gebhart/patrepeval huggingface dataset:
Enhancing the Adaptability of the Deep-Sea Bacterium Shewanella piezotolerans WP3 to High Pressure and Low Temperature by Experimental Evolution under H 2 O 2 Stress (2018)

Oxidative stresses commonly exist in natural environments, and microbes have developed a variety of defensive systems to counteract such events. Although increasing evidence has shown that high hydrostatic pressure (HHP) and low temperature (LT) induce antioxidant defense responses in cells, there is no direct evidence to prove the connection between antioxidant defense mechanisms and the adaptation of bacteria to HHP and LT. In this study, using the wild-type (WT) strain of a deep-sea bacterium, <i>Shewanella piezotolerans</i> WP3, as an ancestor, we obtained a mutant, OE100, with an enhanced antioxidant defense capacity by experimental evolution under H<sub>2</sub>O<sub>2</sub> stress. Notably, OE100 exhibited better tolerance not only to H<sub>2</sub>O<sub>2</sub> stress but also to HHP and LT (20 MPa and 4°C, respectively). Whole-genome sequencing identified a deletion mutation in the <i>oxyR</i> gene, which encodes the transcription factor that controls the oxidative stress response. Comparative transcriptome analysis showed that the genes associated with oxidative stress defense, anaerobic respiration, DNA repair, and the synthesis of flagella and bacteriophage were differentially expressed in OE100 compared with the WT at 20 MPa and 4°C. Genetic analysis of <i>oxyR</i> and <i>ccpA2</i> indicated that the OxyR-regulated cytochrome <i>c</i> peroxidase CcpA2 significantly contributed to the adaptation of WP3 to HHP and LT. Taken together, these results confirmed the inherent relationship between antioxidant defense mechanisms and the adaptation of a benthic microorganism to HHP and LT.<b>IMPORTANCE</b> Oxidative stress exists in various niches, including the deep-sea ecosystem, which is an extreme environment with conditions of HHP and predominantly LT. Although previous studies have shown that HHP and LT induce antioxidant defense responses in cells, direct evidence to prove the connection between antioxidant defense mechanisms and the adaptation of bacteria to HHP and LT is lacking. In this work, using the deep-sea bacterium <i>Shewanella piezotolerans</i> WP3 as a model, we proved that enhancement of the adaptability of WP3 to HHP and LT can benefit from its antioxidant defense mechanism, which provided useful insight into the ecological roles of antioxidant genes in a benthic microorganism and contributed to an improved understanding of microbial adaptation strategies in deep-sea environments.
Paleomagnetism of Rocks from the Island of Viti Levu, Fiji (1985)

Samples were collected at 19 sites in basalts, andesites, dacites, gabbros, sandstones and limestones in the island of Viti Levu. They were dated at about 4 to 40 Ma. New age data have been added in 2 sites. After partial demagnetization by alternating fields to remove unstable components of magnetization, the directions of magnetization became well grouped except for the rocks from a few sites. Both normal and reversed directions are present. The volume susceptibility of each specimen has also been measured. Using the susceptibility data the Königsberger ratio has been calculated. The median destractive field and the magnetic grain size have also been determined for each specimen. As the result, the direction of magnetization for each site does not seem to contradict the hypothesis of anticlockwise rotation of the island.
130 Study on Cycloidal Pendulum Type Dynamic Vibration Absorber (2006)

The dynamic absorber has been widely used for suppressing vibration in structures. In practical application, the optimal tuned absorbers are designed and used in terms of natural frequency and additional damping so that resultant frequency response becomes fully reduced. However, damping performance of ordinal pendulum system may be influenced by levels of excitation because of intrinsic nonlinearity in system which leads to slight change in natural frequency. The present paper deals with a study of new type pendulum dynamic absorber. It is known that pendulum moving along cycloidal curve strictly keeps uniform period. Both analytical and experimental investigations show that a strict optimal damping condition can be satisfied in cycloid pendulum damper, in conjunction with better damping performance compared with normal pendulum.
Prospects for the introduction of targeted antioxidant drugs for the prevention and treatment of diseases related to free radical pathology (2019)

Effective antioxidant therapeutic strategies should include the design of protocols for the inhibition of OST through iron chelation, administration of synthetic and natural antioxidants and enhancement of the antioxidant defences by increasing the production of endogenous antioxidants and activation of antioxidant mechanisms. Different therapeutic strategies apply in the use of antioxidant drugs for one or more targets, for prevention, treatment, or of post-treatment effects and for systematic, long-term or short-term applications. The design of new antioxidant drugs and effective protocols which can include Deferiprone and N-acetylcysteine combinations, could lead to the development of a new class of therapeutics for clinical use.
Heuristic tradeoffs between latency and energy consumption in register assignment (2000)

One of the challenging tasks in code generation for embedded systems is register allocation and assignment, wherein one decides on the placement and lifetimes of variables in registers. When there are more live variables than registers, some variables need to be spilled to memory and restored later. In this paper we propose a policy that minimizes the number of spills — which is critical for portable embedded systems since it leads to a decrease in energy consumption. We argue however, that schedules with a minimal number of spills do not necessarily have minimum latency. Accordingly, we propose a class of policies that explore tradeoffs between assignments leading to schedules with low latency versus those leading to low energy consumption and show how to tune them to particular datapath characteristics. Based on experimental results we propose a criterion to select a register assignment policy that for 99% of the cases we considered minimizes both latency and energy consumption associated with spills to memory.
Novel Gag-Pol Frameshift Site in Human Immunodeficiency Virus Type 1 Variants Resistant to Protease Inhibitors (1998)

Human immunodeficiency virus type 1 (HIV-1) variants resistant to protease inhibitors have been shown to contain a mutation in the p1/p6 Gag precursor cleavage site. At the messenger RNA level, this mutation generates a U UUU UUU sequence that is reminiscent of the U UUU UUA sequence required for ribosomal frameshifting and Gag-Pol synthesis. To test whether the p1/p6 cleavage site mutation was generating a novel frameshift site, HIV sequences were inserted in translation vectors containing a chloramphenicol acetyltransferase (CAT) reporter gene requiring -1 frameshifting for expression. All sequences containing the original HIV frameshift site supported the synthesis of CAT but expression was increased 3- to 11-fold in the presence of the mutant p1/p6 sequence. When the original frameshift site was abolished by mutation, expression remained unchanged when using constructs containing the mutant p1/p6 sequence, whereas it was decreased 2- to 4.5-fold when using wild-type p1/p6 constructs. Similarly, when introduced into HIV molecular clones, the p1/p6 mutant sequence supported Gag-Pol synthesis and protease activity in the absence of the original frameshift site, indicating that this sequence could also promote ribosomal frameshifting in virus-expressing cells.
Back Cover (2020)

The back cover image is based on the Research Article A method for scaling impressions of a scene by Tzuhao Liu et al., https://doi.org/10.1002/col.22516.
Robust multi-objective control for systems involving human-in-the-loop passivity constraints with application to electric power steering (2010)

This paper is concerned with the stability and synthesis of fixed structure controllers satisfying robust multi-objective H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sub> performance for systems involving human-in-the-loop actuation. Closed loop robust stability conditions are studied for both sector-bounded and passive uncertainties. An iterative algorithm comprised of both genetic algorithms and semi-definite programming is presented for control synthesis purposes. This approach is used to design a 2-degree-of-freedom controller for an Electric power steering system. Experimental results using hardware-in-the-loop setup are given. The results indicate that the control design did satisfy the criteria for robust performance.
Theoretical and Experimental Study of Hydrodynamically Modulated Current-Potential Curves at Rotating Disk Electrodes under Conditions of Mixed Electron and Mass Transfer Control (1974)

When a rotating disk electrode is subjected to an appropriate superimposed sinusoidal modulation of its rotation speed, the modulated component of the disk current may be governed by both mass transport and kinetic processes. In this study, mixed electron transfer and convective diffusion control conditions are considered, and the relationships among modulated current response, average current, potential, relevant species concentrations, and kinetic and transport parameters are derived. The theoretical predictions are experimentally verified for the two limiting cases of totally reversible and irreversible reactions, and for the general case of mixed control.
Oligomerization of Aromatic Tertiary Amines (1999)

Abstract The oligomerization of some tertiary aromatic amines was studied using ferric chloride in a variety of solvent. The predominant dimer formation of triphenylamine (TPA) was observed in chloroform at 0 °C where concentration of TPA was 0.125 mmol/l and the molar ratio of ferric chloride to TPA was 4. Except for N-methyldiphenylamine, high molecular weight oligomers were formed in a variety of solvents.
Figure S2 from Discovery of Targets for Immune–Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha (2023)

&lt;p&gt;ESRRA inhibition induces antitumor immunity in vivo.&lt;/p&gt;
An Investigation of Block Coding for Laplacian Noise (2012)

In many communication channels, the ambient disturbance is known through experimental evidence as well as theoretical considerations to deviate strongly from the Gaussian model. In order to evaluate the performance of digital signaling in such channels, the non-Gaussian noise must be properly modeled. The Laplace distribution is used here to model the non-Gaussian noise and study the performance of communication systems employing block data transmission in the presence of impulsive noise. Analytical expressions for assessing codeword error probability and bit error probability are derived for hard-decision decoders, soft-decision decoders and optimum maximum likelihood detectors in both nonfading and quasi-static Rayleigh fading scenarios. Numerical results are presented for different codes, block sizes and error rate levels. The characteristics of error performance are discussed for both nonfading and quasi-static Rayleigh fading channels.
Technical and economic feasibility of a high-temperature self-assembling battery (2006)

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2006.
Bone Marrow Transplantation in Acid Sphingomyelinase-Deficient Mice: Engraftment and Cell Migration Into the Brain as a Function of Radiation, Age, and Phenotype (1997)

Types A and B Niemann-Pick disease (NPD) result from the deficient activity of the lysosomal hydrolase, acid sphingomyelinase (ASM). A long-term goal of our research is to evaluate the effects of bone marrow transplantation (BMT) and hematopoietic stem cell gene therapy (HSCGT) on the NPD phenotype. As an initial step toward this goal, we have undertaken a study aimed at optimizing hematopoietic cell engraftment in acid sphingomyelinase "knock-out" (ASMKO) mice. Several parameters were analyzed, including the effects of radiation and donor cell number on survival and engraftment of newborn and adult animals, the number of donor cells detected in the brain posttransplantation, and the levels of ASM activity achieved in the brain. A total of 202 ASMKO and normal animals were transplanted and studied, and the overall conclusions were: (1) newborn ASMKO animals were more susceptible to radiation-induced mortality than normal animals, (2) at low radiation doses, increasing the donor cell number improved engraftment, while this was less evident at the higher radiation doses, (3) engraftment was easier to achieve in normal as compared with ASMKO animals, (4) among newborn transplants, the number of donor cells detected in the brain was directly correlated with engraftment in the blood, (5) more donor cells were detected in the brains of newborn ASMKO animals as opposed to newborn normal animals, and (6) no donor cells were found in the brains of animals transplanted as adults, including those that were highly engrafted in the blood. These results provide important information regarding the design of future BMT and HSCGT studies in ASMKO mice and other mouse models and demonstrate the potential of altering the NPD phenotype by these therapeutic strategies.
Protein Deimination in the Rat Brain: Generation of Citrulline-Containing Proteins in Cerebrum Perfused with Oxygen-Deprived Media (2000)

The central nervous system contains the posttranslational modification enzyme, peptidylarginine deiminase (PAD; EC 3.5.3.15) type II. This enzyme catalyzes the deimination of arginine residues of proteins in a calcium ion-dependent manner, thereby, forming citrulline residues. Previously, we found postmortem deimination of glial fibrillary acidic protein in rat spinal cord. In the present study, therefore, we studied the deimination further as a possible cause of neurodegeneration in cerebrum. Additionally, as a model oftissue damage, the effect of oxygen deprivation on protein deimination in rat cerebral tissue was also analyzed by applying systemic perfusion with an emulsion of perfluorochemicals. In the presence of sufficient oxygen, such perfusion caused only negligible formation of citrullinated proteins. However, deprivation of oxygen produced by the perfusion medium resulted in preferential deimination of many kinds of high-molecular-weight (>55 kDa) proteins. Deiminated protein immunoreactivity was found in all regions of the cerebrum but was relatively more intense in the hypothalamus and the lateral amygdaloid nucleus. Most of the deiminated protein-positive cells seemed to be astrocytes. Some neuronal cells in the lateral amygdaloid nucleus became positive after prolonged perfusion with oxygen-deprived medium, although the PAD immunoreactivity appeared only in astrocytes. These results indicate that PAD type ll localizes mainly in astrocytes of the cerebrum and that a consequence of hypoxia is enzyme activation that deiminates proteins in astrocytes and some neurons. Such deimination of proteins may be a useful marker of nerve cell degeneration.
ChemInform Abstract: PREPARATION AND REACTION OF STABLE BETA‐KETO‐BIS‐SULFONIUMYLID (1973)

Abstract Die Synthese von neuen, carbonylstabiliserten Bis‐sulfoniumyliden, wie Bis‐ (äthylmethyl‐sulfonium)‐p ,p′‐o xybiphenacylid (IV), p‐Diacetylbenzol‐bis‐ (äthylmethylsulfonium)‐ylid (IX)‐und Bis‐(äthylmethylsulfonium)‐p,p′‐biphenacylid (XII), wird beschrieben.
Laser-induced gas plasma etching of fused silica under ambient conditions (2012)

Laser machining of optics to mitigate surface defects has greatly enhanced the ability to process large optics such as those found in fusion-class lasers. Recently, the use of assist reactive gases has shown promise in enhancing manifold etching rates relative to ambient conditions for CW-laser exposures. However, these methods still require significant heating of the substrate that induce residual stress, redeposit coverage, material flow, and compromise the final surface finish and damage threshold. While very reactive fluorinated gases are capable to reduce treatment temperatures even further, they are also inherently toxic and not readily transferable to large processing facilities. In this report, we look at whether a short-lived gas plasma could provide the safe and effective etchant sought, while still reducing the thermal load on the surface. We test this approach using a YAG laserinduced gas plasma to act as a source of the etchant for fused silica, a common optical material. The configuration and orientation of the beam and optical apparatus with respect to the surface was critical in preventing surface damage while etching the surface. Results with N<sub>2</sub> and air gas plasmas are shown, along with a description of the various experimental implementations attempted.
Effects of Random Dopant Fluctuations (RDF) on the Single Event Vulnerability of 90 and 65 nm CMOS Technologies (2007)

Random dopant fluctuation (RDF) induced threshold voltage variations affect two critical parameters used as a measure of single event (SE) hardness (i) single event transient (SET) pulse widths and (ii) critical charge . This causes an increase in the spread of SET pulse widths in sequential logic circuits and in the required for single event upsets (SEUs) in static random access memory cells (SRAMs). Monte Carlo simulations show this can affect the hardness characterization in a commercial 90 nm process and a generic 65 nm technology. This necessitates statistical design approaches for validating conventional hardening schemes, to assure a required level of radiation tolerance in these deep sub-micron technologies.
Self-assembled Nanomaterials for Hybrid Electronic and Photonic Systems (2015)

This grant studied DNA nanostructures and their applications in a variety of ways, including: (1) the development of thermo-mechanical models, (2) the creation of a new field for circuits of devices that work based on fluorescence resonance energy transfer (RET), ( 3) a new kind of RET switch and several other novel device circuits, and (4) applications in network-on-chip, information assurance, and stochastic computing.
[Immunology in the medical practice. XXVII. Mannose-binding lectin, an important link for nonspecific or hereditary immune reaction]. (2000)

In the course of the past two decennia, a 3rd route of complement activation (next to the classical and the alternative routes) has been identified: the lectin route in which mannose-binding lectin (MBL) plays an essential role. MBL is produced in the liver. From the phylogenetic and functional points of view, complement activation via MBL falls in between the alternative and the classical routes and combines the advantages of the former (an early response, without the intervention of antibodies) with those of the latter (high specificity). The binding of MBL to the surface of a microorganism results in the activation of two serine proteases (MASP1 and MASP2) that are coupled to MBL. These enzymes can activate C4 and C2 so that, via the MBL route, the C3-convertase of the classical route (C4b2b) is produced long before there are any specific antibodies. The gene for MBL is located on the long arm of chromosome 10 and consists of a promoter gene and 4 exons coding for the protein. The prevalence of mutations in the MBL gene is about 10%, but in Africa South of the Sahara it is as high as 30%. MBL deficiency predisposes both children and adults to all sorts of infectious diseases, chronic diarrhoea, tonsillitis, otitis media, pneumonia, (meningococcal) meningitis, sepsis and osteomyelitis. Remarkably, MBL deficiency may actually be advantageous in some infections, because certain microorganisms use MBL or complement to invade the cell.
7/5nm logic manufacturing capabilities and requirements of metrology (2018)

This paper will provide an update to previous works [2][4][9] to our view of the future for in-line high volume manufacturing (HVM) metrology for the semiconductor industry, concentrating on logic technology for foundries. First, we will review of the needs of patterned defect, critical dimensional (CD/3D), overlay and films metrology, and present the extensive list of applications for which metrology solutions are needed. We will then update the industry’s progress towards addressing gating technical limits of the most important of these metrology solutions, highlighting key metrology technology gaps requiring industry attention and investment.
Wegener??s Granulomatosis Presenting as Dacryoadenitis (1991)

Wegener's granulomatosis is a life-threatening condition characterized by the triad of necrotizing granulomatous inflammation of the respiratory tract, vasculitis, and glomerulonephritis. During early stages of the disease, some patients may present with only one or two components of the triad. Other patients may be affected by the limited form of Wegener's which lacks the renal involvement. We report an 18-year-old female who initially presented with bilateral dacryoadenitis. A lacrimal gland biopsy was consistent with Wegener's granulomatosis. A few months later she developed glomerulonephritis and responded well to cyclophosphamide treatment. Wegener's granulomatosis remains a diagnostic challenge and is frequently underdiagnosed. Early diagnosis is crucial in saving many lives because the disease is potentially curable with cytotoxic therapy. Dacryoadenitis may be one of the initial presentations of Wegener's granulomatosis.
Epigenomics meets splicing through the TETs and CTCF (2016)

The cause and consequence of enriched DNA methylation within gene bodies of actively transcribed genes is a mystery that has garnered significant attention in recent years. In particular, elevation...
A Biological sequence compression algorithm based on Variable length LUT and LZ 77 (2010)

This article introduces a new improved Biological sequence compression algorithm which is based on Variable length LUT and LZ77 algorithm and also it combines a LUT-based pre-coding routine and LZ77 compression routine. This algorithm can gains compression ratio lower than the previous Biological Sequence compression algorithm because due to the dynamic creation of look up table with in the encoding and decoding process. The overheads are reduces to maintain look up table and also the execution time decreases, other advantage are leaser memory occupation and easier implementation.
Effect Of Dynamic Stall, Finite Aspect Ratio And Streamtube Expansion On Vawt Performance Prediction Using The Be-M Model (2012)

A multiple-option analytical model for the evaluation of the energy performance and distribution of aerodynamic forces acting on a vertical-axis Darrieus wind turbine depending on both rotor architecture and operating conditions is presented. For this purpose, a numerical algorithm, capable of generating the desired rotor conformation depending on design geometric parameters, is coupled to a Single/Double-Disk Multiple-Streamtube Blade Element – Momentum code. Both single and double-disk configurations are analyzed and model predictions are compared to literature experimental data in order to test the capability of the code for predicting rotor performance. Effective airfoil characteristics based on local blade Reynolds number are obtained through interpolation of literature low-Reynolds airfoil databases. Some corrections are introduced inside the original model with the aim of simulating also the effects of blade dynamic stall, rotor streamtube expansion and blade finite aspect ratio, for which a new empirical relationship to better fit the experimental data is proposed. In order to predict also open field rotor operation, a freestream wind shear profile is implemented, reproducing the effect of atmospheric boundary layer.