gebhart/patrepeval huggingface dataset:
Secondary recovery from the Dune Field, Crane County, Texas, is viable through mine workings (1991)

Data in Report of Investigations No. 168, published by the Bureau of Economic Geology, University of Texas, indicate the Dune field is a good candidate for secondary recovery of mobile residual oil through an oil mine as described in US Patent {number sign}4,458,945. If trends identified in RI No. 168 can be extended into adjacent sections, oil recovery in the range of $10.00 per barrel or less should be possible. Mine workings will permit a more detailed mapping field jointing and fracturing, in turn permitting better placement of wells on 1 acre or closer spacing. Shafts to the surface would be a mile or more apart greatly decreasing environmental impact. Wastewater generated could be re-introduced to assist in retaining reservoir pressures. If mine workings are driven in hard limestones, as would be possible in the Dune field, produced mine spoil would be marketable as gravel for the concrete industry.
Highly efficient generation of isogenic pluripotent stem cell models using prime editing (2022)

SUMMARY The recent development of prime editing (PE) genome engineering technologies has the potential to significantly simplify the generation of human pluripotent stem cell (hPSC)-based disease models. PE is a multi-component editing system that uses a Cas9-nickase fused to a reverse transcriptase (nCas9-RT) and an extended PE guide RNA (pegRNA). Once reverse transcribed, the pegRNA extension functions as a repair template to introduce precise designer mutations at the target site. Here, we systematically compared the editing efficiencies of PE to conventional gene editing methods in hPSCs. This analysis revealed that PE is overall more efficient and precise than homology-directed repair (HDR) of site-specific nuclease-induced double-strand breaks (DSBs). Specifically, PE is more effective in generating heterozygous editing events to create autosomal dominant disease-associated mutations. By stably integrating the nCas9-RT into hPSCs we achieved editing efficiencies equal to those reported for cancer cells, suggesting that the expression of the PE components, rather than cell-intrinsic features, limit PE in hPSCs. To improve the efficiency of PE in hPSCs, we optimized the delivery modalities for the PE components. Delivery of the nCas9-RT as mRNA combined with synthetically generated chemically-modified pegRNAs and nicking guide RNAs (ngRNAs) improved editing efficiencies up to 13-fold compared to transfecting the prime editing components as plasmids or ribonucleoprotein particles (RNPs). Finally, we demonstrated that this mRNA-based delivery approach can be used repeatedly to yield editing efficiencies exceeding 60% and to correct or introduce familial mutations causing Parkinson’s disease in hPSCs.
The crystal and molecular structure of 5-(propyn-1-yl)-1-(β-D-arabinofuranosyl)uracil. A very short C≡C triple bond (1984)

The crystal structure of 5-(propyn-1-yl)-1-(β-D-arabinofuranosyl)uracil, an analog of the active antiherpes nucleoside 1-(β-D-arabinofuranosyl)thymine, was determined by X-ray diffraction. The compound crystallizes in the space group P2 1 2 1 2 1 with a = 4.925(1), b = 14.326(2), c = 17.454 Å. Reflections were measured on a diffractometer and the structure was solved by direct methods. Least-squares refinement converged at R = 0.032 for 1159 observed reflections. The sugar ring exhibits an 3 E or a C(3′)endo conformation with a pseudorotation angle P = 28.3° and puckering amplitude τ m = 31.7°. The orientation of the —CH 2 OH side chain is g + . The base is in an anti conformation with respect to the sugar ring, with a glycosidic torsion angle χ = 33.7°. Changes in the C(5)—C(6) and C(6)—N(1) bond lengths suggest some interaction of the propynyl group with the pyrimidine ring. The C≡C bond length of 1.121 Å is very short. Its shortening could result from intermolecular interactions with the neighboring pyrimidine ring and nearby oxygen atoms.
Association of socioeconomic status with adherence to oral agents in patients with multiple myeloma. (2022)

8023 Background: The introduction of novel oral immunomodulatory drugs has improved the overall survival rates of patients with multiple myeloma (MM). Poor adherence to oral therapies may lead to drug resistance, poor response to treatment and other downstream effects. It is unknown if socioeconomic status (SES) mediates adherence to oral MM agents. Methods: This is a retrospective review of newly diagnosed adult patients with MM with drug coverage through a large pharmacy benefit manager (PBM) who received oral MM agents between September 1, 2016 and September 1, 2020. Patients were excluded if they were not eligible for PBM benefits for the 6 months prior to or the 12 months after the index date and if they had a stem cell transplant based on a proxy signal. Adherence was defined as an annual medication possession ratio between 0.8 and 1.2. An SES composite index was developed using ZIP code level factors in a K-means clustering algorithm. Multivariable logistic regression for adherence was conducted using the SES-index and controlled for other patient-specific demographics. Results: In total, 6,602 patients were enrolled in the study, of which, 4,211 (64.5%) were defined as adherent. There were significant unadjusted differences in age (67.89 vs 64.06, p&lt;0.00001), ZIP code-based SES index (p=0.00049), census region (p&lt;0.00001) and insurance plan type (p&lt;0.00001). Results from multivariable logistic regression are shown in table. Patients residing in Very Low SES ZIP codes were significantly less likely to be adherent to oral MM agents compared to those residing in Very High SES locations. Odds of adherence increased as patient’s age increased. Increasing polypharmacy was negatively associated with oral MM agent adherence. Conclusions: Aside from patients residing in Very Low SES ZIP codes, ZIP code-based SES measures were not associated with worse adherence. Other mediating factors include younger age and number of co-prescribed medications. Further investigations of adherence to oral MM agents with clinically relevant outcomes are warranted. [Table: see text]
Machine learning-based prediction methods for flow boiling in plate heat exchangers (2021)

The present paper describes novel machine learning-based prediction methods for local heat transfer coefficient and local frictional pressure gradient of flow boiling within plate heat exchangers. Plate heat exchangers are becoming a valuable alternative, and in most cases a preferred solution, compared to traditional tube-in-tube and shell-and-tube heat exchangers, as they provide higher flexibility, compactness and lower weight. Using a consolidated dataset from the open literature, the proposed machine learning-based prediction methods take system geometry and flow conditions, such as mass flow rate, saturation temperature, heat flux, etc., as input parameters to predict the local heat transfer coefficient and local frictional pressure gradient. Compared to non-linear regression-based methods previously reported, the new methods significantly improve the prediction accuracy and can be easily adopted to design and analyze thermal performance of two-phase cooling systems. Reliable, accurate and validated prediction methods allow critical two-phase cooling systems to be readily designed given geometric parameters and operating conditions.
Clonal analysis of cytotoxic T cell response against human melanoma. (1983)

We investigated the feasibility of generating cytotoxic T cell clones against autologous human melanoma cells using a melanoma cell line (VIP) and a spontaneously transformed autologous fibroblast line (VIP-F:T). Cytotoxic lymphocytes (CL) generated against the VIP melanoma cells in one-way mixed lymphocyte-tumor cell interactions were expanded in interleukin 2 for 2 wk. The expanded CL were cloned in limiting dilution. Two phenotypically homogeneous clones (3:1 and E.5) were obtained bearing OKT3 phenotype. Both clones expressed cytotoxicity selectively only against the sensitizing autologous target VIP. cytotoxicity assays performed with clone E.5 against the VIP target cells in the presence of autologous unfractionated lymphocytes or serum showed no modulation of autoreactivity of clone E.5. These results indicate that analysis of cellular immune response against autologous tumor cells might be feasible using autoreactive clones generated by the currently available in vitro cloning technology.
Population Pharmacokinetic and Pharmacodynamic Analysis of GLPG1690, an Autotaxin Inhibitor, in Healthy Volunteers and Patients with Idiopathic Pulmonary Fibrosis (2019)

Based on these results, 200 and 600 mg once-daily doses were selected for future clinical trials in patients with idiopathic pulmonary fibrosis.
Porous Ionic Membrane Based Flexible Humidity Sensor and its Multifunctional Applications (2017)

A highly flexible porous ionic membrane (PIM) is fabricated from a polyvinyl alcohol/KOH polymer gel electrolyte, showing well-defined 3D porous structure. The conductance of the PIM changes more than 70 times as the relative humidity (RH) increases from 10.89% to 81.75% with fast and reversible response at room temperature. In addition, the PIM-based sensor is insensitive to temperature (0-95 °C) and pressure (0-6.8 kPa) change, which indicates that it can be used as highly selective flexible humidity sensor. A noncontact switch system containing PIM-based sensor is assembled, and results show that the switch responds favorably to RH change caused by an approaching finger. Moreover, an attachable smart label using PIM-based sensor is explored to measure the water contents of human skin, which shows a great linear relationship between the sensitivity of the sensor and the facial water contents measured by a commercial reference device.
An epidemiological study of subacute sclerosing panencephalitis in Japan, 1976. (1978)

In a PhD study on the heating of monumental churches one of the problems, which was encountered, was the damage to wooden interior parts due to the changing of the indoor climate. Particularly warm air heating frequently leads to sudden changes in relative humidity, which turned out to be dramatically hard for monumental organs during wintertime. The warm air inlet conditions and their result on the airflow and air conditions were examined experimentally and by CFD-simulation. These results provided boundary temperature and humidity conditions, to which the monumental organ was exposed. In an experimental study the response of wooden parts to changing indoor conditions was tested. In a Nuclear Magnetic Resonance (NMR) test setup the moisture content of samples was measured as a function of time and place. These moisture content changes were related to the free mechanical deformation of samples. Together with the measurement of typical material properties of wood, a two-dimensional model was developed in FlexPDE: a finite element program to solve partial differential equations simultaneously.
Neutron interferometer crystallographic imperfections and gravitationally induced quantum interference measurements (2017)

Dynamical diffraction leads to an interesting, unavoidable set of interference effects for neutron interferometers. This experiment studies the interference signal from two and three successive Bragg diffractions in the Laue geometry. We find that intrinsic Bragg-plane misalignment in monolithic, "perfect" silicon neutron interferometers is relevant between successive diffracting crystals, as well as within the Borrmann fan for typical interferometer geometries. We show that the dynamical phase correction employed in the Colella, Overhauser, and Werner gravitationally induced quantum interference experiments is attenuated by slight, intrinsic misalignments between diffracting crystals, potentially explaining the long-standing 1% discrepancy between theory and experiment. This systematic may also impact precision measurements of the silicon structure factor, affecting previous and future measurements of the Debye-Waller factor and neutron-electron scattering length as well as potential fifth-force searches. For the interferometers used in this experiment, Bragg planes of different diffracting crystals were found to be misaligned by 10 to 40 nrad.
Modeling infection methods of computer malware in the presence of vaccinations using epidemiological models: An analysis of real-world data (2019)

Computer malware and biological pathogens often use similar mechanisms of infections. For this reason, it has been suggested to model malware spread using epidemiological models developed to characterize the spread of biological pathogens. However, most work examining the similarities between malware and pathogens using such methods was based on theoretical analysis and simulation. Here we extend the classical Susceptible-Infected-Recovered (SIR) epidemiological model to describe two of the most common infection methods used by malware. We fit the proposed model to malware collected over a period of one year from a major anti-malware vendor. We show that by fitting the proposed model it is possible to identify the method of transmission used by the malware, its rate of infection, and the number of machines which will be infected unless blocked by anti-virus software. The Spearman correlation between the number of actual and predicted infected machines is 0.84. Examining cases where an anti-malware "signature" was transmitted to susceptible computers by the anti-virus provider, we show that the time to remove the malware will be short and independent of the number of infected computers if fewer than approximately 60% of susceptible computers have been infected. If more computers were infected, the time to removal will be approximately 3.2 greater, and will depend on the fraction of infected computers. Our results show that the application of epidemiological models of infection to malware can provide anti-virus providers with information on malware spread and its potential damage. We further propose that similarities between computer malware and biological pathogens, the availability of data on the former and the dearth of data on the latter, make malware an extremely useful model for testing interventions which could later be applied to improve medicine.
Employing Scaled Sigma Sampling for Efficient Estimation of Rare Event Probabilities in the Absence of Input Domain Mapping (2016)

Traditional techniques for statistical analysis of rare events require a good understanding of the dependence of the outputs on the independent input variables. This can sometimes be an insurmountable challenge, especially when the dimensionality of the input variation space is high. In this paper, we present an innovative scaled sigma sampling (SSS) technique that is able to obtain an accurate quantification of the low probability tails without requiring visibility to the failure regions or their input dimensionality. SSS leverages the probability density differences produced by process sigma scale factors to uncover the nature of the population redistribution induced by the circuit. This understanding is used to construct an efficient transform for the circuit metric, one that has the same sigma scale factor dependency of the cumulative probabilities as the SPICE simulations. This transform is then used to obtain the low probability tails corresponding to the original process distribution. We present representative circuit applications to illustrate the large savings in computational costs that one can achieve with SSS and the transparency and accuracy of this approach.
A Comparison of Graphics Processor Architectures for RFID Simulation (2014)

Graphics Processing Units (GPUs) have a huge number of cores to speed up graphical computations and they are being used in a wide area of general-purpose applications that require high performances. In this paper, GPU computing is exploited to model the signal propagation and the interference in large RFID systems, which are a promising solution for achieving pervasive computing since they offer the automatic object identification. The speedup of the parallel algorithm is evaluated with respect to a sequential version. Two popular frameworks for general-purpose computing on GPU are considered in the comparison, i.e. CUDA and OpenCL, and distinct implementations are provided for them, highlighting their differences in code optimization and performance.
Transcription from plasmid expression vectors is increased up to 14- fold when plasmids are transfected as concatemers (1997)

A protocol for increasing transcription from plasmid expression vectors is presented. A vector containing chloramphenicol acetyltransferase (CAT) gene was digested leaving the transcription cassette intact. Heat inactivation of restriction enzymes followed by ligation of the digestion products yielded concatemers which migrated as a single band in agarose gel electrophoresis. Mouse fibroblasts transfected with the concatemers gave a CAT activity that was 14-fold greater than that of cells transfected with a similar mass (equimolar gene number) of the native plasmid. The effect was independent of promoter type, restriction enzyme, number of restriction sites and with a noted exception, cell line.
A MoS2-Based Capacitive Displacement Sensor for DNA Sequencing (2016)

We propose an aqueous functionalized molybdenum disulfide nanoribbon suspended over a solid electrode as a capacitive displacement sensor aimed at determining the DNA sequence. The detectable sequencing events arise from the combination of Watson-Crick base-pairing, one of nature's most basic lock-and-key binding mechanisms, with the ability of appropriately sized atomically thin membranes to flex substantially in response to subnanonewton forces. We employ carefully designed numerical simulations and theoretical estimates to demonstrate excellent (79% to 86%) raw target detection accuracy at ∼70 million bases per second and electrical measurability of the detected events. In addition, we demonstrate reliable detection of repeated DNA motifs. Finally, we argue that the use of a nanoscale opening (nanopore) is not requisite for the operation of the proposed sensor and present a simplified sensor geometry without the nanopore as part of the sensing element. Our results, therefore, potentially suggest a realistic, inherently base-specific, high-throughput electronic DNA sequencing device as a cost-effective de novo alternative to the existing methods.
Microbial subversion of heparan sulfate proteoglycans. (2008)

The interactions between the host and microbial pathogen largely dictate the onset, progression, and outcome of infectious diseases. Pathogens subvert host components to promote their pathogenesis and, among these, cell surface heparan sulfate proteoglycans are exploited by many pathogens for their initial attachment and subsequent cellular entry. The ability to interact with heparan sulfate proteoglycans is widespread among viruses, bacteria, and parasites. Certain pathogens also use heparan sulfate proteoglycans to evade host defense mechanisms. These findings suggest that heparan sulfate proteoglycans are critical in microbial pathogenesis, and that heparan sulfate proteoglycan-pathogen interactions are potential targets for novel prophylactic and therapeutic approaches.
The effect of local disorder on the magnetic, electric and thermal properties of RE(Fe1-xAlx)2(RE=Gd, Dy) (1984)

Measurements of magnetic properties, X-ray and neutron diffraction, differential thermal analysis (DTA), thermal expansion and resistivity were made on Gd(Fe1-xAlx)2 and Dy(Fe1-xAlx)2. Both systems exhibit a line broadening observed by X-ray diffraction on the Al-rich side, indicating a small variation of the lattice constants. This effect leads to a smoothing of the magnetic phase transition at the Curie temperature Tc, which becomes observable in all the measurements mentioned above. The neutron experiments give evidence of a disordered component of the Dy moment due to Fe substitution. By subtracting the thermal expansion of non-magnetic YAl2 from that of the mixed crystal series, a reduction of the spontaneous magnetostriction from its value in the corresponding boundary phase is also obtained. In the case of anisotropic Dy the magnetisation behaviour can be explained by the pinning of narrow domain walls on inhomogeneities caused by chemical substitution. All physical properties indicate a magnetically quasi-amorphous state.
Block Matching in Noise Suppression Filter for Video Coding (2019)

This paper considers specific block matching methods which are used inside Nose Suppression Filter (NSF) in-loop filter for video coding. Different approaches of the block matching procedure, which are combined in NSF are described. In general block matching part of NSF comprises of a specific search region and a statistical search method which are applied to a certain area of a picture. As a result total complexity of block matching part inside NSF significantly decreases while coding efficiency of NSF algorithm is kept. In addition theoretical complexity analysis of the block matching part inside NSF is provided.
DiscPOP: Power-aware buffer management for disk accesses (2011)

Much research has been conducted on energy efficient cache buffer management for disk based storage systems. Some of them use greedy prefetching technique to artificially increase disk idle intervals if there are a large number of known future requests. However, this might result in sub-optimal solution by not exploiting the relationship between I/O access pattern (sequential/random) and application pattern (CPU required for computing time). In a CPU-bound application, by explicitly taking into account this relationship it may reduce energy conservation by up to 50% and increase power cycle number by 100% compared to an existing efficient prefetching scheme without this consideration. In this paper, we consider the tradeoff between disk power consumption, performance guarantee and disk reliability all together by proposing a Disk characteristic based Power-Optimal Prefetching (DiscPOP) scheme. Specifically, we make two contributions: (i) A theoretical model is conducted to analyze energy-efficient cache buffer management in disk I/O system and it is formulated as an optimization problem. We have shown it can be solved via an Integer Linear Programming (ILP) technique. (ii) We propose a simple Divide-and-Conquer based offline algorithm named Greedy Partition (GP) to divide the problem into several small ones and solve them separately via an ILP solver. We use trace-driven simulations to evaluate our proposed scheme. The results show GP outperforms the traditional aggressive prefetching by up to 29.2% more disk energy conservation and 20.6% power cycle reduction.
Short term clinical outcome of acute saddle pulmonary embolism: Figure 1 (2003)

2] It remains unclear whether this may further increase haemodynamic compromise. Also, it is unknown whether saddle PE requires modification of clinical management. We tried to evaluate if saddle thromboembolus affected two week outcome of patients with acute PE.