gebhart/patrepeval huggingface dataset:
Efficiency of Various Lattices from Hard Ball to Soft Ball:  Theoretical Study of Thermodynamic Properties of Dendrimer Liquid Crystal from Atomistic Simulation (2004)

Self-assembled supramolecular organic liquid crystal structures at nanoscale have potential applications in molecular electronics, photonics, and porous nanomaterials. Most of these structures are formed by aggregation of soft spherical supramolecules, which have soft coronas and overlap each other in the packing process. Our main focus here is to study the possible packing mechanisms via molecular dynamics simulations at the atomistic level. We consider the relative stability of various lattices packed by the soft dendrimer balls, first synthesized and characterized by Percec et al. (J. Am. Chem. Soc. 1997, 119, 1539) with different packing methods. The dendrons, which form the soft dendrimer balls, have the character of a hard aromatic region from the point of the cone to the edge with C(12) alkane "hair". After the dendrons pack into a sphere, the core of the sphere has the hard aromatic groups, while the surface is covered with the C(12) alkane "hair". In our studies, we propose three ways to organize the hair on the balls, Smooth/Valentino balls, Sticky/Einstein balls, and Asymmetric/Punk balls, which lead to three different packing mechanisms, Slippery, Sticky, and Anisotropic, respectively. We carry out a series of molecular dynamics (MD) studies on three plausible crystal structures (A15, FCC, and BCC) as a function of density and analyze the MD based on the vibrational density of state (DoS) method to extract the enthalpy, entropy, and free energies of these systems. We find that anisotropic packed A15 is favored over FCC, BCC lattices. Our predicted X-ray intensities of the best structures are in excellent agreement with experiment. "Anisotropic ball packing" proposed here plays an intermediate role between the enthalpy-favored "disk packing" and entropy-favored "isotropic ball packing", which explains the phase transitions at different temperatures. Free energies of various lattices at different densities are essentially the same, indicating that the preferred lattice is not determined during the packing process. Both enthalpy and entropy decrease as the density increases. Free energy change with volume shows two stable phases: the condensed phase and the isolated micelle phase. The interactions between the soft dendrimer balls are found to be lattice dependent when described by a two-body potential because the soft ball self-adjusts its shape and interaction in different lattices. The shape of the free energy potential is similar to that of the "square shoulder potential". A model explaining the packing efficiency of ideal soft balls in various lattices is proposed in terms of geometrical consideration.
The formation of paracetamol (acetaminophen) adducts with hydrogen-bond acceptors (2002)

The crystal structures of five hemiadducts of paracetamol with 1,4-dioxane, N-methylmorpholine, morpholine, N,N-dimethylpiperazine and piperazine and a related 1:1 adduct of paracetamol with 4,4'-bipyridine are described. All structures are characterized by the formation of chains of paracetamol molecules, which are linked via either OHtriplebondO=C interactions [C(9) chains in graph-set notation] or NHtriplebondO=C interactions [C(4) chains], depending on the presence or absence of substituent groups on the guest molecule. In all cases except for the morpholine and bipyridine adducts these chains are connected by hydrogen-bond interactions with the guest molecules, which reside on crystallographic inversion centres. In the bipyridine adduct this linkage also involves a pi-stacking interaction; in the morpholine adduct it is formed between the OH groups of two opposed paracetamol molecules. Most adducts (that with 4,4'-bipyridine is an exception) decompose on heating to give monoclinic paracetamol. This is the first systematic study of a series of co-crystals containing paracetamol.
Processing theta-joins using MapReduce (2011)

Joins are essential for many data analysis tasks, but are not supported directly by the MapReduce paradigm. While there has been progress on equi-joins, implementation of join algorithms in MapReduce in general is not sufficiently understood. We study the problem of how to map arbitrary join conditions to Map and Reduce functions, i.e., a parallel infrastructure that controls data flow based on key-equality only. Our proposed join model simplifies creation of and reasoning about joins in MapReduce. Using this model, we derive a surprisingly simple randomized algorithm, called 1-Bucket-Theta, for implementing arbitrary joins (theta-joins) in a single MapReduce job. This algorithm only requires minimal statistics (input cardinality) and we provide evidence that for a variety of join problems, it is either close to optimal or the best possible option. For some of the problems where 1-Bucket-Theta is not the best choice, we show how to achieve better performance by exploiting additional input statistics. All algorithms can be made 'memory-aware', and they do not require any modifications to the MapReduce environment. Experiments show the effectiveness of our approach.
3D prostate elastography: algorithm, simulations and experiments (2007)

A multi-resolution hybrid strain estimator is presented. The estimator is locally initialized by the B-mode tracking stage. Nonlinear and linear stretching regimes are applied in successive RF tracking stages for refining the estimated axial and lateral displacements. A staggering operator is used to derive the strain images from the reconstructed axial displacements. Simulations and experiments, conducted at a center frequency of 12 MHz, 40% fractional bandwidth, on a 128 element transducer with 0.2 mm pitch, with elastographic window length of 2 mm and overlap of 90%, demonstrate a 3-6 dB improvement in the elastographic contrast-to-noise ratio over the results obtained using conventional multi-stage stretching based strain estimators. The average image cross-correlation coefficient obtained using the proposed algorithm was improved by 6-8%. 3D elastographic simulations conducted to study the performance of a 3D elastographic imaging framework predict achievable axial and lateral resolutions of approximately five and ten wavelengths, respectively. A close correspondence between inclusions reconstructed from experimental elastograms and the known physical shape of actual 3D inclusions demonstrates the potential application of 3D elastography for identifying and classifying the detected lesions (invisible in sonograms) on the basis of their shape.
RNS2: a senescence-associated RNase of Arabidopsis that diverged from the S-RNases before speciation. (1993)

Several self-compatible species of higher plants, such as Arabidopsis thaliana, have recently been found to contain S-like RNases. These S-like RNases are homologous to the S-RNases that have been hypothesized to control self-incompatibility in Solanaceous species. However, the relationship of the S-like RNases to the S-RNases is unknown, and their roles in self-compatible plants are not understood. To address these questions, we have investigated the RNS2 gene, which encodes an S-like RNase (RNS2) of Arabidopsis. Amino acid sequence comparisons indicate that RNS2 and other S-like RNases make up a subclass within an RNase superfamily, which is distinct from the subclass formed by the S-RNases. RNS2 is most similar to RNase LE [Jost, W., Bak, H., Glund, K., Terpstra, P., Beintema, J. J. (1991) Eur. J. Biochem. 198, 1-6.], an S-like RNase from Lycopersicon esculentum, a Solanaceous species. The fact that RNase LE is more similar to RNS2 than to the S-RNases from other Solanaceous plants indicates that the S-like RNases diverged from the S-RNases prior to speciation. Like the S-RNase genes, RNS2 is most highly expressed in flowers, but unlike the S-RNase genes, RNS2 is also expressed in roots, stems, and leaves of Arabidopsis. Moreover, the expression of RNS2 is increased in both leaves and petals of Arabidopsis during senescence. Phosphate starvation can also induce the expression of RNS2. On the basis of these observations, we suggest that one role of RNS2 in Arabidopsis may be to remobilize phosphate, particularly when cells senesce or when phosphate becomes limiting.
Serum Levels of an Isoform of Apolipoprotein A-II as a Potential Marker for Prostate Cancer (2005)

We have identified an isoform of ApoA-II giving rise to an 8.9K m/z SELDI "peak" that is specifically overexpressed in prostate disease. The ability of ApoA-II to detect disease in patients with normal prostate-specific antigen suggests potential utility of the marker in identifying indolent disease.
The Finite-Element Method Contrast Source Inversion Algorithm for 2D Transverse Electric Vectorial Problems (2012)

The contrast source inversion algorithm is formulated using the finite-element method for two-dimensional transverse electric microwave imaging problems. Edge-based triangular elements with vector basis functions are utilized to solve the TE electromagnetic problem. A single finite-element method (FEM) mesh is used to model both the electric field as well as the contrast-source and contrast variables used in the inverse problem. The electromagnetic field is modeled by taking the unknown values to be the tangential components of the transverse electric field along the edges of each triangular element. The unknown contrast-source and contrast variables are located at the centroids of every triangular element of the same FEM mesh, but only inside the imaging domain. The adaptation of the FEM-contrast source inversion (FEM-CSI) algorithm to 2D-TE problems on such an arbitrary mesh requires the implementation of special transformation operators which are presented herein. The algorithm's capabilities are demonstrated by inverting the Fresnel experimental TE datasets as well as synthetically generated data.
Time and frequency synchronization for OFDM using PN-sequence preambles (1999)

Fast and reliable time and frequency synchronization is crucial for packet-based orthogonal frequency division multiplex (OFDM) systems. In this paper we compare and analyze preambles for OFDM systems based on repeated OFDM data symbols or repeated short pseudonoise sequences (PN-sequences). We make an analytical evaluation for AWGN channels and simulate the performance in oneand two-tap Rayleigh fading channels. The PN-based preamble gives better detection properties in terms of lower false detection probability and lower probability of missing the synchronization signal. The PN-based preamble has low peak-to-average power ratio and it makes it possible to use an ADC with one-bit quantization in stand-by mode. For frequency offset estimation both preambles give similar performance, but the PN-based preamble allows for a greater reduction in stand-by mode power consumption.
The primary structure of a glyceraldehyde-3-phosphate dehydrogenase gene from Saccharomyces cerevisiae. (1979)

The complete nucleotide sequence of the coding, as well as the flanking noncoding regions, of a yeast glyceraldehyde-3-phosphate dehydrogenase gene was determined. Both the 5' and 3' noncoding sequences are extremely AT-rich and regions of partial dyad symmetry are present immediately adjacent to the 5' and 3' ends of the translated portion of the gene. The sequence AAUAAA is present in the 3' noncoding region of this gene and is a part of an extensive region of dyad symmetry which is structurally related to the 3'-terminal portion of both procaryotic mRNAs, as well as some eukaryotic mRNAs. The coding region of this gene does not contain intervening sequences. Establishment of the primary structure of this glyceraldehyde-3-phosphate dehydrogenase gene provides a basis for further studies involving in vitro mutation of the gene and subsequent analysis of gene expression in vivo.
On the correlation between stellar chromospheric flux and the surface gravity of close-in planets (2014)

Aims. The chromospheric emission of stars with close-in transiting planets has been found to correlate with the surface gravity of their planets. Stars with low-gravity planets have on average a lower chromospheric flux.
A Practical Synthesis of a COX-2-Specific Inhibitor (2000)

A number of synthetic strategies to the Cox-2 specific inhibitor 1 have been described. These studies have led to the identification of a novel pyridine construction using annulation of ketone 2 using a vinamidinium species 29 and ammonia in 97% assay yield. Three approaches to the synthesis of ketone 2 are described that allow for its preparation in large quantities in >65% overall yield from methyl 6-methylnicotinate.
In Vitro Activities of Two Antimitotic Compounds, Pancratistatin and 7-Deoxynarciclasine, against Encephalitozoon intestinalis , a Microsporidium Causing Infections in Humans (2001)

The antiparasitic effect of a collection of compounds with antimitotic activity has been tested on a mammalian cell line infected with Encephalitozoon intestinalis, a microsporidian causing intestinal and systemic infection in immunocompromised patients. The antiparasitic effect was evaluated by counting the number of parasitophorous vacuoles detected by immunofluorescence. Out of 526 compounds tested, 2 (pancratistatin and 7-deoxynarciclasine) inhibited the infection without affecting the host cell. The 50% inhibitory concentrations (IC(50)s) of pancratistatin and 7-deoxynarciclasine for E. intestinalis were 0.18 microM and 0.2 microM, respectively, approximately eightfold lower than the IC(50)s of these same compounds against the host cells. Electron microscopy confirmed the gradual decrease in the number of parasitophorous vacuoles and showed that of the two life cycle phases, sporogony was more sensitive to the inhibitors than merogony. Furthermore, the persistence of meronts in some cells apparently devoid of sporonts and spores indicated that the inhibitors block development rather than entry of the parasite into the host cell. The occurrence of binucleate sporoblasts and spores suggests that these inhibitors blocked a specific phase of cell division.
Review of Current Evidence for Apoptosis After Spinal Cord Injury (2000)

The initial mechanical tissue disruption of spinal cord injury (SCI) is followed by a period of secondary injury that increases the size of the lesion. The secondary injury has long been thought to be due to the continuation of cellular destruction through necrotic (or passive) cell death. Recent evidence from brain injury and ischemia suggested that cellular apoptosis, an active form of programmed cell death seen during development, could play a role in CNS injury in adulthood. Here, we review the evidence that apoptosis may be important in the pathophysiology of SCI. There is now strong morphological and biochemical evidence from a number of laboratories demonstrating the presence of apoptosis after SCI. Apoptosis occurs in populations of neurons, oligodendrocytes, microglia, and, perhaps, astrocytes. The death of oligodendrocytes in white matter tracts continues for many weeks after injury and may contribute to post-injury demyelination. The mediators of apoptosis after SCI are not well understood, but there is a close relationship between microglia and dying oligodendrocytes, suggesting that microglial activation may be involved. There is also evidence for the activation of important intracellular pathways known to be involved in apoptosis in other cells and systems. For example, some members of the caspase family of cysteine proteases are activated after SCI. It appears that the evolution of the lesion after SCI involves both necrosis and apoptosis. It is likely that better understanding of apoptosis after SCI will lead to novel strategies for therapeutic interventions that can diminish secondary injury.
Clonally Related Cortical Cells Show Several Migration Patterns (1988)

The mammalian cerebral cortex is organized into columns of cells with common functional properties. During embryogenesis, cortical neurons are formed deep, near the lateral ventricles, and migrate radially to their final position. This observation led to the suggestion that the cortex consists of radial, ontogenetic units of clonally related neurons. In the experiments reported here, this hypothesis was tested by studying cell lineage in the rat cortex with a retroviral vector carrying the Escherichia coli beta-galactosidase gene, which can be easily visualized. Labeled, clonally related cortical neurons did not occur in simple columnar arrays. Instead, clonally related neurons entered several different radial columns, apparently by migrating along different radial glial fibers.
Partial-birth abortion (1998)

In the May AAP News, Dr. Scott Spear attacks the comments of Dr. Enrique Canton, who wrote in favor of a ban on partial-birth abortion. In his defense of partial-birth abortion, Dr. Spear dismisses the comments of Dr. Canton as What Dr. Spear fails to comprehend is that his stance on partial-birth abortion is also theologically based. The medical fact is, as the American Medical Association has testified before Congress, that there is simply no valid indication for the procedure. Dr. Spear9s support for partial-birth abortion must, therefore, derive from ideology, not science. Perhaps the god (or gods) that Dr. Spear worships condones, or even encourages, infanticide. But infanticide is something that the American Academy of Pediatrics, in my view, ought to oppose.
Genetically based therapeutics for cancer: similarities and contrasts with traditional drug discovery and development (2005)

The field of molecular therapeutics is in its infancy and represents a promising and novel avenue for targeted cancer treatments. Like the small-molecule and antibody therapeutics before them, however, the genetic-based therapies will face significant research and development challenges in their maturation toward an approved cancer therapy. To facilitate this process, we outline and examine in this review the drug development process, briefly summarizing the research and development paradigms that have accompanied the recent successes of the small-molecule and antibody-based cancer therapeutics. Using this background, we compare and contrast the research and development experiences of small-molecule and antibody therapeutics with genetic-based cancer therapeutics, using oncolytic viruses as a defined example of an experimental molecular therapeutic for cancer.
A Tunable Broadband Photonic RF Phase Shifter Based on a Silicon Microring Resonator (2008)

We propose and demonstrate a tunable broadband photonic radio frequency (RF) phase shifter based on a silicon microring resonator. This scheme utilizes the thermal nonlinear effect of the silicon microring to change the electrical phase of the RF signal with a wide tuning range. A prototype of the phase shifter is experimentally demonstrated for a 40-GHz signal with a 0-4.6-rad tuning range.
The genes of the glutamine synthetase adenylylation cascade are not regulated by nitrogen in Escherichia coli (1993)

Regulation of glutamine-synthetase (GS) activity in enteric bacteria involves a complex cascade of events. In response to nitrogen limitation, a transferase catalyses the uridylylation of the PII protein, which in turn stimulates deadenylylation of GS. Deadenylylated GS is the more active form of the enzyme. Here we characterize in detail the genes from Escherichia coli encoding uridylyl-transferase (glnD), the PII protein (glnB), and adenylyl-transferase (glnE). glnD is transcribed from its own promoter, glnE is contranscribed with another gene, orfXE, whereas glnB is partly contranscribed with a gene encoding a homologue of the transcription activator NtrC. All three gln regulatory genes were constitutively expressed at a low level, i.e. their expression was independent of the nitrogen status and the RNA polymerase sigma factor sigma 54. We conclude that the functioning of the GS adenylylation cascade is regulated by modulation of the activities of uridylyl-transferase and adenylyl-transferase, rather than by changes in the expression of their genes.
LeapFrog: Fast, Timely WiFi Handoff (2007)

Widely used wireless LAN infrastructure often deploys multiple access points to cover a large area. A user terminal needs to handoff between these access points as the user moves. Unfortunately, the IEEE 802.11 standard introduces large latency during the handoff process (> 300ms), which greatly affects the performance of mobile applications. Worse yet, it only attempts a handoff when wireless signal quality degrades to a point where current connectivity is threatened. From the application point of view, a desirable WiFi handoff scheme should have sufficiently low handoff latency to support even the most demanding realtime applications, make timely handoff decisions to always connect the terminal to the access point of the best signal quality and/or the lowest load, not incur significant extra power consumption at the terminal, and facilitate easy deployment and be backwards compatible with the 802.11 standard. Very few existing proposals have all these properties. This paper presents the design, implementation, and experimental evaluation of a scheme called LeapFrog that, with efficient, proactive WiFi channel probing, achieves all the four properties.
Amino acid sequence of the von Willebrand factor-binding domain of platelet membrane glycoprotein Ib. (1987)

We report the amino acid sequence of a 299-residue segment from the alpha chain of the human platelet membrane glycoprotein Ib. This includes the complete sequence of the amino-terminal tryptic fragment of 290 residues comprising the von Willebrand factor-binding domain. Two primary sets of overlapping fragments were obtained by cleavage of the S-carboxymethylated protein at methionyl and lysyl bonds following treatment with cyanogen bromide and Achromobacter protease I, respectively. Additional fragments were obtained by treatment of native glycocalicin with trypsin, Staphylococcus aureus V8 protease, and Serratia marcescens protease. Analysis of all these fragments provided data that allowed determination of the continuous sequence corresponding to approximately half of the alpha-chain polypeptide. This region of glycoprotein Ib is largely hydrophobic and contains only two N-linked and one O-linked carbohydrate chains. A hydrophilic region exists between residues 215 and 299, which contains a cluster of 10 negatively charged residues at 269-287. This area is likely to attract positively charged molecules. The hydrophilic, highly glycosylated (at serine and threonine residues) region corresponding to the previously described "macroglycopeptide" and representing the carboxyl-terminal half of the alpha chain is likely to begin at residue 292. The determined sequence of the alpha chain of glycoprotein Ib contains a region (residues 29-193) with seven repeats, which is indicative of gene duplication and is highly homologous to human leucine-rich alpha 2-glycoprotein. This protein sequence agrees completely with that deduced from the cDNA sequence reported by Lopez et al. [Lopez, J.A., Chung, D.W., Fujikawa, K., Hagen, F.S., Papayannopoulou, T. & Roth, G.J. (1987) Proc. Natl. Acad. Sci. USA 84, 5615-5619].