gebhart/patrepeval huggingface dataset:
Transcriptional activation of promoters of the superoxide and multiple antibiotic resistance regulons by Rob, a binding protein of the Escherichia coli origin of chromosomal replication (1996)

The Rob protein, isolated on the basis of its ability to bind to the right arm of the Escherichia coli origin of chromosomal replication, is about 50% identical in amino acid sequence to SoxS and MarA, the direct regulators of the superoxide (soxRS) and multiple antibiotic resistance (mar) regulons, respectively. Having previously demonstrated that SoxS (as a MalE-SoxS fusion protein) and MarA are essentially identical in their abilities to activate in vitro transcription of genes of the sox-mar regulons, we investigated the properties of Rob as a transcriptional activator. We found that Rob (i) activates the transcription of zwf,fpr,fumC, micF, nfo, and sodA, (ii) requires a 21-bp soxbox-marbox-robbox sequence to activate zwf transcription, (iii) protects the soxbox/marbox/robbox from attack by DNase 1, (iv) is ambidextrous, i.e., requires the C-terminal domain of the alpha subunit of RNA polymerase for activation of zwf but not fumC or micF, (v) bends zwf and fumC DNA, and (vi) binds zwf and fumC DNA as a monomer. Since these transcription activation properties of Rob are virtually identical to those of MalE-SoxS and MarA, it appears as if the E. coli genome encodes three genes with the same functional capacity. However, in contrast to SoxS and MarA, whose syntheses are induced by specific environmental stimuli and elicit a clear defense response, Rob is expressed constitutively and its normal function is unknown.
Mechanisms of Hepatic Very Low Density Lipoprotein Overproduction in Insulin Resistance (2000)

A novel animal model of insulin resistance, the fructose-fed Syrian golden hamster, was employed to investigate the mechanisms mediating the overproduction of very low density lipoprotein (VLDL) in the insulin resistant state. Fructose feeding for a 2-week period induced significant hypertriglyceridemia and hyperinsulinemia, and the development of whole body insulin resistance was documented using the euglycemic-hyperinsulinemic clamp technique. In vivo Triton WR-1339 studies showed evidence of VLDL-apoB overproduction in the fructose-fed hamster. Fructose feeding induced a significant increase in cellular synthesis and secretion of total triglyceride (TG) as well as VLDL-TG by primary hamster hepatocytes. Increased TG secretion was accompanied by a 4.6-fold increase in VLDL-apoB secretion. Enhanced stability of nascent apoB in fructose-fed hepatocytes was evident in intact cells as well as in a permeabilized cell system. Analysis of newly formed lipoprotein particles in hepatic microsomes revealed significant differences in the pattern and density of lipoproteins, with hepatocytes derived from fructose-fed hamsters having higher levels of luminal lipoproteins at a density of VLDL versus controls. Immunoblot analysis of the intracellular mass of microsomal triglyceride transfer protein, a key enzyme involved in VLDL assembly, showed a striking 2.1-fold elevation in hepatocytes derived from fructose-fed versus control hamsters. Direct incubation of hamster hepatocytes with various concentrations of fructose failed to show any direct stimulation of its intracellular stability or extracellular secretion, further supporting the notion that the apoB overproduction in the fructose-fed hamster may be related to the fructose-induced insulin resistance in this animal model. In summary, hepatic VLDL-apoB overproduction in fructose-fed hamsters appears to result from increased intracellular stability of nascent apoB and an enhanced expression of MTP, which act to facilitate the assembly and secretion of apoB-containing lipoprotein particles.
Fabrications of Size- Controlled SiGe Nanowires Using I-Line Lithography and Focused Ion Beam Technique (2014)

In this study, a novel method using Focus Ion Beam (FIB) technique was applied to scale down Si 1-x Ge x wires (x=0.27-0.57) to 20 nm width. Originally, the wires were processed by using I-line lithography and dry etching of SiGe on oxide (SGOI) substrates. The SGOI wafers were processed through condensation method where a SiGe/Si layer was grown in the beginning on SOI wafers and oxidized at 850-1050 °C. The shape of the nanowires (NWs) during the successive FIB cutting was examined by scanning electron microscopy (SEM) and the carrier transport through the NWs was checked by resistivity measurements. The contact resistance was reduced by Ni-silicide prior to metallization. The fabricated NWs were also suspended by tilting FIB. The results present the limitations and challenges of FIB technique to create NWs for advanced sensors and transistors.
The Noise Exposure Structured Interview (NESI): An Instrument for the Comprehensive Estimation of Lifetime Noise Exposure (2018)

Lifetime noise exposure is generally quantified by self-report. The accuracy of retrospective self-report is limited by respondent recall but is also bound to be influenced by reporting procedures. Such procedures are of variable quality in current measures of lifetime noise exposure, and off-the-shelf instruments are not readily available. The Noise Exposure Structured Interview (NESI) represents an attempt to draw together some of the stronger elements of existing procedures and to provide solutions to their outstanding limitations. Reporting is not restricted to prespecified exposure activities and instead encompasses all activities that the respondent has experienced as noisy (defined based on sound level estimated from vocal effort). Changing exposure habits over time are reported by dividing the lifespan into discrete periods in which exposure habits were approximately stable, with life milestones used to aid recall. Exposure duration, sound level, and use of hearing protection are reported for each life period separately. Simple-to-follow methods are provided for the estimation of free-field sound level, the sound level emitted by personal listening devices, and the attenuation provided by hearing protective equipment. An energy-based means of combining the resulting data is supplied, along with a primarily energy-based method for incorporating firearm-noise exposure. Finally, the NESI acknowledges the need of some users to tailor the procedures; this flexibility is afforded, and reasonable modifications are described. Competency needs of new users are addressed through detailed interview instructions (including troubleshooting tips) and a demonstration video. Limited evaluation data are available, and future efforts at evaluation are proposed.
Systematic Review: Antimicrobial Urinary Catheters To Prevent Catheter-Associated Urinary Tract Infection in Hospitalized Patients (2006)

According to fair-quality evidence, antimicrobial urinary catheters can prevent bacteriuria in hospitalized patients during short-term catheterization, depending on antimicrobial coating and several other variables. Older data probably lack current relevance. Cost implications and effect on infectious complications remain undefined.
Design and Development of Miniature Mechanisms for Small Spacecraft (2000)

With the continued push for smaller, faster, and cheaper spacecraft comes a new era in mechanism design. The desire to develop “Micro Satellites”, along with advances in the processing and selection of materials, have created an abundance of opportunities to miniaturize mechanisms. Simple designs with direct applications of developing technologies are ideal for these miniature mechanisms. This paper will focus on the design and development of a miniature satellite “tool kit”. Six mechanisms were developed by Starsys Research and the Applied Physics Laboratory (APL) at John Hopkins University (JHU) under a NASA Advanced Technology Development (ATD) Program. The mechanisms developed included a Micro and Mini Separation Nut, a Mini Rotary Actuator, a Micro Burn Wire Release, a SMA Linear Actuator, and a SMA Redundant Release Mechanism. The paper will discuss the concepts evaluated, designs chosen for fabrications, problems encountered during development, achieved performance characteristics, and recommendations for future development.
A Complex Chromatin Landscape Revealed by Patterns of Nuclease Sensitivity and Histone Modification within the Mouse β-Globin Locus (2003)

In order to create an extended map of chromatin features within a mammalian multigene locus, we have determined the extent of nuclease sensitivity and the pattern of histone modifications associated with the mouse beta-globin genes in adult erythroid tissue. We show that the nuclease-sensitive domain encompasses the beta-globin genes along with several flanking olfactory receptor genes that are inactive in erythroid cells. We describe enhancer-blocking or boundary elements on either side of the locus that are bound in vivo by the transcription factor CTCF, but we found that they do not coincide with transitions in nuclease sensitivity flanking the locus or with patterns of histone modifications within it. In addition, histone hyperacetylation and dimethylation of histone H3 K4 are not uniform features of the nuclease-sensitive mouse beta-globin domain but rather define distinct subdomains within it. Our results reveal a complex chromatin landscape for the active beta-globin locus and illustrate the complexity of broad structural changes that accompany gene activation.
Nonenzymatic Synthesis of Peptides in an Ionic Liquid (2002)

Amino acids, the monomers that comprise proteins, are abundant in nature and have even been found in environments that do not support life, such as meteorites. The origin of proteins, however, is mysterious because the condensation reaction that forms the peptide bond linking two amino acids is thermodynamically disfavored in the aqueous solutions that are required for life. Ionic liquids, which are polar but non-aqueous and which are stable over a wide temperature range, are an ideal medium for testing whether peptide bonds could form spontaneously between amino acids in the absence of water. We have demonstrated that peptides can form non-enzymatically in the molten salt 1-butyl-3-methylimidazolium hexafluorophosphate (BMI-PF6) by incubation of various solid amino acids at temperatures above 100°C. Incubation at temperatures below 100°C did not produce peptides, even when performed under vacuum.
Genistein administered as a once-daily oral supplement had no beneficial effect on the tibia in rat models for postmenopausal bone loss (2013)

Serum levels of genistein similar to those in women consuming a high-soy diet are ineffective in preventing or treating bone loss in rat models for postmenopausal osteoporosis.
A universal and rapid protocol for protein extraction from recalcitrant plant tissues for proteomic analysis (2006)

A simple and universally applicable protocol for extracting high-quality proteins from recalcitrant plant tissues is described. We have used the protocol with no modification, for a wide range of leaves and fruits. In all cases, this protocol allows to obtain good electrophoretic separation of proteins. As the protocol is rapid, universal, and compatible with silver staining, it could be used for routine protein extraction from recalcitrant plant tissues for proteomic analysis.
Hydrogen Storage in the Dehydrated Prussian Blue Analogues M<sub>3</sub>[Co(CN)<sub>6</sub>]<sub>2</sub> (M = Mn, Fe, Co, Ni, Cu, Zn) (2005)

The porosity and hydrogen storage properties for the dehydrated Prussian blue analogues M3[Co(CN)6]2 (M = Mn, Fe, Co, Ni, Cu, Zn) are reported. Argon sorption isotherms measured at 87 K afford BET surface areas ranging from 560 m2/g for Ni3[Co(CN)6]2 to 870 m2/g for Mn3[Co(CN)6]2; the latter value is comparable to the highest surface area reported for any known zeolite. All six compounds show significant hydrogen sorption at 77 K and 890 Torr, varying from 1.4 wt % and 0.018 kg H2/L for Zn3[Co(CN)6]2 to 1.8 wt % and 0.025 kg H2/L for Cu3[Co(CN)6]2. Fits to the sorption data employing the Langmuir-Freundlich equation give maximum uptake quantities, resulting in a predicted storage capacity of 2.1 wt % and 0.029 kg H2/L for Cu3[Co(CN)6]2 at saturation. Enthalpies of adsorption for the frameworks were calculated from hydrogen isotherms measured at 77 and 87 K and found to increase with M varying in the order Mn < Zn < Fe < Co < Cu < Ni. In all cases, the binding enthalpies, which lie in the range of 5.3-7.4 kJ/mol, are higher than the 4.7-5.2 kJ/mol measured for Zn4O(1,4-benzenedicarboxylate)3.
A new control plane for next-generation WDM-PON access systems (2007)

Point-to-point or point-to-multipoint optical access systems are now considered as a viable alternative to xDSL technologies for broadband services. Point-to-multipoint WDM-PONs are the most advanced solution in this matter. Multiple architectures have been proposed since a few years for Next Generation WDM PON (NG-WDM-PON) operating on an hybrid TDMA (Time Division Multiple Access) and WDMA (Wavelength Division Multiple Access) mode. For that purpose, three key optoelectronic devices are considered: reflective modulators, AWG (Arrayed Waveguide Gratings) routers and tunable transceivers. The major investigations in this domain are mainly focused on physical layer aspects and on MAC protocols. In this paper, we propose an original control plane for NG-WDM-PON operating at two timescales: microscopic and macroscopic. The former deals with traditional packet access whereas the latter aims at two objectives. The first objective is to assign connections to upstream optical channels in order to optimize network utilization. The latter enables to reallocate dynamically the number of optical channels to the various PONs of the system. Numerous numerical results are presented in order to outline the benefit of this control plane. It becomes then possible to shift optical resources among the various geographical areas of the system according to their medium term activity.
Streptavidin-biotin-based directional double Nanobody sandwich ELISA for clinical rapid and sensitive detection of influenza H5N1 (2014)

Collectively, these results demonstrated that the proposed detection system is an alternative diagnostic tool that enables a rapid, inexpensive, sensitive and specific detection of the influenza virus.
Insertional Mutagenesis of Genes Required for Seed Development in <i>Arabidopsis thaliana</i> (2001)

The purpose of this project was to identify large numbers of Arabidopsis genes with essential functions during seed development. More than 120,000 T-DNA insertion lines were generated following Agrobacterium-mediated transformation. Transgenic plants were screened for defective seeds and putative mutants were subjected to detailed analysis in subsequent generations. Plasmid rescue and TAIL-PCR were used to recover plant sequences flanking insertion sites in tagged mutants. More than 4200 mutants with a wide range of seed phenotypes were identified. Over 1700 of these mutants were analyzed in detail. The 350 tagged embryo-defective (emb) mutants identified to date represent a significant advance toward saturation mutagenesis of EMB genes in Arabidopsis. Plant sequences adjacent to T-DNA borders in mutants with confirmed insertion sites were used to map genome locations and establish tentative identities for 167 EMB genes with diverse biological functions. The frequency of duplicate mutant alleles recovered is consistent with a relatively small number of essential (EMB) genes with nonredundant functions during seed development. Other functions critical to seed development in Arabidopsis may be protected from deleterious mutations by extensive genome duplications.
Preparation of Polymeric Janus Particles by Directional UV-Induced Reactions (2009)

Polymeric Janus particles are obtained by UV-induced selective surface grafting polymerizations and coupling reactions, in virtue of the light-absorption of photoreactive materials such as the immobilized photoinitiator and spread photoinitiator solution on the surfaces exposed to UV light and the sheltering of densely arrayed immovable particles from light. Varying the monomers or macromolecules applied in photografting polymerization or coupling reaction, and choosing diverse polymeric particles of various size, bicolor and amphiphilic Janus particles could be successfully achieved. Observations by fluorescence microscope, scanning electron microscope ,and transmission electron microscope confirmed the asymmetrical morphology of the resultant Janus particles.
Super Gas Barrier of All-Polymer Multilayer Thin Films (2011)

Thin film assemblies of branched polyethylenimine (PEI) and poly(acrylic acid) (PAA), deposited using the layer-by-layer technique, were studied in an effort to produce all-polymer thin films with low oxygen permeability. Altering the pH of PEI and PAA results in large thickness variations (from 90 nm to 4.74 μm for 30-bilayer films). Cross-linking these films with glutaraldehyde (GA) create an inhibition of polymer interdiffusion, causing exponential film growth to be reset. AFM images show the surface morphology of PEI/PAA assemblies can be controlled by the pH and the final polymer layer deposited, with surface roughness ranging from 2.1 to 49.1 nm. Most pH combinations failed to produce a film with high oxygen barrier, but 8 bilayers of PEI at pH 10 and PAA at pH 4 produce a 305 nm thick film with an oxygen transmission rate below 0.005 cm3/(m2 day). This unique thin film barrier (PO2 < 3.2 × 10−21 cm3 (STP) cm/(cm2 s Pa)) is a promising alternative to current polymeric membranes, flexible electronics, and food packaging materials.
Biomechanics of Spine Stabilization: Principles and Clinical Practice (1994)

Functional Anatomy of the Spine Properties of Spinal Components Properties of the Neural Elements Normal Spine Movement Basic Physics and the Fundamentals of Biomechanics Stability and Instability Biomechanics of Degenerative Spine Diseases Biomechanics of Spine Trauma Biomechanics of Scoliosis and Associated Spine Deformaties Neural Element Injury Spinal Decompression Neural Element Decompression Spinal Fusion Management Fundamentals Spinal Fixation Biomechanics of Anterior Spinal Distraction Fixation Biomechanics of Anterior Spinal Compression Biomechanics of Anterior Cantilever Beam Fixation Anterior Spinal Fixation Constructs and Complex Force Application Biomechanics of Posterior Distraction Biomechanics of Posterior Tension Band Fixation Biomechanics of Posterior Three-point Bending Fixation Biomechanics of Posterior Cantilever Beam Fixation Posterior Spinal Fixation Constructs Biomechanical Characteristics of Spinal Fixation Constructs Biomechnically Complex Constructs Spinal Orthotics Biomechanical Laboratory Testing Modelling the Spine Biomechanics of Injury Prevention.
Screening and Characterization of Purine Nucleoside Degrading Lactic Acid Bacteria Isolated from Chinese Sauerkraut and Evaluation of the Serum Uric Acid Lowering Effect in Hyperuricemic Rats (2014)

Hyperuricemia is well known as the cause of gout. In recent years, it has also been recognized as a risk factor for arteriosclerosis, cerebrovascular and cardiovascular diseases, and nephropathy in diabetic patients. Foods high in purine compounds are more potent in exacerbating hyperuricemia. Therefore, the development of probiotics that efficiently degrade purine compounds is a promising potential therapy for the prevention of hyperuricemia. In this study, fifty-five lactic acid bacteria isolated from Chinese sauerkraut were evaluated for the ability to degrade inosine and guanosine, the two key intermediates in purine metabolism. After a preliminary screening based on HPLC, three candidate strains with the highest nucleoside degrading rates were selected for further characterization. The tested biological characteristics of candidate strains included acid tolerance, bile tolerance, anti-pathogenic bacteria activity, cell adhesion ability, resistance to antibiotics and the ability to produce hydrogen peroxide. Among the selected strains, DM9218 showed the best probiotic potential compared with other strains despite its poor bile resistance. Analysis of 16S rRNA sequences showed that DM9218 has the highest similarity (99%) to Lactobacillus plantarum WCFS1. The acclimated strain DM9218-A showed better resistance to 0.3% bile salt, and its survival in gastrointestinal tract of rats was proven by PCR-DGGE. Furthermore, the effects of DM9218-A in a hyperuricemia rat model were evaluated. The level of serum uric acid in hyperuricemic rat can be efficiently reduced by the intragastric administration of DM9218-A (P<0.05). The preventive treatment of DM9218-A caused a greater reduction in serum uric acid concentration in hyperuricemic rats than the later treatment (P<0.05). Our results suggest that DM9218-A may be a promising candidate as an adjunctive treatment in patients with hyperuricemia during the onset period of disease. DM9218-A also has potential as a probiotic in the prevention of hyperuricemia in the normal population.
Software Fault Localization Using DStar (D*) (2012)

Effective debugging is crucial to producing dependable software. Manual debugging is becoming prohibitively expensive, especially due to the growing size and complexity of programs. Given that fault localization is one of the most expensive activities in program debugging, there has been a great demand for fault localization techniques that can help guide programmers to the locations of faults. In this paper a technique named DStar (D*), which has its origins rooted in similarity coefficient-based analysis, is proposed, which can identify suspicious locations for fault localization automatically without requiring any prior information on program structure or semantics. D* is evaluated across 21 programs and is compared to 16 different fault localization techniques. Both single-fault and multi-fault programs are used. Results indicate that D* is more effective at locating faults than all the other techniques it is compared to.
Towards Analysis of Intra-flow Contention in Multi-hop Wireless Networks (2010)

Based on whether the competing active nodes are forwarding packets of the same flow, the channel access contention in multi-hop wireless networks can be classified into intra-flow contention and inter-flow contention. In this paper, we analyze the effect of intra-flow contention on multi-hop network performance. First, we demonstrate that intra-flow contention makes up a large proportion of contention in the network and may severely degrade the network performance. Then, to understand the performance improvement by eliminating intra-flow contention, we consider an ideal MAC based on 802.11 DCF where intra-flow contention is eliminated. We analyze the performance of the ideal MAC by proposing a three-dimensional Markov model. Furthermore, we present an approximate implementation of the ideal MAC based on simple modifications to 802.11 DCF. Finally, extensive simulations are performed and the results validate the proposed model and reveal the performance improvement by eliminating intra-flow contention.