gebhart/patrepeval huggingface dataset:
A pattern tree-based approach to learning URL normalization rules (2010)

Duplicate URLs have brought serious troubles to the whole pipeline of a search engine, from crawling, indexing, to result serving. URL normalization is to transform duplicate URLs to a canonical form using a set of rewrite rules. Nowadays URL normalization has attracted significant attention as it is lightweight and can be flexibly integrated into both the online (e.g. crawling) and the offline (e.g. index compression) parts of a search engine. To deal with a large scale of websites, automatic approaches are highly desired to learn rewrite rules for various kinds of duplicate URLs. In this paper, we rethink the problem of URL normalization from a global perspective and propose a pattern tree-based approach, which is remarkably different from existing approaches. Most current approaches learn rewrite rules by iteratively inducing local duplicate pairs to more general forms, and inevitably suffer from noisy training data and are practically inefficient. Given a training set of URLs partitioned into duplicate clusters for a targeted website, we develop a simple yet efficient algorithm to automatically construct a URL pattern tree. With the pattern tree, the statistical information from all the training samples is leveraged to make the learning process more robust and reliable. The learning process is also accelerated as rules are directly summarized based on pattern tree nodes. In addition, from an engineering perspective, the pattern tree helps select deployable rules by removing conflicts and redundancies. An evaluation on more than 70 million duplicate URLs from 200 websites showed that the proposed approach achieves very promising performance, in terms of both de-duping effectiveness and computational efficiency.
The First Prokaryotic Trehalose Synthase Complex Identified in the Hyperthermophilic Crenarchaeon Thermoproteus tenax (2013)

The role of the disaccharide trehalose, its biosynthesis pathways and their regulation in Archaea are still ambiguous. In Thermoproteus tenax a fused trehalose-6-phosphate synthase/phosphatase (TPSP), consisting of an N-terminal trehalose-6-phosphate synthase (TPS) and a C-terminal trehalose-6-phosphate phosphatase (TPP) domain, was identified. The tpsp gene is organized in an operon with a putative glycosyltransferase (GT) and a putative mechanosensitive channel (MSC). The T. tenax TPSP exhibits high phosphatase activity, but requires activation by the co-expressed GT for bifunctional synthase-phosphatase activity. The GT mediated activation of TPS activity relies on the fusion of both, TPS and TPP domain, in the TPSP enzyme. Activation is mediated by complex-formation in vivo as indicated by yeast two-hybrid and crude extract analysis. In combination with first evidence for MSC activity the results suggest a sophisticated stress response involving TPSP, GT and MSC in T. tenax and probably in other Thermoproteales species. The monophyletic prokaryotic TPSP proteins likely originated via a single fusion event in the Bacteroidetes with subsequent horizontal gene transfers to other Bacteria and Archaea. Furthermore, evidence for the origin of eukaryotic TPSP fusions via HGT from prokaryotes and therefore a monophyletic origin of eukaryotic and prokaryotic fused TPSPs is presented. This is the first report of a prokaryotic, archaeal trehalose synthase complex exhibiting a much more simple composition than the eukaryotic complex described in yeast. Thus, complex formation and a complex-associated regulatory potential might represent a more general feature of trehalose synthesizing proteins.
Downsampled and Undersampled Datasets in Feature Selective Validation (FSV) (2014)

Feature selective validation (FSV) is a heuristic method for quantifying the (dis)similarity of two datasets. The computational burden of obtaining the FSV values might be unnecessarily high if datasets with large numbers of points are used. While this may not be an important issue per se it is an important issue for future developments in FSV such as real-time processing or where multidimensional FSV is needed. Coupled with the issue of dataset size, is the issue of datasets having “missing” values. This may come about because of a practical difficulty or because of noise or other confounding factors making some data points unreliable. These issues relate to the question “what is the effect on FSV quantification of reducing or removing data points from a comparison-i.e., down- or undersampling data?” This paper uses three strategies to achieve this from known datasets. This paper demonstrates, through a representative sample of 16 pairs of datasets, that FSV is robust to changes providing a minimum dataset size of approximately 200 points is maintained. It is robust also for up to approximately 10% “missing” data, providing this does not result in a continuous region of missed data.
ChAMP: 450k Chip Analysis Methylation Pipeline (2013)

ChAMP is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at bioconductor.org
Room-temperature Coulomb-blockade-dominated transport in gold nanocluster structures (1998)

In this paper we discuss the near-room-temperature electrical transport characteristics of structures made from ligand-stabilized metal clusters. The structures show threshold behaviour, nonlinear current-voltage characteristics and radio-frequency-induced plateaux consistent with Coulomb-blockade-dominated transport in disordered arrays of metal dots. Samples having triphenylphosphine and octadecanethiol ligand shells are found to have a 3 orders of magnitude difference in current above threshold. We discuss a possible explanation for this observation.
GFP-expressing locus ceruleus neurons from Prp57 transgenic mice exhibit CO2/H+ responses in primary cell culture (2008)

The locus ceruleus (LC) contains neurons that increase their firing rate (FR) in vitro when exposed to elevated CO(2)/H(+) and have been proposed to influence the respiratory network to make compensatory adjustments in ventilation. Prp57 transgenic mice express green fluorescent protein (GFP) in the LC and were used to isolate, culture, and target LC neurons for electrophysiological recording. We hypothesized that GFP-LC neurons would exhibit CO(2)/H(+) chemosensitivity under primary culture conditions, evidenced as a change in FR. This is the first study to quantify CO(2)/H(+) responses in LC neuron FR in cell culture. Neurons were continuously bathed with solutions containing antagonists of glutamate and GABA receptors, and the acid-base status was changed from control (5% CO(2); pH approximately 7.4) to hypercapnic acidosis (9% CO(2); pH approximately 7.2) and hypocapnic alkalosis (3% CO(2); pH approximately 7.6). FR was quantified during perforated patch current clamp recordings. Approximately 86% of GFP-LC neurons were stimulated, and approximately 14% were insensitive to changes in CO(2)/H(+). The magnitude of the response of these neurons depended on the baseline FR, ranging from 155.9 +/- 6% when FR started at 2.95 +/- 0.49 Hz to 381 +/- 55.6% when FR started at 1.32 +/- 0.31 Hz. These results demonstrate that cultured LC neurons from Prp57 transgenic mice retain functional sensing molecules necessary for CO(2)/H(+) responses. Prp57 transgenic mice will serve as a valuable model to delineate mechanisms involved in CO(2)/H(+) responsiveness in catecholaminergic neurons.
Robust categorization of microfacet BRDF models to enable flexible application-specific BRDF adaptation (2014)

Since the development of the Torrance-Sparrow bidirectional re ectance distribution function (BRDF) model in 1967, several BRDF models have been created. Previous attempts to categorize BRDF models have relied upon somewhat vague descriptors, such as empirical, semi-empirical, and experimental. Our approach is to instead categorize BRDF models based on functional form: microfacet normal distribution, geometric attenua- tion, directional-volumetric and Fresnel terms, and cross section conversion factor. Several popular microfacet models are compared to a standardized notation for a microfacet BRDF model. A library of microfacet model components is developed, allowing for creation of unique microfacet models driven by experimentally measured BRDFs.
Covalent‐Allosteric Inhibitors to Achieve Akt Isoform‐Selectivity (2019)

Abstract Isoforms of protein kinase Akt are involved in essential processes including cell proliferation, survival, and metabolism. However, their individual roles in health and disease have not been thoroughly evaluated. Thus, there is an urgent need for perturbation studies, preferably mediated by highly selective bioactive small molecules. Herein, we present a structure‐guided approach for the design of structurally diverse and pharmacologically beneficial covalent‐allosteric modifiers, which enabled an investigation of the isoform‐specific preferences and the important residues within the allosteric site of the different isoforms. The biochemical, cellular, and structural evaluations revealed interactions responsible for the selective binding profiles. The isoform‐selective covalent‐allosteric Akt inhibitors that emerged from this approach showed a conclusive structure–activity relationship and broke ground in the development of selective probes to delineate the isoform‐specific functions of Akt kinases.
Amyloidogenic Processing of Amyloid Precursor Protein Drives Stretch-Induced Disruption of Axonal Transport in hiPSC-Derived Neurons (2021)

Traumatic brain injury (TBI) results in disrupted brain function following impact from an external force and is a risk factor for sporadic Alzheimer's disease (AD). Although neurologic symptoms triggered by mild traumatic brain injuries (mTBI), the most common form of TBI, typically resolve rapidly, even an isolated mTBI event can increase the risk to develop AD. Aberrant accumulation of amyloid β peptide (Aβ), a cleaved fragment of amyloid precursor protein (APP), is a key pathologic outcome designating the progression of AD following mTBI and has also been linked to impaired axonal transport. However, relationships among mTBI, amyloidogenesis, and axonal transport remain unclear, in part because of the dearth of human models to study the neuronal response following mTBI. Here, we implemented a custom-microfabricated device to deform neurons derived from human-induced pluripotent stem cells, derived from a cognitively unimpaired male individual, to mimic the mild stretch experienced by neurons during mTBI. Although no cell lethality or cytoskeletal disruptions were observed, mild stretch was sufficient to stimulate rapid amyloidogenic processing of APP. This processing led to abrupt cessation of APP axonal transport and progressive formation of aberrant axonal accumulations that contained APP, its processing machinery, and amyloidogenic fragments. Consistent with this sequence of events, stretch-induced defects were abrogated by reducing amyloidogenesis either pharmacologically or genetically. In sum, we have uncovered a novel and manipulable stretch-induced amyloidogenic pathway directly responsible for APP axonal transport dysregulation. Our findings may help to understand and ultimately mitigate the risk of developing AD following mTBI.<b>SIGNIFICANCE STATEMENT</b> Mild traumatic brain injury is a risk factor for sporadic Alzheimer's disease (AD). Increased amyloid β peptide generation after injury may drive this risk. Here, by using a custom-built device to impose mild stretch to human neurons, we found that stretch triggers amyloid precursor protein (APP) cleavage, and thus amyloid β peptide generation, consequently disrupting APP axonal transport. Compellingly, protecting APP from cleavage was sufficient to spare axonal transport dysregulation and the consequent aberrant axonal accumulation of APP. Supporting such protective mechanism, the expression of the AD-protective APP<sup>A673T</sup> genetic variant conferred protection against stretch-induced APP axonal transport phenotypes. Our data reveal potential subcellular pathways contributing to the development of AD-associated phenotypes following mild traumatic brain injury, and putative strategies for intervening in these pathways.
Numerical Investigation of the Behavior of Reinforced Concrete Beam Reinforced with FRP Bars (2019)

In this study, the behavior of reinforced concrete beams reinforced with FRP bars was investigated. A total of seventeen models were carried out based on the finite element software (ABAQUS). The concrete damage plasticity modeling was considered. Two types of fiber polymer bars, CFRP and GFRP as longitudinal reinforcement for concrete beam were used. The validation of numerical results was confirmed by experimental results, then the parametric study was conducted to evaluate the effect of change in different parameters, such as (diameter size, number of bars), type of FRP bars, longitudinal arrangement for FRP bars. All results were analyzed and discussed through, load-deflection diagram, according, to the difference parameter considered. The results showed that the use of FRP bars in rebar concrete beam improves the beam stiffness and enhance the cracking load. The load capacity enhanced in the range of (7.88-64.82%) when used CFRP bars. The load-carrying capacity of beams strengthened with CFRP is higher than that of strengthened with GFRP. Furthermore, the use of FRP bars in bottom and steel in top reinforcement is useful to overcome the large deflection, and improving the beam ductility. Finally, the results of finite element models were compared with the prediction equation, according to ACI440.1R-15.
Faulty Feeder Detection and Fault Self-Extinguishing by Adaptive Petersen Coil Control (2010)

The characteristic of the single-phase earth fault in the Peterse coil grounded distribution network is discussed in this paper. It is disclosed that only the derivative of the zero-sequence current of the faulty feeder changes with the controllable inductance of the Petersen coil, while the derivative of the zero-sequence current of the sound feeder is kept invariable. Therefore, a novel faulty feeder selection criterion is proposed. A variety of simulation tests is carried out. The exactness and sensitivity of the proposed scheme are verified by simulation test results.
Test Access Mechanism in the Quad-Core AMD Opteron Microprocessor (2009)

Multicore microprocessors provide a natural application environment for IEEE Std 1500 and, as this article proves, allow for innovative approaches that capitalize on the fact that the various cores are identical.
Rescue of Adeno-Associated Virus Production by shRNA Cotransfection (2020)

Adeno-associated virus (AAV) vector technology is rapidly advancing and becoming not only the leading vector platform in the field of gene therapy but also a useful tool for functional genomic studies of novel proteins. As most vectors utilize constitutive promoters, this results in transgene expression during production. Depending on the transgene product, this could induce proapoptotic, cytostatic, or other unknown effects that interfere with producer cell function and, therefore, reduce viral vector yield. This can be a major limitation when trying to characterize poorly described genes. We describe the novel use of shRNA encoding plasmids cotransfected during packaging to limit the expression of the cytotoxic transgene product. This allowed the production of an otherwise unpackageable vector. The approach is simple, versatile, does not require modification of the vector plasmid, and should be easily adaptable to almost any transgene with minimal cost.
Design Considerations for the D-2 NTSC Composite DVTR (1988)

This article discusses the design for the proposed D-2 digital NTSC composite recording format. Both technical and economic criteria used in arriving at the format are enumerated. The relationship among the key parameters and the tradeoffs involved in choosing those parameters are described. Two-channel recording with azimuth heads, Miller <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> code and metal particle tape are key elements of the format. The error-correction coding system, structure of data along the helical tracks, picture-in-shuttle, shuffling, and concealment are also discussed, as are audio timing and editing. Similarities with, and differences from, the D-1 format for recording 4:2:2 component video are noted throughout.
Redox Control of the Solubilization of Benzene with a Ferrocene-Modified Nonionic Surfactant (1998)

Benzene was solubilized in aqueous micellar solutions of a redox-active nonionic surfactant (11-ferrocenylundecyl polyoxyethylene ether : FPEG) and the effect of the redox reactions on the solubilization is studied. The solubilization equilibrium constant (K) of benzene in FPEG micelles, which represents the distribution of solubilizates between micelle and bulk solution, was found to decrease with the oxidation of ferrocenyl moieties of FPEG molecules, but to increase with reduction in ferrocenyl moieties. Active and reversible control of solubilization is thus shown possible through application of the redox reactions of FPEG micellar solution.
Optical characteristics of hexagonal GaN self-assembled quantum dots: Strong influence of built-in electric field and carrier localization (2002)

Optical characteristics of hexagonal GaN self-assembled quantum dots (QDs) were systematically studied by photoluminescence (PL), PL excitation (PLE), time-resolved PL, and cathodoluminescence (CL). We observed a Stokes-like shift between PLE absorption edge and PL emission from the GaN QDs as well as from the Al(Ga)N base layer. With decreasing emission energy, the measured lifetime of the hexagonal GaN QDs emission increased, while that of the cubic GaN QDs kept almost constant. The optical emission from the GaN QDs was measured as a function of temperature from 10 to 300 K, and their properties were compared with GaN quantum-well structures. With increasing temperature, the PL intensity of Al(Ga)N base layer or GaN quantum wells was dramatically decreased, while that of GaN QDs was not changed much. We observed CL images showing strong carrier localization in GaN QDs. Therefore, we conclude that the GaN QD emissions are strongly influenced by built-in electric field as well as by carrier localization in the QDs.
Phenotypic Diversity and Stability of the Intestinal Coliform Flora in Piglets During the First 3 Months of Age (1993)

The intestinal coliform bacterial populations in six piglets and their sows from two litters in the same stable were studied by the aid of an automated system for biochemical fingerprinting (The PhenePlate, or PhP system). Faecal samples from sows were collected once a week until weaning, and from piglets once a week during their first 3 mth of life. Altogether 1248 coliform isolates from 52 faecal samples were studied. The phenotypical diversity of the coliform bacteria in each faecal sample was measured as Simpson’s diversity index (D i ), and the similarities between the bacteria in different samples were measured as population similarity coefficients (S p ). The D i of the sows was initially high, but decreased in one sow during an outbreak of diarrhoea which occurred during week 3 of the study. The D i of the piglets varied between samples, and showed no tendency to increase with age. Two piglets included in the study died during the diarrhoeal outbreak, and they generally carried intestinal floras showing lower D i during their first 3 wk of life than those which survived (mean value 0.454 versus 0.744). The coliform population within each piglet was usually quite stable before the diarrhoeal outbreak, but in all piglets the population was drastically changed during and after the outbreak. Piglets within each litter shared similar coliform populations during the first week of life, but piglets from different litters had no coliforms in common. On day 75, the piglets were removed from their sows and mixed with others in different litters, and after that coliform populations of piglets from different sows showed a tendency to become more similar to each other. Samples collected during the diarrhoeal outbreak from different piglets did not contain similar coliform populations which is a strong indication that the aetiological agent of the outbreak was not any coliform bacterium. The present study shows a useful way to investigate intestinal bacteria in both man and animals. The methods are very simple to use, and fully computerised data treatment makes it possible to study large numbers of bacterial isolates. Keywords - Intestinal bacteria; Coliforms; Piglets; Diversity; Stability.
Systemic Vascular Load in Calcific Degenerative Aortic Valve Stenosis (2015)

Vascular function in calcific degenerative AS is conditioned by the upstream valvular obstruction that dampens forward and backward compression waves in the arterial tree. An increase in vascular load after TAVR limits the procedure's acute afterload relief.
Erratum: Resonant light scattering by fractal clusters [Phys. Rev. B44, 12216 (1991)] (1992)

There is an incorrect statement concerning the mode spacing 6" in comparison with the relaxation constant 5 in our paper. The mode spacing b, "-N 'v ' [compare with (48)], and accordingly is much less than 5 as N~~. However, final formulas ( Let us consider g, (X)-: lXol F, . Integration of the scaling expression (32) in the restricted range lXl R o provides the dom- inant contribution to the integral in the first sum rule (31). This means that the number of eigenmodes contained in the scaling region is on the order of the total amount, 3N, of eigenmodes. Because the integral f g, (X)dX is rapidly conver- gent, it is plausible that the scaling region gives the major contribution to the integral. This suggests that Ro f g, (X)dX [through coefficients K, and IC2, g, (X) ~R 0, reflecting an extensive character of F, : see ( 5 in the essential region of integration and one obtains, in accordance with (47), a simple estimate for the sum rule f g, (X)dX-K, 25 (K, and ICz are of the same order of magnitude). The scale invariance assumption used above is strongly supported by the numerical results of the paper. Considering further the dimensionality arguments, the scaling expression for g, (X) follows: g, (X)-Z, , , 5-'R, '(Ro lXl )' .
Carbohydrate‐linked cisplatin analogue: reactivity studies with RNA and DNA (2017)

With the discovery of cisplatin in the 1960s, it has been widely studied as a precursor for anticancer drug development. Despite its effectiveness against certain cancers, clinical usage of cisplatin is restricted by a number of side effects and resistance. In the past decade, scientists have been exploring biologically important ligands such as sugar derivatives in the hope of overcoming such challenges. Attachment of a sugar moiety could facilitate lower accumulation of platinum drugs in the body as well as enhance cellular uptake. In this study, a carbohydrate‐linked cisplatin analogue, cis ‐dichloro[(2‐ β ‐D‐glucopyranosidyl)propane‐1,3‐diamine]platinum ( 1 ) has been studied. The aim is to evaluate the binding targets and mechanism of action compared to cisplatin. Compound 1 was synthesized and a reactivity study was carried out with deoxy‐/ribonucleosides and nucleic acids using high performance liquid chromatography (HPLC), liquid chromatography mass spectrometry (LC‐MS), and matrix‐assisted laser‐desorption ionization mass spectrometry (MALDI‐MS). A study was done to analyze the effects of compound 1 on DNA duplex structure by measuring the bending angles. Further probing studies on ribosomal RNA showed compound 1 localization on rRNA. Overall, this work allows us to compare ligand binding and subsequent effects on nucleic acids through a series of chemical and biochemical techniques. Support or Funding Information Wayne State University‐Faculty Schaap Fellowship