gebhart/patrepeval huggingface dataset:
Importance of Steric Effects on the Efficiency and Fidelity of Transcription by T7 RNA Polymerase (2011)

DNA-dependent RNA polymerases such as T7 RNA polymerase (T7 RNAP) perform the transcription of DNA into mRNA with high efficiency and high fidelity. Although structural studies have provided a detailed account of the molecular basis of transcription, the relative importance of factors like hydrogen bonds and steric effects remains poorly understood. We report herein the first study aimed at systematically probing the importance of steric and electrostatic effects on the efficiency and fidelity of DNA transcription by T7 RNAP. We used synthetic nonpolar analogues of thymine with sizes varying in subangstrom increments to probe the steric requirements of T7 RNAP during the elongation mode of transcription. Enzymatic assays with internal radiolabeling were performed to compare the efficiency of transcription of modified DNA templates with a natural template containing thymine as a reference. Furthermore, we analyzed effects on the fidelity by measuring the composition of RNA transcripts by enzymatic digestion followed by two-dimensional thin layer chromatography separation. Our results demonstrate that hydrogen bonds play an important role in the efficiency of transcription but, interestingly, do not appear to be required for faithful transcription. Steric effects (size and shape variations) are found to be significant both in insertion of a new RNA base and in extension beyond it.
Pain relief in labour: pharmacological (2017)

This chapter considers the pharmacological options which a woman may choose to utilize during her labour and birth to help her cope with the pain. Options are described in conjunction with the current evidence base for their effectiveness and recommendations for safe use. They include nitrous oxide and oxygen (Entonox®), pethidine, diamorphine, and lumbar epidural anaesthesia.
Automatic segmentation of the optic tracts for computer assistance of deep brain stimulation procedures. (2010)

Deep brain stimulation (DBS) is a surgical treatment involving the implantation of a medical device called a brain pacemaker, which sends electrical impulses to specific regions of the brain for treatment of movement disorders. Because of the small size of the surgical target and possible shift of the deep brain structures due to air invasion when the dura is opened, intra-operative adjustment of the surgical approach is often necessary. Knowledge about the position of the optic tracts gained from intra-operative measurements is useful for placement guidance. Pre-operative knowledge of the location of the optic tracts may not only help the placement and programming of the DBS implant but also prove useful in estimating intra-operative brain shift. In this article we present an automatic method to localize the optic tracts in MR/CT.
Significance of Adrenocorticotropin Stimulation Test in the Diagnosis of an Aldosterone-Producing Adenoma (2011)

Our study indicates that the ACTH stimulation test is useful in the diagnosis of an APA among patients suspected of PA. This test can be used to select patients who are highly suspected of an APA and definitely require adrenal venous sampling.
Rational design of polyhedral oligomeric silsesquioxane fillers for simultaneous improvements of thermomechanical properties and lowering refractive indices of polymer films (2013)

ABSTRACT We describe here the design and synthesis of the polyhedral oligomeric silsesquioxane (POSS)‐based dual‐functional molecular fillers for simultaneously lowering refractive indices and improving thermomechanical properties of conventional polymers. We prepared the composite films with poly(methyl methacrylate) and polystyrene containing the series of the POSS derivatives with the single functional unit for interacting with polymer chains and heptacyclopentyl substituents for creating exclusive volumes around the POSS core. From the measurements of refractive indices of polymer composites, it was revealed that all POSS fillers can lower the refractive index of the films. In addition, thermal stabilities and mechanical properties were enhanced by adding POSS fillers. The filler effect on the thermal properties can be explained by the structural features of POSS: The highly symmetrical structure of the silica cube should suppress thermal motions, resulting in the large enhancement of thermomechanical properties of polymer matrices. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 3583–3589
Alterations in Cardiac Function and Cardiopulmonary Blood Volume in Chronic Sodium Depletion in Dogs (1980)

1. Chronic sodium depletion in dogs is associated with a blunting of the pressor response to carotid occlusion. After section of the vagus nerves this pressor response reverts to normal although atropine is without effect, suggesting a possible role for increased activity of cardiopulmonary vagal afferents in suppressing sympathetic outflow. Since increases in central blood volume stimulate vagal afferents, cardiopulmonary haemodynamics were studied by radioisotope dilution before and after 3 and 4 weeks of dietary sodium restriction together with frusemide. 2. Sodium depletion was associated with significant decreases in cardiac output, ejection fraction and total blood volume; the cardiopulmonary blood volume increased but the change was not statistically significant (P&amp;lt;0.2). These changes were accompanied by a significant increase in the ratio cardiopulmonary blood volume/total blood volume and a decrease in the ratio cardiac output/cardiopulmonary blood volume. 3. Results indicate that sodium depletion may be accompanied by a paradoxical translocation of blood to the cardiopulmonary region in part due to depressed ventricular performance.
ASH DISPOSAL IN DAMS, MOUNDS, STRUCTURAL FILLS, AND RETAINING WALLS (1973)

The properties of fly ash are such that it is possible to utilize ash to construct structural fills, embankments, dams, and dikes but that special care must be taken to ensure against possible liquefaction failure of such a structural fill when subjected to shock loading. It is recommended that for any large project, field trials be enable realistic design parameters to be established and specifications to be prepared. In view of the real risk of liquefaction, the hydrostatic pressure within the body of ash fills should be monitored throughout the construction and operational life of the structure, and construction operations must be adequately controlled to ensure compliance with the specifications, particularly with regard to compaction and drainage details. /Author/
Detecting malicious logins in enterprise networks using visualization (2016)

Enterprise networks have been a frequent target of data breaches and sabotage. In a widely used method, attackers establish a foothold in the target network by compromising a single computer or account. They then move laterally between computers to access valuable resources and information located deeper inside the network. To move laterally, attackers often steal valid user credentials. This paper is based on the observation that an attackers' pattern of access characteristics of the stolen credentials in the form of <;User, Source, Destination> deviates from benign patterns and can be used to detect malicious logins. In this paper, we present APT-Hunter <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> , a visualization tool that helps security analysts to explore login data for discovering patterns and detecting malicious logins. To evaluate the proposed system, a pilot study was conducted over an open dataset of more than one billion logins of an enterprise network, provided by Los Alamos National Lab (LANL). Using APT-Hunter, security analysts (unfamiliar with the dataset) were able to detect 349 of 749 malicious logins related to lateral movements performed by a Red Team during a penetration test conducted at LANL. APT-Hunter is currently deployed in a global financial company and helps security analysts detect account compromises.
Implementation of CNN based Demosaicking on FPGA (2021)

This paper proposes a hardware-friendly Convolutional Neural Network (CNN) based demosaicking scheme. For hardware implementation, we used the KD (Knowledge Distillation) technique for CNN, and the parameters can be reduced by about 97.96% compared to the teacher network. The student network compressed through KD is quantized to 16-bit integer for hardware implementation. The proposed system is implemented on the Xilinx Virtex-7 FPGA. It achieved high PSNR performance 39.47dB.
Infiltrating basal cell carcinoma in the setting of a venous ulcer (2000)

A 77-year-old man was referred with a 5-year history of an intermittently painful, nonhealing right medial ankle ulcer. The ulcer had not responded to multiple treatment modalities, including Unna boots, compression therapy, sclerotherapy, and split-thickness skin grafting. The past medical history was significant for a deep venous thrombosis in the right leg 30 years earlier (treated with warfarin for 3 months) and a history of greater saphenous vein harvesting for coronary bypass grafting 28 years previously. After the vein stripping, the patient had suffered from increasing right leg edema and stasis changes in the right leg. His history was also remarkable for coronary artery disease, dyslipidemia, and lymphoma treated with chemotherapy 8 years before presentation, with no evidence of recurrence. He had stopped smoking approximately 20 years earlier. Medications included atenolol, simvastatin, nicardipine, nitroglycerin, and aspirin. Skin examination revealed a 3.0 x 3.5-cm ulcer adjacent to the medial malleolus. The edges of the ulcer appeared raised and rolled (Fig. 1). Centrally, there was granulation tissue, which appeared healthy. There were surrounding dermatitic changes. Dorsalis pedis and the posterior tibial pulses were normal. Noninvasive vascular studies revealed severe venous incompetence of the right popliteal and superficial veins. Arterial studies and transcutaneous oximetry were normal. Computed tomographic scan of the pelvis did not reveal any adenopathy, and radiographic imaging did not reveal any bony changes suggestive of osteomyelitis. Biopsy of the ulcer edge and base showed infiltrating basal cell carcinoma (Fig. 2). Mohs' micrographic surgery required three layers; the final extent of the ulcer was 7.8 x 6.9 cm. A split-thickness skin graft was placed.
Design of Low-Frequency Impedance Measurement Sensors for Respiratory Health (2018)

Real-time monitoring of environmental exposure causing chronic diseases including asthma and COPD has assumed enormous significance due to prolific advances in materials science and electronics. Such monitoring demands low-power electronic devices for signal conditioning and measurement to be integrated with state-of-the-art environmental sensors. Ozone is a known trigger of asthma causing significant health burden worldwide. In this paper, sensitive detectors based on functionalized (i.e. high specificity) single-walled carbon nanotubes are designed to measure ambient ozone exposure. The electronic interface comprises low-power integration of the chemical sensor with a commercial device to measure the complex (sensor) impedance at a frequency between 40 kHz and 1 MHz. Simultaneous measurement of magnitude and phase on several ozone sensors reveal response change of 35% in the former and 80% in the latter, and a detection limit of only 10 ppb. This innovative chip-based impedance measurement technique has the potential for characterizing the personal exposure to ambient air pollution triggers of respiratory diseases.
ANALYSIS OF INTERPHASE FORMED ON THE ELECTRODES OF LITHIUM ION BATTERIES (2011)

Lithium-ion batteries (LIBs) are one of the most widely used energy sources, especially for portable electronics. However, the development of lithium ion batteries for Electric Vehicle (EV) and Plug-in Hybrid Electric Vehicle (PHEV) requires the research and development of improved electrolytes. The development of electrolytes which allow LIBs to perform over a wide temperature range and operating potential are of significant current interest. The interphase formed on the surface of the electrodes generally governs kinetics of charging and discharging and is an important factor in life of LIBs. Favorable electrode interphases can be generated by altering the composition of the electrolyte. Commercially available LIBs have a normal discharge voltage around 3.7V where the electrolyte oxidation on the surface of cathodes is not a significant problem. Recent research in high voltage cathode materials (>4.5 V vs Li/Li+) to increase the power and energy density of LIBs for EV applications has raised concerns about the stability of LiPF6/carbonate based electrolyte to oxidation. Furthermore, the flammability of organic electrolyte hinders LIBs’ application in the EV market. Detailed investigations of improved electrolyte systems which can address the above issues will be presented. Components of the interphase are detected using various surface analysis techniques such as XPS, FTIR and SEM.
Effect of the micro-environment on α-synuclein conversion and implication in seeded conversion assays (2020)

The variable diagnostic accuracy of current α-synuclein RT-QuIC occurs due to different protocols, cohorts and material etc.. An impact of micro-environmental factors on the α-synuclein aggregation and conversion process and the occurrence and detection of differential misfolded α-synuclein types or strains might underpin the clinical heterogeneity of α-synucleinopathies<b>.</b>
Low‐latitude ionospheric effects of energetic electrons during a recurrent magnetic storm (2014)

Abstract We study a magnetosphere‐ionosphere coupling at low latitudes during a moderate (corotating interaction regions/high‐speed solar wind streams‐driven) geomagnetic storm on 22 July 2009. Recently, it has been shown that during major (coronal mass ejection‐driven) storms, quasi‐trapped &gt;30 keV electrons largely enhance below the radiation belt in the forbidden zone and produce an additional ionization in the topside ionosphere. In this work, we examine a case of the recurrent storm when the magnetosphere‐ionosphere coupling through the quasi‐trapped electrons also may take place. Data from NOAA/Polar‐orbiting Operational Environmental Satellite and Japanese Greenhouse gases Observing Satellite were used to identify the forbidden electron enhancement (FEE). We find a positive vertical gradient of the electron fluxes that indicates to the radiation belt as a source of FEE. Using global ionospheric maps, radiotomography reconstructions from beacon data and COSMIC/FORMOSAT‐3 radio occultation measurements, we have observed an unusually large area in the nighttime ionosphere with increased total electron content (TEC) and prominent elevation of the F layer at low latitudes that coincides with FEEs spatially and temporarily. Ionizing particles are considered as an addition source of ionization along with generally accepted mechanisms for storm time TEC increase (a positive ionospheric storm). We discuss relative contributions of the FEE and disturbance dynamo electric field in the TEC increases during the storm recovery phase.
Hardware scheme of multi-channel audio/video encoder (2003)

This paper realized multi-channel audio/video input by virtue of A/D chip and FPGA chip , cording the multi audio/video by virtue of MPEG-4 encording chip, PCI bridge by virtue of FPGA. Multi-channel audio/video encoder was realized. Experimentation have proved that the scheme is good, function plasticity, high ratio between performance and price.
SARS-CoV-2 Vaccine (2020)

With the SARS-CoV-2 pandemic creating such a wide-reaching health crisis, it is imperative that a safe and effective vaccine be developed promptly for global availability. As such, there are several vaccine development projects currently underway aiming to meet this critical demand. However, COVID vaccine development is not immune to the inherent limitations and challenges that are encountered during vaccine clinical trials.
Kramers’ Turnover Theory: Improvement and Extension to Low Barriers (2016)

Kramers' turnover theory as derived by Pollak, Grabert, and Hänggi (PGH) suffers from a few drawbacks. First, the energy loss in PGH theory is not a monotonic function of the friction. Second, the theory is not applicable to surface diffusion, because the effective potential for the system does not conserve the periodicity of the potential. Third, when the reduced barrier height is low, it is rather inaccurate. In this paper, we present a modification of PGH theory that alleviates these drawbacks. We also introduce a finite barrier correction term which takes into consideration that the energy interval of the escaping particle is bounded from below. The resulting theory is tested for motion on a cubic potential and relatively low reduced barriers.
Structures and isomerization in diamminedichloropalladium(II) (1996)

Three forms ( cis -, trans -, β-trans -) of [Pd(NH 3 ) 2 Cl 2 ] were obtained as pure single-phase powder materials. Ab initio structure determinations using X-ray powder diffraction were carried out. The cis -Pd(NH 3 ) 2 Cl 2 [ a = 6.3121 (2), b = 6.4984 (2), c = 3.3886 (1) Å, α = 96.604 (4), β = 97.290 (4), γ = 104.691 (2)°, Z = 1, space group P 1] and trans -Pd(NH 3 ) 2 Cl 2 [ a = 6.5398 (3), b = 6.8571 (4), c = 6.3573 (3) Å, α = 103.311 (5), β = 102.454 (3), γ = 100.609 (4)°, Z = 2, space group P {\bar 1}] phases have a typical layer-column structure, while β-trans -Pd(NH 3 ) 2 Cl 2 [ a = 8.1540 (2), b = 8.1482 (2), c = 7.7945 (1) Å, Z = 4, space group Pbca ] is described as a parquet-like layer structure. Both trans phases demonstrate the order-disorder phenomenon. The possible ways of phase transitions are discussed. It is noted that the cis phase can transform into trans in the solid state without destroying the crystal body. Further transformation to β-trans follows through a break up of the crystal body.
Least squares acceleration filtering for the estimation of signal derivatives and sharpness at extrema [and application to biological signals] (1999)

A family of finite impulse-response (FIR) filters is derived which estimate the second derivative or "acceleration" of a digitized signal. The acceleration is obtained from parabolas that are continuously fit to the signal using a least squares optimization criterion. A closed-form solution for the filter coefficients is obtained. The general approach is computationally simple, can be performed in real-time, and is robust in the presence of noise. An important application of the method, that of measuring sharpness in biologic signals, is presented using the electroencephalogram (EEG) and electrocardiogram (EKG) signals as examples. Furthermore, the design method is extended to derive FIR filters for estimating derivatives of arbitrary order in digital signals of biologic or other origins.
Reactions with N-(1-benzotriazolylcarbonyl)-amino acids. IV. The use of N-(1-benzotriazolylcarbonyl)-amino acid derivates in peptide synthesis (1991)

The use of the 1-benzotriazolylearbonyl-(Bte)-group as an N-protecting and N-activating group in the synthesis of peptides was investigated. Removal of the Btc group from N-Btc-amino acids, their esters and amides under acidic conditions is possible, but has no advantages over removal of benzyloxyearbonyl-(Z)-group. N-Btc-amino acid esters react with Z-amino acids or Z-dipeptides yielding Z-dipeptide and Z-tripeptide esters, respcetively. This process is aceompanied with separation of benzotriazole and C02. Advantages and disadvantages of this method of peptide bond formation are discussed.
Applying Fast String Matching to Intrusion Detection (2002)

The performance of signature-based network intrusion detection tools is dominated by the string matching of packets against many signatures. In this paper we study how the popular intrusion detection system Snort can be best optimized to utilize different string matching algorithms. We analyze the performance of Snort's current string matching algorithm, Boyer-Moore, and several alternate algorithms.
Redox‐dependent regulation of hepatocyte absent in melanoma 2 inflammasome activation in sterile liver injury in mice (2016)

These findings suggest a novel and important mechanism for regulation of AIM2 inflammasome activation in hepatocytes during redox stress and may suggest broader implications for how this and other inflammasomes are activated and how their activation is regulated during cell stress, as well as the mechanisms of inflammasome regulation in nonimmune cell types. (Hepatology 2017;65:253-268).
Biomechanical effects of double or wide implants for single molar replacement in the posterior mandibular region (2000)

Double implants have been thought to have biomechanical advantages for single molar replacement. To evaluate the effectiveness of double implants versus a wide implant, the vertical forces and torque on each implant were calculated by three-dimensional geometric analysis. Buccal load (100N) perpendicular to cuspal inclination (20 degrees) was applied at the occlusal surface of the superstructure. The three kinds of load points (A, B, C) were 1.5, 3.5, and 5.5 mm from the mesial contact point, respectively. Three implants were compared: mesial and distal double implants (phi 3.3 mm), and a wide implant (phi 5 mm). The wide implant showed torque around the long axis (1.8-15.0 N x cm) whereas double implants had no torque. On the other hand, the vertical forces on the mesial double implant were both smaller (60%: loaded at point C) and larger (140%: loaded at point A) than the wide implant. Given the smaller surface area of the mesial double implant, this large force may generate much higher stress in the peri-implant bone. These results suggest that the biomechanical advantage of double implants for single molar replacement is questionable when the occlusal force is loaded at the occlusal surface near the contact point.
Nitrogen in the environment (2019)

Excess nitrogen causes problems in developed nations, but nitrogen-poor soils threaten food security elsewhere
Deletion Pattern in the 21‐Hydroxylase Gene Detected by Polymerase Chain Reaction (1991)

In order to detect deletion mutation and/or gene conversion in the 21-hydroxylase (21-OH) gene, we adopted the polymerase chain reaction (PCR) method followed by electrophoresis. Two pairs of synthesized primers, Ta/1b and 2a/2b, each corresponding to the sequence at the 5' portion of the 21-OH gene, were set for PCR. TaqI digestion of amplified DNA from normal individuals using Ta/1b as primers gave the following three fragments: an active 21-OH gene-derived 559 bp fragment, and pseudogene-derived 364 and 195 bp fragments. Of 16 patients with 21-hydroxylase deficiency (21-OHD) studied, 6 (37%) lacked the 559 bp fragment. These 6 patients also lacked both the 331 and 117 bp MvaI fragments of the PCR product which were obtained with the primers 2a/2b, both being derived from the active 21-OH gene. These results indicate that 6 of the 16 patients have either deletion of the 21-OH gene or conversion of the gene to its tandemly located pseudogene. The method described here provides a rapid diagnosis of 21-OHD.
Supplementary figure 1 from <i>POLE</i> Proofreading Mutations Elicit an Antitumor Immune Response in Endometrial Cancer (2023)

&lt;p&gt;Supplementary figure 1. Tumor infiltrating lymphocytes and Crohn's like reaction in POLE- mutant endometrioid endometrial cancers&lt;/p&gt;