gebhart/patrepeval huggingface dataset:
In situ DNA synthesis on glass substrate for microarray fabrication using self-focusing acoustic transducer (2006)

This paper presents a droplet-ejection-based technique for synthesizing deoxyribonucleic acid (DNA) sequences on different substrates, such as glass, plastic, or silicon. Any DNA sequence can be synthesized by ejecting droplets of DNA bases by a self-focusing acoustic transducer (SFAT) that does not require any nozzles. An SFAT can eject liquid droplets around 3-5 /spl mu/m in diameter, which is significantly smaller than those ejected by commercial ink jet printers and reduces the amount of reagents needed for the synthesis. An array of SFATs is integrated with microchannels and reservoirs for delivery of DNA bases to the SFATs. Poly-l-lysine-coated glass slide is patterned, and is used as a target substrate for in situ synthesis of multiple T bases. The significant advantage of this scheme over some of the existing commercial solutions is that it can allow geneticists to synthesize any DNA sequence within hours using a computer program at an affordable cost in their own labs. This paper describes the concept and scheme of the on-demand DNA synthesis (with an acoustic ejector integrated with microfluidic components) along with the results of an actual DNA synthesis by an SFAT. Note to Practitioners-Deoxyribonucleic acid (DNA) microarrays allow geneticists to monitor the interactions among thousands of genes simultaneously in a chip. There are commercial systems for producing DNA microarrays, but none of them give flexibility to synthesize DNA microarrays on-demand in the geneticist's own lab. Affymetrix's GeneChip technology produces DNA probe sequences premade at Affymetrix with a set of 4n photomasks for n-mers. Other techniques transfer premade DNA sequences to a substrate (glass, plastic, or silicon) through ink-jet printing or contact dispensing. Agilent and Rosetta use their ink-jet printing technology to produce DNA probe sequences at their factories. The ink-jet print heads used for printing microarrays use either piezoelectric or thermal actuation, and eject liquid droplets through nozzles. Thus, the smallest droplet size ejected from these devices depends on the size of the nozzle. The small nozzles are difficult to construct with good uniformity and tend to get clogged. The idea presented in this paper is to develop a microelectromechanical-system (MEMS)-based portable system for synthesizing DNA on different substrates, using nozzleless, heatless, lensless, acoustic droplet ejectors. The future research is to synthesize longer DNA sequences with a combination of different bases, using directional droplet ejectors.
Retroviruses As Genetic Tools to Isolate Transcriptionally Active Chromosomal Regions (1990)

By exploiting the ability of retroviruses to move genes into random sites of mammalian genomes and by exploiting some features of their replication, retrovirus vectors have been developed that select for instances in which the virus integrates into expressed genes. Since integrated proviruses tag transcriptionally active sites, the vectors provide a means to identify and isolate promoters active in different cell types. Furthermore, the viruses may be useful as insertional mutagens, since they select for instances in which integration occurs into expressed sites. This reduces the number of integrants needed to screen for loss of gene function and may enable genes controlling phenotypes in mammalian cells to be isolated.
Micro ion trap mass spectrometry (2004)

Rapid Commun. Mass Spectrom. 1999; 13: 50–53. The dates for some of the references as originally published were in error. Corrected citations are given below:
Fault-Tolerant Flight Control Using One Aerodynamic Control Surface (2018)

This paper considers a statically stable unmanned aircraft that is equipped with only two aerodynamic control surfaces (called elevons) and one tractor-type propeller. A fault in either of the elevons must, therefore, be managed using only the other elevon and the throttle. Because the fault results in an underactuated aircraft, the reconfiguration possibilities are limited. This paper proposes a strategy of using the throttle for total energy control and the single operable elevon for lateral control. This paper then develops a fault-tolerant controller based on this strategy and demonstrates, via multiple flight tests, the autonomous guidance and final approach of this unmanned aircraft in the presence of a stuck elevon fault. The results indicate that it may be possible to control other aerial bodies, including larger aircraft, using one aerodynamic control surface.
An RGD Motif Present in Cadherin 17 Induces Integrin Activation and Tumor Growth (2014)

Little is known about the mechanism of integrin activation by cadherin 17 (CDH17). Here we observed the presence of a tri-peptide motif, RGD, in domain 6 of the human CDH17 sequence and other cadherins such as cadherin 5 and cadherin 6. The use of CDH17 RAD mutants demonstrated a considerable decrease of proliferation and adhesion in RKO and KM12SM colon cancer cells. Furthermore, RGD peptides inhibited the adhesion of both cell lines to recombinant CDH17 domain 6. The RGD motif added exogenously to the cells provoked a change in β1 integrin to an active, high-affinity conformation and an increase in focal adhesion kinase and ERK1/2 activation. In vivo experiments with Swiss nude mice demonstrated that cancer cells expressing the CDH17 RAD mutant showed a considerable delay in tumor growth and liver homing. CDH17 RGD effects were also active in pancreatic cancer cells. Our results suggest that α2β1 integrin interacts with two different ligands, collagen IV and CDH17, using two different binding sites. In summary, the RGD binding motif constitutes a switch for integrin pathway activation and shows a novel capacity of CDH17 as an integrin ligand. This motif could be targeted to avoid metastatic dissemination in tumors overexpressing CDH17 and other RGD-containing cadherins.
Abstract 009: Genetically Modified Probiotics for Oral Delivery of Angiotensin-(1-7) Confers Protection Against Pulmonary Hypertension (2016)

Background: Previous studies have established that activation of the members of the vasoprotective axis of the renin-angiotensin system [Angiotensin Converting Enzyme 2 (ACE2) or Angiotensin-(1-7) (Ang-(1-7))] prevents and arrests progression of pulmonary hypertension (PH) pathophysiology. Our objective in this present study was to generate a probiotic containing Ang-(1-7) and test the hypothesis that oral administration of such a probiotic would provide cardiopulmonary protection against PH. Methods: In this study, we genetically modified the commensal bacterium Lactobacillus paracasei (LP), commonly found in the gut and used as a probiotic, to serve as a live vector for the oral delivery of Ang-(1-7) and investigated its therapeutic potential in attenuating PH. The vectors pTRKH3- ldh -SP-GFP or pTRKH3- ldh -SP-Ang-(1-7) were introduced by electroporation into LP. PH was induced by a single injection of monocrotaline (MCT; 50 mg/Kg s.c) in rats. A subset of animals was orally gavaged every other day for four weeks with 1x10 9 CFU of LP, LP secreting GFP (LP-GFP), or LP secreting Ang-(1-7) (LP-A). Results: Oral feeding of LP-A significantly reduced MCT-induced right ventricular systolic pressure (RVSP) by 43% (Control: 27±1; MCT: 76±8; MCT+LP: 56±6; MCT+LP-GFP: 59±7; MCT+LP-A: 43±3 mmHg) and RV hypertrophy by 33% (Control: 0.25±0.01; MCT: 0.6+0.02; MCT+LP: 0.48±0.04; MCT+LP-GFP: 0.48±0.04; MCT+LP-A: 0.41±0.03). Moreover, LP-A feeding restored cardiac contractility (Control: 2070±95; MCT: 3133±295; LP-A: 2060±119 mmHg/s) and attenuated myocardial fibrosis. These beneficial effects on the cardiopulmonary system were associated with profound changes in gut pathology. MCT-induced PH was associated with an increase in ileum villus length and thickening of proximal colon, and a decrease in goblet cells/villus area, all of which indicate intestinal injury and altered immune status. However, these parameters were significantly attenuated by oral feeding of LP-A. Conclusions: Oral administration of a genetically modified commensal bacterium that can secrete Ang-(1-7) provides cardiopulmonary protection against PH. Thus, delivery of Ang-(1-7) by probiotic means could be considered an innovative therapeutic strategy for PH.
Multichannel discharges in low-pressure rare-gas–mercury mixtures caused by anode oscillation (1980)

Stable formation of a multichannel arc is observed in low-pressure rare-gas–mercury discharges in a concentric tube where a hot cathode is located in the inner tube and two to six anodes are arranged symmetrically in the space between the inner tube and the outer bulb. The discharge current for each discharge channel is found to be deeply modulated at high frequencies by the anode oscillations which take place in a regular, complex sequence depending on the anode configuration. In a discharge tube with two anodes, anode oscillation occurs alternately, causing discharge transfers between the anodes. With three anodes, the discharge transfers take place in a manner similar to a ring counter, as anode oscillations occur in turn in geometrical order. In the four and five anode configurations, oscillations occur sequentially in time, but not sequentially in the anode configuration. In the case of six anodes, stable formation of a multichannel arc is not observed.
Self-referenced spectral interferometry (2009)

A new femtosecond pulses characterization method is presented and experimentally demonstrated. Linear spectral interferometry becomes a self-referenced measurement by the self-creation of a reference pulse using pulse shaping optimization and non linear temporal filtering.
Plasma Insulin-Like Growth Factor-I and Prostate Cancer Risk: A Prospective Study (1998)

No AccessJournal of UrologyUrological Survey: Abstracts: Benign and Malignant Neoplasms of Prostate1 Jul 1998Plasma Insulin-Like Growth Factor-I and Prostate Cancer Risk: A Prospective Study J.M. Chan, M.J. Stampfer, E. Giovannucci, P.H. Gann, J. Ma, P. Wilkinson, C.H. Hennekens, and M. Pollak J.M. ChanJ.M. Chan More articles by this author , M.J. StampferM.J. Stampfer More articles by this author , E. GiovannucciE. Giovannucci More articles by this author , P.H. GannP.H. Gann More articles by this author , J. MaJ. Ma More articles by this author , P. WilkinsonP. Wilkinson More articles by this author , C.H. HennekensC.H. Hennekens More articles by this author , and M. PollakM. Pollak More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(01)63107-0AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Plasma Insulin-Like Growth Factor-I and Prostate Cancer Risk: A Prospective Study." The Journal of Urology, 160(1), p. 267 Department of Epidemiology, Harvard School of Public Health, Department of Medicine, Division of Preventive Medicine, Departments of Medicine, Ambulatory Care and Prevention, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, Department of Preventive Medicine, Northwestern University Medical School, Chicago, Illinois, and Cancer Prevention Unit, Department of Medicine and Oncology, Lady Davis Research Institute of Jewish General Hospital and McGill University, Montreal, Canada© 1998 by American Urological Association, Inc.FiguresReferencesRelatedDetails Volume 160Issue 1July 1998Page: 267 Advertisement Copyright & Permissions© 1998 by American Urological Association, Inc.MetricsAuthor Information J.M. Chan More articles by this author M.J. Stampfer More articles by this author E. Giovannucci More articles by this author P.H. Gann More articles by this author J. Ma More articles by this author P. Wilkinson More articles by this author C.H. Hennekens More articles by this author M. Pollak More articles by this author Expand All Advertisement PDF downloadLoading ...
Extremely high efficient coupling between long range surface plasmon polariton and dielectric waveguide mode (2009)

To connect the surface plasmon polariton (SPP) based devices with the conventional dielectric devices is a significant issue for the further development of SPP and related applications. In this paper, extremely high efficient coupling (&gt;99%) between long range SPP (LRSPP) waveguide mode and TM mode of dielectric waveguide has been demonstrated from a hybrid coupler, which composed of an Au (LRSPP) waveguide and a SiN (dielectric) waveguide. Based on this hybrid coupler, a polarization splitter with pure TM mode output from one arm and TE mode output from the other arm with high TE/TM extinction ratio has been realized.
Highly efficient tabletop optical parametric chirped pulse amplifier at 1 μm (2002)

Optical parametric chirped pulse amplification (OPCPA) is a scalable technology for ultrashort pulse amplification. Its major advantages include design simplicity, broad bandwidth, tunability, low B-integral, high contrast, and high beam quality. OPCPA is suitable both for scaling to high peak power as well as high average power. We describe the amplification of stretched 100 fs oscillator pulses in a three-stage OPCPA system pumped by a commercial, single- longitudinal-mode, Q-switched Nd:YAG laser. The stretched pulses were centered around 1054 nm with a FWHm bandwidth of 16.5 nm and had an energy of 0.5nJ. Using our OPCPA system, we obtained an amplified pulse energy of up to 31 mJ at a 10 Hz repetition rate. The overall conversion efficiency from pump to signal is 6%, which is the highest efficiency obtained with a commercial tabletop pump laser to date. The overall conversion efficiency is limited due to the finite temporal overlap of the seed (3 ns) with respect to the duration of the pump (8.5 ns). Within the temporal window of the seed pulse the pump to signal conversion efficiency exceeds 20%. Recompression of the amplified signal was demonstrated to 310 fs, limited by the aberrations initially present in the low energy seed imparted by the pulse stretcher. The maximum gain in our OPCPA system is 6x10<SUP>7</SUP>, obtained through single passing of 40 mm of beta- barium borate. We present data on the beam quality obtained from our system (M<SUP>2</SUP>=1.1). This relatively simple system replaces a significantly more complex Ti:sapphire regenerative amplifier-based CPA system used in the front end of a high energy short pulse laser. Future improvement will include obtaining shorter amplified pulses and higher average power.
Quinic Acid Derivatives as Sialyl Lewis<sup>x</sup>-Mimicking Selectin Inhibitors:  Design, Synthesis, and Crystal Structure in Complex with E-Selectin (2005)

A search for noncarbohydrate sLe(x) mimics led to the development of quinic acid derivatives as selectin inhibitors. At Wyeth we solved the first cocrystal structure of a small molecule, quinic acid, with E-selectin. In the cocomplex two hydroxyls of quinic acid mimic the calcium-bound fucose of the tetrasaccharide sLe(x). The X-ray structure, together with structure based computational methods, was used to design quinic acid based libraries that were synthesized and evaluated for their ability to block the interaction of sLex with P-selectin. A large number of analogues were prepared using solution-phase parallel synthesis. Selected compounds showed decrease in leukocyte rolling in the IVM mouse model. Compound 2 inhibited neutrophil influx in the murine TIP model and demonstrated good plasma exposure.
Novel Projection Exposure System Using Gradient-Index Lens Array (2008)

A novel low-cost projection exposure system for printing rough patterns with a width of approximately 10 µm was proposed and its feasibility was verified. In the novel exposure system, a gradient-index (GRIN) lens array was used as the projection optics. The GRIN lens array projects the same-size erect image of the mask patterns onto the wafers. Therefore, arbitrary patterns on a large mask are replicated on a wafer without using a large projection lens by simply scanning the lens array across the whole mask field. Optical lithography for printing rough patterns with widths of 1–10 µm in large areas is widely applied in fabricating various micro-mechanical components. Since the production volumes are usually small, however, expensive optical lithography systems are not easily adopted for production. The new exposure system will provide new advantages for such lithography applications. When the GRIN lens array was fixed steady, line-and-space (L&S) patterns with a line width of 20 µm were printed in spite of the guaranteed low resolution specification of approximately 80 µm. In addition, up to 2.5 µm L&S patterns were locally resolved. Localized high resolution and the uneven resolution performance mainly depend on the periodical light intensity distribution corresponding to the lens array structure. This intensity distribution was greatly improved by scanning the lens array in the direction of the lens array, and averaging the intensity irregularity. By improving the light intensity distribution to be homogeneous, 10 µm L&S patterns were uniformly printed in the whole exposure area.
Demonstration of 640x512 pixel four-band Quantum Well Infrared Photodetector (QWIP) focal plane array (2002)

We have demonstrated the first monolithic spatially separated four-band 640x512 pixel QWIP focal plane array.
Design and development of a MEMS capacitive bending strain sensor (2006)

The design, modeling, fabrication and testing of a MEMS-based capacitive bending strain sensor utilizing a comb drive is presented. This sensor is designed to be integrated with a telemetry system that will monitor changes in bending strain to assist with the diagnosis of spinal fusion. ABAQUS/CAE finite-element analysis (FEA) software was used to predict sensor actuation, capacitance output and avoid material failure. Highly doped boron silicon wafers with a low resistivity were fabricated into an interdigitated finger array employing deep reactive ion etching (DRIE) to create 150 µm sidewalls with 25 µm spacing between the adjacent fingers. The sensor was adhered to a steel beam and subjected to four-point bending to mechanically change the spacing between the interdigitated fingers as a function of strain. As expected, the capacitance output increased as an inverse function of the spacing between the interdigitated fingers. At the unstrained state, the capacitive output was 7.56 pF and increased inversely to 17.04 pF at 1571 µε of bending strain. The FEA and analytical models were comparable with the largest differential of 0.65 pF or 6.33% occurring at 1000 µε. Advantages of this design are a dice-free process without the use of expensive silicon-on-insulator (SOI) wafers.
Multikilohertz Pockels cell driver (1985)

We have developed a Pockels driver, based on field-effect transistors and a microwave tube. This system, capable of generating double voltage steps, operates reliably at repetition rates as high as 10 kHz.
Hafnium oxide gate dielectrics on sulfur-passivated germanium (2006)

Sulfur passivation of Ge(100) is achieved using aqueous ammonium sulfide (NH4)2S(aq). The passivation layer is largely preserved after atomic layer deposition of the high-κ dielectric material HfO2 when sufficiently low growth temperatures (e.g., 220°C) are employed. Oxygen incorporation is moderate and results in an electrically passivating GeOS interface layer. The HfO2∕GeOS∕Ge gate stack exhibits lower fixed charge and interface state density than a more conventional HfO2∕GeON∕Ge gate stack fabricated via an ammonia gas treatment.
Integrated ARROW waveguides for gas/liquid sensing (2004)

We present integrated antiresonant reflecting optical (ARROW) structures with hollow cores as a new paradigm for optical sensing of gases and liquids. ARROW waveguides with micron-sized hollow cores allow for single-mode propagation in low-index non-solid core materials where conventional index guiding is impossible. We review design, fabrication and optical characterization of these devices for possible applications in chemical sensing, single molecule fluorescence and Raman spectroscopy, flow cytometry, and pollution monitoring of picoliter to nanoliter volumes. We describe how to determine and control the waveguide loss and dispersion of the ARROW waveguides and design optimization for realistic structures that are compatible with the fabrication constraints. The technology to realize hollow-core waveguides using conventional silicon microfabrication and sacrificial core layers is discussed. We present the first demonstration of waveguiding in integrated ARROW waveguides with both hollow and liquid cores. Single-mode propagation with mode areas as small as 6mm2 and volumes down to 15 picoliters is observed and the loss characteristics of the waveguides are determined. The observation of fluorescence from dye molecules with concentrations of 10 nmol/l is described. Higher-level integration towards compact, planar, and massively parallel sensors on a chip is discussed.
Isoenzymes of Pig‐Liver Esterase Reveal Striking Differences in Enantioselectivities (2007)

An esterase toolbox: A set of isoenzymes of pig liver esterases (PLE) is identified, cloned, and overexpressed in E. coli. They show striking differences in enantioselectivity and enantiopreference in the kinetic resolution of acetates of secondary alcohols as well as the desymmetrization of cis-3,5-diacetoxycyclopent-1-ene to 1 a and 1 b (see picture: enantiopreference of the new isoenzymes and a commercial PLE isoenzyme mixture). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z703256_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
A Dual Band 1.8GHz/900MHz, 750kb/s GMSK Transmitter Utilizing a Hybrid PFD/DAC Structure for Reduced Broadband Phase Noise (2005)

This paper presents the key circuits of a 1 MHz bandwidth, 750 kb/s GMSK transmitter. The fractional-N synthesizer forming the basis of the transmitter uses a combined phase-frequency detector (PFD) and digital-to-analog converter (DAC) circuit element to obtain > 28 dB high frequency noise reduction when compared to classical /spl Sigma//spl Delta/ frequency synthesis. This large reduction in phase noise makes high bandwidth, low noise (-154 dBc/Hz @ 20 MHz offset for 3.565 GHz output) synthesis possible, allowing direct modulation transmission of GMSK data at 750 kb/s.
Presurgical Maggot Debridement of Soft Tissue Wounds Is Associated with Decreased Rates of Postoperative Infection (2004)

Postoperative complications were assessed for all patients who received presurgical maggot debridement therapy (MDT) and for a matched group of patients who did not. Ten wounds were debrided by maggots within 1-17 days prior to surgical closure. Debridement was effective in all cases, and there were no postoperative wound infections. Six (32%) of 19 wounds not treated presurgically with MDT developed postoperative wound infections (95% CI, 10%-54%; P<.05). Presurgical MDT was effective in preparing the wound bed for surgical closure, without increased risk of postsurgical wound infection.
An electrooptic intensity modulator with improved linearity (1991)

A highly linear electrooptic modulator has been designed, fabricated, and evaluated. The design of this modulator consists of only a simple modification to the directional coupler. Two-tone testing has demonstrated that, for an optical modulation depth of 30% per channel, the third-order intermodulation distortion is more than 30 dB lower than that of the conventional directional coupler or Mach-Zehnder modulators. This improvement was not observed to be accompanied by any increase in second harmonic distortion. Also included are results of two-tone computer simulations which predict the improvement in linearity of this device for a range of modulation depths.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>