. The basic idea for rapid identification is to automatically determine the locations of the nonzero impulse response coefficients for their adaptation and eliminate the unnecessary adaptation of zero coefficients. The proposed method, which is called the Haar-Basis algorithm, employs a transform approach by modeling the sparse impulse response in the Haar domain. The Haar transform has many basis sets and each of them contains basis vectors that span the entire time domain range. This special nature of the Haar transform allows for the selection of one small subset of adaptive filter coefficients whose basis vectors span the entire range of the impulse response. These coefficients are adapted at the beginning and are then used subsequently to identify, from the hierarchical structure of the Haar transform, the rest of the filter coefficients that must be adapted to correctly model the unknown sparse impulse response. The consequence is avoiding adaptation of many zero coefficients, leading to a dramatic improvement in either convergence speed or steady state excess mean-square error (EASE), while requiring no a priori knowledge such as the number of nonzero coefficients in the unknown sparse impulse response. The proposed algorithm has been tested with a variety of unknown sparse systems using both white noise input and colored input whose spectrum closely resembles that of speech. Simulation results show that the new approach provides promising results.
ChemInform Abstract: Synthesis and Biological Activity of an Optically Pure 10‐Spirocyclopropyl Analogue of Huperzine A. (1998)

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.
Interprofessional orientation for health professionals utilising simulated learning: Findings from a pilot study (2016)

We describe a novel, interprofessional educational intervention pilot used to orient new health profession employees through the simulation laboratory. Health profession employees were recruited to engage in a simulation training session that focused on communication, collaboration, and healthcare roles and responsibilities. Learners (N = 11) were divided into two groups with representation from various health disciplines. Each group participated in a simulated patient scenario while the other group actively observed in another classroom. At the end of both sessions, the group reconvened for a debriefing session. Participants were given a survey before and after the training session, to evaluate the content, experience, and value to their practice. The pre- and post-evaluation survey analysis showed improvement in all objectives with a mean (SD) pre-evaluation score of 4.10 (0.40-1.01) and mean (SD) post-evaluation score of 4.73 (0.30-0.81). Results were favourable, and plans to expand this project are under way.
Expression of Siglec-11 by human and chimpanzee ovarian stromal cells, with uniquely human ligands: implications for human ovarian physiology and pathology (2011)

Siglecs (Sialic acid-binding Immunoglobulin Superfamily Lectins) are cell surface signaling receptors of the I-type lectin group that recognize sialic acid-bearing glycans. CD33-related-Siglecs are a subset with expression primarily in cells of hematopoietic origin and functional relevance to immune reactions. Earlier we reported a human-specific gene conversion event that markedly changed the coding region for the extracellular domain of Siglec-11, associated with human-specific expression in microglia (Hayakawa T, Angata T, Lewis AL, Mikkelsen TS, Varki NM, Varki A. 2005. A human-specific gene in microglia. Science. 309:1693). Analyzing human gene microarrays to define new patterns of expression, we observed high levels of SIGLEC11 transcript in the ovary and adrenal cortex. Thus, we examined human and chimpanzee tissues using a well-characterized anti-Siglec-11 mouse monoclonal antibody. Although adrenal expression was variable and confined to infiltrating macrophages in capillaries, ovarian expression of Siglec-11 in both humans and chimpanzees was on fibroblasts, the first example of Siglec expression on mesenchyme-derived stromal cells. Cytokines from such ovarian stromal fibroblasts play important roles in follicle development and ovulation. Stable transfection of SIGLEC11 into a primary human ovarian stromal fibroblast cell line altered the secretion of growth-regulated oncogene α, interleukin (IL)-10, IL-7, transforming growth factor β1 and tumor necrosis factor-α, cytokines involved in ovarian physiology. Probing for Siglec-11 ligands revealed distinct and strong mast cell expression in human ovaries, contrasting to diffuse stromal ligands in chimpanzee ovaries. Interestingly, there was a trend of increased Siglec-11 expression in post-menopausal ovaries compared with pre-menopausal ones. Siglec-11 expression was also found on human ovarian stromal tumors and in polycystic ovarian syndrome, a human-specific disease. These results indicate potential roles for Siglec-11 in ovarian physiology and human evolution.
Development of depth-image-based three-dimensional mobile broadcasting system in terrestrial digital media broadcasting (2010)

We present a 3-D mobile broadcasting system based on a depth-image-based rendering (DIBR) technique in terrestrial digital multimedia broadcasting (T-DMB). It is well known that a 3-D mobile broadcasting service based on the DIBR technique can be one of the solutions to meet service requirements, because the required bit rates of depth images in DIBR schemes are less than additional video bit rates of other 3-D formats, while keeping good 3-D quality and guaranteeing backward compatibility with conventional broadcasting systems. We propose an implementation of a DIBR-based 3-D T-DMB system that supports real-time rendering with good image quality and realistic depth effect at the receiver, verifying that it could be perfectly applicable in mobile broadcasting. Specifically, the proposed 3-D T-DMB receiver adopts a look-up table (LUT)-based simultaneous method to accomplish the real-time implementation of DIBR algorithms, including warping, hole filling, and interleaving. Moreover, we establish the parameter values that are needed for generating the LUT based on theoretical analysis. The verification is accomplished through objective and subjective evaluations, based on simulation and real-time implementation of the system under actual service conditions.