gebhart/patrepeval huggingface dataset:
Flexible regression models with cubic splines (1989)

We describe the use of cubic splines in regression models to represent the relationship between the response variable and a vector of covariates. This simple method can help prevent the problems that result from inappropriate linearity assumptions. We compare restricted cubic spline regression to non-parametric procedures for characterizing the relationship between age and survival in the Stanford Heart Transplant data. We also provide an illustrative example in cancer therapeutics.
24.2: Investigation of Flexoelectric Effect in Vertically‐Aligned In‐Plane‐Switching Mode by Low Frequency Driving (2014)

Abstract Due to the inhomogeneous electric field, liquid crystal molecules reveal splay deformation in vertically‐aligned in‐plane‐switching mode. The flexoelectric effect from the splay is confirmed by fast CCD images. We introduce a model to explain the mechanism of such phenomenon and to determine the sign of flexoelectric coefficient.
Synthesis and psychotropic properties of furyl‐ and thienyl‐germatranes (1988)

Abstract Trihalogermyl‐furans and ‐thiophenes magnified image were prepared by inserting germanium dibromide (GeBr 2 ) generated from the dibromogermane(II) dioxanate complex into the carbon‐halogen bond of halo‐furans and ‐thiophenes. Their ethanolysis and transesterification by triethanolamine yielded the germatranes magnified image which were subjected to psychotropic activity assays. The psychotropic properties of germatranes were found to depend on the type of the heterocycle and on the position of the germatrane moiety.
Experience with the double lumen Silastic catheter for hemoaccess. (1990)

Transvenous access for acute hemodialysis has advanced recently with the introduction of a double lumen Silastic (silicone rubber), Dacron-cuffed (polyester) catheter (Quinton PermCath), which has a better patient acceptance than the stiff Teflon (polytetrafluoroethylene) catheters. We present our experience with 53 PermCath catheters placed in 49 patients (eight to 80 years old). Twenty-two catheters were used for initiation of dialysis, 17 as a bridge to permanent hemoaccess, two as a bridge to peritoneal dialysis and 12 for chronic hemoaccess. We have achieved better success with insertion of catheters through the jugular system (external in 22 instances and internal in 30) by cutdown with fluoroscopic positioning of the catheter tip at the second to third intercostal space. Arterial port alignment was toward the center of the vena cava to reduce sucking against the caval wall during dialysis. No catheter failed to function with this positioning technique. Average catheter use was 84 days with a range of one to 573 days. Catheter thrombosis occurred 40 times in ten patients and was treated successfully in all with the infusion of streptokinase or urokinase. Four patients received chronic warfarin for repeated clotting. Four patients had catheter sepsis that resolved with removal of the catheter and administration of antibiotics. We conclude that the PermCath is an improved means for hemoaccess with a low complication rate. Our key to successful functioning of the PermCath is careful fluoroscopic positioning of the catheter tip.
Preserving geometry and topology for fluid flows with thin obstacles and narrow gaps (2016)

Fluid animation methods based on Eulerian grids have long struggled to resolve flows involving narrow gaps and thin solid features. Past approaches have artificially inflated or voxelized boundaries, although this sacrifices the correct geometry and topology of the fluid domain and prevents flow through narrow regions. We present a boundary-respecting fluid simulator that overcomes these challenges. Our solution is to intersect the solid boundary geometry with the cells of a background regular grid to generate a topologically correct, boundary-conforming cut-cell mesh. We extend both pressure projection and velocity advection to support this enhanced grid structure. For pressure projection, we introduce a general graph-based scheme that properly preserves discrete incompressibility even in thin and topologically complex flow regions, while nevertheless yielding symmetric positive definite linear systems. For advection, we exploit polyhedral interpolation to improve the degree to which the flow conforms to irregular and possibly non-convex cell boundaries, and propose a modified PIC/FLIP advection scheme to eliminate the need to inaccurately reinitialize invalid cells that are swept over by moving boundaries. The method naturally extends the standard Eulerian fluid simulation framework, and while we focus on thin boundaries, our contributions are beneficial for volumetric solids as well. Our results demonstrate successful one-way fluid-solid coupling in the presence of thin objects and narrow flow regions even on very coarse grids.
Classical Swine Fever Virus Leader Proteinase N <sup>pro</sup> Is Not Required for Viral Replication in Cell Culture (1998)

The sequence encoding the viral leader proteinase Npro was replaced by the murine ubiquitin gene in a full-length cDNA clone of the classical swine fever virus (CSFV) strain Alfort/187. The recombinant virus vA187-Ubi showed growth characteristics similar to those of the parent vA187-1 virus. At two occasions cells infected with vA187-Ubi exhibited a cytopathic effect and were found to contain a subgenomic viral RNA. This RNA lacked the same viral genes as the subgenomic RNA which has been found in all cytopathogenic CSFV strains analyzed so far, but it maintained the ubiquitin sequence.
A Novel Regioselective Desulfation Method Specific to Silyl Ester of Primary Sulfate Using Silylating Agents. Selective Preparation of Secondary Alkyl Sulfates Having a Primary Hydroxy Group (2001)

Abstract The treatment of bis(trimethylsilyl)ester of 1-O-decylglycerol-2,3-disulfate with trimethylsilyl-N-trimethylsilylacetimidate (BSA) or (dimethylamino)trimethylsilane caused regioselective desulfation to afford 1-O-decyl glycerol-2-sulfate selectively in good yield. Silylating agents, having nitrogen, seems to be responsible for facilitating trimethylsiloxysulfonyl cation transfer.
CRAMM: virtual memory support for garbage-collected applications (2006)

Existing virtual memory systems usually work well with applications written in C and C++, but they do not provide adequate support for garbage-collected applications. The performance of garbage-collected applications is sensitive to heap size. Larger heaps reduce the frequency of garbage collections, making them run several times faster. However, if the heap is too large to fit in the available RAM, garbage collection can trigger thrashing. Existing Java virtual machines attempt to adapt their application heap sizes to fit in RAM, but suffer performance degradations of up to 94% when subjected to bursts of memory pressure.We present CRAMM (Cooperative Robust Automatic Memory Management), a system that solves these problems. CRAMM consists of two parts: (1) a new virtual memory system that collects detailed reference information for (2) an analytical model tailored to the underlying garbage collection algorithm. The CRAMM virtual memory system tracks recent reference behavior with low overhead. The CRAMM heap sizing model uses this information to compute a heap size that maximizes throughput while minimizing paging. We present extensive empirical results demonstrating CRAMM's ability to maintain high performance in the face of changing application and system load.
Efficient Genetic Algorithm sets for optimizing constrained building design problem (2016)

The main aim of this paper is to find the appropriate set of Genetic Algorithm (GA), control parameters that attain the optimum, or near optimum solutions, in a reasonable computational time for constrained building optimization problem. Eight different combinations of control parameters of binary coded GA were tested in a hypothetical building problem by changing 80 variables. The results showed that GA performance was insensitive to some GA control parameter values such as crossover probability and mutation rate. However, population size was the most influential control parameter on the GA performance. In particular, the population sizes (15 individuals) require less computational time to reach the optimum solution. In particular, a binary encoded GA with relatively small population sizes can be used to solve constrained building optimization problems within 750 building simulation calls.
Creative Problem Solving (1996)

This paper reports on the experience of third year Chemical Engineering students at the University of Canterbury who have undertaken a lecture course on problem solving techniques supplemented with interactive computer instruction - Strategies for Creative Problem Solving. Problem solving strategies were taught as an integral part of engineering design. In addition to lectures, students worked together in pairs to complete the assigned six computer modules as part of their assessment which contributed 10% towards their course work. Performance for each module was measured by an in-built code. Student opinion of this alternative assessment method and issues related to interactive computer learning were evaluated by questionnaire. 79% of the students who responded to the questionnaire found the computer modules useful.
The effect of film thickness on Curie temperature distribution and magnetization reversal mechanism for granular L1<sub>0</sub>FePt films (2017)

Structural and magnetic properties of granular L10 FePt films are investigated as a function of film thickness in the range 3–11 nm. Scanning transmission electron microscopy observations indicate an increasing contribution of in-plane variants to the L10 FePt crystalline structure with increasing film thickness, which may explain the noticed degradation of the perpendicular anisotropy. The temperature dependence of coercivity suggests a progressive deviation of the magnetization reversal mechanism from coherent rotations with increasing film thickness above ~6 nm, corresponding to a domain-wall width. The anisotropy field distribution (〈HK〉, ) is estimated using Monte Carlo (MC) simulations of AC transverse susceptibility (ACTS). The average anisotropy field 〈HK〉 displays a similar temperature dependence to (MS)1.1, where MS is the film saturation magnetization, consistent with the theoretical predictions for L10 FePt. The Curie temperature distribution (〈TC〉, ) is evaluated using two methods: fast (ns) thermal erasure (ThEr) of remanent magnetization and MC modeling of the temperature dependence of AC susceptibility (ACS). The values evaluated by the two methods are in agreement, indicating an increase of in the range 2–6% with decreasing film thickness. The observed increase of 〈TC〉 in the range 620–680 K with increasing film thickness is explained using the finite-size scaling law with the critical exponent set to the theoretical value for L10 FePt. A general procedure to extract 〈TC〉 and using MC modeling of ACS, essentially independent of the magnetization reversal mechanism, is proposed. MC simulations of ACS confirm the deviation of the magnetization reversal mechanism from coherent rotations with increasing film thickness above ~6 nm.
Cryoprotective Activities of Group 3 Late Embryogenesis Abundant Proteins from<i>Chlorella vulgaris</i>C-27 (2000)

The nucleotide sequence of hiC12, isolated as a cDNA clone of hardening-induced Chlorella (hiC) genes, was identified. The clone encodes a late embryogenesis abundant (LEA) protein having six repeats of a 11-mer amino acid motif, although in a slightly imperfect form. To overexpress the hiC61) and hiC12 genes, their coding regions were PCR amplified and subcloned into a pGEX-1lambdaT vector. The HIC6 and HIC12 proteins were expressed as GST fusion proteins in E. coli, then purified. The two HIC proteins were found to be effective in protecting a freeze-labile enzyme, LDH, against freeze-inactivation. On a molar concentration basis, they were about 3.1 x 10(6) times more effective in protecting LDH than sucrose and as effective as BSA. Cryoprotection tests with five kinds of chain-shortened polypeptides, synthesized based on the 11-mer amino acid motif of the HIC6 protein showed that the cryoprotective activity decreased with a decrease in the repeating units of the 11-mer motif. In fact, cryoprotective activities of three kinds of single 11-mer amino acids were very low even at high concentrations. All the results suggested that the sufficiently repeated 11-mer motif is required for the cryoprotective activities of Chlorella LEA proteins.
Palladium-Catalyzed Coupling Reaction of Iodouracil Having Acetamidine Moiety with Olefins (2000)

Abstract The reaction of 6-[1-Aza-2-(dimethylamino)prop-l-enyl]-5-iodo-1,3-dimethyluracil (3) with various olefins in the presence of a catalytic amount of Pd(OAc)2 and 1.5 equiv. of K2CO3 in DMF at 120 °C gave the pyrido[2,3-d]pyrimidine derivatives (5a-b and 7a-d) in moderate to high yield.
kBF: A Bloom Filter for key-value storage with an application on approximate state machines (2014)

Key-value (k-v) storage has been used as a crucial component for many network applications, such as social networks, online retailing, and cloud computing. Such storage usually provides support for operations on key-value pairs, and can be stored in memory to speed up responses to queries. So far, existing methods have been deterministic: they will faithfully return previously inserted key-value pairs. Providing such accuracy, however, comes at the cost of memory and CPU time. In contrast, in this paper, we present an approximate k-v storage that is more compact than existing methods. The tradeoff is that it may, theoretically, return a null value for a valid key with a low probability, or return a valid value for a key that was never inserted. Its design is based on the probabilistic data structure called the “Bloom Filter”, which was originally developed to test element membership in sets. In this paper, we extend the bloom filter concept to support key-value operations, and demonstrate that it still retains the compact nature of the original bloom filter. We call the resulting design as the kBF (key-value bloom filter), and systematically analyze its performance advantages and design tradeoffs. Finally, we apply the kBF to a practical problem of implementing a state machine in network intrusion detection to demonstrate how the kBF can be used as a building block for more complicated software infrastructures.
Transfer function method for measuring characteristic impedance and propagation constant of porous materials (1989)

A method for measuring the characteristic impedance and propagation constant of porous materials is described in this paper. Measurements were performed based on a surface impedance method that required a set of distinct acoustic impedances derived at the material surface. This requirement is satisfied by arbitrarily changing the air space depth behind the material, and then a new formulation is derived so that a recently developed method of determination, called the transfer function method, can be applied. An appropriate set of air space depths is also discussed. Glass wool and porous aluminum were used to assess the usefulness of the present method. The normal acoustic impedance and normal absorption coefficient of the test materials with arbitrary thicknesses or with an arbitrary air space depth behind them were calculated from the obtained characteristic impedance and propagation constant and were compared with the measured values that were obtained directly by using the transfer function method. The good agreement achieved suggests that the present method is reliable and effective enough to measure the characteristic impedance and propagation constant over a broadband frequency range.
Anti-ampicillin monoclonal antibodies and their cross-reactivities to various β-lactams (1991)

Two cell lines producing monoclonal antibodies, Abp4 (IgM) and Abp7 (IgG1) against ampicillin were established. The epitopes and the cross-reactions of the antibodies with various beta-lactams were examined by enzyme-linked immunosorbent assay (ELISA) and ELISA inhibition test. Abp4 showed broad cross-reaction to human serum albumin (HSA) conjugates of several beta-lactams, 6-aminopenicillanic acid and 7-aminocephalosporanic acid. Abp7 reacted only with ampicillin and cephalexin, which have the same acyl side chain. In ELISA inhibition tests, Abp4 inhibited binding to ampicillin-HSA by benzylpenicilloyl-epsilon-amino-n-caproic acid, and strongly inhibited the binding by penicillamine. Abp7 strongly inhibited the reaction by aminobenzylpenicilloyl-epsilon-amino-n-caproic acid, but benzylpenicilloyl-epsilon-amino-n-caproic acid was less effected. These data suggest that Abp4 recognizes the thiazolidine ring and Abp7 recognizes the acyl side chain. Therefore, the thiazolidine ring-epitope acts in broad cross-reaction among beta-lactams, and the acyl side chain acts only in the cross-reactivity between penam and cephem, which have a similar acyl side chain.
Electrochemical Design of Ultrathin Platinum-Coated Gold Nanoparticle Monolayer Films as a Novel Nanostructured Electrocatalyst for Oxygen Reduction (2004)

The deliberate tailoring of nanostructured metallic catalysts at the monolayer-level is an ongoing challenge and could lead to new electronic and catalytic properties, since surface-catalyzed reactions are extremely sensitive to the atomic-level details of the catalytic surface. In this article, we present a novel electrochemical strategy to nanoparticle-based catalyst design using the recently developed underpotential deposition (UPD) redox replacement technique. A single UPD Cu replacement with Pt2+ yielded a uniform Pt layer on colloid gold surfaces. The ultrathin (nominally monolayer-level) Pt coating of the novel nanostructured particles was confirmed by cyclic voltammetry and X-ray photoelectron spectra (XPS). The present results demonstrate that ultrathin Pt coating effects efficiently and behaves as the nanostructured monometallic Pt for electrocatalytic oxygen reduction, and also shows size-dependent, tunable electrocatalytic ability. The as-prepared ultrathin Pt-coated Au nanoparticle monolayer electrodes reduce O2 predominantly by four electrons to H2O, as confirmed by the rotating ring-disk electrode (RRDE) technique.
α‐Synuclein–synaptosomal membrane interactions (2004)

alpha-Synuclein exists in two different compartments in vivo-- correspondingly existing as two different forms: a membrane-bound form that is predominantly alpha-helical and a cytosolic form that is randomly structured. It has been suggested that these environmental and structural differences may play a role in aggregation propensity and development of pathological lesions observed in Parkinson's disease (PD). Such effects may be accentuated by mutations observed in familial PD kindreds. In order to test this hypothesis, wild-type and A53T mutant alpha-synuclein interactions with rat brain synaptosomal membranes were examined. Previous data has demonstrated that the A30P mutant has defective lipid binding and therefore was not examined in this study. Electron microscopy demonstrated that wild-type alpha-synuclein fibrillogenesis is accelerated in the presence of synaptosomal membranes whereas the A53T alpha-synuclein fibrillogenesis is inhibited under the same conditions. These results suggested that subtle sequence changes in alpha-synuclein could significantly alter interaction with membrane bilayers. Fluorescence and absorption spectroscopy using environment sensitive probes demonstrated variations in the inherent lipid properties in the presence and absence of alpha-synuclein. Addition of wild-type alpha-synuclein to synaptosomes did not significantly alter the membrane fluidity at either the fatty acyl chains or headgroup space, suggesting that synaptosomes have a high capacity for alpha-synuclein binding. In contrast, synaptosomal membrane fluidity was decreased by A53T alpha-synuclein binding with concomitant packing of the lipid headgroups. These results suggest that alterations in alpha-synuclein-lipid interactions may contribute to physiological changes detected in early onset PD.
Interacting valley Chern insulator and its topological imprint on moiré superconductors (2019)

One salient feature of systems with moir\'e superlattice is that the Chern number of ``minibands'' originating from each valley of the original graphene Brillouin zone becomes a well-defined quantized number because the miniband from each valley can be isolated from the rest of the spectrum due to the moir\'e potential. Then a moir\'e system with a well-defined valley Chern number can become a nonchiral topological insulator with $\mathrm{U}(1)\ifmmode\times\else\texttimes\fi{}{Z}_{3}$ symmetry and a $\mathbb{Z}$ classification at the free fermion level. Here we demonstrate that the strongly interacting nature of the moir\'e system reduces the classification of the valley Chern insulator from $\mathbb{Z}$ to ${\mathbb{Z}}_{3}$, and it is topologically equivalent to a bosonic symmetry-protected topological state made of local boson operators. We also demonstrate that even if the system becomes a superconductor when doped away from the valley Chern insulator, the valley Chern insulator still leaves a topological imprint as the localized Majorana fermion zero mode in certain geometric configuration.
Inhibition of Phosphatidylinositol-3-OH Kinase/Akt Signaling Impairs DNA Repair in Glioblastoma Cells following Ionizing Radiation (2007)

Radiation therapy is a mainstay in the treatment of glioblastomas, but these tumors are often associated with radioresistance. Activation of the phosphatidylinositol-3-OH kinase (PI3K)/Akt pathway, which occurs frequently in glioblastomas due to inactivation of the tumor suppressor phosphatase and tensin homologue (PTEN), correlates with radioresistance. To directly test the link between Akt activation and radioresistance, we utilized PTEN-deficient U251 glioblastoma cells engineered to inducibly restore PTEN upon exposure to doxycycline. These cells showed high basal levels of Akt activation (i.e. high levels of phospho-Akt), but induction of PTEN led to substantially decreased phospho-Akt and was associated with radiosensitization. To investigate whether the PTEN-induced radiosensitization was attributable to impaired sensing versus repair of DNA damage, we assessed levels of gamma-H2AX after ionizing radiation in U251 cells induced for PTEN. Initial post-radiation levels of gamma-H2AX foci were not decreased in PTEN-induced cells; however, the resolution of these foci was significantly delayed. In contrast to these results, induction of phosphatase-dead PTEN showed no appreciable effect. Finally, exposure of cells to the PI3K inhibitor LY294002 did not decrease the occurrence of gamma-H2AX foci after irradiation but did markedly delay their resolution. These results together support a direct link between Akt activation, repair of DNA damage, and radioresistance in glioblastoma. Targeting the PI3K/Akt pathway may modulate DNA repair to improve the efficacy of radiation therapy.