gebhart/patrepeval huggingface dataset:
Role of the Reverse Transcriptase, Nucleocapsid Protein, and Template Structure in the Two-step Transfer Mechanism in Retroviral Recombination (2003)

Template switching during reverse transcription promotes recombination in retroviruses. Efficient switches have been measured in vitro on hairpin-containing RNA templates by a two-step mechanism. Pausing of the reverse transcriptase (RT) at the hairpin base allowed enhanced cleavage of the initial donor RNA template, exposing regions of the cDNA and allowing the acceptor to base pair with the cDNA. This defines the first or docking step. The primer continued synthesis on the donor, transferring or locking in a second step. Here we determine the enzyme-dependent factors that influence template switching by comparing the RTs from human immunodeficiency virus, type 1 (HIV-1), and equine infectious anemia virus (EIAV). HIV-1 RT promoted transfers with higher efficiency than EIAV RT. We found that both RTs paused strongly at the base of the hairpin. While stalled, HIV-1 RT made closely spaced cuts, whereas EIAV RT made only a single cut. Docking occurred efficiently at the multiply cut but not at the singly cut site. HIV-1 nucleocapsid (NC) protein stimulated strand transfers. It improved RNase H activity of both RTs. It allowed the EIAV RT to make a distribution of cuts, greatly stimulating docking at the base of the hairpin. Most likely, it also promoted strand exchange, allowing transfers to be initiated from sites throughout the hairpin. Minor pause sites beyond the base of the hairpin correlated with the locking sites. The strand exchange properties of NC likely promote this step. We present a model that explains the roles of RNase H specificity, template structure, and properties of NC in the two-step transfer reaction.
Genetic manipulation of lignin profiles: a realistic challenge towards the qualitative improvement of plant biomass (1998)

Lignins represent an important proportion of the plant biomass (up to 35% of the dry weight for some woody species). Despite their role in the adaptative strategies of vascular plants, they have a negative impact on the agroindustrial utilization of crops and woody species. They reduce forage digestibility and are difficult to extract from lignocelluloses during the pulping process. The recent characterization of lignification genes and their exploitation for modulation of lignin profiles in transgenic plants was a breakthrough in the area of lignification. A large number of transformed plants exhibiting qualitative and quantitative changes in lignins have already been obtained. For some of these plants, preliminary data have already demonstrated their potential industrial interest. In this review, particular attention is paid to features that are critical in the exploitation of these transgenic approaches: compensation mechanisms, potential unwanted side-effects, stability of transgene expression and so on. In addition, the integration of these new materials in the general strategies of breeders and chemists working for the pulp industry is considered. Transgenic plants provide a source of insight into the processes of lignification and generate new plant products which extend the natural chemical variability observed for lignins. It is clear that genetically engineered trees that developed normally but which produced modified lignins (in lower amounts or that can be more easily processed) would lead to substantial industrial and environmental benefits.
Temperature Measurement by Use of Variations of the Planck Equation (1970)

A temperature-measurement technique is described that compares measurements of the radiated power of a source with its radiated photon flux. The ratio of such measurements is shown to be a direct function of temperature of a graybody source. For nongraybody sources, the technique yields Kelvin temperatures that are the equivalent of the best-fit graybody.
Session 24 overview: GaN drivers and converters: Power management subcommittee (2018)

GaN power devices have garnered significant attention for their reduced switching losses leading to small-form-factor high-frequency switching converters. However, issues related to reliable GaN gate drivers, level shifters with high common-mode immunity and zero-voltage switching detection remain. This session presents recent advances in gate drivers and ZVS detection schemes for GaNbased power converters.
Optimal code size reduction for software-pipelined and unfolded loops (2003)

Software pipelining and unfolding are commonly used techniques to increase parallelism for DSP applications. However, these techniques expand the code size of the application significantly. For most DSP systems with limited memory resources, code size becomes one of the most critical concerns for the high-performance applications. In this paper, we present the code size reduction theory based on retiming and unfolding concepts. We propose a code size reduction framework to achieve the optimal code size of software-pipelined and unfolded loops by using conditional registers. The experimental results on several well-known benchmarks show the effectiveness of our code size reduction technique in controlling the code size of optimized loops.
Refractory post-transplant airway strictures: successful management with wire stents (1999)

The airway complication of stricture, broncho-malacia or dehiscence following lung transplantation can be managed effectively and easily with the use of balloon catheter dilation followed by precise placement of a self-expandable wire stent. The Wallstent is the superior stent for this application.
Polycystic ovary syndrome: clinical considerations. (2001)

Polycystic ovary syndrome (PCOS) is one of the most frequently encountered endocrine disorders occurring in women of reproductive age. Clinically, a patient usually presents with menstrual irregularities, infertility, and hirsutism. If not treated properly, a patient is at risk for type 2 diabetes, cardiovascular disease, and hyperestrogen-related cancers. The hallmark endocrine disorders of this syndrome are hyperandrogenism and hyperinsulinemia. Great controversy exists as to which state precedes the other. There also appears to be a defect in the hypothalamic-pituitary-adrenal (HPA) axis in patients presenting with polycystic ovary syndrome. Research consistently demonstrates that the first line of treatment for this condition is weight loss. Weight loss and dietary changes appear to affect all parameters of hormonal fluctuation. Due to the vast array of side effects associated with many pharmaceutical agents typically prescribed to treat PCOS, natural therapeutics including nutrient supplementation and botanicals may be a less invasive and equally effective approach. Due to the seriousness of this syndrome when left untreated, prompt evaluation and treatment is essential.
HPLC purification of RNA for crystallography and NMR. (1996)

Homogeneous preparations of milligram quantities of RNA are a prerequisite for their characterization by biophysical methods such as crystallography or NMR spectroscopy. Methods for obtaining milligram quantities of pure synthetic RNA are described in this paper. These methods employ anion exchange HPLC for purifying full-length sequence from failure sequences and incompletely deprotected material. RNA molecules with little or extensive amounts of secondary structure could be purified. In cases where the RNA molecule was tightly folded, the cation in the eluent buffer influenced both the distinction of the peaks during chromatography and the final folded conformation. Finally, two RNA sequences were chemically synthesized, deprotected, purified, and crystallized using this methodology.
Two-reservoir model of quantum error correction (2006)

We consider a two-reservoir model of quantum error correction with a hot bath causing errors in the qubits and a cold bath cooling the ancilla qubits to a fiducial state. We consider error correction protocols both with and without measurement of the ancilla state. The error correction acts as a kind of refrigeration process to maintain the data qubits in a low entropy state by periodically moving the entropy to the ancilla qubits and then to the cold reservoir. We quantify the performance of the error correction as a function of the reservoir temperatures and cooling rate by means of the fidelity and the residual entropy of the data qubits. We also make a comparison with the continuous quantum error correction model of Sarovar and Milburn [Phys. Rev. A 72, 012306 (2005)].
Synthesis, Characterization, and DNA Adsorption Studies of Ampholytic Model Conetworks Based on Cross-Linked Star Copolymers (2007)

Five model conetworks based on cross-linked star ampholytic copolymers were synthesized by group transfer polymerization. The ampholytic copolymers were based on two hydrophilic monomers: the positively ionizable 2-(dimethylamino)ethyl methacrylate (DMAEMA) and the negatively ionizable methacrylic acid (MAA). Ethylene glycol dimethacrylate was used as the cross-linker. These five ampholytic model conetworks were isomers based on equimolar DMAEMA-MAA copolymer stars of different architectures: heteroarm (two), star block (two), and statistical. The two networks based on the homopolymer stars were also synthesized. The MAA units were introduced via the polymerization of tetrahydropyranyl methacrylate and the acid hydrolysis of the latter after network formation. All the precursors to the (co)networks were characterized in terms of their molecular weights using gel permeation chromatography (GPC). The mass of the extractables from the (co)networks was measured and characterized in terms of molecular weight and composition using GPC and proton nuclear magnetic resonance (1H NMR) spectroscopy, respectively. The degrees of swelling (DS) of all the ampholytic conetworks were measured as a function of pH and were found to present a minimum at a pH value which was taken as the isoelectric point, pI. The DS and the pI values did not present a dependence on conetwork architecture. Finally, DNA adsorption studies onto the ampholyte conetworks indicated that DNA binding was governed by electrostatics.
Water absorption and retention of porous ceramics fabricated by waste resources (2008)

Several counter measures have been carried out for mitigating heat island effect. One of those is installing on top of the roof with base materials having planted vegetation. The base materials are required good water absorption and retention which is necessary for the plant to survive. Therefore, in this study, we investigate the relationship between water absorption and water retention within the pore structures of porous ceramics. The raw materials of the ceramics were used waste resources. The structures were changed by different state foaming additive. It was found that the water absorption was dependent on open porosity and the pore size. The water retention, was reduced excessively with high porosity. Accordingly, the control of pore structure is described in details in this study.
Acute and chronic immune biomarker changes during interferon/ribavirin treatment in HIV/HCV co‐infected patients (2014)

Chronic viral infections lead to persistent immune activation, which is alleviated by eradicating or suppressing the infection. To understand the effects of interferon treatment on immune system activation by chronic infections, we evaluated kinetic patterns of a broad spectrum of serum biomarkers during HCV treatment in HIV/HCV co-infected patients. HCV viral load and 50 biomarkers were analysed at baseline and 27 time points during pegylated interferon-alpha and ribavirin (IFN/RBV) treatment of 12 HIV/HCV co-infected patients. We evaluated biomarker changes from baseline for each time point and biomarker correlations with clinical parameters, treatment response and liver histopathology. IL-1α, IL-12p40, IL-1RA, IP-10, MIG, MIP-1α/1β, HGF, sCD40L, TRAIL and leptin increased in the first day. IL-12p70, IL-17A, IL-10, GROα, IL-8, MCP-3, IL-4 and M-CSF peaked later during week 1. IL-1α, HGF, IP-10, MIP-1α, TRAIL, sCD40L, IL-10, IL-12p70, MCP-3, FGFb, ENA-78, TGF-β, IL-2, IFN-γ, IL-6, IL-15, IL-7 and PDGF-BB decreased below baseline over the course of treatment. Higher BMI, baseline HCV viral load and leptin levels were associated with lack of sustained virologic response. ENA-78 was associated with sustained viral response. Positive correlations were found between liver inflammation and baseline CD4 count, sVCAM and HGF; fibrosis stage and HGF; liver steatosis, BMI and leptin. Our findings suggest IFN/RBV treatment initially increases levels of several biomarkers, but eventually leads to a decline in many immune markers. These findings shed light on the relationship between IFN treatment and immune activation by chronic viral infections, such as HCV.
Initial Stages of Oxidation on Graphitic Surfaces: Photoemission Study and Density Functional Theory Calculations (2009)

The initial oxidation stages of perfect and defective graphitic surfaces exposed to atomic oxygen have been studied with a combined high-resolution photoemission spectroscopy (HR-PES) and density functional theory (DFT) computational approach. The resulting oxygen-containing surface functional groups are identified by analyzing the multicomponent C 1s and O 1s core level spectra that are then interpreted on the basis of DFT calculations. In the initial oxidation stage, epoxy groups are formed on perfect graphene, whereas the preferential adsorption of the O atoms on the vacancies of the defective surfaces results in structures containing pairs of oxygen atoms in ether and carbonyl (semiquinone) configurations. The formation of these functional groups is preceded by metastable structures consisting of single O atoms occupying single C vacancies.
Phase II Study of Oxaliplatin and Fluorouracil in Taxane- and Anthracycline-Pretreated Breast Cancer Patients (2002)

This oxaliplatin/5-FU combination is effective with an excellent safety profile in anthracycline/taxane-pretreated ABC patients, showing encouraging activity in patients with anthracycline/taxane-resistance or visceral disease.
A Case of Gastric Metastasis of Hepatocellular Carcinoma (2016)

症例は59歳，男性．2005年より肝細胞癌および再発に対しラジオ波焼灼術を施行．2007年８月，門脈腫瘍栓（Vp3）を伴う再発に対し肝動注化学療法を施行後，肝右葉切除術および門脈腫瘍栓摘出術を施行．その後も繰り返す再発にラジオ波焼灼術や肝動脈化学塞栓術で治療しながら経過観察していたところ，2009年12月，上部消化管内視鏡検査で胃噴門部に易出血性の巨大な不整形の腫瘤性病変を認め，生検にて肝細胞癌の胃転移と診断され，胃全摘術を施行した．病理学的に胃壁内の静脈内に腫瘍栓が認められており，経門脈的に転移したと考えられた．術後経過は良好であり，術後21日目に退院となったが，その後肺転移，脳転移をきたし，胃全摘術後２年３カ月で脳転移巣からの出血により死亡した．肝細胞癌の胃転移は比較的稀であり，若干の文献的考察を加え報告する．
ChemInform Abstract: Antifungal Agents. Part 30. Novel Substituted 3‐(2‐Furanyl)‐3‐(1H‐imidazol‐1‐ylmethyl)‐2‐methyl‐5‐phenyl(or phenyloxymethyl)isoxazolidines. (1990)

Abstract The in vitro antifungal activity of the title compounds (III) and (IV) is investigated.
Neutron star properties with in-medium vector mesons (2002)

We explore the impact of in-medium modification of the properties of vector mesons on the nuclear equation of state and neutron star properties. It is found that in-medium modifications stiffen the nuclear equation of state considerably. If this feature has its correspondence in the full treatment of dense hadronic matter, then very little room is left for the existence of exotic phases like quark matter or boson condensates in the centers of neutron stars of canonical mass.
An access control for IoT based on network community perception and social trust against Sybil attacks (2021)

Summary The evolution of the Internet of things (IoT) has increased the connection of personal devices, mainly taking into account the habits and behavior of their owners. These environments demand access control mechanisms to protect them against intruders, like Sybil attacks, that can compromise data privacy or disrupt the network operation. The social IoT paradigm enables access control systems to aggregate community context and sociability information from devices to enhance robustness and security. This work introduces the ELECTRON mechanism to control access in IoT networks based on social trust between devices to protect the network from Sybil attackers. ELECTRON groups IoT devices into communities by their social similarity and evaluates their social trust, strengthening the reliability between legitimate devices and their resilience against the interaction of Sybil attackers. NS‐3 simulations show the ELECTRON performance under Sybil attacks on several IoT communities so that it has gotten to detect more than 90% of attackers in a scenario with 150 nodes into offices, schools, gyms, and parks communities, and in other scenarios for same communities, it achieved around of 90% of detection. Furthermore, it provided high accuracy, over 90%–95%, and false positive rates closer to zero.
A Highly cis-Selective Synthesis of 2-Ethynylaziridines by Intramolecular Amination of Chiral Bromoallenes:  Improvement of Stereoselectivity Based on the Computational Investigation (2002)

The base-mediated intramolecular amination of bromoallenes having an axial chirality is described. The treatment of (4S,aR)-4-alkyl-4-[N-(arylsulfonyl)amino]-1-bromobuta-1,2-dienes with NaH in DMF affords 2,3-cis-2-ethynylaziridines in good to excellent selectivity (2,3-cis:trans = 92:8-99:1). The reaction of (4S,aS)-bromoallenes with NaH/DMF also gives 2,3-cis-2-ethynylaziridines selectively (79:21-91:9). These experimental results have been rationalized by B3LYP density functional calculations together with the 6-31+G(d) basis set and the Onsager solvation model. The transition structures for cis-aziridine formation of both (4S,aR)- and (4S,aS)-bromoallenes in DMF are favored over the corresponding trans transition structures by 4.35 and 1.41 kcal/mol, respectively. Furthermore, the calculations predicted that a less polar solvent gives higher cis selectivity for (4S,aS)-bromoallenes. In fact, improvement of the cis selectivity to 99:1 has been realized by using a less polar solvent such as THF. The cyclization of bromoallenes bearing a beta- or gamma-amino group also affords four- and five-membered azacycles in a highly cis-selective manner.
Activation Energy for Dc-drift in X-cut LiNbO_3 Optical Intensity Modulators (1998)

Existence of a wafer axial dependency in the activation energy (Ea) for the dc-drift of LiNbO3 modulators has been experimentally found. The Ea for the x-cut modulators is derived to be 0.2~0.5 eV, and 1 eV for the z-cut ones.
Presence of type I and VI collagen mRNAs in endothelial cells in cutaneous neurofibromas. (1991)

In situ hybridization and peroxidase anti-peroxidase immunodetection were used in the same tissue sections to elucidate the spatial distribution of collagen gene expression in cutaneous neurofibromas, particularly in relation to blood vessels; the latter structures were identified by the presence of factor VIII-related antigen. The data indicate a clear relationship between the vascular structures and sites of locally elevated expression of type I and VI collagen genes. Specifically, some, but not all, blood vessels were surrounded by stromal cells highly active in expressing pro alpha 1(I) and alpha 2(VI) collagen genes. Furthermore, these genes were expressed by a subpopulation of endothelial cells within the walls of blood vessels traversing the lesion. To quantitate the overall expression of five genetically distinct collagen genes in cutaneous neurofibromas, we performed Northern analyses and slot blot hybridizations with pro alpha 1 (I), pro alpha 2 (I), pro alpha 1 (III), pro alpha 1 (IV) and alpha 2(VI) collagen cDNAs. Although the mRNA levels for all five genes were slightly increased in neurofibroma tissue, only the abundance of alpha 2(VI) collagen mRNAs was significantly elevated, as compared with normal skin. We conclude that endothelial cell populations with different levels of collagen gene expression exist within cutaneous neurofibromas: some are actively expressing type I and VI collagen genes, whereas in other the expression of these genes is effectively down-regulated. The markedly elevated steady-state levels of type VI collagen mRNAs suggest that synthesis of type VI collagen may contribute to the growth and architecture of cutaneous neurofibromas.
Scenario-based threat metric evaluation based on the highd dataset (2020)

Scenario-based approaches have gained popularity in the context of automated vehicles. As in any model-based approach, validation to real data needs to be considered. This work studies concrete scenarios based on real data from a large-scale and open road user trajectory dataset. In particular, we detail on cut-ins and (hard) braking maneuvers and study them based on existing threat metrics. In this work, we present the complete workflow starting from the pre-processing and validation of the data, the definition of concrete scenarios based on how we extract them from the dataset and their evaluation based on several threat metrics. We identify peculiarities of the dataset itself, as well as of the driving behavior of vehicles therein. As this work relies on an open dataset, results can be reproduced and readily compared.
Use time series NDVI and EVI to develop dynamic crop growth metrics for yield modeling (2020)

The normalized difference vegetation index (NDVI) and enhanced vegetation index (EVI) derived from Moderate Resolution Imaging Spectroradiometer (MODIS) satellite imagery are widely used for crop yield analysis. However, the growth metrics derived from the MODIS NDVI or EVI have so far not been explored and applied to crop yield yet. To the best of our knowledge, this study is the first to design NDVI- and EVI-based crop growth metrics, which biometrically capture the status and trend of crop growth and thus could be more powerful for growth yield management. We developed 19 NDVI- and EVI-based growth metrics, respectively, to monitor crop growth and yield, which is based on a time series of MODIS Terra 16-day 250 m data product from 2000 to 2018. Among the NDVI- and EVI-based vegetation growth metrics (VGM), the maximum (VGMmax), the integrated (VGMinteg), the sum of green-up (VGMsumgrn), the 70 days growth stage (VGM70), 85 days growth stage (VGM85), and 98 days growth stage (VGM98), the sum of 85 days growth stage (VGM85total), and the sum of 98 days growth stage (VGM98total) are mentionable. In this study, we implemented these crop growth metrics for soybean crop yield modeling at Mississippi Delta, Mississippi, USA. Soybean is a major crop cultivated in this region that is consisted of a total of 18 counties with similar agricultural cropping patterns. We observed that NDVI- and EVI-based VGMmax, VGM70, VGM85, VGM98total fitted models best with R-Square about 0.95. Using cross-validation of 80% train and 20% test size, we found NDVI-based VGM85 (e.g., normalized mean prediction error (NMPE) = 0.034) and EVI-based VGMmax (NMPE = 0.033) were the best fit linear yield models for this region. Designing novel crop growth indices based on crop phenological and ecological characteristics, this study further showed NDVI- and EVI-based growth metrics for crop growth monitoring and yield modeling. These growth metrics can be applied to other types of crop monitoring in different climate zones.