gebhart/patrepeval huggingface dataset:
4D-Fingerprints, Universal QSAR and QSPR Descriptors (2004)

An elusive goal in the field of chemoinformatics and molecular modeling has been the generation of a set of descriptors that, once calculated for a molecule, may be used in a wide variety of applications. Since such universal descriptors are generated free from external constraints, they are inherently independent of the data set in which they are employed. The realization of a set of universal descriptors would significantly streamline such chemoinformatics tasks as virtual high-throughout screening (VHTS) and toxicity profiling. The current study reports the derivation and validation of a potential set of universal descriptors, referred to as the 4D-fingerprints. The 4D-fingerprints are derived from the 4D-molecular similarity analysis. To evaluate the applicability of the 4D-fingerprints as universal descriptors, they are used to generate descriptive QSAR models for 5 independent training sets. Each of the training sets has been analyzed previously by several varying QSAR methods, and the results of the models generated using the 4D-fingerprints are compared to the results of the previous QSAR analyses. It was found that the models generated using the 4D-fingerprints are comparable in quality, based on statistical measures of fit and test set prediction, to the previously reported models for the other QSAR methods. This finding is particularly significant considering the 4D-fingerprints are generated independent of external constraints such as alignment, while the QSAR methods used for comparison all require an alignment analysis.
Genotyping Schemes for Polyomavirus BK, Using Gene-Specific Phylogenetic Trees and Single Nucleotide Polymorphism Analysis (2008)

BK virus (BKV) genotyping has been historically based on nucleotides 1744 to 1812 in the VP1 gene. We reevaluated this practice by making BKV whole-genome and gene-specific phylogenetic trees as well as performing single nucleotide polymorphism (SNP) analysis of 162 sequences available in the public domain. It was found that currently known BKV subtypes and subgroups can no longer be reliably determined by sequencing certain partial gene sequences. Phylogenetic trees based on large T-antigen (LTA) allow separation of subtype I into subgroups Ia, Ib1, Ib2, and Ic, with bootstrap values of 100%, which are better than bootstraps obtained using VP1 sequences (bootstrap values of 71 to 97%). Subtype IV can be subdivided into subgroups, but LTA bootstrap values (33 to 80%) are lower than those obtained by whole-genome analysis (68 to 87%). Subtypes V and VI provisionally identified earlier on the basis of more limited sequence data are better classified as subgroups Ib2 and Ib1, respectively. LTA positions 3634, 3772, 3934, and 4339 can serve as a minimal SNP set to distinguish between the four major BKV subtypes. No subtype II-, IVa-, or IVb-defining SNPs are available in the VP1 gene. However, the overall congruence of viral strain classification based on either VP1 or LTA phylogenetic analysis indicates that these two areas of the viral genome are genetically linked. Interstrain genetic recombination between distant loci in the VP1 and LTA areas is not a common event.
<i>Xa26</i>, a gene conferring resistance to <i>Xanthomonas oryzae</i> pv. <i>oryzae</i> in rice, encodes an LRR receptor kinase‐like protein (2004)

Rice bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most serious rice diseases worldwide. A rice gene, Xa26, conferring resistance against Xoo at both seedling and adult stages was isolated by map-based cloning strategies from the rice cultivar Minghui 63. Xa26 belongs to a multigene family consisting of four members. It encodes a leucine-rich repeat (LRR) receptor kinase-like protein and is constitutively expressed. Sequence analysis revealed that IRBB3 and Zhachanglong lines that are resistant to a broad range of Xoo strains, also carry Xa26. However, significant difference in lesion length was observed among these lines after inoculation with a set of Xoo strains. Moreover, transgenic plants carrying Xa26 showed enhanced resistance compared with the donor line of the gene in both seedling and adult stages. These results suggest that the resistance conferred by Xa26 is influenced by the genetic background.
Occurrence of paedogenetic cecidomyiids (Diptera: Cecidomyiidae) in casing layer materials used in the Australian mushroom industry. (1980)

Both composted sugar mill by-products and New South Wales peat are being used in mixtures with imported sphagnum peat as alternative casing layer materials in the Australian mushroom industry. Larvae of 'Heteropeza pygmaea' Winnertz were found in sphagnum peat imported from West Germany and also in composted sugar mill by-products from Southport, Queensland. Larvae of 'Mycophila barnesi' Edwards were found in sedge peat from Robertson, New South Wales.
Signal reduction in fluorescence imaging using radio frequency-multiplexed excitation by compressed sensing (2014)

Fluorescence imaging using radio frequency-multiplexed excitation (FIRE) has emerged to enable an order-of-magnitude higher frame rate than the current technologies. Similar to all high-speed realtime imaging modalities, FIRE inherently generates massive image data continuously. While this technology entails high-throughput data sampling, processing, and storage in real-time, strategies in data compression on the fly is also beneficial. We here report that it is feasible to exploit the radio frequency-multiplexed excitation scheme in FIRE for implementing compressed sensing (CS) without any modification of the FIRE system. We numerically demonstrate that CS-FIRE can reduce the effective data rate by 95% without severe degradation of image quality.
Thermoplastic 3D Printing—An Additive Manufacturing Method for Producing Dense Ceramics (2014)

In our new approach—thermoplastic 3D printing—a high‐filled ceramic suspension based on thermoplastic binder systems is used to produce dense ceramic components by additive manufacturing. Alumina (67 vol%) and zirconia (45 vol%) suspensions were prepared by ball milling at a temperature of about 100°C to adjust a low viscosity. After the preparation the suspension solidified at cooling. For the sintered samples (alumina at 1600°C, zirconia at 1500°C), a density of about 99% and higher was obtained. FESEM studies of the samples' cross section showed a homogenous microstructure and a very good bond between the single printed layers.
Empirical study of tolerating denial-of-service attacks with a proxy network (2005)

Proxy networks have been proposed to protect applications from Denial-of-Service (DoS) attacks. However, since large-scale study in real networks is infeasible and most previous simulations have failed to capture detailed network behavior, the DoS resilience and performance implications of such use are not well understood in large networks. While post-mortems of actual large-scale attacks are useful, only limited dynamic behavior can be understood from these single instances. Our work provides the first detailed and broad study of this problem in large-scale realistic networks. The key is that we use an online network simulator to simulate a realistic large-scale network (comparable to several large ISPs). We use a generic proxy network, and deploy it in a large simulated network using typical real applications and DoS tools directly. We study detailed system dynamics under various attack scenarios and proxy network configurations. Specific results are as follows. First, rather than incurring a performance penalty, proxy networks can improve usersí experienced performance. Second, proxy networks can effectively mitigate the impact of both spread and concentrated large-scale DoS attacks in large networks. Third, proxy networks provide scalable DoS-resilience ñ resilience can be scaled up to meet the size of the attack, enabling application performance to be protected. Resilience increases almost linearly with the size of a proxy network; that is, the attack traffic that a given proxy network can resist, while preserving a particular level of application performance, grows almost linearly with proxy network size. These results provide empirical evidence that proxy networks can be used to tolerate DoS attacks and quantitative guidelines for designing a proxy network to meet a resilience goal. 1
Synthesis and biological activities of angiotensin II, sarilesin, and sarmesin analogs containing Aze or Pip at position 7 (1993)

Analogues of [Sar1]angiotensin II, Sarilesin (type I antagonist), and Sarmesin (type II antagonist) with L-azetidine-2-carboxylic acid (Aze) and L-pipecolic acid (Pip) at position 7 have been prepared by the solid-phase method, purified by reverse-phase HPLC, and bioassayed in the rat uterus. Analogues of the superagonist [Sar1]ANGII with Aze or Pip at position 7 and sarcosine (Sar) or aminoisobutyric acid (Aib) at position 1 had high intrinsic activity in the rat isolated uterus assay (34-184%). Analogues of Sarilesin ([Sar1,Ile8]ANGII) with Aze or Pip at position 7 and Sar or Aib at position 1 retained high antagonist activity (pA2 = 7.1-8.3). Analogues of Sarmesin ([Sar1,Tyr-(OMe)4]ANGII) with Aze and Pip at position 7 had pA2 values of 7.4 and 6.5, respectively. [Aze7]-ANGII and [Pip7]ANGII had low activities (12% and 1%, respectively), and deletion of Sar at position 1 of Sarmesin analogues abolished binding (or affinity) as judged from pA2 values. Nuclear Overhauser effect (NOE) spectroscopy studies of [Sar1,Aze7]ANGII in DMSO-d6 have indicated a clustering of the three aromatic rings (Tyr, His, Phe) and proximity of Sar C alpha and Arg C delta protons to the Tyr/Phe ring protons. These data emphasize that replacement of Pro with the lower and higher homologs Aze and Pip does not greatly alter the structural requirements necessary for expression of agonist or antagonist activity, when sarcosine occupies position 1, but not when Asp occupies position 1, suggesting that there is an intimate relationship between the N-terminal and penultimate residues of the molecule in the biologically active conformation of the molecule.
Synthesis and antitumor activity evaluation of new 2-(4-aminophenyl)benzothiazole derivatives bearing different heterocyclic rings (2014)

Twenty-five new N-[4-(benzothiazole-2-yl)phenyl]acetamide derivatives bearing different heterocyclic ring systems were synthesized using 2-(4-aminophenyl)benzothiazole structure as a pharmacophoric group. Final compounds were screened for their potential antitumor activity in vitro against approximately 60 human tumor cell lines derived from nine neoplastic diseases at National Cancer Institute, USA. 2-(4-Aminophenyl)benzothiazole structure was prepared by the reaction of 4-aminobenzoic acid and 2-aminothiophenol in polyphosphoric acid using microwave irradiation. After acetylation reaction, amide compounds 2a and 2b were obtained, which were then reacted with 2-mercapto(benz)imidazole/benzothiazole/benzoxazole derivatives in acetone with the presence of potassium carbonate to gain final compounds (3-27). Among all tested compounds, compound 10, namely N-[4-(benzothiazole-2-yl)-3-chlorophenyl]-2-[(benzimidazole-2-yl)thio]acetamide, and compound 16, namely N-[4-(benzothiazole-2-yl)phenyl]-2-[(1,5-diphenyl-1H-imidazole-2-yl)thio]acetamide, were found to be of considerable anticancer activity against some cancer cell lines.
Multi-stage switching system using optical wdm grouped links based on dynamic bandwidth sharing (2003)

A three-stage Clos switch architecture is attractive because of its scalability. From an implementation point of view, it allows us to relax the cooling limitation, but there is a problem interconnecting different stages. This article presents a three-stage switching system that uses optical WDM grouped links and dynamic bandwidth sharing. We call it a WDM grouped-link switch. The introduction of WDM makes the number of cables used in the system proportional to the switch size. Dynamic bandwidth sharing among WDM grouped links prevents the statistical multiplexing gain offered by WDM from falling even if the switching system becomes large. The WDM grouped-link switch uses cell-by-cell wavelength routing. A performance evaluation confirms the scalability and cost-effectiveness of this switch. An implementation of the WDM grouped link and a compact planar lightwave circuit platform is described. This architecture allows us to expand the throughput of the switching system up to 5 Tb/s.
Modular Typestate Verification of Aliased Objects (2007)

A number of type systems have used typestates to specify and statically verify protocol compliance.Aliasing is a major challenge for these systems.This paper proposes a modular type system for a core object-oriented language that leverages linear logic for verifying compliance to more expressive protocol specifications than previously supported.The system improves reasoning about aliased objects by associating references with access permissions that systematically capture what aliases know about and can do to objects.Permissions grant full, shared, or read-only access to a certain part of object state and allow aliasing both on the stack and in the heap.The system supports dynamic state tests, arbitrary callbacks, and open recursion.The system's expressiveness is illustrated with examples from the Java I/O library.
Synergistic Co‐Delivery of Membrane‐Disrupting Polymers with Commercial Antibiotics against Highly Opportunistic Bacteria (2013)

A series of vitamin E-containing biodegradable antimicrobial cationic polycarbonates is designed and synthesized via controlled organocatalytic ring-opening polymerization. The incorporation of vitamin E significantly enhances antimicrobial activity. These polymers demonstrate broad-spectrum antimicrobial activity against various microbes, e.g., S. aureus (Gram-positive), E-coli (Gram-negative) and C. albicans (fungi). More importantly, the co-delivery of such polymers with selected antibiotics (e.g., doxycycline) shows high synergism towards difficult-to-kill bacteria P. aeruginosa. These findings suggest that these vitamin E-functionalized polycarbonates are potentially useful antimicrobial agents against challenging bacterial/fungal infections.
Improved High-Performance Liquid Chromatographic Method for the Analysis of Potato (<i>Solanum tuberosum</i>) Glycoalkaloids (1996)

An improved high-performance liquid chromatographic (HPLC) method for the determination of the potato glycoalkaloids, α-solanine and α-chaconine, is described. The glycoalkaloids were extracted with aqueous acetic acid, concentrated, and cleaned up by solid phase extraction using C18 cartridge columns and separated using a reverse phase C18 HPLC column. Recoveries averaged 93% ± 1.3 for α-solanine and 99% ± 3.1 for α-chaconine. Comparisons were made at each step with existing published methods. We conclude that trifunctional endcapped C18 SPE cartridges were more reliable than traditional monofunctional non-endcapped cartridges and that low carbon load C18 HPLC columns provided an improved separation of glycoalkaloids when compared to columns with a high carbon loading. An acidic extraction medium excluding organic solvents is recommended. Keywords: α-Chaconine; glycoalkaloids; HPLC; potato; α-solanine; Solanum tuberosum
Interaction of<i>Escherichia coli</i>Cobalamin-Dependent Methionine Synthase and Its Physiological Partner Flavodoxin:  Binding of Flavodoxin Leads to Axial Ligand Dissociation from the Cobalamin Cofactor (1997)

Cobalamin-dependent methionine synthase from Escherichia coli catalyzes the last step in de novo methionine biosynthesis. Conversion of the inactive cob(II)alamin form of the enzyme, formed by the occasional oxidation of cob(I)alamin during turnover, to an active methylcobalamin-containing form requires a reductive methylation of the cofactor in which an electron is supplied by reduced flavodoxin and the methyl group is derived from S-adenosyl-L-methionine. E. coli flavodoxin acts specifically in this activation reaction, and neither E. coli ferredoxin nor flavodoxin from the cyanobacterium Synechococcus will substitute, despite their highly similar midpoint potentials for one-electron transfer. As assessed by EPR spectroscopy, the binding of flavodoxin to cob(II)alamin methionine synthase results in a change in the coordination geometry of the cobalt from five-coordinate to four-coordinate. Histidine 759 of methionine synthase, which replaces the normal lower ligand dimethylbenzimidazole on binding of methylcobalamin to methionine synthase, is dissociated from the cobalt of the cobalamin by the binding of flavodoxin. The association of flavodoxin and methionine synthase depends on ionic strength and pH; the pH dependence corresponds to the uptake of one proton on association. The formation of a complex between flavodoxin and methionine synthase perturbs the midpoint potentials of the flavin and cobalamin cofactors only marginally and without any significant thermodynamic advantage for electron transfer to the cobalamin of methionine synthase. No significant binding was seen between oxidized flavodoxin and methylcobalamin methionine synthase. A model for the interaction of methionine synthase with flavodoxin is proposed in which flavodoxin binding leads to changes in the distribution of methionine synthase conformations.
Description and detection of moving sample zones in zone electrophoresis: Zone spreading due to the sample as a necessary discontinuous element (1983)

Abstract This paper deals with the description and detection of moving sample zones in free zone electrophoresis. It is shown that the shape of a sample zone never reaches a steady‐state. However, either the front or the rear boundary of the sample zones, but not both, can represent steady‐state concentration distributions with decreasing peak heights. This results in an unsymmetrical broadening of the moving zones. With a multichannel detection device, consisting of 255 equidistant detectors along the separation trough, asymmetric electric field distributions of the sample components are measured. These are shown to agree with theoretical predictions, made by a model based on migration only. This clarifies the fact that in zone electrophoresis migrational dispersion due to the applied electric field is usually much larger than diffusional spreading.
Telangiectatic Osteosarcoma: Radiologic-Pathologic Comparison (2003)

CT and MR imaging findings of telangiectatic osteosarcoma often include thick nodular tissue (and matrix mineralization at CT) in a largely hemorrhagic and/or necrotic osseous lesion with an associated soft-tissue mass, which allows distinction from aneurysmal bone cyst.
Particle trajectories and terminal velocities in vertically oscillating fluids (1966)

Abstract The trajectories and terminal velocities of particles in vertically oscillating fluids have been studied by obtaining analytic and numerical solutions to the nonlinear Langevin equation representing a superposition of forces arising from particle acceleration, displaced fluid acceleration, buoyancy and particle‐fluid drag as represented by an n th ‐power drag law. In vibrating fluids the directional particle velocities are found to be lower than in stationary fluids for drag exponents n > 1 and correspondingly higher for 0 < n < 1. The engineering significance of the results is discussed in relation to hold‐up, separation and transport phenomena in vertically oscillating multiparticle‐fluid systems.
Nanostructuring Borosilicate Glass With Near-Field Enhanced Energy Using a Femtosecond Laser Pulse (2006)

A model based on the evolution of electron density derived from the Fokker-Planck equation has been built to describe ablation of dielectrics during femtosecond laser pulses. The model is verified against an experimental investigation of borosilicate glass with a 200fs laser pulse centered at 780nm wavelength in a range of laser energies. The ablation mechanisms in dielectrics include multi-photon ionization (MPI) and avalanche ionization. MPI dominates the ionization process during the first stages of the laser pulse, contributing seed electrons which supply avalanche ionization. The avalanche process initiates and becomes responsible for the majority of free-electron generation. The overall material removal is shown to be highly dependent upon the optical response of the dielectric as plasma is formed. The ablation model is employed to predict the response of borosilicate glass to an enhanced electromagnetic field due to the presence of microspheres on the substrate surface. It is shown that the diffraction limit can be broken, creating nanoscale surface modification. An experimental study accompanies the model, with AFM and SEM characterizations that are consistent with the predicted surface modifications.
Radium Removal Using Sorption to Filter Sand (1987)

This study evaluated the use of a novel sand filtration process that exploits the natural capacity of filter sand to sorb radium through the use of a periodic dilute acid rinse to maintain its sorptive capacity. Batch studies were conducted to determine distribution coefficients so that performance estimates could be made. Laboratory pilot studies using a partially softened groundwater showed the process capable of reducing 226 Ra concentrations by 80 to 90 percent in the presence of iron flocs when daily rinsing was practiced using pH 1 (0.36 percent) or pH 2 (0.04 percent) HCl. Similar removals could be achieved in field studies using water containing 9–11 pCi 226 Ra/L obtained from the existing sand filters in a city whose supply is treated for iron removal. Removals in the field were less when simultaneous iron and radium removal was attempted. In addition, estimates of the total sorptive capacity of the sand obtained in continuous‐flow experiments were generally significantly greater than those predicted based on batch results.
Simple hybrid type II ARQ technique using softoutputinformation (2000)

The authors present a simple automatic repeat request (ARQ) scheme for turbo codes which uses the soft output information, available as a by-product of the decoding process, to indicate the need for retransmission of a particular data block. The technique utilises the punctured data, not normally sent in recursive systematic convolutional (RSC) turbo code systems, to improve the operation of the decoder rather than the retransmission of the whole block, thus maximising the throughput. Furthermore, as no cyclic redundancy check (CRC) is included there is no overhead on transmission rate. The scheme is capable of correctly identifying a large proportion of all errors across a range of Eb/No whilst minimising incorrect retransmission requests.
Does parkin play a role in the peripheral nervous system? A family report (2004)

Two genes were identified for autosomal recessive forms of early onset Parkinson's disease: parkin and DJ-1. We describe 2 siblings with EOPD due to parkin mutations and peripheral neuropathy, which presented as neuropathy with liability to pressure palsies (HNPP) in the index case. RT-PCR experiments revealed that the parkin gene is expressed in sural nerves from both controls and patient with parkin-related disease. Our findings support the view that parkin may play a role in the peripheral nervous system.