gebhart/patrepeval huggingface dataset:
Finding effective support-tree preconditioners (2005)

In 1995, Gremban, Miller, and Zagha introduced support-tree preconditioners and a parallel algorithm called support-tree conjugate gradient (STCG) for solving linear systems of the form Ax = b, where A is an n x n Laplacian matrix. A Laplacian is a symmetric matrix in which the off-diagonal entries are non-positive, and the row and column sums are zero. A Laplacian A with 2m off-diagonal non-zeros can be interpreted as an undirected positively-weighted graph G with n vertices and m edges, where there is an edge between two vertices i and j with weight c((i,j)) = --Ai,j = --Aj,i if Ai,j = Aj,i ‹ 0. Gremban et al showed experimentally that STCG performs well on several classes of graphs commonly used in scientific computations. In his thesis, Gremban also proved upper bounds on the number of iterations required for STCG to converge for certain classes of graphs. In this paper, we present an algorithm for finding a preconditioner for an arbitrary graph G = (V,E) with n vertices, m edges, and a weight function c › 0 on the edges, where w.l.o.g., mine∈ec(e) = 1. Equipped with this preconditioner, STCG requires O(log4n · √Δ/α) iterations, where α = minU⊂V,|U|≤|V|/2c(U,V\U)/|U| is the minimum edge expansion of the graph, and Δ = maxυ∈Vc(υ) is the maximum incident weight on any vertex. Each iteration requires O(m) work and can be implemented in O(log n) steps in parallel, using only O(m) space. Our results generalize to matrices that are symmetric and diagonally-dominant (SDD).
Cogeneration of mechanical, electrical, and software designs for printable robots from structural specifications (2014)

Designing and fabricating new robotic systems is typically limited to experts, requiring engineering background, expensive tools, and considerable time. In contrast, to facilitate everyday users developing custom robots for personal use, this work presents a new system to easily create printable foldable robots from high-level structural specifications. A user merely needs to select electromechanical components from a library of basic building blocks and pre-designed mechanisms, then connect them to define custom robot assemblies. The system then generates complete mechanical drawings suitable for fabrication, instructions for the assembly of electronics, and software to control and drive the final robot. Several robots designed in this manner demonstrate the ability and versatility of this process.
Up to 100-Fold Increase of Apparent Gene Expression in the Presence of Epstein-Barr Virus oriP Sequences and EBNA1: Implications of the Nuclear Import of Plasmids (1998)

A 100-fold increase in luciferase activity was observed in 293 cells, stably expressing Epstein-Barr nuclear antigen 1 (EBNA1; 293-EBNA1 cells), that had been transiently transfected with plasmids carrying Epstein-Barr virus (EBV) oriP sequences. This increase was observed in comparison to reporter gene activity obtained after transfection with a plasmid carrying no oriP sequences. The luciferase gene on these plasmids was under the control of either the cytomegalovirus immediate-early 1 gene enhancer-promoter (CMV IE1) or the Rous sarcoma virus promoter. The increase of reporter gene activity was not due to plasmid replication, since a similar enhancement was observed in the presence of aphidicolin, an inhibitor of replicative DNA synthesis, or after deletion of the dyad symmetry (DS) element within oriP. Luciferase production was not increased in the presence of only the DS element. Microinjection of plasmids carrying the CMV IE1 promoter-driven luciferase gene with or without oriP sequences into the nuclei of 293-EBNA1 cells resulted in a 17-fold increase in luciferase activity. Cytoplasmic injection of these plasmids led to an enhancement of luciferase activity of up to 100-fold. This difference in the factor of activation after nuclear or cytoplasmic injection could be ascribed to increased transport of plasmids carrying oriP from the cytoplasm to the nucleus in the presence of EBNA1. These data suggest the possibility of substantially increasing the apparent expression of a gene under the control of a strong constitutive promoter in the presence of oriP sequences and EBNA1. This improvement in expression is due to intranuclear enhancement of gene expression. oriP-specific transport of plasmid DNA from the cytoplasm of 293-EBNA1 cells to the nucleus seems to contribute to the observed effect.
The Membrane-Proximal External Region of the Human Immunodeficiency Virus Type 1 Envelope: Dominant Site of Antibody Neutralization and Target for Vaccine Design (2008)

Enormous efforts have been made to produce a protective vaccine against human immunodeficiency virus type 1; there has been little success. However, the identification of broadly neutralizing antibodies against epitopes on the highly conserved membrane-proximal external region (MPER) of the gp41 envelope protein has delineated this region as an attractive vaccine target. Furthermore, emerging structural information on the MPER has provided vaccine designers with new insights for building relevant immunogens. This review describes the current state of the field regarding (i) the structure and function of the gp41 MPER; (ii) the structure and binding mechanisms of the broadly neutralizing antibodies 2F5, 4E10, and Z13; and (iii) the development of an MPER-targeting vaccine. In addition, emerging approaches to vaccine design are presented.
Genetically Engineered Clostridial C2 Toxin as a Novel Delivery System for Living Mammalian Cells (2009)

The C2 toxin of Clostridium botulinum is a binary bacterial protein toxin, comprising the enzyme component C2I and the separate binding/translocation component C2IIa. C2IIa mediates the transport of C2I into the host cell cytosol. The N-terminal domain of C2I (C2IN) is enzymatically inactive but essential for C2IIa-mediated internalization of C2I. Here, we exploit the C2IIa/C2IN system to generate a recombinant C2IN−streptavidin fusion protein allowing for the delivery of biotinylated molecules into the cytosol of mammalian cells. C2IN−streptavidin overproduced in E. coli was affinity-purified and capable of binding biotinylated proteins in a concentration-dependent manner. Real-time surface plasmon resonance confirmed the biotin-mediated interaction yielding a KD-value of ∼0.75 μM. Internalization of C2IN−streptavidin into the cytosol of epithelial cells and macrophages was demonstrated by immunoblot analysis and confirmed by confocal microscopy. Cell viability studies showed no cytotoxic effects of the novel transporter. Furthermore, Vero cells treated with biotin−fluorescein or biocytin−Alexa488 as model cargo displayed a specific C2IN−streptavidin/C2IIa-dependent uptake, providing proof-of-principle for the functionality of this novel delivery system.
Efficient removers for poly(methylmethacrylate) (2002)

As nanotechnology approaches molecular scales, issues of surface contamination by unremoved resists will play an important role in device fabrication. Electron beam lithography of polymethylmethacrylate (PMMA) resist is still among the most widely used nanofabrication techniques, so it is relevant to study its residual contamination on both exposed and unexposed surfaces using a variety of resist removers. We systematically characterized the effectiveness of several different strippers. Our experiments show that 1,2-dichloroethane is an efficient PMMA remover, and can produce almost the same surface roughness as the original SiO2 surface (i.e., no contamination), whereas the popular PMMA remover, acetone, cannot. Estimates of the polymer–solvent Flory–Huggins interaction parameters and surface–solvent interfacial energy (from contact angle measurements) satisfactorily predict the effectiveness of the solvents. This method should also be applicable to any PMMA-like films on any substrate to find a good surface cleaner.
Stable low-loss proton-exchanged LiNbO_3 waveguide devices with no electro-optic degradation (1988)

Channel waveguides and Mach-Zehnder interferometers were fabricated in LiNbO(3) by annealed proton exchange. The waveguides had a loss of 0.15 dB/cm and a fiber-to-fiber insertion loss of 1.2 dB at 0.8 microm. The measured r(33) electro-optic coefficient of the interferometers was 30 x 10(-12) m/V +/-5%, which agrees well with theory, indicating that there is no degradation in the r(33) coefficient. No variation in insertion loss or switching voltage was observed over 8 months for devices stored at room temperature.
Transplantation of Specific Human Astrocytes Promotes Functional Recovery after Spinal Cord Injury (2011)

Repairing trauma to the central nervous system by replacement of glial support cells is an increasingly attractive therapeutic strategy. We have focused on the less-studied replacement of astrocytes, the major support cell in the central nervous system, by generating astrocytes from embryonic human glial precursor cells using two different astrocyte differentiation inducing factors. The resulting astrocytes differed in expression of multiple proteins thought to either promote or inhibit central nervous system homeostasis and regeneration. When transplanted into acute transection injuries of the adult rat spinal cord, astrocytes generated by exposing human glial precursor cells to bone morphogenetic protein promoted significant recovery of volitional foot placement, axonal growth and notably robust increases in neuronal survival in multiple spinal cord laminae. In marked contrast, human glial precursor cells and astrocytes generated from these cells by exposure to ciliary neurotrophic factor both failed to promote significant behavioral recovery or similarly robust neuronal survival and support of axon growth at sites of injury. Our studies thus demonstrate functional differences between human astrocyte populations and suggest that pre-differentiation of precursor cells into a specific astrocyte subtype is required to optimize astrocyte replacement therapies. To our knowledge, this study is the first to show functional differences in ability to promote repair of the injured adult central nervous system between two distinct subtypes of human astrocytes derived from a common fetal glial precursor population. These findings are consistent with our previous studies of transplanting specific subtypes of rodent glial precursor derived astrocytes into sites of spinal cord injury, and indicate a remarkable conservation from rat to human of functional differences between astrocyte subtypes. In addition, our studies provide a specific population of human astrocytes that appears to be particularly suitable for further development towards clinical application in treating the traumatically injured or diseased human central nervous system.
Stat3 Activation Is Limiting for Reprogramming to Ground State Pluripotency (2010)

The cytokine leukemia inhibitory factor (Lif) sustains self-renewal of mouse embryonic and induced pluripotent stem cells by activating Jak kinase and the transcription factor Stat3. Here we investigate whether Jak/Stat3 may also contribute to induction of pluripotency. EpiSCs derived from postimplantation embryos express low levels of Lif receptor and Stat3. We introduced into EpiSCs a Jak/Stat3 activating receptor (GY118F) responsive to granulocyte colony stimulating factor (Gcsf). On transfer to ground state culture, in which MAPK signaling and glycogen synthase kinase are inhibited, Gcsf induced transcriptional resetting and functional reprogramming. Activation of a tamoxifen-regulatable fusion, Stat3ER(T2), also converted EpiSCs into chimera-competent iPSCs. We exploited GY118F to increase Jak/Stat3 activity during somatic cell reprogramming. Incompletely reprogrammed cells derived from neural stem cells or fibroblasts responded to Gcsf with elevated frequencies of progression to ground state pluripotency. These findings indicate that Jak/Stat3 participate directly in molecular reprogramming and that activation of this pathway is a limiting component.
Lymphoma-associated translocation t(14;18) in blood B cells of normal individuals (1995)

Successive oncogenic steps are necessary to generate cancer. In many B-cell lymphomas, chromosomal translocations are considered to be an early oncogenic hit. We investigated whether the lymphoma-associated t(14;18) involving the BCL2 oncogene can occur outside the context of malignancy. To this end, we extensively screened blood cells from healthy blood donors by a very sensitive seminested polymerase chain reaction (PCR) for breakpoint junctions at JH1-5 on 14q32 and the major breakpoint region of BCL2 on 18q21. In each individual, mononuclear cells, granulocytes, flow-sorted B cells, and T cells were separately tested in five to seven independently performed PCRs (in total, 0.5 x 10(6) to 1.0 x 10(6) cells per fraction per individual). Amplification products that hybridized with an internal BCL2 probe and a JH probe were sequenced. Six of nine individuals harbored t(14;18) breakpoints. Translocations were restricted to B cells, with an estimated frequency of 1 in 10(5) or less circulating B cells. In total, 23 of 51 experiments on B cells were positive in contrast to 1 of 48 on T cells and 2 of 47 experiments on granulocytes. Consistent with the presence of 4.7% to 13.0% B cells in the mononuclear cell fractions, only very few (4 of 47) tests were positive in these fractions. Sequence analysis showed that four of six individuals harbored two to five unrelated t(14;18)-carrying B-cell clones. All breakpoints had a structure similar to that in follicular lymphoma. We propose that B cells with the t(14;18) translocation are regularly generated in normal individuals, but that only very few cells with the translocation will acquire the additional oncogenic hits necessary to establish the malignant phenotype.
Esophageal Temperature Monitoring During Radiofrequency Ablation of Atrial Fibrillation (2005)

The location of the esophagus relative to the back of the left atrium displays considerable variability. It is rarely midline and most often lies in close proximity to the left-sided veins. Ablation in close radiographic proximity (approximately 1 cm) to the esophagus as defined by a radio-opaque temperature probe can result in heating at the esophageal lumen.
Discovery of I-BRD9, a Selective Cell Active Chemical Probe for Bromodomain Containing Protein 9 Inhibition (2015)

Acetylation of histone lysine residues is one of the most well-studied post-translational modifications of chromatin, selectively recognized by bromodomain "reader" modules. Inhibitors of the bromodomain and extra terminal domain (BET) family of bromodomains have shown profound anticancer and anti-inflammatory properties, generating much interest in targeting other bromodomain-containing proteins for disease treatment. Herein, we report the discovery of I-BRD9, the first selective cellular chemical probe for bromodomain-containing protein 9 (BRD9). I-BRD9 was identified through structure-based design, leading to greater than 700-fold selectivity over the BET family and 200-fold over the highly homologous bromodomain-containing protein 7 (BRD7). I-BRD9 was used to identify genes regulated by BRD9 in Kasumi-1 cells involved in oncology and immune response pathways and to the best of our knowledge, represents the first selective tool compound available to elucidate the cellular phenotype of BRD9 bromodomain inhibition.
Crossover behavior in the hydrogen sensing mechanism for palladium ultrathin films (2010)

Palladium has been extensively studied as a material for hydrogen sensors because of the simplicity of its reversible resistance change when exposed to hydrogen gas. Various palladium films and nanostructures have been used, and different responses have been observed with these diverse morphologies. In some cases, such as with nanowires, the resistance will decrease, whereas in others, such as with thick films, the resistance will increase. Each of these mechanisms has been explored for several palladium structures, but the crossover between them has not been systematically investigated. Here we report on a study aimed at deciphering the nanostructure-property relationships of ultrathin palladium films used as hydrogen gas sensors. The crossover in these films is observed at a thickness of approximately 5 nm. Ramifications for future sensor developments are discussed.
Separation of positional isomers of oligosaccharides and glycopeptides by high-performance anion-exchange chromatography with pulsed amperometric detection. (1988)

High-performance anion-exchange (HPAE) chromatography under alkaline conditions (pH congruent to 13) has been found to efficiently separate neutral oligosaccharides (triose to undecaose) according to molecular size, sugar composition, and linkage of monosaccharide units. The method was able to resolve 1----3, 1----4, and 1----6 positional isomers of neutral oligosaccharides, which are defined as having the same number, type, sequence, and anomeric configurations of monosaccharides but differing in the linkage position of a single sugar. From correlating structural features of different oligosaccharides and retention times, we deduced that at least two factors are operative to determine the superior resolution of oligosaccharides by this type of chromatography: (i) the relative acidities of the hydroxyl groups and (ii) the accessibility of oxyanions of the oligosaccharides to the functional groups of the stationary phase. Splitting of peaks attributable to mutarotation was not observed. Reducing oligosaccharides were much more retained than their reduced counterparts. Linkage of Fuc(alpha 1-3) to GlcNAc of oligosaccharides markedly decreased retention times. Positional isomers of two branched monosaccharides, which differed by 1----6 and 1----4 linkages, were widely separated. The separation of 1----3 and 1----4 positional isomers of both tetrasaccharides and glycopeptides containing undecasaccharides demonstrated the significant improvement in resolution of HPAE compared to previous chromatographic methods by either reverse-phase or amine-bonded stationary phases. Picomole quantities of underivatized oligosaccharides have been detected by triple-pulse amperometric detection, which produced similar responses for a wide range of structures. Quantification of two triantennary glycopeptides from bovine fetuin by using either detector response or 1H NMR was comparable. The N-glycanase-catalyzed release of two 1----4 and 1----3 positional isomers of an undecasaccharide from a tryptic glycopeptide of bovine fetuin could be observed and quantified by direct injection of the enzyme mixture into the chromatograph.
Hafnium Oxide Based CMOS Compatible Ferroelectric Materials (2013)

S.N69-N72
Fast bistable all-optical switch and memory on a silicon photonic crystal on-chip (2005)

We demonstrate extremely low-power all-optical bistability by utilizing silicon photonic crystal nanocavities, based on the plasma effect of carriers generated by two-photon absorption. Owing to the high quality factor and the small volume of the nanocavities, the photon density inside the cavity becomes extremely high, which leads to a large reduction in operation power. Optical bistable operation in a single nanocavity permits optical read-write memory operation, which opens the possibility of an integrated optical logic circuit on a single chip, based on photonic crystals. The demonstrated bistable threshold power is 0.4 mW with a set pulse energy of 74 fJ, at a switching speed of <100 ps.
Aggregative adherence fimbriae I of enteroaggregative Escherichia coli mediate adherence to HEp-2 cells and hemagglutination of human erythrocytes (1992)

Strains of enteroaggregative Escherichia coli (EAggEC) have been implicated in several studies as important agents of persistent diarrhea among infants in the developing world. We have previously shown that the aggregative adherence (AA) property of EAggEC is associated with the presence of a 60-MDa plasmid which confers AA when introduced into E. coli HB101. Here, we report the cloning of the AA determinant from EAggEC strain 17-2 into the 21.5-kb cosmid vector pCVD301. TnphoA mutagenesis of the AA cosmid clone pJPN31 implicated an AA region of approximately 12 kb. Transmission electron microscopy of HB101 (pJPN31) revealed the presence of bundle-forming fimbriae, which were absent in AA- TnphoA insertion mutants. The presence of these fimbriae, AA, and hemagglutination (HA) of human erythrocytes were all concurrently lost by single-insertion mutations. A 14-kDa protein was seen on polyacrylamide gel electrophoresis and Western blotting (immunoblotting) of surface shear preparations from fimbriated clones. Twelve of nineteen volunteers fed EAggEC 17-2 developed rises in antibodies to the 14-kDa protein as determined by Western blot. We have termed the cloned bundle-forming fimbriae aggregative adherence fimbriae I (AAF/I); positivity with a previously described EAggEC probe and human erythrocyte HA appear to correlate with the presence of AAF/I.
Tuning memory performance of sequential and parallel programs (1995)

To improve program memory performance, programmers and compiler writers can transform the application so that its memory-referencing behavior better exploits the memory hierarchy. The challenge in achieving these program transformations is overcoming the difficulty of statically analyzing or reasoning about an application's referencing behavior and interactions. In addition, many performance-monitoring tools collect high-level information that is inadequately detailed to analyze specific memory performance bugs. We describe MemSpy, a performance-monitoring tool we designed to help programmers discern where and why memory bottlenecks occur. MemSpy guides programmers toward program transformations that improve memory performance through detailed statistics on cache-miss causes and frequency. Because of the natural link between data-reference patterns and memory performance, MemSpy helps programmers comprehend data structure and code segment interactions by displaying statistics in terms of both the program's data and code structures, rather than for code structures alone.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A novel solid freeforming method using simultaneous part and mould construction (2008)

Purpose The purpose of this paper is to present a new powder‐based solid freeforming method based on conventional furnace sintering after co‐deposition of mould and part powder materials. Design/methodology/approach Based on acoustic powder deposition, both mould and part powder materials are delivered simultaneously into the forming area according to the cross section of the 3D computer file. The part is formed in the form of loose powder surrounded by the mould powder again in a loose state. The whole assembly can then be sintered by a conventional method and the mould powder, which has a higher sintering temperature than that of part powder, remains in the loose state after sintering and can be removed. Findings Complex‐shaped components containing re‐entrant cavities and the capability of being made with 3D functional gradients can be rendered directly as a powder preform suitable for subsequent compaction or direct sintering in a conventional furnace. The flowability and compatibility of the powders need to be selected carefully and the track distance between part/mould powders is important for forming a vertical wall. Research limitations/implications The main factors affecting building from powder tracks are identified, including the effect of track distance at an interface on integrity, discontinuous feeding on bends and the effects of fill strategies. The flow rates of the part and mould powder as well as their geometrical maps are controlled computationally. Materials and instrumental aspects are discussed. Originality/value This paper describes a method to produce complex‐shaped object without residual stress and expensive lasers and the process could be modified to include 3D functional gradients.