gebhart/patrepeval huggingface dataset:
Design and Evaluation of a Perceptual-Based Object Group Selection Technique (2010)

Selecting groups of objects is a frequent task in graphical user interfaces since it precedes all manipulation operations. Current selection techniques such as lasso become time-consuming and error-prone in dense configurations or when the area covered by targets is large or hard to reach. Perceptual-based selection techniques can considerably improve the selection task when the targets have a perceptual structure, driven by Gestalt principles of proximity and good continuity. However, current techniques use ad hoc grouping algorithms that often lack evidence from perception science. Moreover, they do not allow selecting arbitrary groups (i.e. without a perceptual structure) or modifying a selection. This paper presents a domain-independent perceptual-based selection technique that addresses these issues. It is built upon an established group detection model from perception research and provides intuitive interaction techniques for selecting (whole or partial) groups with curvilinear or random structures. Our user study shows that this technique not only outperforms rectangle selection and lasso techniques when targets have perceptual structure, but also it is competitive when targets have arbitrary arrangements.
Mycobacterium avium subspecies paratuberculosis triggers intestinal pathophysiologic changes in beige/scid mice. (2001)

We investigated whether infection of beige/scid mice with Mycobacterium avium subspecies paratuberculosis can induce intestinal pathophysiologic changes. Six-week-old beige/scid mice were inoculated intraperitoneally with M. paratuberculosis, then were killed 32 weeks after inoculation when the small intestine was evaluated for physiologic and morphologic abnormalities. All infected mice developed clinical disease. The lamina propria of the intestine from infected mice was mildly infiltrated with mononuclear cells containing acid-fast bacteria, and had significantly increased villus width. In vitro physiologic studies in Ussing chambers indicated that M. paratuberculosis infection caused significant abnormalities in intestinal transport parameters. Baseline short circuit current and potential difference were abnormally high in tissues from infected, compared with control mice, indicative of increased ion secretion. Baseline conductance was significantly decreased in infected mice, suggesting that intestinal tissue from infected mice was less permeable to ions. The change in short circuit current following transmural electrical and glucose stimulation was significantly reduced in intestines from infected mice, suggesting that inflamed intestine had neural and/or epithelial cell damage. We conclude that infection of beige/scid mice with M. paratuberculosis triggers significant intestinal pathophysiologic changes consistent with chronic inflammation. These functional abnormalities may contribute to the pathogenesis of the wasting syndrome seen in bovids with paratuberculosis. This animal model provides evidence that T cell-independent mechanisms are sufficient to cause mucosal pathophysiologic changes and inflammation in response to a specific pathogen, and may be of relevance to inflammatory bowel disease in humans.
Genetic interaction mapping informs integrative structure determination of protein complexes (2020)

Determining structures of protein complexes is crucial for understanding cellular functions. Here, we describe an integrative structure determination approach that relies on in vivo measurements of genetic interactions. We construct phenotypic profiles for point mutations crossed against gene deletions or exposed to environmental perturbations, followed by converting similarities between two profiles into an upper bound on the distance between the mutated residues. We determine the structure of the yeast histone H3-H4 complex based on ~500,000 genetic interactions of 350 mutants. We then apply the method to subunits Rpb1-Rpb2 of yeast RNA polymerase II and subunits RpoB-RpoC of bacterial RNA polymerase. The accuracy is comparable to that based on chemical cross-links; using restraints from both genetic interactions and cross-links further improves model accuracy and precision. The approach provides an efficient means to augment integrative structure determination with in vivo observations.
Engineered Two‐Helix Small Proteins for Molecular Recognition (2009)

Less is more: By starting with a high-affinity HER2-binding 3-helix affibody molecule, we successfully developed 2-helix small protein binders with 5 nM affinities by using a combination of several different strategies. Our efforts clearly suggest that 2-helix small proteins against important tumor targets can be obtained by rational protein design and engineering.
Effect of Antibiotic and Sulphonamide Treatment on the Development of Post-vaccination Immunity to Trichophytosis in Cattle (1991)

Calves treated with chloramphenicol or apramycin at the time of vaccination against trichophytosis were less resistant to experimental infection with Trichophyton verrucosum culture than vaccinated calves not treated with these antibiotics. Treatment with preparations containing penicillin, streptomycin, oxytetracycline, rolitetracycline, tylosine or sulphonamide had no immunosuppressive effect on the development of post-vaccination immunity.
ChemInform Abstract: Role of Steric, Electrostatic, and Hydrogen Bonding Effects as Face Selectivity Controlling Factors in Nitrone Cycloadditions. (1987)

Abstract 1,3‐Dipolar cycloaddition reaction of the bicyclooctenes (II) with the nitrone (I) yields the syn‐ or anti‐isoxazolidines (III) and (IV).
Superior Performance of Metal–Organic Frameworks over Zeolites as Solid Acid Catalysts in the Prins Reaction: Green Synthesis of Nopol (2013)

The catalytic performance of a set of metal-organic frameworks [CuBTC, FeBTC, MIL-100(Fe), MIL-100(Cr), ZIF-8, MIL-53(Al)] was investigated in the Prins condensation of β-pinene with formaldehyde and compared with the catalytic behavior of conventional aluminosilicate zeolites BEA and FAU and titanosilicate zeolite MFI (TS-1). The activity of the investigated metal-organic frameworks (MOFs) increased with the increasing concentration of accessible Lewis acid sites in the order ZIF-8<MIL-53(Al)<FeBTC<MIL-100(Cr)<MIL-100(Fe). Unwanted β-pinene-like isomerization takes place on the strong Brønsted acid sites of zeolites BEA and FAU, which showed significantly lower selectivity to the target nopol than the MOFs. Its high activity, the preservation of its structure and active sites, and the possibility to use it in at least three catalytic cycles without loss of activity make MIL-100 (Fe) the best performing catalyst of the series for the Prins condensation of β-pinene and paraformaldehyde. Our report exemplifies the advantages of MOFs over zeolites as solid catalysts in liquid-phase reactions for the production of fine chemicals.
First Step toward Cloud-Based Firewalling (2012)

With the explosive growth of network-based services and attacks, the complexity and cost of firewall deployment and management have been increasing rapidly. Yet, each private network, no matter big or small, has to deploy and manage its own firewall, which is the critical first line of defense. To reduce the complexity and cost in deploying and managing firewalls, businesses have started to outsource the firewall service to their Internet Service Providers (ISPs), such as AT&T, which provide cloud-based firewal service. Such fire walling model saves businesses in managing, deploying, and upgrading firewalls. The current firewall service outsourcing model requires businesses fully trust their ISPs and give ISPs their firewall policies. However, businesses typically need to keep their firewall policies confidential. In this paper, we propose the first privacy preserving firewall outsourcing approach where businesses outsource their firewall services to ISPs without revealing their firewall policies to the ISPs. The basic idea is that businesses first anonymize their firewall policies and send the anonymized policies to their ISP, then the ISP performs packet filtering based on the anonymized firewall policies. For anonymizing firewall policies, we use Firewall Decision Diagrams to cope with the multi-dimensionality of policies and Bloom Filters for the anonymization purpose. This paper deals with a hard problem. By no means that we claim our scheme is perfect, however, this effort represents the first step towards privacy preserving outsourcing of firewall services. We implemented our scheme and conducted extensive experiments. Our experimental results show that our scheme is efficient in terms of both memory usage and packet lookup time. The firewall throughput of our scheme running at ISPs is comparable to that of software firewalls running at businesses themselves.
Ion transport in gel and gel–liquid systems for LiClO4-doped PMMA at the meso- and nanoscales (2017)

Solid and gel electrolytes offer significant advantages for cycle stability and longevity in energy storage technologies. These advantages come with trade-offs such as reduced conductivity and ion mobility, which can impact power density in storage devices even at the nanoscale. Here we propose experiments aimed at exploring the ion transport properties of a hybrid electrolyte system of liquid and gel electrolytes with meso and nanoscale components. We focus on single pore systems featuring LiClO<sub>4</sub>-propylene carbonate and LiClO<sub>4</sub>-PMMA gel, which are model electrolytes for energy storage devices. We identified conditions at which the systems considered featured rectifying current-voltage curves, indicating a preferential direction of ion transport. The presented ion current rectification suggests different mechanisms arising from the unique hybrid system: (i) PMMA structure imposing selectivity in fully immersed systems and (ii) ionic selectivity linked to ion sourcing from media of different ionic mobility. These mechanisms were observed to interplay with ion transport properties linked to nanopore structure i.e. cylindrical and conical.
Reward-dependent plasticity in the primary auditory cortex of adult monkeys trained to discriminate temporally modulated signals (2003)

Adult owl monkeys were trained to detect an increase in the envelope frequency of a sinusoidally modulated 1-kHz tone. Detection was positively correlated with the magnitude of the change in the envelope frequency. Surprisingly, neuronal responses recorded in the primary auditory cortex of trained monkeys were globally suppressed by the modulated tone. However, the contrast in neuronal responsiveness to small increases versus large increases in envelope frequencies was actually enhanced in the trained animals. The results suggest behaviorally contingent inhibitory and excitatory processes that are modulated by the probability that a particular signal predicts a reward.
Role of Macroautophagy in Anti‐Cancer Effects of the Novel Sphingolipid, Enigmol (2015)

Enigmol ([2S,3S,5S]‐2‐amino‐3,5‐dihydroxyoctadecane) is a novel sphingolipid analog that inhibits tumor growth in preclinical models of human prostate cancer; however, little is known about mechanisms contributing to this efficacy. Since sphingolipids can affect macroautophagy (hereafter “autophagy”), the purpose of this research was to investigate whether autophagy is involved in Enigmol's anti prostate cancer activity. Although the role of autophagy in cancer is complex, several studies have shown that blocking the pH‐dependent fusion of autophagosomes with lysosomes is detrimental to cancer cells. We demonstrate here a robust, dose‐dependent accumulation of autophagosomes in PC‐3 prostate cancer cells treated with Enigmol, evidenced by Western blot and immunofluorescence monitoring of an autophagosome marker (LC3‐II) and by electron microscopy. At doses near the EC 50 for cancer cell killing, Enigmol neutralized lysosomal pH and inhibited autophagosome turnover. Enigmol also caused inhibition of Akt kinase and mammalian target of rapamycin (mTOR), which contributed to autophagosome accumulation. Enigmol analogs deficient in Akt/ mTOR inhibition caused a much lesser degree of LC3‐II accumulation and were markedly less cytotoxic to prostate cancer cells, linking these molecular actions to anti‐cancer effects. We propose a model in which Enigmol's blockade of lysosome‐mediated autophagosome degradation enhances the anti‐cancer effects of Akt/ mTOR inhibition.
Investigation of p-type depletion doping for InGaN/GaN-based light-emitting diodes (2017)

Due to the limitation of the hole injection, p-type doping is essential to improve the performance of InGaN/GaN multiple quantum well light-emitting diodes (LEDs). In this work, we propose and show a depletion-region Mg-doping method. Here we systematically analyze the effectiveness of different Mg-doping profiles ranging from the electron blocking layer to the active region. Numerical computations show that the Mg-doping decreases the valence band barrier for holes and thus enhances the hole transportation. The proposed depletion-region Mg-doping approach also increases the barrier height for electrons, which leads to a reduced electron overflow, while increasing the hole concentration in the p-GaN layer. Experimentally measured external quantum efficiency indicates that Mg-doping position is vitally important. The doping in or adjacent to the quantum well degrades the LED performance due to Mg diffusion, increasing the corresponding nonradiative recombination, which is well supported by the measured carrier lifetimes. The experimental results are well numerically reproduced by modifying the nonradiative recombination lifetimes, which further validate the effectiveness of our approach.
Viscosity and Density of Lactulose Solutions (1996)

The density and viscosity of solutions of lactulose and solutions of lactulose and boric acid were determined using calibrated viscometers and a nominal 10-ml pycnometer, respectively. These data were necessary for the development of the recovery section of a continuous pilot plant process to produce lactulose, a valuable pharmaceutical, from lactose.
Structural and temporal characteristics of the flow in a plane asymmetric diffuser with 8.5 degrees opening angle (2006)

The separating turbulent flow in a plane asymmetric diffuser with 8.5 degrees opening angle is investigated experimentally and computationally. The considered flow case is suitable for fundamental studies of separation, separation control and turbulence modelling. The flow case has been studied in a specially designed wind-tunnel under well controlled conditions. The average velocity and fluctuation fields have been mapped out with stereoscopic particle image velocimetry (PIV). Knowledge of all velocity components allows the study of several quantities of interest in turbulence modelling such as the turbulence kinetic energy, the turbulence anisotropy tensor and the turbulence production rate tensor. Pressures are measured through the diffuser. The measured data will form a reference database which can be used for evaluation of turbulence models and other computational investigations. Time-resolved stereoscopic PIV is used in an investigation of turbulence structures in the flow and their temporal evolution. A comparative study is made where the measured turbulence data are used to evaluate an explicit algebraic Reynolds stress turbulence model (EARSM). A discussion regarding the underlying reasons for the discrepancies found between the experimental and the model results is made. A model for investigations of separation suppression by means of vortex generating devices is presented together with results from the model in the plane asymmetric diffuser geometry. A short article on the importance of negative production-rates of turbulent kinetic energy for the reverse flow region in separated flows is presented. A detailed description of the experimental setup and PIV measurement procedures is given in a technical report.
Suppression of cytokine storm with a sphingosine analog provides protection against pathogenic influenza virus (2011)

Human pandemic H1N1 2009 influenza virus rapidly infected millions worldwide and was associated with significant mortality. Antiviral drugs that inhibit influenza virus replication are the primary therapy used to diminish disease; however, there are two significant limitations to their effective use: (i) antiviral drugs exert selective pressure on the virus, resulting in the generation of more fit viral progeny that are resistant to treatment; and (ii) antiviral drugs do not directly inhibit immune-mediated pulmonary injury that is a significant component of disease. Here we show that dampening the host's immune response against influenza virus using an immunomodulatory drug, AAL-R, provides significant protection from mortality (82%) over that of the neuraminidase inhibitor oseltamivir alone (50%). AAL-R combined with oseltamivir provided maximum protection against a lethal challenge of influenza virus (96%). Mechanistically, AAL-R inhibits cellular and cytokine/chemokine responses to limit immunopathologic damage, while maintaining host control of virus replication. With cytokine storm playing a role in the pathogenesis of a wide assortment of viral, bacterial, and immunologic diseases, a therapeutic approach using sphingosine analogs is of particular interest.
A micropower battery current sensor with &#x00B1;0.03% (3&#x03C3;) inaccuracy from &#x2212;40 to +85&#x00B0;C (2013)

This paper presents a micropower current-sensing system (CSS) for battery monitoring, which consists of a calibrated shunt resistor, a ΔΣ ADC, and a dynamic bandgap reference (BGR). For currents ranging from 0 to 1A over the industrial temperature range (-40°C to +85°C), it exhibits 10μA offset and ±0.03% (3σ) gain error, which is a 3× improvement on systems with off-chip external references [1,2]. This level of accuracy is achieved by the use of dynamic error-correction techniques, digital temperature compensation, and an on-chip dynamic BGR, whose spread is corrected by a single room-temperature trim.
MINIMALLY INVASIVE SURGERY FOR THE MANAGEMENT OF CERVICAL SPONDYLOSIS (2007)

Dorsal surgical procedures have a well-established role in the treatment of both radiculopathy and myelopathy caused by cervical spondylosis. Laminectomy and laminoplasty procedures can both lead to postoperative kyphosis because of the removal of the dorsal supporting structures of the neck. Minimally invasive or minimal-access spinal surgery procedures of the dorsal cervical spine are evolving techniques with the goal of decompressing the neural structures with minimal disruption of the dorsal supporting structures. We think that this will lead to less postoperative pain and a decreased incidence of post-decompression kyphotic deformity. Patient selection, techniques, and results are discussed for both minimally invasive cervical laminoforaminotomy and stenosis decompression.
DNA Recognition by Synthetic Constructs (2011)

The interaction of transcription factors with specific DNA sites is key for the regulation of gene expression. Despite the availability of a large body of structural data on protein-DNA complexes, we are still far from fully understanding the molecular and biophysical bases underlying such interactions. Therefore, the development of non-natural agents that can reproduce the DNA-recognition properties of natural transcription factors remains a major and challenging goal in chemical biology. In this review we summarize the basics of double-stranded DNA recognition by transcription factors, and describe recent developments in the design and preparation of synthetic DNA binders. We mainly focus on synthetic peptides that have been designed by following the DNA interaction of natural proteins, and we discuss how the tools of organic synthesis can be used to make artificial constructs equipped with functionalities that introduce additional properties to the recognition process, such as sensing and controllability.
A design for computer nucleic-acid-sequence storage, retrieval, and manipulation (1982)

We have designed and built a data-base system for the storage of nucleic-acid sequences. The system consists of a data base ("the library") and software that manages and provides access to that data base ("the Librarian").
Data Compilation for AGC-2 Matrix-only Compact Lot A3-H08 (2010)

This document is a compilation of fabrication and characterization data for the compact lot A3-H08, which was produced for possible insertion into the second ATR Graphite Creep irradiation test capsule (AGC-2). The compacts were produced by Oak Ridge National Laboratory (ORNL) for the Advanced Gas Reactor Fuel Development and Qualification (AGR) program. This compact lot was fabricated using a graphite/resin blend formulated by INL as a candidate matrix precursor for scale-up of overcoating and compacting processes. The matrix precursor powder for compact lot A3-H08 was a jet milled blend of 64 wt% natural graphite (Asbury 3482), 16 wt% synthetic graphite (Graftech GTI-D), and 20 wt% high purity novolac resin (Hexion D_SD-1708 with 7.5% hexamethylenetetramine added). The “Matrix Compacts for AGC-2 Irradiation” Specification (INL SPC-1285, Rev. 1) provides the requirements necessary for acceptance of the compacts. Sections 2.03 and 2.04 of SPC-1285 provide the property requirements for the heat-treated compacts. There are requirements on the length, diameter, and matrix density. Section 2.02.01.01 further requests impurity analysis on representative samples from the final compact lot, but there are no specified acceptance criteria. The impurity information will be evaluated by INL as part of a final decision on whether to insert the compacts into the AGC-2 experiment. The procedures for characterizing and qualifying the compacts are outlined in ORNL product inspection plan AGR-CHAR-PIP-16. The measurement of compact length, diameter, and matrix density was performed according to data acquisition method AGR-CHAR-DAM-39. The data report forms generated by this procedure document the product acceptance for the property requirements listed in sections 2.03 and 2.04 of SPC-1285. All compacts selected for irradiation conformed to the specified requirements for length, diameter, and density. In addition to the characterization data, this report also contains other records relevant to the product acceptance. A history of the material flow and sample naming is included and the compacting process is summarized. In addition to results of the impurity analysis on representative samples from the final compact lot, impurity analysis results are also provided for samples of the graphite, resin, and the graphite/resin blend. A Certificate of Conformance to SPC-1285, Rev. 1 is attached in Appendix B.
Antibodies to Human c- myc Oncogene Product: Evidence of an Evolutionarily Conserved Protein Induced During Cell Proliferation (1984)

Antisera to a synthetic c-myc peptide and to c-myc antigens synthesized from various portions of the human gene expressed in Escherichia coli were used in order to characterize the protein product of the human c- myc oncogene. Although the deduced molecular weight of the human c-myc protein is 49,000, these antisera precipitate a protein from human cells that migrates in sodium dodecyl sulfate-polyacrylamide gel as if its molecular weight were 65,000. In addition, the mouse c-myc protein, whether synthesized in cells or in a cell-free system directed by pure, synthetic messenger RNA, has analogous properties and is immunoprecipitated by the antiserum to the human c-myc protein. Similar proteins are immunoprecipitated from monkey, rat, hamster, and frog cells, suggesting evolutionary conservation of antigenic structure of the c-myc protein among vertebrates. In addition, and in a manner consistent with the behavior of its messenger RNA, the immunoprecipitable c-myc protein is sharply induced by the action of mitogens on resting human T cells.