gebhart/patrepeval huggingface dataset:
Fast and flexible string matching by combining bit-parallelism and suffix automata (2000)

The most important features of a string matching algorithm are its efficiency and its flexibility. Efficiency has traditionally received more attention, while flexibility in the search pattern is becoming a more and more important issue. Most classical string matching algorithms are aimed at quickly finding an exact pattern in a text, being Knuth-Morris-Pratt (KMP) and the Boyer-Moore (BM) family the most famous ones. A recent development uses deterministic "suffix automata" to design new optimal string matching algorithms, e.g. BDM and TurboBDM. Flexibility has been addressed quite separately by the use of "bit-parallelism", which simulates automata in their nondeterministic form by using bits and exploiting the intrinsic parallelism inside the computer word, e.g. the Shift-Or algorithm. Those algorithms are extended to handle classes of characters and errors in the pattern and/or in the text, their drawback being their inability to skip text characters. In this paper we merge bit-parallelism and suffix automata, so that a nondeterministic suffix automaton is simulated using bit-parallelism. The resulting algorithm, called BNDM, obtains the best from both worlds. It is much simpler to implement than BDM and nearly as simple as Shift-Or. It inherits from Shift-Or the ability to handle flexible patterns and from BDM the ability to skip characters. BNDM is 30%-40% faster than BDM and up to 7 times faster than Shift-Or. When compared to the fastest existing algorithms on exact patterns (which belong to the BM family), BNDM is from 20% slower to 3 times faster, depending on the alphabet size. With respect to flexible pattern searching, BNDM is by far the fastest technique to deal with classes of characters and is competitive to search allowing errors. In particular, BNDM seems very adequate for computational biology applications, since it is the fastest algorithm to search on DNA sequences and flexible searching is an important problem in that area. As a theoretical development related to flexible pattern matching, we introduce a new automaton to recognize suffixes of patterns with classes of characters. To the best of our knowledge, this automaton has not been studied before.
Pain treatment by transcutaneous electrical nerve stimulation. A practical manual (1989)

Pain: July 1989 - Volume 38 - Issue 1 - p 119-120 doi: 10.1016/0304-3959(89)90084-5
P-SAMS: a web site for plant artificial microRNA and synthetic <i>trans</i>-acting small interfering RNA design (2015)

acarbonell@ibmcp.upv.es or nfahlgren@danforthcenter.org.
The effect of surface roughness on direct wafer bonding (1999)

A theory is presented which describes the initial direct wafer bonding process. The effect of surface microroughness on the bondability is studied on the basis of the theory of contact and adhesion of elastic solids. An effective bonding energy, the maximum of which is the specific surface energy of adhesion, is proposed to describe the real binding energy of the bonding interface, including the influence of the wafer surface microroughness. Both the effective bonding energy and the real area of contact between rough surfaces depend on a dimensionless surface adhesion parameter, θ. Using the adhesion parameter as a measure, three kinds of wafer contact interfaces can be identified with respect to their bondability; viz. the nonbonding regime (θ &gt;12), the bonding regime (θ &lt;1), and the adherence regime (1&lt;θ &lt;12). Experimental data are in reasonable agreement with this theory.
A Combined Chemical and Electrochemical Approach Using Bis(trifluoroacetoxy)iodobenzene and Glucose Oxidase for the Detection of Chlorinated Phenols (1997)

A novel electrocatalytic approach using a chemical reaction and an enzymatic reaction has been developed for the measurement of 18 chlorophenol congeners, including highly chlorinated pollutants such as pentachlorophenol, 2,3,5,6-tetrachlorophenol, 2,3,4,6-tetrachlorophenol, and several trichlorophenols. Chlorophenols were oxidized to chlorobenzoquinones with very high yields using bis(trifluoroacetoxy)iodobenzene in 0.1 M trichloroacetic acid, pH 1.5, at ambient temperature. UV-visible spectrophotometry, cyclic voltammetry, and HPLC have been used to characterize the reaction products and yields. Together with glucose oxidase immobilized on a working glassy carbon electrode (+0.45 V vs Ag/AgCl), chlorinated benzoquinones have been demonstrated to be efficient mediators in a glucose oxidase/glucose system. In this approach, glucose oxidase was readily reduced by excess glucose to provide a non-rate-limiting source of electron flow toward the electrode. The oxidation products of chlorophenols then recycled the reduced glucose oxidase to its active oxidative state, i.e., mediating the rate-limiting electron transfer from the enzyme to the electrode. At pH 3.5, linear behavior of the current response was observed up to 200 nM for all chlorophenol oxidation products. The detection limit of this method for both pentachlorophenol and 2,3,5,6-tetrachlorophenol was about 4 nM, which is close to the maximum allowable contamination level of pentachlorophenol in water samples (2.7 nM). The detection limit obtained for pentachlorophenol could also be considered superior to the result obtained with the PCP immunoassay technology (13.3 nM).
Fast Methods for Solving Rough Contact Problems: A Comparative Study (1999)

A realistic description of rough surfaces will generally involve very large arrays of surface height data, which makes the application of conventional numerical methods of contact mechanics to rough contact analyses impractical. Recently, two fast numerical techniques have been applied to rough contact problems: the multi-level multi-summation (MLMS) and the fast Fourier transform (FFT). In this work, the computational efficiency of the two methods is compared by applying them to an example concentrated contact problem. It is shown that to achieve a numerical accuracy comparable to that of MLMS, the grid on which FFT is performed needs to be extended far beyond the contact area, which results in a dramatic increase in the computation time. When such a high accuracy is unnecessary. FFT can be applied on a smaller grid. However, the computational speed of MLMS can also be increased in this case by modifying certain algorithm parameters. Numerical results demonstrate that MLMS is more advantageous than FFT for solving three-dimensional concentrated contact problems, both when the maximum possible accuracy is desired and when a moderate accuracy goal is specified. [S0742-4787(00)00601-9]
Multiple‐view Shape and Deformation Measurement by Combining Fringe Projection and Digital Image Correlation (2011)

Abstract: We present a new method that combines the fringe projection and the digital image correlation (DIC) techniques on a single hardware platform to simultaneously measure both shape and deformation fields of three‐dimensional (3‐D) surfaces with complex geometries. The method in its basic form requires only a single camera and single projector, but this can be easily extended to a multi‐camera multi‐projector system to obtain complete 360° measurements. Multiple views of the surface profile and displacement field are automatically co‐registered in a unified global coordinate system, thereby avoiding the significant errors that can arise through the use of statistical point cloud stitching techniques. Experimental results from a two‐camera two‐projector sensor are presented and compared with results from both a standard stereo‐DIC approach and a finite element model.
Mechanism and Specificity of DNA Strand Exchange Catalyzed by Vaccinia DNA Topoisomerase Type I (2010)

The type I DNA topoisomerase from vaccinia virus (vTopo) forms a reversible covalent 3'-phosphotyrosyl linkage with a single strand of duplex DNA at the preferred sequence 5'-(C/T)CCTTp downward arrowN(-1)N(-2)N(-3)-3'. The enzyme-DNA covalent adduct is recombinogenic in cells, because the nicked strand downstream of the cleavage site can dissociate and be replaced by another DNA strand, potentially resulting in genome rearrangements if the enzyme executes strand ligation. Topo I could play an active role in strand exchange, either by altering the kinetics or thermodynamics of DNA strand binding or by serving as a proofreading gate to prevent ligation of incoming DNA strands containing mismatches. To address these questions, we have measured the kinetic and thermodynamic parameters for strand annealing to a purified vaccinia Topo I-DNA (vTopo-DNA) covalent complex containing a single-strand overhang and then compared them with the same overhang duplex in the absence of vTopo. We found that vTopo accelerates the strand association rate by 2-fold but has no effect on the rate of strand dissociation. vTopo has a similar small effect on the annealing parameters of a series of DNA strands containing single mismatches. In contrast, single base mismatches at the -1, -2, or -3 positions decreased the forward rate and equilibrium constant for reversible strand ligation by 10-fold. These data establish that while vTopo is a bystander during the annealing step of strand exchange, the enzyme strongly discriminates against mismatches close to the cleavage site during the subsequent events leading to strand ligation. A mechanism emerges where vTopo oscillates between an open state where the downstream DNA segment does not interact with the enzyme and a closed state where catalytically important contacts are formed with this region. This oscillation between an open and closed state of the covalently bound enzyme is likely important for regulating the number of DNA superhelical turns that are removed during the lifetime of the covalent complex with supercoiled substrates.
Synthesis of vitamin K<sub>1</sub> analogs. A new class of vitamin K<sub>1</sub> antagonists (1970)

The synthesis of two analogs of vitamin K 1 , namely, 2-chloro (2) and 2-bromo (3) analogs, is described. The separation of cis and trans isomers of both these compounds on preparative t.l.c. is reported along with the spectral data.
Efficient Generation of Dopamine Neurons from Human Embryonic Stem Cells (2007)

In this chapter, we introduce a co-culture protocol for human embryonic stem (hES) cell differentiation in which dopamine (DA) neurons with midbrain-specific markers are efficiently derived. Human ES cells on a feeder layer of stromal cells are induced to differentiate into neuroepithelial or neural precursor cells with embryonic midbrain precursor properties. The resulting neural precursor cells are then selectively expanded and serially passaged to obtain a large, homogeneous population of these cells. Under the conditions for terminal differentiation, the majority of hES-derived neural precursors differentiate into neuronal cells that are positive for DA neuronal markers such as tyrosine hydroxylase (TH) and function in vitro as presynaptic DA neurons.
Optimum recall period for reporting persons injured in motor vehicle accidents. (1972)

Details of injury on accident reports were compared with those later remembered by the victims in interviews, to determine if the recall period could be increased without jeopardizing accuracy, and to identify a possible optimum length of recall time. A sample was selected from persons involved in injury-producing motor vehicle accidents in Durham, Orange, and Wake counties of North Carolina, February 1966-February 1967. Detailed statistical data are tabulated. The study indicated that the optimum recall period for estimating the total number of persons injured in motor vehicle accidents is less than three months. This is a conservative choice, since the bias component of relative root mean square error, which is a function of the ability of a responder to recall a motor vehicle injury, increases over time at a rate greater than that estimated from the methodology study.
A finite element analysis of generalized Newtonian fluids through spiral mandrel dies (1986)

Abstract A method is described which calculates the fluid flow pattern for any generalized Newtonian fluid forced through the narrow annular space between two concentric cylindrical surfaces. The inner surface is engraved with a number of identical equally spaced spiral channels of small constant pitch angle but of varying cross‐sectional area. For equal flow into the spiral passages, the pressure distribution along them is described by a quasi‐linear ordinary difference‐differential equation. A finite element approximation is employed to solve this equation for the pressure and resultant flow field. The method is illustrated by calculating and comparing flow patterns through two different spiral geometries.
Room-temperature continuous wave operation of distributed feedback quantum cascade lasers with watt-level power output (2010)

We demonstrate surface-grating distributed feedback quantum cascade lasers (QCLs) with a watt-level power output at 4.75 μm. A device with a 5 mm cavity length exhibits an output power of 1.1 W in room-temperature cw operation. Single-mode operation with a side mode suppression ratio of 30 dB is obtained in the working temperature of 15–105 °C. A double-lobed far field with negligible beam steering is observed. The significance of this demonstration lies in its simplicity and readiness to be applied to standard QCL wafers with the promise of high-power performances.
Corneal epithelial healing after photorefractive keratectomy: Analytical study (2005)

Analysis of the data shows that epithelial migration along the photoablated corneal surface depends on the ablation pattern. The epithelial sliding is highly influenced by local variations in the curvature of the stromal surface. The data demonstrate that faster epithelial wound healing after PRK is predictive of optimal visual performance.
Langmuir monolayers and Langmuir–Blodgett multilayers containing macrocyclic ionophores (1996)

Macrocyclic ionophores in thin films are of interest for sensors or novel ionophotoswitching devices. Continuing work on floating monolayers and Langmuir–Blodgett multilayers of macrocyclic ionophores—such as crown ether ionophores, cyclodextrins and valinomycin—is reviewed. The figure shows a schematic representation of the complex of valinomycin (a biopolymer based on a 36‐membered ring) with potassium. magnified image
Association of diabetes duration and diabetes treatment with the risk of hepatocellular carcinoma (2010)

Diabetes appears to increase the risk of HCC, and such risk is correlated with a long duration of diabetes. Relying on dietary control and treatment with sulfonylureas or insulin were found to confer the highest magnitude of HCC risk, whereas treatment with biguanides or thiazolidinediones was associated with a 70% HCC risk reduction among diabetics.
Investigation of Fixed Oxide Charge and Fin Profile Effects on Bulk FinFET Device Characteristics (2013)

The effect of positive fixed oxide charge (Q <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</sub> ) on the electrical characteristics of bulk FinFET devices is investigated and newly addressed as a Fin scaling detractor. The aggressively scaled Fin width leads to abnormal subthreshold slope (SS) degradation in nMOS devices even with a long channel length, while pMOS is free of such degradation. This observation is reproduced and analyzed by a well-calibrated TCAD simulation deck with Q <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</sub> introduced. A new Fin profile suppressing the Q <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</sub> effect is proposed, and the benefits of the new profile are predicted in terms of variability reduction and mobility improvement, as well as Q <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</sub> immunity.
RhoA and the Function of Platelet Integrin αIIbβ3 (1998)

Integrins respond to “inside-out” signals, which enable them to bind adhesive ligands, and ligand binding initiates “outside-in” signals that mediate anchorage-dependent cellular responses. RhoA is a GTPase that regulates certain actin rearrangements and transcriptional events. It has also been implicated in integrin signaling, but the exact relationship is not understood. To examine this further, platelets were incubated with C3 exoenzyme to adenine diphosphate (ADP)-ribosylate and inactivate RhoA, and the function of integrin αIIbβ3 was studied. Despite inactivation of ≥ 90% of RhoA, platelets exhibited normal inside-out signaling, as monitored by agonist-induced binding of a fibrinogen-mimetic anti-αIIbβ3 antibody and normal fibrinogen-dependent aggregation. On the other hand, RhoA inactivation decreased the adhesion of agonist-stimulated platelets to fibrinogen (P < .04) and the formation of vinculin-rich focal adhesions in platelets that did adhere (P < .001). These effects were selective because fibrin clot retraction, a response also dependent on αIIbβ3 and actin contractility, was unaffected by C3, as was the content of F-actin in resting or agonist-stimulated platelets. Similar results were obtained in a Chinese hamster ovary (CHO) cell model system of αIIbβ3: C3 exoenzyme (or overexpression of dominant-negative N19RhoA) failed to influence integrin activation state, but it blocked the formation of focal adhesions in cells spread on fibrinogen. These studies establish that RhoA plays a highly selective role in αIIbβ3 signaling, and they identify a subset of responses to integrin ligation that may be uniquely dependent on the actin rearrangements regulated by this GTPase.
Synthesis of <scp>l</scp>-Cysteine and <scp>l</scp>-Cysteic Acid by Paired Electrolysis Method (2004)

Abstract l-Cysteine and l-cysteic acid were synthesized by paired eletrolysis method. A high purity over 98% and high yield over 90% of both products were gained. When current density was 7 A/dm2 and concentration of l-cysteine was 0.6 mol/dm3, the highest current efficiency of anode and cathode was achieved. Total current efficiency was over 180%. The cyclic voltammetry behaviors of hydrobromic acid and cystine showed that a typical EC reaction took place in the anodic cell. The anode reaction and successive chemical reaction accelerated each other to get a high speed and current efficiency.
Strategies for Making More Organs Available for Transplantation (2000)

Organ transplantation has evolved rapidly from the first early successes1 to the current widespread use of donated organs for the treatment of end-stage kidney, heart, and liver failure. With limited supplies of organs and an increasing demand for them, however, many patients who need transplants do not receive them (Figure 1).2 Each year, about 3000 patients in the United States die while waiting for an organ transplant, and about 100,000 potential candidates for transplantation die before they are placed on a waiting list.2 There is an 11 percent annual increase in the number of patients placed on waiting lists for . . .
miRNA-939 regulates human inducible nitric oxide synthase posttranscriptional gene expression in human hepatocytes (2012)

Human inducible nitric oxide synthase (hiNOS) gene expression is regulated by transcriptional and posttranscriptional mechanisms. The purpose of this study was to determine whether specific microRNA (miRNA) directly regulate hiNOS gene expression. Sequence analysis of the 496-bp hiNOS 3'-untranslated region (3'-UTR) revealed five putative miR-939 binding sites. The hiNOS 3'-UTR conferred significant posttranscriptional blockade of luciferase activity in human A549, HCT8, and HeLa cells. The hiNOS 3'-UTR also exerted basal and cytokine-stimulated posttranscriptional repression in an orientation-dependent manner. Functional studies demonstrated that transfection of miR-939 into primary human hepatocytes (HCs) significantly inhibited cytokine-induced NO synthesis in a dose-dependent manner that was abrogated by a specific miR-939 inhibitor. MiR-939 (but not other miRNAs) abolished cytokine-stimulated hiNOS protein in human HC, but had no effect on hiNOS mRNA levels. Site-directed mutagenesis of miR-939 bindings sites at +99 or +112 bp in the hiNOS 3'-UTR increased reporter gene expression. Furthermore, intact miR-939 binding sites at +99 or +112 positions were required for posttranscriptional suppression by miR-939. Cytokine stimulation directly increased miR-939 levels in human HC. Transfection of miR-939 inhibitor (antisense miR-939) enhanced cytokine-induced hiNOS protein and increased NO synthesis in vitro in human HC. Finally, cytokine or LPS injection in vivo in mice increased hepatic miR-939 levels. Taken together, these data identify that miR-939 directly regulates hiNOS gene expression by binding in the 3'-UTR to produce a translational blockade. These findings suggest dual regulation of iNOS gene expression where cytokines induce iNOS transcription and also increase miR-939, leading to translational inhibition in a check-and-balance system.
Overexpression of the rice AKT1 potassium channel affects potassium nutrition and rice drought tolerance (2016)

Potassium (K(+)) is the most important cationic nutrient for all living organisms and has roles in most aspects of plant physiology. To assess the impact of one of the main K(+) uptake components, the K(+) inward rectifying channel AKT1, we characterized both loss of function and overexpression of OsAKT1 in rice. In many conditions, AKT1 expression correlated with K(+) uptake and tissue K(+) levels. No salinity-related growth phenotype was observed for either loss or gain of function mutants. However, a correlation between AKT1 expression and root Na(+) when the external Na/K ratio was high suggests that there may be a role for AKT1 in Na(+) uptake in such conditions. In contrast to findings with Arabidopsis thaliana, we did not detect any change in growth of AKT1 loss of function mutants in the presence of NH4 (+) Nevertheless, NH4 (+)-dependent inhibition was detected during K(+) uptake assays in loss of function and wild type plants, depending on pre-growth conditions. The most prominent result of OsAKT1 overexpression was a reduction in sensitivity to osmotic/drought stress in transgenic plants: the data suggest that AKT1 overexpression improved rice osmotic and drought stress tolerance by increasing tissue levels of K(+), especially in the root.
Author response: ATP hydrolysis by the viral RNA sensor RIG-I prevents unintentional recognition of self-RNA (2015)

Mutations within the ATPase domain of RIG-I in patients with Singleton-Merten Syndrome prevent ATP-hydrolysis dependent dissociation of RIG-I from double-stranded RNA and lead to unintentional constitutive signaling through increased binding of endogenous RNA.
Effect of Low Aluminum Silicon on the Direct Process (2003)

GE Silicones ran a commercial direct process production unit with low aluminum content silicon, and very poor reaction yields were obtained. The direct process is used to react silicon with methyl chloride to produce methylchlorosilanes, which are used to produce silicone materials. Laboratory experiments were conducted that allowed GE to generate a plausible hypothesis to explain the commercial failure. The commercial and laboratory results have been used by GE to diagnose additional direct process reaction problems. Aluminum is an important impurity found in chemical-grade silicon. Aluminum acts as one of many promoters in the direct process. Laboratory experiments indicated that the presence of aluminum is required to increase the vapor pressure of the zinc promoter at direct process reaction conditions. Increased vapor pressure allows movement of zinc within the solid reaction mass present in the fluid-bed reactor. Insufficient zinc vapor pressure causes severe problems with raw material yields and product quality that translates to uneconomic operation of the commercial direct process reaction unit.