gebhart/patrepeval huggingface dataset:
Conformational Analyses of Native and Permethylated Disaccharides (2002)

Effects of permethylation on disaccharide conformation were studied with relaxed-residue φ,ψ maps for eight disaccharides of glucose and their permethylated derivatives. Many orientations of the methyl groups were generated with the conformation generator in the Chem-X software program and filtered with a rules-based method. For native molecules, clockwise and counterclockwise rings of hydrogen bonds were also used. MM3(96) energies were calculated with a dielectric constant (ε) of 1.5. The native disaccharide maps were also calculated at ε = 3.5 and 7.5 to reduce hydrogen-bonding strength. Maps for native and permethylated structures were generally similar. The permethylated structures, which do not make hydrogen bonds, gave maps that were most similar to the native maps that had reduced hydrogen-bonding strength. All φ,ψ values for the global minima of the permethylated models fell within the 1-kcal/mol contours on the ε = 7.5 maps. Flexibility values based on a partition function were substantially less for permethylated α,α-trehalose and laminarabiose, compared to their native counterparts at any ε. On the other hand, strong interresidue hydrogen bonding at ε = 1.5 for the global minimum structures of cellobiose and maltose caused those models to be more rigid than their permethylated counterparts. All permethylated models were less flexible than their native counterparts at ε = 7.5 and their backbone analogues based on tetrahydropyran calculated at ε = 1.5.
Coupled Geodesic Active Regions for Image Segmentation (1999)

This paper presents a novel variational method for image segmentation which is obtained by unifying boundary and region-based information sources under the Geodesic Active Region framework. A statistical analysis over the observed density function (image histogram) using a mixture of Gaussian elements, indicates the number of the different regions and their intensity properties. Then, the boundary information is determined using a probabilistic edge detector, while the region information is given directly from the observed image using the conditional probability density functions of the mixture model. The defined objective function is minimized using a gradient-descent method where a level set approach is used to implement the resulting PDE system. According to the motion equations (PDE), the set of initial curves is propagated towards the segmentation result under the influence of boundary and region-based segmentation forces, and being constrained by a regularity force. The changes of topology are naturally handled thanks to the level set implementation, while a coupled multi-phase propagation is adopted that increases the robustness and the convergence rate by introducing a coupled system of equations for the different level set functions. Besides, to reduce the required computational cost and to decrease the risk of convergence to a local minimum, a multi-scale approach is also considered. The performance of our method is demonstrated on a variety of synthetic and real images.
Reduction of the concentration of slow insulator states in SiO2/InP metal-insulator semiconductor structures (1987)

Spatially distributed states within the insulator are thought to be the origin of the well‐known drift phenomena usually found in InP metal–insulator semiconductor (MIS) devices. This paper will show that the concentration of these states can be reduced drastically by applying a suitable deposition technique. Plasma‐enhanced chemical vapor deposited SiO2 is used as the insulator in a process involving low substrate temperatures (200 °C), spatial separation of sample and plasma (indirect plasma method), and the addition of phosphorus into the reaction chamber during the initial stage of insulator deposition. The influence of several process parameters on the properties of the silicon dioxide films as well as the SiO2/InP interface characteristics are investigated. Deep level transient spectroscopy and C(V) measurements of InP MIS capacitors yield concentrations of slow insulator states of only 1–2×1011 cm−1 eV−1 for the best of our samples.
Enzymology Fundamentals of Enzymology: Rate Enhancement, Specificity, Control, and Applications Garfield P. Royer (1983)

Journal Article Enzymology Get access Fundamentals of Enzymology: Rate Enhancement, Specificity, Control, and Applications, by Royer Garfield P.. John Wiley & Sons, Inc., New York, 1982, 232 p., illus., $27.50 (81-11359). Perry A. Frey Perry A. Frey Institute for Enzyme Research, University of Wisconsin-Madison, Madison, WI 53706 Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 33, Issue 11, December 1983, Page 724, https://doi.org/10.2307/1309373 Published: 01 December 1983
Sputter-deposited erbium-doped Y 2 O 3 active optical waveguides (1993)

A signal enhancement of 10dB at 1535nm with a low launched pump power of 1 mW at 1480nm is achieved for sputtered Er3+ : Y2O3 channel waveguides on oxidised silicon substrates. With the developed reactive co-sputtering process using sputterguns the erbium concentration can be varied easily and reproducibly.
A simplified fuzzy model based on grey relation and data transformation techniques (2002)

Unlike previous methods which relied on the given data, the paper depends on preprocessed patterns to construct a satisfactory fuzzy model. The grey relational method is exploited to help determine the most appropriate premise variables for the fuzzy rules such that a simplified modeling procedure can be achieved. There is no need to refine the membership functions used in the fuzzy rules. Only the transformation functions and the consequent real numbers are required to be adjusted to satisfy the identification purpose. To validate how well the consequent singletons are adjusted, the refined parameters are compared with the desired values calculated by the least squares method. The results show that the adjusted parameters from the proposed model conform to the desired ones. Simulation results from different examples are presented to demonstrate the superiority of the proposed model over conventional methodologies.
Serum Matrix Metalloprotease-1 and Vascular Endothelial Growth Factor-A Predict Cardiac Allograft Rejection (2008)

Cardiac allograft rejection is currently diagnosed from endomyocardial biopsies (EMB) that are invasive and impractical to repeat. A serological marker could facilitate rejection monitoring and minimize EMB-associated risks. We investigated the relation of serum matrix metalloprotease (MMP)-1 and vascular endothelial growth factor (VEGF)-A concentrations to cardiac allograft rejection, using 1176 EMBs and serum samples obtained from 208 recipients. Acute cellular rejection was diagnosed in 186 EMBs. Mean week 1 and week 2 serum MMP-1 concentrations predicted rejection (p = 0.001, AUC = 0.80). At the optimal cut-off level of >or=7.5 ng/mL, MMP-1 predicted rejection with 82% sensitivity and 72% specificity. Initial serum MMP-1 <5.3 ng/mL (lowest quartile) was associated with rejection-free outcome in 80% of patients. Both MMP-1 (p < 0.001, AUC = 0.67-0.75) and VEGF-A (p < 0.01, AUC = 0.62-0.67) predicted rejection on the next EMB, while rejection at EMB was identified only by VEGF-A (p < 0.02, AUC = 0.70-0.77). Patients receiving combined cyclosporine-A and everolimus had the lowest serum MMP-1 concentrations. While serum MMP-1 predicts rejection-free outcome and VEGF-A identifies rejection on EMB, both markers predict rejection in follow-up of cardiac transplant recipients. Combination of serum MMP-1 and VEGF-A concentration may be a noninvasive prognostic marker of cardiac allograft rejection, and could have important implications for choice of surveillance and immunosuppression protocols.
Streptococcus pneumoniae Enhances Human Respiratory Syncytial Virus Infection In Vitro and In Vivo (2015)

Human respiratory syncytial virus (HRSV) and Streptococcus pneumoniae are important causative agents of respiratory tract infections. Both pathogens are associated with seasonal disease outbreaks in the pediatric population, and can often be detected simultaneously in infants hospitalized with bronchiolitis or pneumonia. It has been described that respiratory virus infections may predispose for bacterial superinfections, resulting in severe disease. However, studies on the influence of bacterial colonization of the upper respiratory tract on the pathogenesis of subsequent respiratory virus infections are scarce. Here, we have investigated whether pneumococcal colonization enhances subsequent HRSV infection. We used a newly generated recombinant subgroup B HRSV strain that expresses enhanced green fluorescent protein and pneumococcal isolates obtained from healthy children in disease-relevant in vitro and in vivo model systems. Three pneumococcal strains specifically enhanced in vitro HRSV infection of primary well-differentiated normal human bronchial epithelial cells grown at air-liquid interface, whereas two other strains did not. Since previous studies reported that bacterial neuraminidase enhanced HRSV infection in vitro, we measured pneumococcal neuraminidase activity in these cultures but found no correlation with the observed infection enhancement in our model. Subsequently, a selection of pneumococcal strains was used to induce nasal colonization of cotton rats, the best available small animal model for HRSV. Intranasal HRSV infection three days later resulted in strain-specific enhancement of HRSV replication in vivo. One S. pneumoniae strain enhanced HRSV both in vitro and in vivo, and was also associated with enhanced syncytium formation in vivo. However, neither pneumococci nor HRSV were found to spread from the upper to the lower respiratory tract, and neither pathogen was transmitted to naive cage mates by direct contact. These results demonstrate that pneumococcal colonization can enhance subsequent HRSV infection, and provide tools for additional mechanistic and intervention studies.
Pressure Probes Physiology and Membrane Protein Dynamics in Yeast (2004)

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Visualizing Chemomechanical Degradation of a Solid-State Battery Electrolyte (2019)

Transformations at interfaces between solid-state electrolytes (SSEs) and lithium metal electrodes can lead to high impedance and capacity decay during cycling of solid-state batteries, but the links between structural/chemical/mechanical evolution of interfaces and electrochemistry are not well understood. Here, we use in situ X-ray computed tomography to reveal the evolution of mechanical damage within a Li1+xAlxGe2–x(PO4)3 (LAGP) SSE caused by interphase growth during electrochemical cycling. The growth of an interphase with expanded volume drives fracture in this material, and the extent of fracture during cycling is found to be the primary factor causing the impedance increase, as opposed to the resistance of the interphase itself. Cracks are observed to initiate near the edge of the lithium/LAGP interface, which agrees with simulations. The chemomechanical effects of interphase growth studied here are expected to play a role in a variety of SSE materials, and this work is a step toward designing durable interfaces.
Enhanced photophysics from self-assembled cyclometalated Ir(iii) complexes in water (2016)

Two water-soluble anionic cyclometalated Ir(iii) complexes, Ir(ppy)2BPS [] and Ir(F-mppy)2BPS [] have been synthesized and display clear evidence of self-assembly in water. Concentration-induced aggregation enhances the excited-state properties of both complexes, blue-shifting the photoluminescence emission energies as well as increasing the corresponding excited state lifetimes and quantum yields up to a factor of 5.
Prognostic implications of PD-L1 expression in patients with soft tissue sarcoma (2016)

We have confirmed PD-L1 expression in various STS of young population and demonstrated its independent negative prognostic role, thereby suggesting the PD-1/PD-L1 axis as a potential therapeutic target for the treatment of young STS patients.
Stilbenoid molecules: An experimental and theoretical study of trans-1-(2-pyridyl)-2-(4-pyridyl)-ethylene and the parent molecule (1997)

Free-jet absorption millimeter-wave spectroscopy and gradient-corrected density-functional calculations are combined to study trans-1-(2-pyridyl)-2-(4-pyridyl)-ethylene, 2,4-DPE, a stilbenelike molecule. The interplay between experiments and computational theory backed by the large amount of data and modeling already available for stilbene allows us to establish the parameters of the two-dimensional potential of the pyridyl torsions which well reproduce the experimental defect of inertia (−1.295 uÅ2). The large difference between the defects of inertia of 2,4-DPE and stilbene (≈−15 uÅ2) and further computer simulations suggest that the latter may warrant a reinvestigation. The effect of introducing a weakly binding N⋯H interaction in the stilbene frame is discussed and a very simple model based on the ab initio calculations is found to rationalize the energetics and structural differences of the two conformers of 2,4-DPE.
Response to “Effect of the fill factor of CCD pixels on digital holograms: comment on the papers ‘Frequency analysis of digital holography’ and ‘Frequency analysis of digital holography with reconstruction by convolution’ ” (2003)

Nanjing UniversityNational Laboratory of Solid State MicrostructuresNanjing 210093, ChinaSubject terms: holography; digital holography; fourier optics; coher-ent optical system; point spread function; charge-coupled devices.Paper 030066 received Feb. 6, 2003; accepted for publicationMar. 7, 2003.[DOI: 10.1117/1.1599841]
Midazolam Prevents the Adverse Outcome of Neonatal Asphyxia (2022)

The disease-modifying effect of midazolam identified here strongly suggests that this drug provides a valuable option for improving the treatment and outcome of BA. ANN NEUROL 2023;93:226-243.
A Gadolinium Complex Confined in Silica Nanoparticles as a Highly Efficient T1/T2 MRI Contrast Agent (2013)

Gd in silica: Noncovalent confinement of a monoaqua Gd chelate into biocompatible silica nanoparticles (NPs; see figure) by a sol-gel method affords a new example of nanosized contrast agents with very high per-Gd relaxivities. Such NPs provide a route to highly efficient multimodal contrast agents.
Non-aureus staphylococci in fecal samples of dairy cows: First report and phenotypic and genotypic characterization (2019)

The aims of this study were to determine whether non-aureus staphylococci (NAS) are present in rectal feces of healthy dairy cows, and if so, to delineate species to which they belong and to study several phenotypic and genotypic traits as a first step toward determining the potential impact of fecal shedding of NAS on bovine udder health. Fecal samples were aseptically collected from the rectum of 25 randomly selected clinically healthy dairy cows in a commercial dairy herd using an automated milking system. Fecal NAS were isolated and then identified at the species level using transfer RNA-intergenic spacer PCR and sequencing of the 16S rRNA housekeeping gene. Strain typing was performed using random amplification of polymorphic DNA (RAPD)-PCR. The antimicrobial resistance profiles, biofilm formation, and growth and inhibitory characteristics of all NAS isolates were evaluated. Half of the cows were shedding NAS, resulting in 31 NAS isolates belonging to 11 different species. The most prevalent species were Staphylococcus rostri (23%, n = 7), Staphylococcus cohnii (16%, n = 5), and Staphylococcus haemolyticus (13%, n = 4) with all Staphylococcus agnetis, Staphylococcus chromogenes, and Staph. rostri isolates belonging to the same strain according to RAPD banding patterns. Acquired antimicrobial resistance was observed in 28 of the 31 NAS isolates, mainly due to β-lactamase production. Most of the isolates (84%, n = 27) had a weak biofilm-forming potential, but only 2 contained the bap gene. The ica and aap genes were not detected in any of the isolates. In vitro growth of Staphylococcus aureus and Streptococcus dysgalactiae was inhibited by Staph. agnetis isolates, and Staph. chromogenes isolates were able to inhibit the growth of Strep. dysgalactiae and Streptococcus uberis. All fecal isolates were able to grow when oxygen and iron were limitedly available, mimicking the growth conditions in the mammary gland.
NASA’s propulsion airframe aeroacoustics research (2004)

The integration of propulsion and airframe is a fundamental consideration in the design of an aircraft system. Many considerations influence the integration, such as structural, aerodynamic, and maintenance factors. In the future, a focus on the aerodynamic and acoustic interaction effects of installation, propulsion airframe aeroacoustics will become more important as noise reduction targets become more difficult to achieve. In addition to continued fundamental component reduction efforts, a system level approach that includes propulsion airframe aeroacoustics will be required in order to achieve the 20-dB noise reductions envisioned by the aggressive NASA goals. This emphasis on the aeroacoustics of propulsion airframe integration is a new part of NASA’s ongoing acoustics research. The presentation will review current efforts and highlight technical challenges and approaches.
1987 target values for uncertainty components in fissile isotope and element assay (1987)

The Working Group on Techniques and Standards for Destructive Analysis (WGDA) of the European Safeguards Research and Development Association (ESARDA), which at present includes the representation of 37 nuclear analytical laboratories, has long been concerned with defining realistic performance characteristics of destructive analysis techniques. One of the terms of reference of the working groups is: ''to evaluate and recommend criteria for destructive analysis of nuclear materials for use by plant operators and safeguarding authorities''. Some of the most important and most badly needed criteria are those to be used for judging results of quantitative determinations of fissile isotope and element amounts. The working group has recognized and discussed this problem at several meetings and decided that it was appropriate to fix reasonable levels of performance as ''goals'' for nuclear analytical laboratories.
Alignment system using voltage contrast images for low-energy electron-beam lithography (2001)

We have proposed an alignment system for low-energy electron-beam lithography. The proposed alignment system is based on the following unique concepts: (1) an alignment mark is detected using voltage contrast images caused by charging, and (2) to improve the alignment accuracy of global alignment, the alignment accuracy can be inspected before the pattern exposure without any loss of time. In order to verify these concepts, we performed a series of experiments. Using an electron beam of a few keV, we detected a mark buried by thick insulator films; even if direct access to the marks by the primary beam is prevented, the mark detection is possible. Also, we confirmed that the simultaneous observation of exposure patterns and alignment mark is possible using the voltage contrast images caused by charging: the inspection is possible for the exposure status without resist development.
The prevalence of knee osteoarthritis in the elderly. the framingham osteoarthritis study (1987)

To investigate the prevalence of osteoarthritis (OA) of the knee in elderly subjects, we studied the Framingham Heart Study cohort, a population-based group. During the eighteenth biennial examination, we evaluated the cohort members for OA of the knee by use of medical history, physical examination, and anteroposterior (standing) radiograph of the knees. Radiographs were obtained on 1,424 of the 1,805 subjects (79%). Their ages ranged from 63-94 years (mean 73). Radiographs were read by a radiologist who specializes in bone and joint radiology, and were graded 0-4 according to the scale described by Kellgren and Lawrence. OA was defined as grade 2 changes (definite osteophytes), or higher, in either knee. Radiographic evidence of OA increased with age, from 27% in subjects younger than age 70, to 44% in subjects age 80 or older. There was a slightly higher prevalence of radiographic changes of OA in women than in men (34% versus 31%); however, there was a significantly higher proportion of women with symptomatic disease (11% of all women versus 7% of all men; P = 0.003). The age-associated increase in OA was almost entirely the result of the marked age-associated increase in the incidence of OA in the women studied. This study extends current knowledge about OA of the knee to include elderly subjects, and shows that the prevalence of knee OA increases with age throughout the elderly years.
PRESSURE DROP DURING FORCED-AIR VENTILATION OF VARIOUS HORTICULTURAL PRODUCE IN CONTAINERS WITH DIFFERENT OPENING CONFIGURATIONS (2004)

The pressure drop through 25 different fruits and vegetables in separate containers was measured during forced-air ventilation. The commodities were separated into six different categories: leafy, spherical, long, with leaves or peel, complexgeometry, and bulk. Coefficients a and b of the Ramsin equation were established for the 25 commodities with airflowvelocity varying from 0.05 to 3.72 m s-1. The results demonstrated that the geometry of the produce and their particularcharacteristics play a significant part in decreasing the pressure during forced-air ventilation. The effects of the pressure dropwith respect to the physical characteristics of the containers and produce were also studied for three orifice configurationsand venting areas equal to 25% and 88% (mesh). The porosity of the produce was not enough to distinguish the pressure dropbetween them, except for spherical produce where an equation was developed for predicting the pressure drop.
Tandem scanning microscope--a new tool for three-dimensional microanatomy. (1989)

Tandem Scanning Microscope enables us to observe in real time one thin layer under the surface of a highly complex semitransparent object (e. g. living tissue), make photographs of thick layers in such objects and observe (by means of a stereoscope) three dimensional images of such objects. Important results can be obtained with moderate expenditure on basic hardware and the equipment can be expanded steadily according to the state of our budget.
Distributed-fountain network code (DFNC) for content delivery in vehicular networks (2013)

Vehicle-to-vehicle (V2V) communication utilizing dedicated short range communication (DSRC) has already been tested in field trials and is ready for potential deployment. This deployment would enable the possibility of large scale content delivery over small and large geographical areas. While content delivery in such vehicular networks can take advantage of the broadcast nature of DSRC, it has to cope with new challenges presented by dynamic topology, unpredictable erasures and lack of acknowledgements. Random linear network coding (RLNC) can address these challenges in theory, but the high decoding complexity limits its applicability in practice, especially for large scale content delivery. Motivated by this, a new network coding scheme for vehicular networks, distributed-fountain network code (DFNC), that has low encoding, re-encoding and decoding complexity is presented in this paper. DFNC uses a fountain code at the source and re-encoding at intermediate vehicles that approximate a fountain code. Re-encoding at intermediate vehicles comprises an innovative approach of low complexity degree reduction and random linear combination of degree-reduced packets to satisfy the degree distribution of the fountain code. Low-complexity belief propagation (BP) decoding is applied at the destinations. Through extensive simulations on two mobility models, random waypoint and Boston urban area, this paper establishes that DFNC performance is close to RLNC performance at order-wise lower complexity. DFNC significantly outperforms other relevant epidemic algorithms in literature.