gebhart/patrepeval huggingface dataset:
Effects of human papillomavirus type 18-specific antisense oligonucleotides on the transformed phenotype of human carcinoma cell lines. (1993)

DNA of human papillomavirus type 18 is present in several human cancer cell lines that were derived from oral or cervical tumors, and it is known that several features of the transformed phenotype can be inhibited by expression of antisense RNA to human papillomavirus (HPV). The present study was performed to find out whether antisense oligonucleotides were also inhibitory. Synthetic oligonucleotides were made that were complementary to regions of the start codons of the E6 and E7 genes of HPV-18. These were added to cultures of the oral cancer cell line 1483 and the cervical cancer cell line C4-1, each of which contain DNA of HPV-18. As controls we used the oral cancer cell line 183 and the monkey kidney cell line Vero, which do not contain HPV. Anti-E6 and anti-E7 oligonucleotides, in concentrations between 1 and 5 microM, significantly inhibited the growth of the 1483 and C4-1 cells, but not the 183 or Vero cell lines. Treatment of the 1483 cells with a combination of 2.5 microM of each of the antisense oligonucleotides was a more effective inhibitor than 5 microM of either one used alone. Antisense oligonucleotides had no effect on the ability of 1483 cells to form foci in soft agar, nor on their plating efficiency or serum requirements. Microscopic examination of 1483 cells showed that the antisense E7 oligonucleotide produced cell-rounding, detachment from the surface of the culture flask, and cell death, while the antisense E6 oligonucleotide had none of these effects. Random-sequence oligonucleotides had no effects of any type on any cells that were growing in culture. However, if random-sequence oligonucleotides were added to cells at the time they were passed to a new culture vessel, they produced severe nonspecific toxic effects. These results show that the use of synthetic oligonucleotides is an effective way of producing antisense-mediated changes in the behavior of human cancer cells that contain DNA of HPV-18.
RobustSTL: A Robust Seasonal-Trend Decomposition Algorithm for Long Time Series (2019)

Decomposing complex time series into trend, seasonality, and remainder components is an important task to facilitate time series anomaly detection and forecasting. Although numerous methods have been proposed, there are still many time series characteristics exhibiting in real-world data which are not addressed properly, including 1) ability to handle seasonality fluctuation and shift, and abrupt change in trend and reminder; 2) robustness on data with anomalies; 3) applicability on time series with long seasonality period. In the paper, we propose a novel and generic time series decomposition algorithm to address these challenges. Specifically, we extract the trend component robustly by solving a regression problem using the least absolute deviations loss with sparse regularization. Based on the extracted trend, we apply the the non-local seasonal filtering to extract the seasonality component. This process is repeated until accurate decomposition is obtained. Experiments on different synthetic and real-world time series datasets demonstrate that our method outperforms existing solutions.
Development of metabolic and inflammatory mediator biomarker phenotyping for early diagnosis and triage of pediatric sepsis (2015)

In children ages 2-17 years, combining metabolomic and inflammatory protein mediator profiling early after presentation may differentiate children with sepsis requiring care in a PICU from children with or without sepsis safely cared for outside a PICU. This may aid in making triage decisions, particularly in an ED without pediatric expertise. This finding requires validation in an independent cohort.
Carrier-Resolved Photo-Hall Effect: Unlocking a 140-year-old secret in Hall effect (2020)

Majority and minority carrier properties such as type, density and mobility represent fundamental yet difficult to access parameters governing semiconductor device performance, most notably solar cells. Obtaining this information simultaneously under light illumination would unlock many critical parameters such as recombination lifetime, recombination coefficient, and diffusion length; while deeply interesting for optoelectronic devices, this goal has remained elusive. We demonstrate here a new carrier-resolved photo-Hall technique that rests on a new equation relating hole-electron mobility difference (Δμ), Hall coefficient ( H), and conductivity ( σ), and a rotating parallel dipole line ac-field Hall system with Fourier/lock-in detection for clean Hall signal measurement [1]. We successfully apply this technique to recent world-record-quality perovskite film and map the results against varying light intensities, demonstrating unprecedented simultaneous access to the above-mentioned parameters.
Long-Term Immunity to Lethal Acute or Chronic Type II<i>Toxoplasma gondii</i>Infection Is Effectively Induced in Genetically Susceptible C57BL/6 Mice by Immunization with an Attenuated Type I Vaccine Strain (2009)

C57BL/6 (B6) mice are genetically highly susceptible to chronic type II Toxoplasma gondii infections that invariably cause lethal toxoplasmic encephalitis. We examined the ability of an attenuated type I vaccine strain to elicit long-term immunity to lethal acute or chronic type II infections in susceptible B6 mice. Mice immunized with the type I cps1-1 vaccine strain were not susceptible to a lethal (100-cyst) challenge with the type II strain ME49. Immunized mice challenged with 10 ME49 cysts exhibited significant reductions in brain cyst and parasite burdens compared to naive mice, regardless of the route of challenge infection. Remarkably, cps1-1 strain-immunized B6 mice chronically infected with ME49 survived for at least 12 months without succumbing to the chronic infection. Potent immunity to type II challenge infections persisted for at least 10 months after vaccination. While the cps1-1 strain-elicited immunity did not prevent the establishment of a chronic infection or clear established brain cysts, cps1-1 strain-elicited CD8(+) immune T cells significantly inhibited recrudescence of brain cysts during chronic ME49 infection. In addition, we show that uracil starvation of the cps1-1 strain induces early markers of bradyzoite differentiation. Collectively, these results suggest that more effective immune control of chronic type II infection in the genetically susceptible B6 background is established by vaccination with the nonreplicating type I uracil auxotroph cps1-1 strain.
Neurokinin B Administration Induces Hot Flushes in Women (2015)

Neurokinin B (NKB) is a hypothalamic neuropeptide binding preferentially to the neurokinin 3 receptor. Expression of the gene encoding NKB is elevated in postmenopausal women. Furthermore, rodent studies suggest that NKB signalling may mediate menopausal hot flushes. However, the effects of NKB administration on hot flushes have not been investigated in humans. To address this, we performed a randomised, double-blinded, placebo-controlled, 2-way cross-over study. Ten healthy women were admitted to a temperature and humidity-controlled research unit. Participants received 30 minute intravenous infusions of NKB and vehicle in random order. Symptoms, heart rate, blood pressure, sweating and skin temperature were compared between NKB and vehicle in a double-blinded manner. Eight of ten participants experienced flushing during NKB infusion with none experiencing flushing during vehicle infusion (P = 0.0007). Significant elevations in heart rate (P = 0.0106 vs. pre-symptoms), and skin temperature measured using skin probe (P = 0.0258 vs. pre-symptoms) and thermal imaging (P = 0.0491 vs. pre-symptoms) characteristic of menopausal flushing were observed during hot flush episodes. Our findings provide evidence that NKB administration can cause hot flushes in women. Further studies are required to determine if pharmacological blockade of NKB signalling could inhibit hot flushes during the menopause and during treatment for sex-steroid dependent cancers.
A fully digital frequency shift keying demodulator chip for wireless biomedical implants (2003)

A fully digital frequency shift keying (D-FSK) data transfer protocol and demodulator circuit has been developed with the data-rate to carrier-frequency ratio of up to 67%. Its primary application is in the magnetically coupled wireless systems such as biomedical implants and RFID-tags with high data rates above 1 Mbps. The demodulator circuit extracts the serial data bit stream and a constant-frequency clock from an FSK carrier signal in the 4/spl sim/20 MHz range, which can power the wireless system as well. The circuit occupies 0.29 mm/sup 2/ in the AMI 1.5 /spl mu/m 2M/2P standard CMOS process and has a simulated data-rate of up to 2 Mbps and a measured rate of 200 Kbps while consuming less than 0.4 mW.
Room Temperature Sub-Wavelength Plasmon Laser (2010)

We report plasmon lasers with optical confinement of 1/20th wavelength operating at room temperature. The strong confinement and efficient feedback arising from plasmonic total internal reflection enhance the spontaneous emission rate up to 20 times.
Antipsychotic drug-induced weight gain mediated by histamine H <sub>1</sub> receptor-linked activation of hypothalamic AMP-kinase (2007)

The atypical antipsychotic drugs (AAPDs) have markedly enhanced the treatment of schizophrenias but their use has been hindered by the major weight gain elicited by some AAPDs. We report that orexigenic AAPDs potently and selectively activate hypothalamic AMP-kinase, an action abolished in mice with deletion of histamine H1 receptors. These findings may afford a means of developing more effective therapeutic agents and provide insight into the hypothalamic regulation of food intake.
ON THE ADDITIVITY OF ENTROPY, THE GEOMETRY OF THERMODYNAMICS, AND THE MAXIMIZING OF POWER-PLANT THERMAL EFFICIENCY AT NO COST. JOINT VENTURE WITH IGNS LTD, NEW-ZEALAND (2013)

Predictions of power plant efficiency improvement due to machinery repair, modification, replacements, or new desig n can be made by way of mathematical models (What If). No such model can solve the converse question of finding root-causes of efficiency variations of an existing plant. Here it is demons trated how these can be found automatically. A natural extension of diagnostics is the finding of values for available set-point s which maximize thermal efficiency - a decades-old quest. The solut ion is demonstrated for a steam-turbine coal fired plant. Method of approach. The facilitating underlining physics are the Balance Equations and the additivity of entropy. These yield thermodynamic availability with no further definitions and assu mption. The automatic maximization of thermal efficiency is ti ed to the geometrical formulation of thermodynamics, which is briefly discussed. Results. The example of automatic diagnostics was recorded on line under routine running of a Combined Cycle plant. The example shows graphics of automated diagnostics of efficiency drop, and remedy action. In passing a natural way t o normalize thermal efficiency against variable environment is devised. Another example shows a 4% gain in efficiency recorded during the maximization tests. The analysis of the gains provides a quantitative proof of why a generic efficiency maximi zing set of fixed values for set-points (which is the entrenche d conventions) does not exist. Conclusions. Remedies following real-time automatic diagnostics can improve plant thermal performance in a measurable way mostly at no capital cost. Efficiency maximization can be fully automated by integrating the tuning algorithm into plant’s controls. Even if controllab le parameters are set manually 1% improvement is achievable.
Functional Properties of Polyurethane-Shape Memory Polymer (2000)

The main functional properties of shape memory polymer are shape fixity and shape recovery. Gas permeability is also observed in polyurethane-shape memory polymer. Shape memory polymer is light, shows large deformation and is easy to be formed. The glass transition temperature of shape memory polymer can be set around the room temperature. Shape memory polymer is expected to be applied as an intelligent material.
Resistance to<i>Coccidioides immitis</i>in Mice after Immunization with Recombinant Protein or a DNA Vaccine of a Proline-Rich Antigen (1999)

Two inbred strains of mice (BALB/c and C57BL/6) were vaccinated with either recombinant expression protein of a Coccidioides immitis spherule-derived proline-rich antigen (rPRA) in monophosphoryl lipid A-oil emulsion adjuvant or a DNA vaccine based on the same antigen. Four weeks after vaccination, mice were infected intraperitoneally with arthroconidia. By 2 weeks, groups of mice receiving saline or plasmids with no PRA insert exhibited significant weight loss, and quantitative CFUs in the lungs ranged from 5.9 to 6.4 log10. In contrast, groups of mice immunized with either rPRA or DNA vaccine had significantly smaller pulmonary fungal burdens, ranging from 3.0 to 4.5 log10 fewer CFUs. In vitro immunologic markers of lymphocyte proliferation and gamma interferon (IFN-gamma) release after splenocytes were stimulated with rPRA correlated with protection. Also, plasma concentrations of rPRA-specific total immunoglobulin G (IgG), IgG1, and IgG2a showed increases in vaccinated mice. These studies expand earlier work by demonstrating protection in mice which differ in H-2 background, by using an adjuvant that is potentially applicable to human use, and by achieving comparable protections with a DNA-based vaccine. Our in vitro results substantiate a Th1 response as evidenced by IFN-gamma release and increased IgG2a. However, IgG1 was also stimulated, suggesting some Th2 response as well. PRA is a promising vaccine candidate for prevention of coccidioidomycosis and warrants further investigation.
<i>DAXX</i> / <i>ATRX</i> , <i>MEN1</i> , and mTOR Pathway Genes Are Frequently Altered in Pancreatic Neuroendocrine Tumors (2011)

Pancreatic neuroendocrine tumors (PanNETs) are a rare but clinically important form of pancreatic neoplasia. To explore the genetic basis of PanNETs, we determined the exomic sequences of 10 nonfamilial PanNETs and then screened the most commonly mutated genes in 58 additional PanNETs. The most frequently mutated genes specify proteins implicated in chromatin remodeling: 44% of the tumors had somatic inactivating mutations in MEN1, which encodes menin, a component of a histone methyltransferase complex, and 43% had mutations in genes encoding either of the two subunits of a transcription/chromatin remodeling complex consisting of DAXX (death-domain-associated protein) and ATRX (α thalassemia/mental retardation syndrome X-linked). Clinically, mutations in the MEN1 and DAXX/ATRX genes were associated with better prognosis. We also found mutations in genes in the mTOR (mammalian target of rapamycin) pathway in 14% of the tumors, a finding that could potentially be used to stratify patients for treatment with mTOR inhibitors.
Hydrophilic iminosugar active‐site‐specific chaperones increase residual glucocerebrosidase activity in fibroblasts from Gaucher patients (2006)

Gaucher disease is an autosomal recessive lysosomal storage disorder caused by the deficient activity of glucocerebrosidase. Accumulation of glucosylceramide, primarily in the lysosomes of cells of the reticuloendothelial system, leads to hepatosplenomegaly, anemia and skeletal lesions in type I disease, and neurologic manifestations in types II and III disease. We report herein the identification of hydrophilic active-site-specific chaperones that are capable of increasing glucocerebrosidase activity in the cultured fibroblasts of Gaucher patients. Screening of a variety of natural and synthetic alkaloid compounds showed isofagomine, N-dodecyl deoxynojirimycin, calystegines A3, B1, B2 and C1, and 1,5-dideoxy-1,5-iminoxylitol to be potent inhibitors of glucocerebrosidase. Among them, isofagomine was the most potent inhibitor of glucocerebrosidase in vitro, and the most effective active-site-specific chaperone capable of increasing residual glucocerebrosidase activity in fibroblasts established from Gaucher patients with the most prevalent Gaucher disease-causing mutation (N370S). Intracellular enzyme activity increased approximately two-fold after cells had been incubated with isofagomine, and the increase in glucocerebrosidase activity was both dose-dependent and time-dependent. Western blotting demonstrated that there was a substantial increase in glucocerebrosidase protein in cells after isofagomine treatment. Immunocytochemistry revealed an improvement in the glucocerebrosidase trafficking pattern, which overlaps that of lysosome-associated membrane protein 2 in Gaucher fibroblasts cultivated with isofagomine, suggesting that the transport of mutant glucocerebrosidase is at least partially improved in the presence of isofagomine. The hydrophilic active-site-specific chaperones are less toxic to cultured cells. These results indicate that these hydrophilic small molecules are suitable candidates for further drug development for the treatment of Gaucher disease.
A Two-Gene Blood Test for Methylated DNA Sensitive for Colorectal Cancer (2015)

Detection of methylated BCAT1 and/or IKZF1 DNA in plasma may have clinical application as a novel blood test for CRC. Combining the results from the two methylation-specific PCR assays improved CRC detection with minimal change in specificity. Further validation of this two-gene blood test with a view to application in screening is now indicated.
A mobile autonomous robot for radiological surveys (1992)

The Robotics Development Group at the Savannah River Site is developing an autonomous robot (SIMON) to perform radiological surveys of potentially contaminated floors. The robot scans floors at a speed of one-inch/second and stops, sounds an alarm, and flashes lights when contamination in a certain area is detected. The contamination of interest here is primarily alpha and beta-gamma. The robot, a Cybermotion K2A base, is radio controlled, uses dead reckoning to determine vehicle position, and docks with a charging station to replenish its batteries and calibrate its position. It uses an ultrasonic ranging system for collision avoidance. In addition, two safety bumpers located in the front and the back of the robot will stop the robots motion when they are depressed. Paths for the robot are preprogrammed and the robots motion can be monitored on a remote screen which shows a graphical map of the environment. The radiation instrument being used is an Eberline RM22A monitor. This monitor is microcomputer based with a serial I/0 interface for remote operation. Up to 30 detectors may be configured with the RM22A.
Nonblocking broadcast switching networks (1991)

Results are presented for nonblocking multistage broadcast networks wherein a request from an idle input port to be connected to some set of idle output ports can be satisfied without any disturbance of other broadcast connections already existing in the network. Furthermore, a linear network control algorithm for realizing such a broadcast connection request is given. These results represent the best known explicit constructions with limited numbers of stages relative to both crosspoint and control algorithm complexity. Thus, these networks are highly useful for practical applications involving the movement of and collaboration with voice/video/text/graphics information that require broadcast capability. These networks are also useful for the interconnection of processor and memory units in parallel processing systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Applications and Extensions of Fourier Ptychography (2022)

Abstract: This is the third article within a three-part series on Fourier ptychography, which is a computational microscopy technique for high-resolution, large field-of-view imaging. While the previous articles introduced the working principles of the technique, in this article we focus on the practical benefits that it brings to the imaging community. We present a didactic overview of the most important and well-established practical use-cases such as gigapixel imaging, quantitative phase contrast, thick sample imaging, and aberration metrology. We also discuss how Fourier ptychography can leave the visible light domain and venture into the realm of smaller wavelengths such as X-rays and electrons, among other topics.
Physics-guided probabilistic modeling of extreme precipitation under\n climate change (2017)

Earth System Models (ESMs) are the state of the art for projecting the\neffects of climate change. However, longstanding uncertainties in their ability\nto simulate regional and local precipitation extremes and related processes\ninhibit decision making. Stakeholders would be best supported by probabilistic\nprojections of changes in extreme precipitation at relevant space-time scales.\nHere we propose an empirical Bayesian model that extends an existing skill and\nconsensus based weighting framework and test the hypothesis that nontrivial,\nphysics-guided measures of ESM skill can help produce reliable probabilistic\ncharacterization of climate extremes. Specifically, the model leverages\nknowledge of physical relationships between temperature, atmospheric moisture\ncapacity, and extreme precipitation intensity to iteratively weight and combine\nESMs and estimate probability distributions of return levels. Out-of-sample\nvalidation shows evidence that the Bayesian model is a sound method for\nderiving reliable probabilistic projections. Beyond precipitation extremes, the\nframework may be a basis for a generic, physics-guided approach to modeling\nprobability distributions of climate variables in general, extremes or\notherwise.\n
Partial oxidation of methane to methanol on boron nitride at near critical acetonitrile (2022)

Direct catalytic conversion of methane to methanol with O<sub>2</sub> has been a fundamental challenge in unlocking abundant natural gas supplies. Metal-free methane conversion with 17% methanol yield based on the limiting reagent O<sub>2</sub> at 275 °C was achieved with near supercritical acetonitrile in the presence of boron nitride. Reaction temperature, catalyst loading, dwell time, methane-oxygen molar ratio, and solvent-oxygen molar ratios were identified as critical factors controlling methane activation and the methanol yield. Extension of the study to ethane (C2) showed moderate yields of methanol (3.6%) and ethanol (4.5%).
A new species of multicopy single-stranded DNA from Myxococcus xanthus with conserved structural features. (1988)

Myxobacteria have been shown to contain a large number of branched RNA-linked single-stranded DNA (multicopy single-stranded DNA (msDNA] molecules. In addition, we found that Myxococcus xanthus contains another smaller msDNA-like molecule, designated mrDNA, consisting of a 65-base single-stranded DNA covalently linked by a 2',5'-phosphodiester linkage to a 49-base branched RNA. In spite of their different primary sequences, the RNA-linked mrDNA is remarkably similar in secondary structure to msDNA, sharing similar stem-loop folding as well as the unique 2',5'-phosphodiester linkage. These results indicate that these novel molecules are synthesized by common molecular mechanisms.