gebhart/patrepeval huggingface dataset:
Identification and characterization of critical cis-acting sequences within the yeast Ty1 retrotransposon (2005)

The yeast long terminal repeat (LTR) retrotransposon Ty1, like retroviruses, encodes a terminally redundant RNA, which is packaged into virus-like particles (VLPs) and is converted to a DNA copy by the process of reverse transcription. Mutations predicted to interfere with the priming events during reverse transcription and hence inhibit replication are known to dramatically decrease transposition of Ty1. However, additional cis-acting sequences responsible for Ty1 replication and RNA dimerization and packaging have remained elusive. Here we describe a modular mini-Ty1 element encoding the minimal sequence that can be retrotransposed by the Ty1 proteins, supplied in trans by a helper construct. Using a mutagenic screening strategy, we recovered transposition-deficient modular mini-Ty1-HIS3 elements with mutations in sequences required in cis for Ty1 replication and integration. Two distinct clusters of mutations mapped near the 5'-end of the Ty1 RNA. The clusters define a GAGGAGA sequence at the extreme 5'-end of the Ty1 transcript and a complementary downstream UCUCCUC sequence, 264 nt into the RNA. Disruption of the reverse complementarity of these two sequences decreased transposition and restoration of complementarity rescued transposition to wild-type levels. Ty1 cDNA was reduced in cells expressing RNAs with mutations in either of these short sequences, despite nearly normal levels of Ty1 RNA and VLPs. Our results suggest that the intramolecular interaction between the 5'-GAGGAGA and UCUCCUC sequences stabilizes an RNA structure required for efficient initiation of reverse transcription.
Accessing Social Support and Overcoming Judgment on Social Media among Parents of Children with Special Needs (2014)

Over 10 million children are diagnosed with a special need in the United States each year. For their parents, the economic and emotional costs can be overwhelming. Using a mixed methods approach, we show that parents of children with special needs rely primarily on Facebook pages, Facebook groups, and Yahoo! groups for accessing information and social support. Specifically, these groups offer geographic communities for local needs (e.g. school services) and case-based communities for specific conditions (e.g. autism). Promisingly, parents perceive less judgment online than offline when talking about their children’s special needs; however, these perceptions are nuanced. In particular, posts containing humor, achievement, or treatment suggestions are perceived to be more socially appropriate than posts containing judgment, violence, or social comparisons. However, results show that social media generally fails at connecting special needs families over time and across the life span. We discuss implications for social media site design and for supporting special needs families.
New materials and devices for optical interconnect (2015)

In this paper we show how new materials such as InP epitaxially grown on silicon, graphene and ferroelectric materials with strong electro-optic coefficient can be integrated with silicon waveguides and enhance the functionality of the silicon photonics platform.
System modeling of small bore DOI-PET scanners for fast and accurate 3D image reconstruction (2007)

We are developing a small bore PET scanner with four-layer depth-of-interaction (DOI) detectors arranged in a hexagonal shape for small animal imaging. In image reconstruction of the small bore DOI-PET, the difficulty is irregular detector sampling caused by inter-detector gaps and the dimension of data increases in proportion to the square of the number of DOI layers. We need to apply an accurate system model based on an on-the-fly calculation because it is difficult to pre-compute and preserve a huge number of lines of response (LORs). In this work, we propose a system model of small bore DOI-PET scanners for fast and accurate 3D image reconstruction. First, we compare two system models which represent the detector response function (DRF) as the combination of several flight paths of gamma-rays and an optimized number of flight paths. Second, we propose anew ray-tracing method based on the Zhao-Reader algorithm. The results show that a high resolution image is reconstructed in 3 hours per OSEM iteration from 1.0times 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sup> LORs.
Fluorescent Melting Curve Analysis Compatible With a Flowing Polymerase Chain Reactor (2005)

A primary tool for analysing PCR product is the Fluorescent Melting Curve Analysis (FMCA). The temperature at which a double helix DNA strand denatures depends both on its length and base pair composition. Accurate measurement of this melting temperature using fluorescence allows estimations be made regarding DNA product length and composition. Current progress in development of PCR thermal cyclers has been primarily aimed at micro-channel based flowing devices. This paper addresses the challenges associated with performing FMCA analysis which is compatible with the output from a flowing PCR thermocycler. Two PCR products of significantly different lengths and base pair composition are compared using space domain FMCA. Results allow for differentiation of the PCR product, and compare favourably with results from a commercial thermal cycler. The successful application of FMCA within a channel shows its potential for use in high throughput flow based total analysis systems (μTAS).
Preparation of an Antibacterial Poly(ionic liquid) Graft Copolymer of Hydroxyethyl Cellulose (2015)

Poly(ionic liquid)s (P(IL)s) of different degrees of polymerization (10, 50, and 100) were prepared via RAFT polymerization using an alkyne-terminated xanthate as transfer agent, with a monomer conversion of up to ∼80% and a ĐM of 1.5 for P(IL)100. Subsequently, P(IL) chains were coupled to (15)N-labeled azido-functionalized hydroxyethyl cellulose (HEC), forming graft copolymers of HEC with different chain length and graft densities, which were characterized using ((13)C and (15)N) CP-MAS NMR and FT-IR spectroscopies. The antibacterial activities of HEC-g-P(IL)s were tested against Escherichia coli and Staphylococcus aureus and were comparable to ampicillin, a well-known antibiotic, demonstrating efficient activity of the graft copolymers against bacteria. Moreover, HEC-g-P(IL)s were slightly more effective against E. coli than S. aureus. A decrease in graft density of P(IL)10 on the HEC backbone decreased the activity of the graft copolymers against both bacteria. These findings suggest that HEC-g-P(IL) could find applications as an antiseptic compound, for example, in paint formulation.
Zirconocene‐Mediated Carbonylative Coupling of Grignard Reagents (2016)

Abstract Organozirconocenes are versatile synthetic intermediates that can undergo carbonylation to yield acyl anion equivalents. Zirconocene hydrochloride ([Cp 2 ZrHCl]) is often the reagent of choice for accessing these intermediates but generates organozirconocenes only from alkenes and alkynes. This requirement eliminates a broad range of substrates. For example, organozirconocenes in which the zirconium center is bonded to an aromatic ring, a benzylic group, or an alkyl group that possesses a tertiary or quaternary carbon atom α to the carbon–zirconium bond can not be formed in this way. To provide more generalized access to acyl zirconium reagents, we explored the transmetalation of Grignard reagents with zirconocene dichloride under a CO atmosphere. This protocol generates acyl zirconium(IV) complexes that are inaccessible with the Schwartz reagent, including those derived from secondary and tertiary alkyl and aryl Grignard reagents.
L Band Phased Array Feed Noise Figure and Radiation Efficiency Measurement with the Antenna Y Factor Method (2023)

The noise performance of a high sensitivity, wide-field astronomical phased array feed receiver can be characterized by measurements using the antenna Y factor method. These measurements are used to determine figures of merit for an active array receiver. Antenna elements for the Advanced L Band Phased Array Camera for Astronomy (ALPACA) were measured using the antenna Y factor method to determine the active array and receiver noise figure, the antenna loss, receiver equivalent noise temperature, and radiation efficiency of the system over its 500[Formula: see text]MHz operating bandwidth. The completed ALPACA instrument will feature a fully cryogenic design with both the low-noise amplifiers and array elements cryogenically cooled. The uncooled performance measurements from the antenna Y factor method are used to extrapolate the elements cryogenic radiation efficiency and antenna loss showing that it is expected that the elements will contribute less than 1 K to the overall system noise temperature. These results validate the antenna Y factor method to measure key antenna parameters such as the antenna radiation efficiency and show that the instruments front-end array and electronics meets expected performance targets.
Functional Expression of Soluble Human Interleukin-11 (IL-11) Receptor α and Stoichiometry of in Vitro IL-11 Receptor Complexes with gp130 (1996)

The interleukin-6 (IL-6) family of cytokines activates signaling through the formation of either gp130 homodimers, as for IL-6, or gp130-leukemia inhibitory factor receptor (LIFR) heterodimers as for ciliary neurotrophic factor (CNTF), leukemia inhibitory factor, oncostatinM, and cardiotrophin-1. Recent in vitro studies with IL-6 and CNTF have demonstrated that higher order hexameric receptor complexes are assembled in which signaling chain dimerization is accompanied by the dimerization of both the cytokine molecule and its specific receptor alpha subunits (IL-6Ralpha or CNTFRalpha, respectively). IL-11 is a member of the IL-6 family and known to require gp130 but not LIFR for signaling. In this study we investigate the functional and biochemical composition of the IL-11 receptor complex. The human IL-11 receptor alpha-chain was cloned from a human bone marrow cDNA library. IL-11Ralpha was shown to confer IL-11 responsiveness to human hepatoma cells either by cDNA transfection or by adding a soluble form of the receptor (sIL11Ralpha) expressed in the baculovirus system to the culture medium. In vitro immunoprecipitation experiments showed that sIL11Ralpha specifically binds IL-11 and that binding is enhanced by gp130. Similarly to IL-6 and CNTF, gp130 is able to induce dimerization of the IL-11.IL-11Ralpha subcomplex, the result of which is the formation of a pentameric receptor complex. However, in contrast to the other two cytokines, IL-11 was unable to induce either gp130 homodimerization or gp130/LIFR heterodimerization. These results strongly suggest that an as yet unidentified receptor beta-chain is involved in IL-11 signaling.
Health care burden of cervical spine fractures in the United States: analysis of a nationwide database over a 10-year period (2010)

OBJECT The objective of this work was to search a national health care database of patients diagnosed with cervical spine fractures in the US to analyze discharge, demographic, and hospital charge trends over a 10-year period. METHODS Clinical data were derived from the Nationwide Inpatient Sample (NIS) for the years 1997 through 2006. The NIS is maintained by the Agency for Healthcare Research and Quality and represents a 20% random stratified sample of all discharges from nonfederal hospitals within the US. Patients with cervical spine fractures with and without spinal cord injury (SCI) were identified using the appropriate ICD-9-CM codes. The volume of discharges, length of stay (LOS), hospital charges, total national charges, discharge pattern, age, and sex were analyzed. National estimates were calculated using the HCUPnet tool. RESULTS Approximately 200,000 hospitalizations were identified. In the non-SCI group, there was a 74% increase in hospitalizations and charges between 1997 and 2006, but LOS changed minimally. There was no appreciable change in the rate of in-hospital mortality (< 3%), but discharges home with home health care and to skilled rehabilitation or nursing facilities increased slightly. In the SCI group, hospitalizations and charges increased by 29 and 38%, respectively. There were no significant changes in LOS or discharge status in this group. Spinal cord injury was associated with increases in LOS, charges, and adverse outcomes compared with fractures without SCI. Total national charges associated with both groups combined exceeded $1.3 billion US in 2006. CONCLUSIONS During the studied period, increases in hospitalizations and charges were observed in both the SCI and non-SCI groups. The percentage increase was higher in the non-SCI group. Although SCI was associated with higher adverse outcomes, there were no significant improvements in immediate discharge status in either group during the 10 years analyzed.
Ambient air quality monitoring plan, Johnsonville Steam Plant (1982)

TVA has operated an ambient air quality monitoring network at Johnsonville Steam Plant since 1950. The monitoring was initially conducted to collect background information prior to plant startup (1951) and ultimately to document the impact of plant emissions on ambient air quality after it reached full operating capacity in 1959. In 1976, TVA implemented a plan to bring the steam plant into compliance with provisions of the Clean Air Act by demonstrating that it met applicable ambient air quality standards for sulfur dioxide (SO/sub 2/). This option was allowed at that time under the Tennessee State Implementation Plan (SIP) and was selected by TVA as being the most practical means of achieving compliance. This air quality monitoring plan is described in this report. TVA's strategy for meeting ambient standards was its Sulfur Dioxide Emission Limitation (SDEL) program. This program provided for the control of plant emissions through the intermittent reduction of power generation under meteorological conditions conducive to ambient SO/sub 2/ concentrations in excess of National Ambient Air Quality Standards (NAAQS). Seven SO/sub 2/ monitors were added to the existing network to provide monitoring support for the SDEL program. Data from the monitoring network were used to verify that SO/submore » 2/ standards were not exceeded and to upgrade SDEL program effectiveness. The SDEL program has operated continuously at Johnsonville since its implementation in 1976. It was integrated into the Consent Decree interim control plan in 1978 to control SO/sub 2/ emissions until July 1982 when the plant will meet the required 3.4 lb/10/sup 6/ Btu emission standard. Compliance with this standard will be met by burning low- to medium-sulfur coel.« less
Free Viewpoint Virtual Try-On With Commodity Depth Cameras (2011)

Figure 1: An illustration of the concept of our system. A user is recorded at a shop entrance. He can take his avatar home, and view and interact with it on his own computer equipped with a depth camera. The user’s avatar wears augmented, reconstructed or virtual garments to create a comfortable, private try-on experience. We present a system that allows users to interactively control a 3D model of themselves at home using a commodity depth camera. It augments the model with virtual clothes that can be downloaded. As a result, users can enjoy a private, virtual try-on experience in their own homes. As a prerequisite, the user needs to enter or pass through a multi-camera setup that captures him or her in a fraction of a second. From the captured data, a 3D model is created. The model is transmitted to the user’s home system to serve as a realistic avatar for the virtual try-on application. The system provides freeviewpoint high quality rendering with smooth animations and correct occlusion, and therefore improves the state of the art in terms of quality. It utilizes cheap hardware and therefore is affordable for and accessible to a wide audience. 1
The future of extracorporeal support (2008)

Extracorporeal therapy has expanded significantly over the past few decades from solely artificial renal replacement therapy. In patients with multiple organ dysfunction syndrome, it becomes necessary to provide multiple organ support therapy. Technological advances have opened the door to a multifaceted intervention directed at supporting the function of multiple organs through the treatment of blood. Indications for "old" therapies such as hemofiltration and adsorption have been expanded, and using these therapies in combination further enhances blood detoxification capabilities. Furthermore, new devices are constantly in development. Nanotechnology allows us to refine membrane characteristics and design innovative monitoring/biofeedback devices. Miniaturization is leading down the path of wearable/implantable devices. With the incorporation of viable cells within medical devices, these instruments become capable not only of detoxification but synthetic functions as well, bringing us closer to the holy grail of complete replacement of organ function. This article provides a brief overview of current and future direction in extracorporeal support in the critical care setting.
Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel (2017)

Genetic imputation is a cost-efficient way to improve the power and resolution of genome-wide association (GWA) studies. Current publicly accessible imputation reference panels accurately predict genotypes for common variants with minor allele frequency (MAF)≥5% and low-frequency variants (0.5≤MAF<5%) across diverse populations, but the imputation of rare variation (MAF<0.5%) is still rather limited. In the current study, we evaluate imputation accuracy achieved with reference panels from diverse populations with a population-specific high-coverage (30 ×) whole-genome sequencing (WGS) based reference panel, comprising of 2244 Estonian individuals (0.25% of adult Estonians). Although the Estonian-specific panel contains fewer haplotypes and variants, the imputation confidence and accuracy of imputed low-frequency and rare variants was significantly higher. The results indicate the utility of population-specific reference panels for human genetic studies.
Risk Factors for Pneumococcal Carriage in Day Care Centers (2013)

In this retrospective epidemiologic study, we present pneumococcal carriage data from 109 Swedish day care centers over a period of 10 years. Aspects of season, age, personnel and group size were studied. We found a significant seasonal variation in pneumococcal carriage. Group size was a significant risk factor for pneumococcal carriage. Pneumococcal carriage was 4.5 % in personnel.
High-Power Broadband Dual Comb Spectroscopy in the Mid Infrared (2020)

We present results of directly measured acetone absorption in the mid infrared using high-powered broadband dual comb spectroscopy. The technique developed is applicable to a wide variety of systems with mid infrared spectral features.
A Time-Resolved CMOS Image Sensor With Draining-Only Modulation Pixels for Fluorescence Lifetime Imaging (2012)

This paper presents a time-resolved CMOS image sensor with draining-only modulation (DOM) pixels, for time-domain fluorescence lifetime imaging. In the DOM pixels using a pinned photodiode (PPD) technology, a time-windowed signal charge transfer from a PPD to a pinned storage diode (PSD) is controlled by a draining gate only, without a transfer gate between the two diodes. This structure allows a potential barrierless and trapless charge transfer from the PPD to the PSD. A 256 × 256 pixel time-resolved CMOS imager with 7.5 × 7.5 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> DOM pixels has been implemented using 0.18-μm CMOS image sensor process technology with PPD option. The prototype demonstrates high sensitivity for weak signal of less than one electron per light pulse and accurate measurement of fluorescence decay process with subnanosecond time resolution.
Double-Layer Silicon Photonic Crystal Fiber-Tip Temperature Sensors (2014)

This letter describes the manufacture and performance of a monolithic double-layer silicon photonic crystal temperature sensor. The sensor is fabricated on standard silicon wafers using oxide passivation and a combination of isotropic and anisotropic etching, and mounted on the facet of a standard single-mode optical fiber using template-assisted epoxy bonding. The double-layer configuration leads to coupling of the guided resonances in the two photonic crystals and enables sharper resonances and consequently higher temperature sensitivity and better detection limit (0.011 °C) than the single-layer counterpart. We experimentally demonstrate that the sensor has a twofold increased temperature sensitivity in terms of reflectivity change at a fixed wavelength (-0.00576/°C), and report on electromagnetic simulations explaining the enhanced sensor operation. The photonic crystal fabrication method and template-assisted bonding enable batch-fabrication of the sensors. Their small size, robust construction, and fiber interface make the sensors promising for numerous applications, including sensing in harsh environments.
Tailored intestinal IgA responses can set an evolutionary trap for Salmonella Typhimurium (2020)

Secretory antibody responses (Immunoglobulin A, IgA) against repetitive bacterial surface glycans, such as O-antigens, can protect against intestinal pathogenic bacteria. However, vaccines that rely predominantly on secretory IgA for protection against non-Typhoidal salmonellosis often fail. Here we demonstrate that a major contributor to this failure is rapid immune escape, due to strong selective pressure exerted by high-avidity intestinal IgA. Interestingly, we found that IgA-escape initially occurs via a predictable narrow spectrum of Salmonella O-antigen variants that are fitness-neutral in naïve hosts. This could be attributed both to phase-variation, and to loss-of-function mutations in O-antigen-modifying enzymes. Via a vaccination regimen that simultaneously induced IgA against all observed O-antigen variants, rapid bacterial evolution could be switched from a hindrance into an advantage. Here, IgA generated a selective pressure resulting in fixation of mutations causing loss of polymerized O-antigen. When transmitted into naive hosts, these short O-antigen variants display compromised fitness and virulence, i.e. IgA-mediated pressure generates an evolutionary trade-off. Rational induction of IgA specificities that set “evolutionary traps” could reduce virulent enteropathogen reservoirs, even when sterilizing immunity cannot be achieved. This may become a powerful tool in the management of increasingly drug-resistant enteropathogenic bacteria.
<title>Internet's impact on publishing</title> (1997)

In 1990, the first monochrome print-on-demand (POD) systems wee successfully brought to market. Subsequent color versions have been less successful, in my view mostly because they require a different workflow than traditional systems and the highly skilled specialists have not been trained. This hypothesis is based on the observation that direct-to-plate systems for short run printing, which do not require a new workflow, are quite successful in the market place. The internet and the World Wide Web are the enabling technologies that are fostering a new print model that is very likely to replace color POD before the latter can establish itself. In this model the consumers locate the material they desire from a contents provider, pay through a digital cash clearinghouse, and print the material at their own cost on their local printer. All the basic technologies for this model are in place; the main challenge is to make the workflow sufficiently robust for individual use.