gebhart/patrepeval huggingface dataset:
The Electricidal Effect Is Active in an Experimental Model of <i>Staphylococcus epidermidis</i> Chronic Foreign Body Osteomyelitis (2009)

Treatment with low-amperage (200 microA) electrical current was compared to intravenous doxycycline treatment or no treatment in a rabbit model of Staphylococcus epidermidis chronic foreign body osteomyelitis to determine if the electricidal effect is active in vivo. A stainless steel implant and 10(4) CFU of planktonic S. epidermidis were placed into the medullary cavity of the tibia. Four weeks later, rabbits were assigned to one of three groups with treatment administered for 21 days. The groups included those receiving no treatment (n = 10), intravenous doxycycline (n = 14; 8 mg/kg of body weight three times per day), and electrical current (n = 15; 200 microA continuous delivery). Following treatment, rabbits were sacrificed and the tibias quantitatively cultured. Bacterial load was significantly reduced in the doxycycline (median, 2.55 [range, 0.50 to 6.13] log10 CFU/g of bone) and electrical-current (median, 1.09 [range, 0.50 to 2.99] log10 CFU/g of bone) groups, compared to the level for the control group (median, 4.16 [range, 3.70 to 5.66] log10 CFU/g of bone) (P < 0.0001). Moreover, treatment with electrical current was statistically significantly more efficacious (P = 0.035) than doxycycline treatment. The electricidal effect (the bactericidal activity of low-amperage electrical current against bacterial biofilms) is active in vivo in the treatment of experimental S. epidermidis chronic foreign body osteomyelitis.
Simulation of Two Phase Flow in Reservoir Rocks Using a Lattice Boltzmann Method (2009)

Abstract We present results from simulations of two-phase flow directly on digitized rock microstructure images of porous media using a lattice Boltzmann method. The implemented method is done on a D3Q19 lattice with fluid-fluid and fluid-solid interaction rules to handle interfacial tension and wetting properties. We demonstrate that the model accurately reproduces capillary and wetting effects in pores with non-circular shape. The model is applied to study viscous coupling effects for two-phase cocurrent annular flow in circular tubes. Simulated relative permeabilities for this case agree with analytical predictions and show that the non-wetting phase relative permeability might greatly exceed unity when the wetting phase is less viscous than the non-wetting phase. Two-phase lattice Boltzmann simulations are performed on microstructure images derived from X-ray microtomography and process based reconstructions of Bentheimer sandstone. By imposing a flow regulator to control the capillary number of the flow, the lattice Boltzmann model can closely mimic typical experimental setups, such as centrifuge capillary pressure and un-steady and steady-state relative permeability measurements. Computed drainage capillary pressure curves are found to be in excellent agreement with experimental data. Simulated steady-state relative permeabilities at typical capillary numbers in the vicinity of 10−5 are in fair agreement with measured data. The simulations accurately reproduce the wetting phase relative permeability, but tend to under-predict the non-wetting phase relative permeability at high wetting phase saturations. For higher capillary numbers, we correctly observe increased relative permeability for the non-wetting phase due to mobilization and flow of trapped fluid. It is concluded that the lattice Boltzmann model is a powerful and promising tool for deriving physically meaningful constitutive relations directly from rock microstructure images.
A Template‐assembled Model of the N‐peptide Helix Bundle from HIV‐1 Gp‐41 with High Affinity for C‐peptide (2007)

The infection of target cells by HIV-1 is initiated by fusion of the viral and cell membranes, which is mediated by the viral glycoproteins, gp120 and gp41. After initial cell binding by gp120, the folding of gp41 to form a stable six-helix bundle structure is directly associated with membrane fusion. This helix bundle is composed of an alpha-helical trimer of gp41 N-peptide, with three copies of the alpha-helical gp41 C-peptide folded onto it in an antiparallel orientation. This report describes the synthesis and study of an N-peptide three-helix bundle structure, KTA-3N29b, that is assembled on a threefold symmetric template derived from Kemp's triacid. At neutral pH and in the presence of physiologic salt, KTA-3N29b, exists as a monomer with high helix content. Binding isotherms measured by circular dichroism spectropolarimetry indicate that KTA-3N29b binds three copies of the C-peptide native sequence, with a KD of about 260 nM. These features of KTA-3N29b demonstrate that this templated three-helix bundle serves as a functional model for the native N-peptide structure that will allow detailed studies of the folding and thermodynamic stability of the gp41 six-helix bundle, and may aid the future development of potent HIV-1 fusion inhibitors and immunogens.
Glutamate dehydrogenase from Escherichia coli: purification and properties (1975)

Glutamate dehydrogenase (L-glutamate:NADP+ oxidoreductase [deaminating], EC 1.4.1.4) has been purified from Escherichia coli B/r. The purity of the enzyme preparation has been established by polyacrylamide gel electrophoresis, ultracentrifugation, and gel filtration. A molecular weight of 300,000 +/- 20,000 has been calculated for the enzyme from sedimentation equilibrium measurements. Polyacrylamide gel electrophoresis in sodium dodecyl sulfate and sedimentation equilibrium measurements in guanidine hydrochloride have revealed that glutamate dehydrogenase consists of polypeptide chains with the identical molecular weight of 50,000 +/- 5,000. The results of molecular weight determination lead us to propose that glutamate dehydrogenase is a hexamer of subunits with identical molecular weight. We also have studied the stability and kinetics of purified glutamate dehydrogenase. The enzyme remains active when heat treated or when left at room temperature for several months but is inactivated by freezing. The Michaelis constants of glutamate dehydrogenase are 1,100,640, and 40 muM for ammonia, 2-oxoglutarate, and reduced nicotinamide adenine dinucleotide phosphate, respectively.
ChemInform Abstract: Synthesis of 1‐Substituted 5‐Aminoimidazole‐4‐carbaldehydes and 8‐Amino‐1‐(2‐fluorobenzyl)imidazo[4′,5′:5,6]pyrido[2,3‐d]pyrimidine. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Color and Fluorescent Imaging of <i>t</i>-BOC-Protected Quinizarin Methacrylate Polymers (2002)

A polymerizable quinizarin (Qz) dye precursor having both methacrylate and tert-butoxycarbonyl (t-BOC) groups has been prepared and radically copolymerized to obtain mono-t-BOC-protected quinizarin polymers as fluorescent imaging materials. The mono-t-BOC-protected quinizarin methacylate 3 (t-BQzMA) is a unique monomer having an acid-labile t-BOC blocking group along with a polymerizable methacrylate group. The t-BOC-protected quinizarin polymers obtained by copolymerization of t-BQzMA with methyl methacrylate were readily modified to regenerate phenol groups by deprotection of t-BOC groups in the quinizarin moieties with photochemical treatment in the presence of a photoacid generator. The polymers rendered color and fluorescent imaging properties based on a photolithographic method: fluorescent images obtained without wet development and fluorescent relief patterns after wet development followed by flood exposure.
New ARQ based on code combining applicable to HF channels (2000)

The highly time varying nature of the HF radio channel makes the design of coding schemes extremely difficult. The designer must make the choice between a code which is powerful enough to allow error free communication in the worst channel state or a code which will allow communication only when the channel is good and risk the introduction of errors in to the received data. Clearly, what is required is an adaptive system which uses a high rate code for high throughput when channel conditions are good and a more powerful, low rate code to ensure reliable reception when the channel is poor. An adaptive system must monitor the channel state and ensure that the correct code is selected, this requires accurate real time channel evaluation data. Code combining hybrid ARQ systems provide continuous adaptive operation, without relying on channel evaluation data, ensuring that the correct amount of error control is added to any transmitted data. This is achieved using a system of incremental redundancy where progressively more parity symbols are transmitted as errors are detected. This paper describes a code combining, hybrid ARQ system based on the Reed Muller code using a full, trellis based, soft maximum likelihood decoder. The system is capable of providing reliable communication over widely varying channel conditions using a low complexity decoder.
Splash: fast data dissemination with constructive interference in wireless sensor networks (2013)

It is well-known that the time taken for disseminating a large data object over a wireless sensor network is dominated by the overhead of resolving the contention for the underlying wireless channel. In this paper, we propose a new dissemination protocol called Splash, that eliminates the need for contention resolution by exploiting constructive interference and channel diversity to effectively create fast and parallel pipelines over multiple paths that cover all the nodes in a network. We call this tree pipelining. In order to ensure high reliability, Splash also incorporates several techniques, including exploiting transmission density diversity, opportunistic overhearing, channel-cycling and XOR coding. Our evaluation results on two large-scale testbeds show that Splash is more than an order of magnitude faster than state-of-the-art dissemination protocols and achieves a reduction in data dissemination time by a factor of more than 20 compared to DelugeT2.
A Review of Recent Advances in Speaker Diarization with Bayesian Methods (2011)

This chapter aims to present some of the recent Bayesian approaches to speaker diarization (SD). SD is the task of grouping an audio document into homogenous regions, where each region should ideally correspond to the complete set of utterances that belong to a single speaker. Rich transcription, speaker adaptation of speech recognition systems and speaker recognition are some of the applications that require such a clustering procedure. Broadcast News, meeting, and telephone conversations are the main domains that SD is applied to. SD is a fully unsupervised clustering task. Not only we are not allowed to use any target-speaker enrollment data to detect the target speakers through the acoustic stream, but the number of speakers should be considered as an unknown, too. Moreover, text-independence should also be assumed, meaning that no transcript is available, either. Despite the effectiveness of several approaches and frameworks that have been proposed and tested in literature, the most natural and systematic approach to SD is to treat it as a model’s order selection task. Once the order is estimated (i.e. the number of speakers) the task reduces to a familiar (but not trivial at all) machine learning task where the latent variables (i.e. the speaker indicators of each utterance) of given cardinality should be estimated from the observations. Therefore, a major issue we deal with is how to assess the number of speakers in a way that is simultaneously robust and efficient. Bayesian machine learning is a highly principled paradigm and can naturally tackle model selection problems. It does so by applying consistently the rules of probability in order to infer the desired quantities, including the order of the model. Its superiority over the frequentistic statistical framework (e.g. Maximum Likelihood estimates, Classical Hypothesis testing) or semi-Bayesian approaches (e.g. MAP estimation, penalized maximum likelihood criteria) in model selection, averaging and density estimation has been verified in most (if not all) of the speaker related tasks, including identification and verification. Several drawbacks however still exist, most of which stem from the intractability of the majority of the ideal Bayesian solutions. Many well known and effective machine learning tools cannot be applied or require severe adaptation that may drastically increase their computational complexity. Nevertheless, the introduction of powerful approximate inference method (e.g. Variational Bayes, Expectation Propagation), novel Markov-Chain Monte Carlo techniques, along with the rapid development of the Bayesian nonparametric models 11
Update on <i>Pneumocystis carinii</i> f. sp. <i>hominis</i> Typing Based on Nucleotide Sequence Variations in Internal Transcribed Spacer Regions of rRNA Genes (1998)

Pneumocystis carinii f. sp. hominis isolates from 207 clinical specimens from nine countries were typed based on nucleotide sequence variations in the internal transcribed spacer regions I and II (ITS1 and ITS2, respectively) of rRNA genes. The number of ITS1 nucleotides has been revised from the previously reported 157 bp to 161 bp. Likewise, the number of ITS2 nucleotides has been changed from 177 to 192 bp. The number of ITS1 sequence types has increased from 2 to 15, and that of ITS2 has increased from 3 to 14. The 15 ITS1 sequence types are designated types A through O, and the 14 ITS2 types are named types a through n. A total of 59 types of P. carinii f. sp. hominis were found in this study.
Dynamic correction for parallel conductance, G<sub>P</sub>, and gain factor, α, in invasive murine left ventricular volume measurements (2009)

The conductance catheter technique could be improved by determining instantaneous parallel conductance (G(P)), which is known to be time varying, and by including a time-varying calibration factor in Baan's equation [alpha(t)]. We have recently proposed solutions to the problems of both time-varying G(P) and time-varying alpha, which we term "admittance" and "Wei's equation," respectively. We validate both our solutions in mice, compared with the currently accepted methods of hypertonic saline (HS) to determine G(P) and Baan's equation calibrated with both stroke volume (SV) and cuvette. We performed simultaneous echocardiography in closed-chest mice (n = 8) as a reference for left ventricular (LV) volume and demonstrate that an off-center position for the miniaturized pressure-volume (PV) catheter in the LV generates end-systolic and diastolic volumes calculated by admittance with less error (P < 0.03) (-2.49 +/- 15.33 microl error) compared with those same parameters calculated by SV calibrated conductance (35.89 +/- 73.22 microl error) and by cuvette calibrated conductance (-7.53 +/- 16.23 microl ES and -29.10 +/- 31.53 microl ED error). To utilize the admittance approach, myocardial permittivity (epsilon(m)) and conductivity (sigma(m)) were calculated in additional mice (n = 7), and those results are used in this calculation. In aortic banded mice (n = 6), increased myocardial permittivity was measured (11,844 +/- 2,700 control, 21,267 +/- 8,005 banded, P < 0.05), demonstrating that muscle properties vary with disease state. Volume error calculated with respect to echo did not significantly change in aortic banded mice (6.74 +/- 13.06 microl, P = not significant). Increased inotropy in response to intravenous dobutamine was detected with greater sensitivity with the admittance technique compared with traditional conductance [4.9 +/- 1.4 to 12.5 +/- 6.6 mmHg/microl Wei's equation (P < 0.05), 3.3 +/- 1.2 to 8.8 +/- 5.1 mmHg/microl using Baan's equation (P = not significant)]. New theory and method for instantaneous G(P) removal, as well as application of Wei's equation, are presented and validated in vivo in mice. We conclude that, for closed-chest mice, admittance (dynamic G(P)) and Wei's equation (dynamic alpha) provide more accurate volumes than traditional conductance, are more sensitive to inotropic changes, eliminate the need for hypertonic saline, and can be accurately extended to aortic banded mice.
Design considerations for circularly form-birefringent optical fibres (1986)

Single-lobe and multiple-lobe single-mode fibre core structures which are twisted at a uniform rate along the fibre axis are proposed as candidates for achieving very high circular birefringence in optical fibres. The main characteristics of these structures are analysed in general terms using ray optics. These circularly birefringent fibres can give 100% twisting efficiency without any linear birefringence effects. Even with parameters similar to conventional monomode fibres, the maximum obtainable birefringence can be a few rotations/mm.
Two Arabidopsis cytochrome P450 monooxygenases, CYP714A1 and CYP714A2, function redundantly in plant development through gibberellin deactivation (2011)

The rice gene ELONGATED UPPERMOST INTERNODE1 (EUI1) encodes a P450 monooxygenase that epoxidizes gibberellins (GAs) in a deactivation reaction. The Arabidopsis genome contains a tandemly duplicated gene pair ELA1 (CYP714A1) and ELA2 (CYP714A2) that encode EUI homologs. In this work, we dissected the functions of the two proteins. ELA1 and ELA2 exhibited overlapping yet distinct gene expression patterns. We showed that while single mutants of ELA1 or ELA2 exhibited no obvious morphological phenotype, simultaneous elimination of ELA1 and ELA2 expression in ELA1-RNAi/ela2 resulted in increased biomass and enlarged organs. By contrast, transgenic plants constitutively expressing either ELA1 or ELA2 were dwarfed, similar to those overexpressing the rice EUI gene. We also discovered that overexpression of ELA1 resulted in a severe dwarf phenotype, while overexpression of ELA2 gave rise to a breeding-favored semi-dwarf phenotype in rice. Consistent with the phenotypes, we found that the ELA1-RNAi/ela2 plants increased amounts of biologically active GAs that were decreased in the internodes of transgenic rice with ELA1 and ELA2 overexpression. In contrast, the precursor GA(12) slightly accumulated in the transgenic rice, and GA(19) highly accumulated in the ELA2 overexpression rice. Taken together, our study strongly suggests that the two Arabidopsis EUI homologs subtly regulate plant growth most likely through catalyzing deactivation of bioactive GAs similar to rice EUI. The two P450s may also function in early stages of the GA biosynthetic pathway. Our results also suggest that ELA2 could be an excellent tool for molecular breeding for high yield potential in cereal crops.
Reversion of cardiac dysfunction by a novel orally available calcium/calmodulin-dependent protein kinase II inhibitor, RA306, in a genetic model of dilated cardiomyopathy (2019)

This work supports the feasibility of identifying potent orally available CaMKII inhibitors suitable for clinical use to treat heart disease.
Laser Hair Removal (1998)

The use of lasers for hair removal has generated tremendous interest. In the treatment of cutaneous pigmented disorders, lasers are used at relatively
Social Media Content Ranking Based on Social Computing and User Influence (2015)

In this paper an innovative social media content ranking scheme is proposed. The proposed unsupervised architecture takes into consideration user-content interactions, since social media posts receive likes, comments and shares from friends and other users. Additionally the influence of each user is modeled, based on the centrality theory. Towards this direction both the degree and Bonacich's centrality are estimated for each user. Finally, a novel content ranking component is introduced, which ranks posted items based on a social computing method, driven by the power and influence of social network users. Initial experiments on real life social networks content illustrate the promising performance of the proposed architecture. Additionally comparisons with random selection chronological ordering (RSPICO), random selection non-chronological ordering (RSPIn-CO) and “My Facebook Movie” algorithms are provided.
Heavy Oil Dilution (2004)

Heavy crude oils cannot be transported by pipeline without a prior reduction of their viscosity. This is commonly obtained by blending the oil with light hydrocarbons. In that case, the resulting viscosity of the mixture depends only on the dilution rate, on the respective viscosities and densities of the oil, and of the diluent. The addition of a polar solvent to a solution of asphaltenes in toluene acts on the colloidal structure of the asphaltenes. The relative viscosity of the solution decreases. Small-angle X-ray scattering (SAXS) measurements show that the radius of gyration of the aggregates of asphaltenes decreases too. In the same way, by mixing hydrocarbons and solvents owning polar functional groups in their molecule, it is shown that the efficiency of the dilution of heavy crude oils is enhanced. Hansen's theory can be used to screen the solvent efficiency. At constant dilution rate, the higher the polarity parameter or the hydrogen bonding parameter of the solvent, the greater the relative viscosity reduction of the diluted crude oil. Nevertheless, solvent owning high hydrogen bonding are generally more viscous than hydrocarbons. The influence of their interactions with the asphaltenes is hidden when the results are expressed in absolute viscosity. Only polar solvents giving few hydrogen bonding give a significant reduction of the viscosity of the diluted crude oil.
Improving Automatic Polyp Detection Using CNN by Exploiting Temporal Dependency in Colonoscopy Video (2019)

Automatic polyp detection has been shown to be difficult due to various polyp-like structures in the colon and high interclass variations in polyp size, color, shape, and texture. An efficient method should not only have a high correct detection rate (high sensitivity) but also a low false detection rate (high precision and specificity). The state-of-the-art detection methods include convolutional neural networks (CNN). However, CNNs have shown to be vulnerable to small perturbations and noise; they sometimes miss the same polyp appearing in neighboring frames and produce a high number of false positives. We aim to tackle this problem and improve the overall performance of the CNN-based object detectors for polyp detection in colonoscopy videos. Our method consists of two stages: a region of interest (RoI) proposal by CNN-based object detector networks and a false positive (FP) reduction unit. The FP reduction unit exploits the temporal dependencies among image frames in video by integrating the bidirectional temporal information obtained by RoIs in a set of consecutive frames. This information is used to make the final decision. The experimental results show that the bidirectional temporal information has been helpful in estimating polyp positions and accurately predict the FPs. This provides an overall performance improvement in terms of sensitivity, precision, and specificity compared to conventional false positive learning method, and thus achieves the state-of-the-art results on the CVC-ClinicVideoDB video data set.