gebhart/patrepeval huggingface dataset:
Why and how to benchmark XML databases (2001)

Benchmarks belong to the very standard repertory of tools deployed in database development. Assessing the capabilities of a system, analyzing actual and potential bottlenecks, and, naturally, comparing the pros and cons of different systems architectures have become indispensable tasks as databases management systems grow in complexity and capacity. In the course of the development of XML databases the need for a benchmark framework has become more and more evident: a great many different ways to store XML data have been suggested in the past, each with its genuine advantages, disadvantages and consequences that propagate through the layers of a complex database system and need to be carefully considered. The different storage schemes render the query characteristics of the data variably different. However, no conclusive methodology for assessing these differences is available to date.In this paper, we outline desiderata for a benchmark for XML databases drawing from our own experience of developing an XML repository, involvement in the definition of the standard query language, and experience with standard benchmarks for relational databases.
Systemic toxicity and dermal irritation of Tołpa Peat Preparation. (1993)

The systemic toxicity of the peat preparation in rats and rabbits was assessed. Dermal irritation tests were conducted on rabbits. In acute and chronic toxicity studies TPP was well tolerated in both animal species. Laboratory findings revealed no hematologic abnormalities as well as disturbances in liver and kidney function. No local irritancy of TPP was found. The results show that TPP may be considered as practically non toxic.
Binding to Nonmethylated CpG DNA Is Essential for Target Recognition, Transactivation, and Myeloid Transformation by an MLL Oncoprotein (2004)

The MLL gene is a frequent target for leukemia-associated chromosomal translocations that generate dominant-acting chimeric oncoproteins. These invariably contain the amino-terminal 1,400 residues of MLL fused with one of a variety of over 30 distinct nuclear or cytoplasmic partner proteins. Despite the consistent inclusion of the MLL amino-terminal region in leukemia oncoproteins, little is known regarding its molecular contributions to MLL-dependent oncogenesis. Using high-resolution mutagenesis, we identified three MLL domains that are essential for in vitro myeloid transformation via mechanisms that do not compromise subnuclear localization. These include the CXXC/Basic domain and two novel domains of unknown function. Point mutations in the CXXC domain that eliminate myeloid transformation by an MLL fusion protein also abolished recognition and binding of nonmethylated CpG DNA sites in vitro and transactivation in vivo. Our results define a critical role for the CXXC DNA binding domain in MLL-associated oncogenesis, most likely via epigenetic recognition of CpG DNA sites within the regulatory elements of target genes.
Cyclodextrin overcomes the transport defect in nearly every organ of NPC1 mice leading to excretion of sequestered cholesterol as bile acid (2009)

A mutation in NPC1 leads to sequestration of unesterified cholesterol in the late endosomal/lysosomal compartment of every cell culminating in the development of pulmonary, hepatic, and neurodegenerative disease. Acute administration of 2-hydroxypropyl-β-cyclodextrin (CYCLO) rapidly overcomes this transport defect in both the 7-day-old pup and 49-day-old mature npc1−/− mouse, even though this compound is cleared from the body and plasma six times faster in the mature mouse than in the neonatal animal. The liberated cholesterol flows into the cytosolic ester pool, suppresses sterol synthesis, down-regulates SREBP2 and its target genes, and reduces expression of macrophage-associated inflammatory genes. These effects are seen in the liver and brain, as well as in peripheral organs like the spleen and kidney. Only the lung appears to be resistant to these effects. Forty-eight h after CYCLO administration to the 49-day-old animals, fecal acidic, but not neutral, sterol output increases, whole-animal cholesterol burden is reduced, and the hepatic and neurological inflammation is ameliorated. However, lifespan is extended only when the CYCLO is administered to the 7-day-old animals. These studies demonstrate that CYCLO administration acutely reverses the cholesterol transport defect seen in the NPC1 mouse at any age, and this reversal allows the sequestered sterol to be excreted from the body as bile acid.
HIGH-IMPEDANCE ELECTROMAGNETIC SURFACES FOR MITIGATION OF SWITCHING NOISE IN HIGH-SPEED CIRCUITS (2003)

With the increasing gate density, the rising clock frequency, printed circuit board (PCB) level simultaneous switching noise (SSN) has become a major bottleneck for the signal integrity in high-speed microprocessors and computers. All approaches that are currently being used to address this problem have been proven inefficient for switching frequencies of 500 MHz and above. The research work carried out in this dissertation addresses a novel technique for mitigating high-frequency SSN by suppressing the natural parallel-plate resonant modes encountered in traditional power planes. This is done by replacing at least one of the power planes of the power distribution network with a high-impedance electromagnetic surface (HIS). The high-impedance electromagnetic surface, which indeed is an artificial magnetic conductor, prevents any surface wave propagation in its forbidden band-gap, therefore leading to the suppression of resonant modes. Using full wave electromagnetic simulation and experimental verification, the fundamental limitations of SSN mitigation using standard HIS is investigated. It is found that the thickness of the dielectric substrate and the metal line spacing offered by most PCB technologies are fundamental limitations for achieving broadband simultaneous switching noise mitigation at frequencies below 3 GHz for high-density packaging. This restriction is addressed by developing a new family of HIS, whose surface impedance is mainly controlled by the inductance density. These novel inductively-tuned HIS offer the possibility of mitigating switching noise at frequencies of 1 GHz and below frequencies and can be fabricated using conventional PCB technology. It is also demonstrated that the combination of these novel HIS with RC dissipative edge termination (DET) leads to broadband simultaneous switching noise mitigation from DC to about 3 or 4 GHz. Finally physics-based compact models that allow the use of the novel power planes with other components for full package simulation are developed and validated for power planes with integrated standard and double-layer HIS. These models utilize only frequency independent lumped-components and are, therefore, particularly attractive for transient analysis.
Metal–biomolecule frameworks (MBioFs) (2011)

Biomolecules are the building blocks of life. Nature has evolved countless biomolecules that show promise for bridging metal ions. These molecules have emerged as an excellent source of biocompatible building blocks that can be used to design Metal-Biomolecule Frameworks (MBioFs). This feature article highlights the advances in the synthesis of this class of MOFs. Special emphasis is provided on the crystal structures of these materials, their miniaturization to the submicron length scale, and their new potential storage, catalytic, and biomedical applications.
Expression of mutant amyloid precursor proteins induces apoptosis in PC12 cells (1997)

The cause of neuronal loss in Alzheimer disease is unknown. We investigated the effects on survival of PC12 cells expressing A692G, E693Q, and V717F mutant amyloid precursor proteins (APP). Differentiated cells expressing mutant APPs exhibited somal shrinkage, followed by cell detachment from the plates. Increased levels of oligonucleosome-sized DNA ladders and TUNEL-positive nuclei were observed, and electron microscopy revealed extensive plasma membrane blebbing, margination of condensed chromatin, and well-preserved organelles in these transfectants. The levels of TUNEL-positive cells, analyzed by a flow-cytometric method, were increased by four- to sevenfold in mutant APP transfectants, but less than twofold in wild-type APP transfectants relative to untransfected cells. Our results provide evidence that expression of mutant APPs in differentiated PC12 cells induces cell death via an apoptotic pathway.
Human immune response to polydimethylsiloxane (silicone): screening studies in a breast implant population (1993)

Although initially it was thought that polydimethylsiloxane (silicone) was biologically inert, recent published studies have demonstrated varying levels of IgG antibody reactive with this structure in humans. The objective of our study was to determine whether silicone implanted in humans results in a measurable immune response directed against a 3700 mol wt hydroxyl terminated silicone molecule and whether that response could be correlated with the level of presumed silicone exposure as inferred by clinical history. In a blind study, sera from 111 patients, with and without breast implants, were sent to a laboratory using an enzyme-linked immunosorbent assay to determine specific anti-silicone IgG antibody levels. Test results showed that patients with implants demonstrated statistically significant elevation in anti-silicone antibodies compared with the unimplanted control groups. The highest anti-silicone antibody levels were measured in implanted women with either frank implant ruptures or leakage of their silicone gel implants.
Homology between the DNA-binding domain of the GCN4 regulatory protein of yeast and the carboxyl-terminal region of a protein coded for by the oncogene jun. (1987)

The product of the recently described oncogene jun shows significant amino acid sequence homology with the GCN4 yeast transcriptional activator protein. The similarity is restricted to the 66 carboxyl-terminal amino acids, thought to be the DNA-binding domain of the GCN4 protein. In these alpha-helix-permissive regions of the jun and GCN4 products there is also a lesser but still significant amino acid resemblance to the fos protein and a marginal degree of similarity to myc proteins. The amino acid sequence homology between GCN4 and jun gene products suggests that the jun protein may bind to DNA in a sequence-specific way and exert a regulatory function.
Identification of a Peroxisome Proliferator-responsive Element Upstream of the Human Peroxisomal Fatty Acyl Coenzyme A Oxidase Gene (1996)

Peroxisome proliferators cause a rapid and coordinated transcriptional activation of genes encoding the enzymes of the peroxisomal beta-oxidation pathway in rats and mice. Cis-acting peroxisome proliferator responsive elements (PPREs) have been identified in the 5'-flanking region of H202-producing rat acyl-CoA oxidase (ACOX) gene and in other genes inducible by peroxisome proliferators. To gain more insight into the purported nonresponsiveness of human liver cells to peroxisome volume density and in the activity of the beta-oxidation enzyme system, we have previously cloned the human ACOX gene, the first and rate-limiting enzyme of the peroxisomal beta-oxidation system. We now present information on a regulatory element for the peroxidase proliferator-activated receptor (PPAR)/retinoid X receptor (RXR) heterodimers. The PPRE, consists of AGGTCA C TGGTCA, which is a direct repeat of hexamer half-sites interspaced by a single nucleotide (DR1 motif). It is located at -1918 to -1906 base pairs upstream of the transcription initiation site of this human ACOX gene. This PPRE specifically binds to baculovirus-expressed recombinant rat PPAR alpha/RXR alpha heterodimers. In transient transfection experiments, the maximum induction of luciferase expression by ciprofibrate and/or 9-cis-retinoic acid is dependent upon cotransfection of expression plasmids for PPAR alpha and RXR alpha. The functionally of this human ACOX promoter was further demonstrated by linking it to a beta-galactosidase reporter gene or to a rat urate oxidase cDNA and establishing stably transfected African green monkey kidney (CV1) cell lines expressing reporter protein. The human ACOX promoter has been found to be responsive to peroxisome proliferators in CV1 cells stably expressing PPAR alpha, whereas only a basal level of promoter activity is detected in stably transfected cells lacking PPAR alpha. The presence of a PPRE in the promoter of this human peroxisomal ACOX gene and its responsiveness to peroxisome proliferators suggests that factors other than the PPRE in the 5'-flanking sequence of the human ACOX gene may account for differences, if any, in the pleiotropic responses of humans to peroxisome proliferators.
Porous Semiconductor Chalcogenide Aerogels (2005)

Chalcogenide aerogels based entirely on semiconducting II-VI or IV-VI frameworks have been prepared from a general strategy that involves oxidative aggregation of metal chalcogenide nanoparticle building blocks followed by supercritical solvent removal. The resultant materials are mesoporous, exhibit high surface areas, can be prepared as monoliths, and demonstrate the characteristic quantum-confined optical properties of their nanoparticle components. These materials can be synthesized from a variety of building blocks by chemical or photochemical oxidation, and the properties can be further tuned by heat treatment. Aerogel formation represents a powerful yet facile method for metal chalcogenide nanoparticle assembly and the creation of mesoporous semiconductors.
Optical Neural Networks (1990)

The trade-off between the number of neurons that can be implemented with a single correlator and the shift invariance that each neuron has is investigated. A new type of correlator implemented with a planar hologram is described whose shift invariance can be controlled by setting the position of the hologram properly. The shift invariance and the capacity of correlators implemented with volume holograms is also investigated.
Towards quantum-resistant cryptosystems from supersingular elliptic curve isogenies. (2011)

We present new candidates for quantum-resistant public-key cryptosystems based on the conjectured difficulty of finding isogenies between supersingular elliptic curves. The main technical idea in our scheme is that we transmit the images of torsion bases under the isogeny in order to allow the parties to construct a shared commutative square despite the noncommutativity of the endomorphism ring. Our work is motivated by the recent development of a subexponential-time quantum algorithm for constructing isogenies between ordinary elliptic curves. In the supersingular case, by contrast, the fastest known quantum attack remains exponential, since the noncommutativity of the endomorphism ring means that the approach used in the ordinary case does not apply. We give a precise formulation of the necessary computational assumptions along with a discussion of their validity, and prove the security of our protocols under these assumptions. In addition, we present implementation results showing that our protocols are multiple orders of magnitude faster than previous isogeny-based cryptosystems over ordinary curves. This paper is an extended version of [19]. We add a new zero-knowledge identification scheme, and detailed security proofs for the protocols. We also present a new, asymptotically faster, algorithm for key generation, a thorough study of its optimization, and new experimental data.
Discovery and Analysis of Evolutionarily Conserved Intronic Splicing Regulatory Elements (2007)

Knowledge of the functional cis-regulatory elements that regulate constitutive and alternative pre-mRNA splicing is fundamental for biology and medicine. Here we undertook a genome-wide comparative genomics approach using available mammalian genomes to identify conserved intronic splicing regulatory elements (ISREs). Our approach yielded 314 ISREs, and insertions of ~70 ISREs between competing splice sites demonstrated that 84% of ISREs altered 5' and 94% altered 3' splice site choice in human cells. Consistent with our experiments, comparisons of ISREs to known splicing regulatory elements revealed that 40%-45% of ISREs might have dual roles as exonic splicing silencers. Supporting a role for ISREs in alternative splicing, we found that 30%-50% of ISREs were enriched near alternatively spliced (AS) exons, and included almost all known binding sites of tissue-specific alternative splicing factors. Further, we observed that genes harboring ISRE-proximal exons have biases for tissue expression and molecular functions that are ISRE-specific. Finally, we discovered that for Nova1, neuronal PTB, hnRNP C, and FOX1, the most frequently occurring ISRE proximal to an alternative conserved exon in the splicing factor strongly resembled its own known RNA binding site, suggesting a novel application of ISRE density and the propensity for splicing factors to auto-regulate to associate RNA binding sites to splicing factors. Our results demonstrate that ISREs are crucial building blocks in understanding general and tissue-specific AS regulation and the biological pathways and functions regulated by these AS events.
Semiconductor Optical Amplifiers (2006)

# Basic Concepts # Recombination Mechanisms and Gain # Epitaxial Growth and Amplifier Designs # Low Reflectivity Facet Designs # Amplifier Rate Equations and Operating Characteristics # Photonic Integrated Circuit Using Amplifiers # Functional Properties and Applications # Optical Logic Operations # Optical Logic Circuits
Identification of a novel exon and spliced form of Duffy mRNA that is the predominant transcript in both erythroid and postcapillary venule endothelium (1996)

The Duffy gene has been shown not to be split by introns, even in its 5' untranslated region, and to be expressed not only in erythroid but in postcapillary venule endothelium of almost every organ in the body. To further investigate the transcriptional start position in erythroid and postcapillary venule endothelium, we performed 5'-rapid amplification of cDNA ends (5'-RACE). While every positive clone of 5'-RACE encoded the identical sequence of previously identified cDNA downstream from nucleotide 203, the upstream sequences were different. The upstream sequences corresponded to the sequence from nucleotide -279 to -308/-357 in erythroblasts and from -279 to -355/-383 in lung and were regarded as comprising a novel exon. This novel exon encoded seven residues initiated with a methionine, linked to nucleotide 203 in-frame and in agreement with the GT-AG splicing rule. The major erythroid transcriptional start position was identified in human erythroleukemia cells by primer extension and in bone marrow by ribonuclease protection analysis at 34 bases upstream from the first ATG codon. Distinctively, in lung and kidney, the transcription was started at 82 bases upstream from the ATG. Both Northern blotting and reverse transcription-polymerase chain reaction followed by Southern analysis indicated a predominance of the novel spliced form of mRNA of about 50- to 200-fold comparing with the unspliced form, in every studied organ and erythroid lineage cells. The spliced form of cDNA has been transfected into a human erythroleukemic cell line, K562, and the expressed protein reacted with Duffy-specific murine monoclonal antibody Fy6. These studies indicate that the product from the spliced form of mRNA is the major product of the Duffy gene in the erythroid lineage and postcapillary venule endothelium.
A Survey of Database Marketing (1999)

This working paper surveys the current state of database marketing.Database marketing, usually associated with customer relationship marketing (CRM), is concerned with the application of information systems to direct marketing.The current state of database marketing varies widely across industries and even between companies within the same industry.Proponents of database marketing speak often and loudly of its role as a source of competitive advantage.Yet surveys of database practitioners show few companies realize significant advantages from their systems.This paper discusses the drivers, the stages of development, the current state of the field, and the obstacles to database marketing.The drivers include the changes in the roles of direct marketing, cost structures, technology, and economic conditions.The development of database marketing sophistication in individual firms is described by a number of models, four of which are discussed here.These models agree on how such systems are started and their ultimate stage of development, but differ in how they describe the middle phases.Database marketing is seen as a source of strategic and tactical competitive advantage by some firms and a competitive burden or strategic necessity by others.Obstacles to database marketing, including environmental, technical, marketing, and strategic problems, are discussed in detail.
Ontogeny of Th1 Memory Responses against a<i>Brucella abortus</i>Conjugate (2001)

Protective immune responses to intracellular pathogens such as Brucella abortus are characteristically Th1-like. Recently we demonstrated that heat-killed B. abortus (HKBa), a strong Th1 stimulus, conjugated to ovalbumin (HKBA-OVA), but not B. abortus alone, can alter the antigen-specific cytokine profile from Th2- to Th1-like. In this report we study the ability of a single injection of B. abortus to switch a Th2 to a Th1 response in immature mice. One-day- and 1-week-old mice were given a single injection of B. abortus in the absence or presence of OVA, and at maturity mice were challenged with an allergenic preparation, OVA with alum (OVA-A). B. abortus given without OVA did not diminish the subsequent Th2 response in either age group. In contrast, mice receiving a single injection of B. abortus-OVA at the age of 1 week, but not those injected at the age of 1 day, had reversal of the ratio of OVA-specific Th1 to Th2 cells and decreased immunoglobulin E levels after allergen challenge as adults. Within 6 h both 1-day- and 1-week-old mice expressed interleukin-12 p40 mRNA following either B. abortus or B. abortus-OVA administration. However, only the 1-week-old mice exhibited increased expression of gamma interferon (IFN-gamma) mRNA. The absence of the early IFN-gamma response in 1-day-old mice may explain their inability to generate a Th1 memory response. These results suggest that at early stages of immune development, responses to intracellular bacteria may be Th2- rather than Th1-like. Furthermore, they suggest that the first encounter with antigen evokes either a Th1- or a Th2-like response which becomes imprinted, so that subsequent memory responses conform to the original Th bias. This has implications for protection against infectious agents and development of allergic responses.
Membrane potential stimulated binding of the maltose-binding protein to membrane vesicles of Escherichia coli. (1982)

We show in this study that radioactively labelled purified maltose-binding protein of Escherichia coli binds specifically to membrane vesicles, in the presence of maltose. When a potential is imposed across the membrane, the specific binding is increased, dependent on maltose, abolished in a mutant defective in the tar-gene product, one of the methyl-accepting chemotaxis proteins.
A programmable polarization-mode dispersion emulator for systematic testing of 10 Gb/s PMD compensators (2002)

A programmable polarization-mode dispersion emulator is demonstrated first and higher-order PMD is systematically generated. Twelve birefringent crystals with 10 ps differential-group-delay apiece are mounted in twelve computer controlled motorized rotating stages.