gebhart/patrepeval huggingface dataset:
The bop gene regulon (2000)

Halobacterium sp. sustains a short Period of phototrophic growth by synthesizing ATP using a light-driven proton pump, bacteriorhodopsin. The expression of bop, which encodes the protein component of bacteriorhodopsin, bacterioopsin, is induced in mid- to late-log phase with maximal expression in the stationary phase. Three cis-acting elements within the minimal 53 bp bop promoter were predicted to be responsible in mediating expression and regulation of this gene, viz. UAS, TATA box, and RY box. Finally, computational analysis of the complete genome sequence was projected as a means of identifying putative transcription factors and regulators. I have used a saturation mutagenesis approach to derive a consensus for 35 bp of the 53 bp minimal bop promoter. In the process, we identified two cis-acting elements required for transcription of bop (TATA box and UAS). Based on the presence of an alternate TATA box consensus sequence and lack of a TFB responsive element (BRE) we predicted presence of multiple TBPs and TFBs in Halobacterium NRC-1. Complete genome sequence analysis identified a total of six TBPs and seven TF13s. The UAS was highly immutable at its 3′ and 5 ′ extremities. Three nucleotides (−27A, −23 A and −19A), within the RY box, were identified to be the major sites for DNA supercoiling mediated regulation of bop. We identified the UAS upstream to three other genes, viz. brp, blp and crtB1. Expression profiles for these genes indicated that (a) they are coordinately regulated in Halobacterium NRC-1 and S9, (b) Bat, the putative bacterio-opsin activator, is required for expression of bop, blp and crtB1 and (c) like the bop promoter, the crtB1 and brp promoters contain alternating purine-pyrimidine sequences (10 and 11 bp long respectively), and are also regulated by changes in DNA supercoiling. A detailed analysis of Bat revealed the presence of a redox-sensing PAS/PAC domain, a cGMP responsive GAF domain and a DNA-binding helix-turn-helix motif. These results lead us to conclude that carotenoid and bacterio-opsin biosyntheses are coordinately regulated by Bat in Halobacterium NRC-1. Also, Bat probably functions as a repressor and activator in high- and low-oxygen tension respectively; and the repressor state is transdominant. A model has been proposed to explain bop gene regulation by DNA supercoiling, multiple transcription factors, and Bat. (Abstract shortened by UMI.)
Replication Data for: Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints (2021)

A diverse panel of domesticated hexaploid and tetraploid wheat lines and their tetraploid and diploid wild relatives were genotyped using the DArtSeq technology and characterized in a global wheat diversity analysis.
A Kernelized Architecture for Multilevel Secure Object-Oriented Databases Supporting Write-Up (1993)

This paper presents a kernelized architecture (i.e., an architecture in which no subject is exempted from the simple-security and ⋆-properties) for multilevel secure (mls) object-oriented database management systems (DBMS’s) which support write-up. R
Genome Analysis of Haplotype D of Candidatus Liberibacter Solanacearum (2018)

Candidatus Liberibacter solanacearum (Lso) haplotype D (LsoD) is a suspected bacterial pathogen, spread by the phloem-feeding psyllid Bactericera trigonica Hodkinson and found to infect carrot throughout the Mediterranean. Haplotype D is one of six haplotypes of Lso that each have specific and overlapping host preferences, disease symptoms, and psyllid vectors. Genotyping of rRNA genes has allowed for tracking the haplotype diversity of Lso and genome sequencing of several haplotypes has been performed to advance a comprehensive understanding of Lso diseases and of the evolutionary relationships among the haplotypes. To further pursue that aim we have sequenced the genome of LsoD from its psyllid vector and report here its draft genome. Genome-based single nucleotide polymorphism analysis indicate LsoD is most closely related to the A haplotype. Genomic features and metabolic potential of LsoD are assessed in relation to Lso haplotypes A, B, and C, as well as the facultative strain Liberibacter crescens. We identify genes unique to haplotype D as well as putative secreted effectors that may play a role in disease characteristics specific to this haplotype of Lso.
2309 Introduction of IT Technology into D & D Process of JAXA's Rocket Engine Valves for Reliability Improvement (2007)

This paper describes recent activity in JAXA aiming reformation of design and development (D & D) process by introduction of information technology, simulation technology, reliability engineering, etc for rocket valve reliability improvement. In this activity, JAXA's information system for rocket valve D & D will be developed by the end of FY2007. This information system consists of detailed FMEA/FTA utilization support tool, QFD utilization support tool, and material database system and material database utilization support tool. This information system will help to improve efficiency and reliability of D & D process of JAXA's rocket valves and other JAXA's products.
Transition-metal Complexes of Pyrrole Pigments. XV. Coordination of Pyridine Bases to the Axial Sites of Cobalt Corroles (1978)

Abstract Cobalt(III) corroles exist predominantly as polymeric species in a concentration range above 5×10−3 M in chloroform at room temperature as confirmed by NMR measurements. The coordination behavior of pyridine bases at the axial sites of cobalt(III) corroles, in a concentration range where they are present exclusively in the monomeric species, has been investigated by measuring electronic spectra in acetone at 25.0±0.1 °C. Penta- and hexa-coordination processes were found to take place, and the stepwise formation constants were interpreted by means of the equations logKi=a·pKa+b and logKi⁄Ki0=ρσ. When the cobalt corrole was reduced at the nuclear cobalt from trivalent to bivalent state, only one pyridine molecule was coordinated at its axial sites, hexa-coordination being no longer possible as confirmed by ESR measurements. The axial ligation behavior of cobalt corroles is quite analogous in nature to that of cobalt corrinoid.
Effects of Structural Modification of Calcium Spirulan, a Sulfated Polysaccharide from Spirulina Platensis, on Antiviral Activity. (2001)

Calcium ion binding with the anionic part of a molecule was replaced with various metal cations and their inhibitory effects on the replication of herpes simplex virus type 1 were evaluated. Replacement of calcium ion with sodium and potassium ions maintained the antiviral activity while divalent and trivalent metal cations reduced the activity. Depolymerization of sodium spirulan with hydrogen peroxide decreased in antiviral activity as its molecular weight decreased.
Correlating Structural and Functional Heterogeneity of Immobilized Enzymes (2018)

Many nanobiotechnology applications rely on stable and efficient integration of functional biomacromolecules with synthetic nanomaterials. Unfortunately, the reasons for the ubiquitous loss of activity of immobilized enzymes remain poorly understood due to the difficulty in distinguishing between distinct molecular-level mechanisms. Here, we employ complementary single-molecule fluorescence methods that independently measure the impact of immobilization on the structure and function ( i. e., substrate binding kinetics) of nitroreductase (NfsB). Stochastic statistical modeling methods were used to unambiguously quantify the effects of immobilized NfsB structural dynamics on function, allowing us to explicitly separate effects due to conformation and accessibility. Interestingly, we found that nonspecifically tethered NfsB exhibited enhanced stability compared to site-specifically tethered NfsB; however, the folded state of site-specifically tethered NfsB had faster substrate binding rates, suggesting improved active site accessibility. This demonstrated an unexpected intrinsic trade-off associated with competing bioconjugation methods, suggesting that it may be necessary to balance conformational stability versus active site accessibility. This nuanced view of the impact of immobilization will facilitate a rational approach to the integration of enzymes with synthetic nanomaterials.
Adipose Stem Cell Coating of Biomimetic β -TCP Macrospheres by Use of Laboratory Centrifuge (2012)

Biomimetic materials such as coral exoskeletons possess unique architectural structures with a uniform and interconnected porous network that can be beneficial as a scaffold material. In addition, these marine structures can be hydrothermally converted to calcium phosphates, while retaining the original structural properties. The ability of biomaterials to stimulate the local microenvironment is one of the main focuses in tissue engineering, and directly coating the scaffold with stem cells facilitates future potential applications in therapeutics and regenerative medicine. In this article we describe a new and simple method that uses a laboratory centrifuge to coat hydrothermally derived beta-tricalcium phosphate macrospheres from coral exoskeleton with stem cells. In this research the optimal seeding duration and speed were determined to be 1 min and 700 g. Scanning electron micrographs showed complete surface coverage by stem cells within 7 days of seeding. This study constitutes an important step toward achieving functional tissue-engineered implants by increasing our understanding of the influence of dynamic parameters on the efficiency and distribution of stem cell attachment to biomimetic materials and how stem cells interact with biomimetic materials.
ULTRASTRUCTURAL CHANGES AND LIPID PEROXIDATION IN RAT ADIPOMUSCULOCUTANEOUS FLAP ISOTRANSPLANTS AFTER NORMOTHERMIC STORAGE AND REPERFUSION (1992)

Parallel in vivo, histological, and ultrastructural studies were carried out and markers of lipid peroxidation (Schiff's bases [SB] and thiobarbituric-acid-reactive material [TBAR]) were measured in rat adipomusculocutaneous flap isotransplants that had been stored for 0, 2, 4, 6, and 8 hr under normothermic (37 degrees C) conditions and reperfused for specific periods. Flaps stored for 4 hr and treated with intravenous desferrioxamine (DFX) or hypertonic citrate flush (HCA) were also evaluated. In vivo assessment was made after 7 days of reperfusion. Flaps stored for 4 hr eventually exhibited partial necrosis in vivo, and neither DFX or HCA flush increased the area of surviving skin. Electron microscopy revealed extensive storage damage in epidermal, follicle, fat, and smooth muscle cells and in endothelium. HCA significantly preserved fat cells (P = 0.0035) and DFX diminished smooth muscle damage. Reperfusion injury was seen in endothelial cells in the form of swelling that was not prevented by HCA or DFX. Ultrastructural alterations correlated with changes in susceptibility to lipid peroxidation in fat but not in skin. The results of these parallel studies indicate that both free radical-dependent and independent mechanisms operate in ischemia and reperfusion injury in flap tissue and that fat has a greater predisposition to free radical damage than skin.
Differential privacy and robust statistics (2009)

We show by means of several examples that robust statistical estimators present an excellent starting point for differentially private estimators. Our algorithms use a new paradigm for differentially private mechanisms, which we call Propose-Test-Release (PTR), and for which we give a formal definition and general composition theorems.
Low-Grade Fibrosarcoma With Palisaded Granulomalike Bodies (Giant Rosettes) (1999)

"Hyalinizing spindle cell tumor with giant rosettes" is a tumor recently described by Lane et al. and thought by them possibly to represent a form of low-grade fibromyxoid sarcoma. Proof of a metastatic potential was lacking. We report an example of this tumor on the arm of a 28-year-old woman. The ultrastructural study of the tumor confirmed the fibroblastic nature of the lesion, which subsequently metastasized to the lung. Histologically, the giant rosettes simulated palisaded granulomas. Our findings warrant classifying the tumor as a sarcoma, and we suggest the designation low-grade fibrosarcoma with palisaded granulomalike bodies (giant rosettes).
The design of adaptive acquisition of users feedback: An empirical study (2014)

Users' feedback is a main source of knowledge on how users perceive the role of software in meeting their requirements. Collectively, such feedback helps shaping software autonomous and semi-autonomous adaptation decisions of what is called Social Adaptation. It also helps developers to identify loci in the system where an evolution should be introduced in the next release. Despite this role of users' feedback, there is a lack of systematic engineering approaches on how to design its acquisition mechanisms. In this paper, we observe that the acquisition of feedback should be itself adaptive to the context of use. We conduct an empirical study following a mixed-method sequential exploratory approach to explore the main drivers of such adaptation and understand users' attitude when being asked to provide feedback. Our findings are meant to enrich the knowledge base for developers and researchers in users-centric, or crowd-centric, adaptation. It also highlights areas of study for a future research in the area.
Dynamical simulation of molecular-beam epitaxial growth of a model crystal (1989)

Molecular-dynamics simulation is used to study molecular-beam epitaxial growth of a model fcc system where the atoms interact via the Lennard-Jones (LJ) potential. Dependence of the growth profile on the substrate temperature, the rate of the incident atomic flux, annealing, and on the orientation of the crystal surface is examined. Roles of various kinetic processes in epitaxial growth properties are discussed. We find that for a LJ system the best epitaxial growth occurs at low to intermediate temperatures along the [111] and [100] directions.
Long-Term Ambulatory Continuous Nerve Blocks for Terminally Ill Patients: A Case Series (2010)

CPNBs are a reasonably effective modality to decrease opioid usage when side effects are undesirable for end-of-life care. The risk of unfavorable coagulation status, poor lung function, and risk of infection was outweighed by the benefit in this patient population.
Effect of Solutionizing Duration and Temperature on the Electrochemical Corrosion and Pitting Resistance of Cold-Rolled Super Austenitic Stainless Steel (2022)

The solution annealing of cold rolled super austenitic stainless steel UN08029 alloy was carried out to investigate the role of solutionizing duration and temperature on the electrochemical corrosion and pitting resistance of the alloy. Linear polarization, cyclic potentiodynamic, and electrochemical impedance spectroscopy techniques were used to evaluate the electrochemical behavior in 3.5% NaCl solution. The microstructural analysis of the solutionized samples revealed the formation of uniform equiaxed grains from elongated columnar grains, which size increases with duration and temperature. The charge transfer resistance shows an increasing corrosion protectiveness of 46 to 60% with increasing solutionizing duration from 30 to 120 min. Similarly, a 45, 52, 60, and 26% improvement in the corrosion performance was obtained for sample solutionized at 1000, 1100, 1200, and 1300 °C, respectively. In general, the solutionized samples demonstrated improved resistance over the as-received alloy, and this behavior increases with solutionizing duration and temperature. Though the pitting potential drops below that of the as-received alloy, the hysteresis loop revealed that the solutionized samples are less prone to pitting damage, and the sample solutionized at 1200 °C for 120 min exhibited optimum pitting corrosion resistance. The microstructural influence on corrosion was also discussed.
Corrosion experiments in a pulsed electric field (PEF) treatment chamber with stainless steel electrodes fed with three different pulse shapes (2003)

Liquid pumpable food is mostly pasteurised by heat treatment. One of the new methods is an intense pulsed electric fields (PEF) treatment. The treated food is pumped between two metal electrodes and exposed to very short high voltage pulses, typically tens of kV during several microseconds. During this treatment the electrodes are in direct contact with the food product. The interfacial charge, which must be transferred between electrode and food, can cause serious electrode damage, depending on many factors such as current magnitude, pulse duration, pulse shape and fluid constitution. In this contribution three different topologies of a high-voltage pulse generator, resulting in three different pulse shapes, are compared in relation to treatment chamber corrosion. The experiments indicate that during repeated PEF treatment different dissolved metal concentrations are found in the liquid. The results are qualitatively clarified from theory. (4 pages)
A Method for the Neutralization of Electron Space Charge by Positive Ionization at Very Low Gas Pressures (1923)

Neutralization of space charge around a hot filament by imprisoned positive ions in gas at very low pressures.---(I) Design of tube. If a very small filament, diameter 0.01 cm, is run axially through a cylindrical anode with closed ends, positive ions formed between the electrodes can only rarely escape and will describe orbits around the filament until they lose sufficient energy by collision with gas molecules to enable them to fall into the cathode. The imprisoned ions, during their lives, neutralize a certain amount of the space charge between the electrodes. The effect should increase with the absolute temperature and with the ratio of the cross-section of the anode cylinder to that of the filament. A theoretical calculation indicates that in He at ${10}^{\ensuremath{-}5}$ mm, an ion which misses the filament on its first passage across the tube may circulate around the filament 300 times before discharging to the cathode. (2) Results in $\mathrm{He}$, $H$, $\mathrm{Ne}$, and $\mathrm{Hg}$ at pressures ranging from ${10}^{\ensuremath{-}2}$ to ${10}^{\ensuremath{-}7}$ mm are shown in curves. Comparison of the currents when the cylinder ends were connected (1) to the anode and (2) to the cathode gave the effect of the positive ions, and also their number, and therefore the increase in current per ion, $\ensuremath{\alpha}$. At pressures so low that the 3/2 power space-charge law holds in an ordinary tube, imprisoned ions may still produce large deviations from this law, in favorable cases the current with the ions being 5 or 10 times the current as ordinarily limited by space charge. The relatively much greater effect in Hg vapor than in He is shown to agree well with the theory. If $\ensuremath{\alpha}$ depended only on mean free path, however, it should vary as $\frac{1}{p}$, but the results gave ${(\frac{1}{p})}^{\frac{2}{3}}$. This difference shows the influence of other factors. However, theoretical mean free paths are of the same order of magnitude as those calculated from $\ensuremath{\alpha}$. Moreover, in Hg vapor at 4.2 \ifmmode\times\else\texttimes\fi{} ${10}^{\ensuremath{-}7}$ mm, the time required to reach equilibrium after the positive ions began to accumulate was found by oscillograms to be about the same as the calculated life of an ion, 1.4 \ifmmode\times\else\texttimes\fi{} ${10}^{\ensuremath{-}3}$ sec. The simple theory, then, seems to be pretty well verified.
Measurement Quality of Blood Glucose Meters: Is There a Need for an Institution with an Unbiased View? (2007)

The quality of self-monitoring of blood glucose (SMBG) with modern blood glucose meters is considered by many as not being a relevant topic anymore. However, in reality, a number of open questions about the quality of the measurement exists. Even if the meters fulfill the established quality criteria when they receive approval, there is no independent institution that performs a regular, critical comparison of the quality of the measurement of all blood glucose meters after their approval. Such an institute could also evaluate the quality of the different batches of test strips. In addition, it can evaluate the impact of other factors that are known to have an impact on the quality of measurement, e.g., the ambient temperature and the hematocrit. Such an institution will be very helpful to counterbalance complaints by the patients, physicians and authorities about an industry that earns a lot of money but does not provide solutions for the topics raised.
Complete Metabolic Evaluation is Indicated after a First Stone Event (2016)

No AccessJournal of UrologyOpposing Views1 Mar 2017Complete Metabolic Evaluation is Indicated after a First Stone EventCon Ryan S. Hsi and Marshall L. Stoller Ryan S. HsiRyan S. Hsi More articles by this author and Marshall L. StollerMarshall L. Stoller More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2016.12.028AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail © 2017 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 197Issue 3 Part 1March 2017Page: 545-547 Advertisement Copyright & Permissions© 2017 by American Urological Association Education and Research, Inc.MetricsAuthor Information Ryan S. Hsi More articles by this author Marshall L. Stoller More articles by this author Expand All Advertisement PDF downloadLoading ...
Stimulated photon echo for angular analysis of elastic and depolarizingYb/emph>–noble-gas collisions (1985)

Elastic and depolarizing collisions between excited ytterbium atoms (6s6p ${}^{3}$${P}_{1}$ level) and noble gases (He, Ne, and Xe) are investigated using a stimulated-photon-echo technique. The method is sensitive to collisional velocity changes concerning both the total population ${\ensuremath{\rho}}^{0}$ and the alignment ${\ensuremath{\rho}}^{2}$ of the level. More specifically, it enables us to compare precisely the velocity changes associated with elastic scattering and with alignment-preserving scattering. This represents an improvement with regard to previous works. A detailed theoretical discussion of depolarizing collisions in laser spectroscopy is presented. A simplified density-matrix equation is derived under appropriate approximations. Stimulated photon-echo data for elastic scattering are interpreted within the limits of small-angle scattering in a long-range van der Waals potential; total elastic scattering cross sections are derived from comparison between experiment and calculation: ${\mathit{\ensuremath{\sigma}}}_{\mathrm{He}}^{\mathrm{el}}$=220(20) A${\r{}}^{2}$, ${\mathit{\ensuremath{\sigma}}}_{\mathrm{Ne}}^{\mathrm{el}}$=320(20) A${\r{}}^{2}$, ${\mathit{\ensuremath{\sigma}}}_{\mathrm{Xe}}^{\mathrm{el}}$=1240(60) A${\r{}}^{2}$. Total rates for destruction of alignment are measured in an auxiliary standard photon-echo experiment; the corresponding cross sections are ${\mathit{\ensuremath{\sigma}}}_{\mathrm{He}}^{(2)}$=94(3) A${\r{}}^{2}$, ${\mathit{\ensuremath{\sigma}}}_{\mathrm{Ne}}^{(2)}$=123(7) A${\r{}}^{2}$, ${\mathit{\ensuremath{\sigma}}}_{\mathrm{Xe}}^{(2)}$=300(20) A${\r{}}^{2}$. Stimulated photon-echo data for depolarizing collisions are successfully compared with a calculation that we develop starting from a long-range anisotropic model potential.