gebhart/patrepeval huggingface dataset:
Homogeneous Amplification and Variant Detection by Fluorescent Hybridization Probes (2000)

Over the past 5 years, there has been substantial progress in sequencing the human genome and identifying clinically significant genes (1). Genes that are clinically significant are diagnostic or prognostic for disease and/or helpful in guiding treatment. Unknown gene mutations, resulting from germline or somatic DNA alterations, are initially defined by direct sequencing. Other methods that detect specific mutations can then be used for higher throughput.

Recently developed instrumentation and techniques for genotyping combine PCR and fluorescent hybridization probes for homogeneous amplification and product analysis within 1 h (2)(3)(4)(5). The target is amplified from genomic DNA by rapid-cycle PCR (6) with all the reagents needed for genotyping present from the beginning of the reaction. After 15–20 min, PCR is completed and the instrument automatically begins a melting curve protocol. Fluorescence is acquired continuously as the reaction is slowly heated and genotypes are identified by their characteristic melting curves. Because amplification and genotyping occur in the same instrument in a closed tube format, there is no concern of contamination by previously amplified product.

Hybridization probes are oligonucleotides that are singly labeled with a donor or acceptor fluorophore. During probe/target hybridization, these fluorophores are brought into close proximity and fluorescence resonance energy transfer occurs. Two hybridization probe schemes for fluorescent resonance energy transfer have been developed (3)(5). One method uses a 3′-labeled hybridization probe designed to anneal to a PCR strand …
Cooperative and Competitive Occlusion of Organic and Inorganic Structure-Directing Agents within Chabazite Zeolites Influences Their Aluminum Arrangement (2020)

We combine experiment and theory to investigate the cooperation or competition between organic and inorganic structure-directing agents (SDAs) for occupancy within microporous voids of chabazite (CHA) zeolites and to rationalize the effects of SDA siting on biasing the framework Al arrangement (Al-O(-Si-O)<sub><i>x</i></sub>-Al, <i>x</i> = 1-3) among CHA zeolites of essentially fixed composition (Si/Al = 15). CHA zeolites crystallized using mixtures of TMAda<sup>+</sup> and Na<sup>+</sup> contain one TMAda<sup>+</sup> occluded per cage and Na<sup>+</sup> co-occluded in an amount linearly proportional to the number of 6-MR paired Al sites, quantified by Co<sup>2+</sup> titration. In contrast, CHA zeolites crystallized using mixtures of TMAda<sup>+</sup> and K<sup>+</sup> provide evidence that three K<sup>+</sup> cations, on average, displace one TMAda<sup>+</sup> from occupying a cage and contain predominantly 6-MR isolated Al sites. Moreover, CHA crystallizes from synthesis media containing more than 10-fold higher inorganic-to-organic ratios with K<sup>+</sup> than with Na<sup>+</sup> before competing crystalline phases form, providing a route to decrease the amount of organic SDA needed to crystallize high-silica CHA. Density functional theory calculations show that differences in the ionic radii of Na<sup>+</sup> and K<sup>+</sup> determine their preferences for siting in different CHA rings, which influences their energy to co-occlude with TMAda<sup>+</sup> and stabilize different Al configurations. Monte Carlo models confirm that energy differences resulting from Na<sup>+</sup> or K<sup>+</sup> co-occlusion promote the formation of 6-MR and 8-MR paired Al arrangements, respectively. These results highlight opportunities to exploit using mixtures of organic and inorganic SDAs during zeolite crystallization in order to more efficiently use organic SDAs and influence framework Al arrangements.
Parallelism-Aware Batch Scheduling: Enabling High-Performance and Fair Shared Memory Controllers (2009)

Uncontrolled interthread interference in main memory can destroy individual threads' memory-level parallelism, effectively serializing the memory requests of a thread whose latencies would otherwise have largely overlapped, thereby reducing single-thread performance. The parallelism-aware batch scheduler preserves each thread's memory-level parallelism, ensures fairness and starvation freedom, and supports system-level thread priorities.
The dispersion-OTDR (2003)

We have developed an optical time domain reflectometer (OTDR)-like instrument that measures dispersion as a function of distance along fiber spans of up to 50 km, quickly and with great accuracy. Its range is extended to at least 75 km with the use of Raman gain.
Post-CMOS process for high-aspect-ratio monolithically integrated single crystal silicon microstructures (2005)

A novel modular fabrication process for bulk integrated single-crystal-silicon microstructures designed and manufactured in a post-CMOS process is presented in this paper, which can increase the accuracy and reliability of MEMS sensors as well as lower the fabricating cost. The process involves the conventional CMOS circuit formation, the electrical isolation trench etching and refilling, backside silicon etching, interconnection formation, and structure releasing. The performance of integrated Schottky diodes was tested to have reverse leakage of 10/sup -7/A, and breakdown voltage of 57V. A new method for fabricating void-free isolation trenches is also developed. The resistance of void-free isolation trench is more than 10/sup 12//spl Omega/. The influence of LPCVD high temperature on the doping distribution is simulated.
Adaptive output feedback control of a class of multi-input multi-output systems using neural networks (2004)

For a class of uncertain multi-input multi-output non-linear systems an adaptive output feedback control methodology is developed using linearly parameterized neural networks. The neural network operates over a tapped delay line of memory units, comprised of system input/output signals. The adaptive laws for neural network parameters are written in terms of a linear observer of the nominal system's error dynamics. Ultimate boundedness of the error signals is shown through Lyapunov's direct method. Simulations illustrate the theoretical results.
Automating statistics management for query optimizers (2001)

Statistics play a key role in influencing the quality of plans chosen by a database query optimizer. In this paper, we identify the statistics that are essential for an optimizer. We introduce novel techniques that help significantly reduce the set of statistics that need to be created without sacrificing the quality of query plans generated. We discuss how these techniques can be leveraged to automate statistics management in databases. We have implemented and experimentally evaluated our approach on Microsoft SQL Server 7.0.
<title>Use of holography for imaging through inhomogeneous media</title> (1993)

Electronic holography for imaging through biological tissue is described. A number of processes are given, including the holographic implementation of the first arriving light method, the broad source method, as well as variations on these methods. The equipment is discussed in some detail, including the camera-computer interactions.
13 EMBRYONIC CELIAC ANTIGENS (ECA). (1996)

The antigens reactive to serum anti-endomysial antibodies and anti-reticulin antibodies were isolated from human placenta following our observation that sera from patients with celiac disease (CD) binds to placenta tissue sections. We designated the antigens as “Embryonic Celiac Antigens” (ECA). Microscopic evaluation of placenta tissue sections indicate that the antigens were expressed on the cell membrane and cytoplasm of the trophoblast cells. Placental cells grown in primary culture also express the ECA. However, ECA was not found in the culture media. Proteins were extracted from lysed cultured cells, and identified by SDS-PAGE gel electrophoresis and western blotting. Nine protein molecules were bound to the IgA of CD patients. The molecular weights ranged from 22kd - 110kd. High pressure liquid chromatography (HPLC) was used to purify these single proteins. 110kd protein inhibited binding of CD patients IgA to rat kidney (reticulin like antigen). The 65kd protein, on the other hand, inhibited the binding of IgA to the monkey esophagus (endomysium like antigen). Both protein molecules had 60% of cross inhibition activity. The 110kd protein is a heat labile protein and tends to break down to a 55kd molecule without loosing its activity. Low molecular weight proteins (ranging 22kd-45kd) inhibited binding of celiac patient sera to gliadin. High resolution two dimensional electrophoresis demonstrated that the above antigen have isoelectricpoint between 5.1 - 5.9 ECA (110kd; 65kd and 55kd). Protein isolation method; Proteins collected from the cultured placental cell lysate were applied to a DEAE sephadex column and subsequently to Gel Chromatography Sephacryl S-200 HR Column. The ECA does not bind to the IgA or IgG contained in the sera of normal patients, those with inflammatory bowel disease or other immunologic conditions. These findings indicate that celiac antigens are expressed during fetal development. Their investigation may offer insight into the pathomechanism of celiac disease and provide a new tool for diagnosis of the condition.
<title>Fast and compact adaptive mirror</title> (1997)

Adaptive mirrors are used in laser material processing machines in order to control the propagation of the raw beam through the beam-guiding system as well as the geometry of the focused beam. As modern machine concepts for laser material processing tend to operate at increasing working speed, fast and lightweight adaptive mirrors with excellent optical properties and a large range of radius variation are needed. In this paper, a new approach for a fast, compact and lightweight adaptive mirror is discussed. In the approach the deformation of a circular plate under pressure is used. The pressure is generated by a small piezoelectric actuator which presses against a small water layer behind the mirror plate, thereby deforming it. The deformation of the mirror surface is almost parabolic across a large area of the overall surface, which results in a high optical quality even at large deformations. Based on this concept, an adaptive mirror was designed that can be operated at a bandwidth up to 400 Hz at maximum deformation (which results in a range of radius-variation from -20 m to +20 m) and about 2 kHz at smaller deformations. Furthermore, extensive investigations have been performed using FEM analysis of the adaptive mirrors in order to understand the influence of mirror thickness, diameter and operating pressure on the deformation and the resulting radii of curvature. The result is an analytical method which allows to calculate the mirror dimensions in order to achieve a desired characteristic of deformation for given beam diameters.
Effect of heat treatment on stress corrosion of Alloy 718 in pressurized-water-reactor primary water (1992)

Stress corrosion cracking (SCC) tests were conducted in 360{degrees}C pressurized-water-reactor (PWR) primary water using alloy 718 in various heat treatment conditions. Alloy X-750 in the HTH condition and an experimental heat of an alloy 718 variation, Hicoroy, were also tested for comparison. Fatigue-precracked, 12.5-mm-thick compact fracture specimens were subjected to a constant extension rate of 1.3 x 10{sup {minus}9} m/s. Crack growth rate was measured during testing using a reversing DC potential drop technique. Results in the form of SCC crack growth rate versus applied stress intensity demonstrate that the SCC resistance of alloy 718 in the PWR primary-side environment can be improved by changes in heat treatment.
CD40-targeted adenoviral GM-CSF gene transfer enhances and prolongs the maturation of human CML-derived dendritic cells upon cytokine deprivation (2003)

Vaccination with autologous leukaemia-derived dendritic cells (DC) presents an adjuvant treatment option for chronic myeloid leukaemia (CML). Here, we show that high-efficiency CD40-targeted adenoviral gene transfer of GM-CSF to CML-derived DC induces long-lived maturation in the absence of exogenous cytokines and may thus ensure protracted stimulation of CML-specific T cells upon vaccination.
Decreased burden among caregivers of patients with Parkinson’s disease psychosis (PDP) treated with pimavanserin, a selective 5-HT2A inverse agonist (P6.044) (2015)

OBJECTIVE: To determine the effect of pimavanserin, a selective 5-HT2A inverse-agonist, on caregiver burden. BACKGROUND: Parkinson's Disease Psychosis (PDP) is associated with functional and cognitive decline, morbidity/mortality, and increased caregiver burden often leading to early institutionalization. Pimavanserin is a potent 5-HT2A inverse-agonist being developed for PDP. Unlike current antipsychotics, it has no dopaminergic, histaminergic, adrenergic or muscarinic activity. Pimavanserin 40mg demonstrated improvements in psychosis, nighttime sleep and daytime wakefulness in randomized controlled trials (RCTs) in PDP. RCT completers could roll into a long-term open-label study (OLS). A consented caregiver had to attend all RCT and OLS visits and complete the Zarit 22-item caregiver burden scale (CBS). METHOD: In an integrated analysis of the 6-week RCTs, CBS scores were evaluated among caregivers of 268 PDP patients in N.America who received pimavanserin 40mg or placebo. Most caregivers were spouses or other family. Continued effect was assessed in the OLS. RESULTS: Mean baseline (pretreatment) CBS scores were 30.6 for placebo (N=133) and 28.8 for pimavanserin 40mg (N=135). Significant improvement in burden was observed for the pimavanserin group (-4.8 points) over placebo (-1.1 points) at 6 weeks (p=0.0009). These results did not strongly correlate with psychosis or sleep improvements, suggesting broader benefits of pimavanserin not captured by other study measures. More caregiver benefit was observed for patients with less dementia and less co-morbid disease. In the OLS, CBS scores remained generally stable (+1-point difference) for up to 9 months.CONCLUSIONS: Improvements on caregiver burden among pimavanserin-treated people with PDP, provide important context around the benefit-risk profile of this selective 5-HT2A inverse-agonist that has shown significant benefit on psychosis and sleep and a well-tolerated safety profile.
PCR identification of four medically important Candida species by using a single primer pair (1994)

A single pair of primers was used in a PCR assay to amplify and identify the DNAs from four medically important Candida species: C. albicans, C. parapsilosis, C. tropicalis, and C. (Torulopsis) glabrata. The report describes the first successful amplification of a chitin synthase-specific fragment from the four Candida species responsible for more than 90% of all cases of neonatal candidemia. The primer pair sequence was based on that from the C. albicans chitin synthase gene, CHS1 (J. Au-Young and P.W. Robbins, Mol. Microbiol. 4:197-207, 1990). Each of the four amplified products is a single band of a different size. The DNA sequence of each PCR product was determined, and four species-specific probes were synthesized. The DNAs from as few as 10 organisms in 100 microliters of plasma could be detected after amplification and Southern blot analysis. In a retrospective study of 27 paired blood samples from 16 patients with culture-proven candidemia, PCR analysis was successful at detecting and correctly identifying to the species level 26 of the 27 Candida isolates. The speed and accuracy of this PCR-based technology make it a very powerful tool for detecting and diagnosing candidemia. Implementation of this assay for analyzing blood samples should result in the more timely treatment of neonatal candidemia, thereby reducing morbidity and mortality.
Quantifying tissue viscoelasticity using optical coherence elastography and the Rayleigh wave model (2016)

This study demonstrates the feasibility of using the Rayleigh wave model (RWM) in combination with optical coherence elastography (OCE) technique to assess the viscoelasticity of soft tissues. Dispersion curves calculated from the spectral decomposition of OCE-measured air-pulse induced elastic waves were used to quantify the viscoelasticity of samples using the RWM. Validation studies were first conducted on 10% gelatin phantoms with different concentrations of oil. The results showed that the oil increased the viscosity of the gelatin phantom samples. This method was then used to quantify the viscoelasticity of chicken liver. The Young’s modulus of the chicken liver tissues was estimated as E=2.04±0.88??kPa with a shear viscosity ?=1.20±0.13??Pa?s. The analytical solution of the RWM correlated very well with the OCE-measured phased velocities (R2=0.96±0.04). The results show that the combination of the RWM and OCE is a promising method for noninvasively quantifying the biomechanical properties of soft tissues and may be a useful tool for detecting disease.
Five New <i>Ent</i>-Atisene Glycosides From <i>Stevia rebaudiana</i> (2019)

Five new ent-atisene diterpene glycosides (1-5) have been isolated from Stevia rebaudiana Bertoni. This adds to a list of only 2 new ent-atisene diterpene glycosides isolated previously from S. rebaudiana. Diterpene glycosides isolated from S. rebaudiana, such as the rebaudiosides, are typically associated with the ent-kaurene core and glycosylation at the C-13 and C-19 positions. Extensive application of nuclear magnetic resonance spectroscopy techniques ( 1 H, 13 C, 1D-TOCSY, COSY, HSQC-DEPT, HMBC, and ROESY) as well as high-resolution mass spectrometry demonstrated that the ent-atisenes 1 to 5 had glycosylation patterns identical to rebaudiosides J, N, O, K, and T, respectively. We have named these compounds stevatisene J, N, O, K, and T, respectively.
Zeolite Rho: a highly selective adsorbent for CO<sub>2</sub>/CH<sub>4</sub>separation induced by a structural phase modification (2011)

Zeolite Rho is able to successfully separate CO(2) from CH(4) with the highest selectivity ever observed on the basis of pore diameter and surface polarity. The adsorption of CO(2) provokes structural changes in the zeolite Rho.
Novel Variants of Angiotensin Converting Enzyme-2 of Shorter Molecular Size to Target the Kidney Renin Angiotensin System (2019)

ACE2 is a monocarboxypeptidase which generates Angiotensin (1-7) from Angiotensin II (1-8). Attempts to target the kidney Renin Angiotensin System using native ACE2 to treat kidney disease are hampered by its large molecular size, 100 kDa, which precludes its glomerular filtration and subsequent tubular uptake. Here, we show that both urine and kidney lysates are capable of digesting native ACE2 into shorter proteins of ~60-75 kDa and then demonstrate that they are enzymatically very active. We then truncated the native ACE2 by design from the C-terminus to generate two short recombinant (r)ACE2 variants (1-605 and 1-619AA). These two truncates have a molecular size of ~70 kDa, as expected from the amino acid sequence and as shown by Western blot. ACE2 enzyme activity, measured using a specific substrate, was higher than that of the native rACE2 (1-740 AA). When infused to mice with genetic ACE2 deficiency, a single i.v. injection of 1-619 resulted in detectable ACE2 activity in urine, whereas infusion of the native ACE2 did not. Moreover, ACE2 activity was recovered in harvested kidneys from ACE2-deficient mice infused with 1-619, but not in controls (23.1 ± 4.3 RFU/µg creatinine/h and 1.96 ± 0.73 RFU/µg protein/hr, respectively). In addition, the kidneys of ACE2-null mice infused with 1-619 studied ex vivo formed more Ang (1-7) from exogenous Ang II than those infused with vehicle (AUC 8555 ± 1933 vs. 3439 ± 753 ng/mL, respectively, <i>p</i> < 0.05) further demonstrating the functional effect of increasing kidney ACE2 activity after the infusion of our short ACE2 1-619 variant. We conclude that our novel short recombinant ACE2 variants undergo glomerular filtration, which is associated with kidney uptake of enzymatically active proteins that can enhance the formation of Ang (1-7) from Ang II. These small ACE2 variants may offer a potentially useful approach to target kidney RAS overactivity to combat kidney injury.
Circulating FGF19 closely correlates with bile acid synthesis and cholestasis in patients with primary biliary cirrhosis (2017)

These findings demonstrate that the regulation of BA synthesis in response to cholestasis is primarily controlled by circulating FGF19 and that under cholestatic conditions, the FGF19-BA synthesis feedback mechanism remains intact. Administering FGF19, or suitable mimetic, as a pharmacological intervention to increase circulating levels of FGF19 and suppress BA synthesis by inhibiting CYP7A1 gene expression is likely to provide therapeutic benefits for many PBC patients.
Secure transcoding of internet content (2002)

In this paper, we introduce a secure transcoding framework that enables network intermediaries such as proxies to transcode multimedia data without violating end-to-end security guarantees. In our approach, an encoder decomposes a data stream at the source into multiple streams, encrypts each stream independently, and annotates each stream with clear-text metadata. An intermediary performs transcoding by prioritizing the data streams based only on the clear-text metadata, and then dropping lower priority streams. The destination can then decrypt the remaining received streams and recombine them into the transcoded output stream. Our solution offers true end-to-end security since there is no decryption and re-encryption of the data stream midway. As a result, the proxy/intermediary may employ compression-based transcoding of encrypted multimedia data to improve speed of delivery over slow access links without having to decrypt the data.
Functionality Selection Principle for High Voltage Lithium-ion Battery Electrolyte Additives (2017)

A new class of electrolyte additives based on cyclic fluorinated phosphate esters was rationally designed and identified as being able to stabilize the surface of a LiNi<sub>0.5</sub>Mn<sub>0.3</sub>Co<sub>0.2</sub>O<sub>2</sub> (NMC532) cathode when cycled at potentials higher than 4.6 V vs Li<sup>+</sup>/Li. Cyclic fluorinated phosphates were designed to incorporate functionalities of various existing additives to maximize their utilization. The synthesis and characterization of these new additives are described and their electrochemical performance in a NMC532/graphite cell cycled between 4.6 and 3.0 V are investigated. With 1.0 wt % 2-(2,2,2-trifluoroethoxy)-1,3,2-dioxaphospholane 2-oxide (TFEOP) in the conventional electrolyte the NMC532/graphite cell exhibited much improved capacity retention compared to that without any additive. The additive is believed to form a passivation layer on the surface of the cathode via a sacrificial polymerization reaction as evidenced by X-ray photoelectron spectroscopy (XPS) and nuclear magnetic resonsance (NMR) analysis results. The rational pathway of a cathode-electrolyte-interface formation was proposed for this type of additive. Both experimental results and the mechanism hypothesis suggest the effectiveness of the additive stems from both the polymerizable cyclic ring and the electron-withdrawing fluorinated alkyl group in the phosphate molecular structure. The successful development of cyclic fluorinated phosphate additives demonstrated that this new functionality selection principle, by incorporating useful functionalities of various additives into one molecule, is an effective approach for the development of new additives.
Fine-Grained All-Optical Switching Based on Optical Time Slice Switching for Hybrid Packet-OCS Intra-Data Center Networks (2016)

We propose a hybrid packet-OCS intra-datacenter network architecture with bufferless sub-wavelength all-optical time slice switching enabled by high-precision time synchronization. We experimentally demonstrate flex-capacity sub-wavelength circuit establishment among the ToR switches without buffers and contention.