gebhart/patrepeval huggingface dataset:
Immobilization Strategies for Functional Complement Convertase Assembly at Lipid Membrane Interfaces (2017)

The self-assembly formation of complement convertases-essential biomacromolecular complexes that amplify innate immune responses-is triggered by protein adsorption. Herein, a supported lipid bilayer platform was utilized to investigate the effects of covalent and noncovalent tethering strategies on the self-assembly of alternative pathway C3 convertase components, starting with C3b protein adsorption followed bythe addition of factors B and D. Quartz crystal microbalance-dissipation (QCM-D) experiments measured the real-time kinetics of convertase assembly onto supported lipid bilayers. The results demonstrate that the nature of C3b immobilization onto supported lipid bilayers is a key factor governing convertase assembly. The covalent attachment of C3b to maleimide-functionalized supported lipid bilayers promoted the self-assembly of functional C3 convertase in the membrane-associated state and further enabled successful evaluation of a clinically relevant complement inhibitor, compstatin. By contrast, noncovalent attachment of C3b to negatively charged supported lipid bilayers also permitted C3b protein uptake, albeit membrane-associated C3b did not support convertase assembly in this case. Taken together, the findings in this work demonstrate that the attachment scheme for immobilizing C3b protein at lipid membrane interfaces is critical for downstream C3 convertase assembly, thereby offering guidance for the design and evaluation of membrane-associated biomacromolecular complexes.
Clinical outcomes following ankle fracture: a cross‐sectional observational study (2014)

NCT01127776.
A Diffusion-Tensor-Based White Matter Atlas for Rhesus Macaques (2014)

Atlases of key white matter (WM) structures in humans are widely available, and are very useful for region of interest (ROI)-based analyses of WM properties. There are histology-based atlases of cortical areas in the rhesus macaque, but none currently of specific WM structures. Since ROI-based analysis of WM pathways is also useful in studies using rhesus diffusion tensor imaging (DTI) data, we have here created an atlas based on a publicly available DTI-based template of young rhesus macaques. The atlas was constructed to mimic the structure of an existing human atlas that is widely used, making results translatable between species. Parcellations were carefully hand-drawn on a principle-direction color-coded fractional anisotropy image of the population template. The resulting atlas can be used as a reference to which registration of individual rhesus data can be performed for the purpose of white-matter parcellation. Alternatively, specific ROIs from the atlas may be warped into individual space to be used in ROI-based group analyses. This atlas will be made publicly available so that it may be used as a resource for DTI studies of rhesus macaques.
PIPEFLOW CONTRIBUTING AREAS AND RUNOFF RESPONSE (1997)

Links that have been established between the characteristic responses of hillslope drainage processes and the size of drainage catchments enable valuable extrapolations and comparisons to be made, both within and beyond the range of the field data. To date, flow through natural soil pipes has not been included in these investigations. A methodology is offered for achieving this and the first such analyses of field data on pipeflow. The results indicate that pipeflow responses follow trends which are broadly similar to other hillslope drainage processes and are intermediate between throughflow and saturation overland flow. © 1997 by John Wiley & Sons, Ltd.
Aerosol route enhances the contamination of intact eggs and muscle of experimentally infected laying hens by Salmonella typhimurium DT104 (1999)

Commercial laying hens were infected with Salmonella typhimurium DT104 strain 16 alternatively via the crop (107 cfu per bird) or by an aerosol delivered directly to the beaks using a Collison nebuliser and Henderson apparatus (2×102 or 2×104 cfu per bird). Infection by both routes caused systemic infection and prolonged contamination of faeces. Contamination rates of eggs and muscle were much higher following the aerosol challenges despite the much lower doses given by this route. The frequency of Salmonella isolation from eggs rose from 1.7% following oral challenge to 14% and 25%, for each of the aerosol challenges respectively, and the frequency of isolation from muscle rose from 0% following the oral challenge to 27% following each of the aerosol challenges.
A new single carrier FDMA system based on the discrete cosine transform (2009)

In this paper, a new single carrier frequency division multiple access (SC-FDMA) system based on the discrete cosine transform (DCT) for uplink wireless transmissions, is introduced. The time domain expressions of the DCT SC-FDMA signals are derived. The peak to average power ratio (PAPR) of the DCT SC-FDMA signals is compared with that of the discrete Fourier transform (DFT) SC-FDMA and orthogonal frequency division multiple access (OFDMA) signals. Simulation results show that the proposed DCT SC-FDMA system provides a better bit error rate (BER) performance than the DFT SC-FDMA and the OFDMA systems. In addition, it is found that the PAPR of the DCT SC-FDMA signals is lower than that of OFDMA signals.
Administration time-dependent effects on ambulatory blood pressure of doxazosin gits as added therapy in uncontrolled hypertensive patients (2004)

improvement in BP control without metabolic disturbances. The higher the baseline BP values were the greater the lowering effect was.
Molecular approach toward information storage based on the redox properties of porphyrins in self-assembled monolayers (2000)

A molecular approach to information storage is described that uses porphyrins attached to a Au microelectrode as the memory storage element. A set of four zinc porphyrins has been examined, with each porphyrin bearing three mesityl groups and one S-acetylthio-derivatized linker of structure 1-[AcS-(CH2)n]-4-phenylene (n=0, 1, 2, or 3). Each porphyrin forms a self-assembled monolayer (SAM) on the Au microelectrode. Information is stored in the multiple oxidation states (neutral, monocation, dication) of the porphyrin. The charge retention time for each of the porphyrin monocations is in the regime of hundreds of seconds and varies with molecular structure (t1/2=116, 167, 656, and 885 s for n=0–3, respectively). The redox process in the SAM can be cycled thousands of times under ambient conditions without loss of signal, thus the loss in charge does not stem from decomposition. The fact that the system (1) is fabricated by self-assembly, (2) is addressed electrically, (3) operates under ambient conditions, (4) can be cycled multiple times, (5) requires no moving parts for reading and writing, and (6) is scalable to small dimensions make this approach attractive for molecular-based information storage.
Atlas for optogalvanic wavelength calibration (1980)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Richard A. Keller, Rolf Engleman, and Byron A. Palmer, "Atlas for optogalvanic wavelength calibration," Appl. Opt. 19, 836-837 (1980) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Tandem mass spectrometric analysis of a complex triterpene saponin mixture of Chenopodium quinoa (2006)

A nano-HPLC electrospray ionization multi-stage tandem mass spectrometry (nLC-ESI-MS/MS) approach was applied to a complex crude triterpene saponin extract of Chenopodium quinoa seed coats. In ESI-MS/MS spectra of triterpene saponins, characteristic fragmentation reactions are observed and allow the determination of aglycones, saccharide sequences, compositions, and branching. Fragmentation of aglycones provided further structural information. The chemical complexity of the mixture was resolved by a complete profiling. Eighty-seven triterpene saponins comprising 19 reported and 68 novel components were identified and studied by MS. In addition to four reported, five novel triterpene aglycones were detected and characterized according to their fragmentation reactions in ESI-MS/MS and electron ionization mass spectrometry (EI-MS). As a novelty fragmentation pathways were proposed and analyzed based upon quantum chemical calculations using a hybrid Hartree-Fock density functional method. Accuracy of the assignment procedure was proven by isolation and structure determination of a novel compound. As the relative distribution and composition of saponins varies between different cultivars and soils, the presented strategy allows a rapid and complete analysis of Chenopodium quinoa saponin distribution and composition, and is particularly suitable for quality control and screening of extracts designated for pharmaceutical, agricultural, and industrial applications.
Adaptive power control design for microwave communication system (2003)

Terrestrial point-to-point microwave communication link in tropical region faces excess path attenuation due to rainfall. The rain attenuation causes the receiving signal to fall below threshold level required for specific bit-error-rate (BER) performance. Adaptive power control is design to solve this problem. It increases the transmitting power level according to the signal level arriving in the receiver. This paper describes the design of adaptive power control system and illustrates the operation of the system.
Formulating a Stable Emulsified Acid at High Temperatures: Stability and Rheology Study (2016)

Abstract Matrix acidizing is a means to stimulate wells; in order to increase the productivity or injectivity. Amongst the wide acidizing fluids, emulsified acids are the most commonly used. Emulsified acids have a reputation to retard the reaction with formation rock, hence they cause deeper penetration. Apart from that, they need minimum additives, since acid is encapsulated by oil phase. That being said, only the oil phase is in immediate contact with the tubing. Thus, granting less corrosion issues. All of these perks of emulsified acids are based on the mere condition that they are stable during their journey in the well to reach the formation rock. Therefore, a stable emulsion (emulsified acid) is extremely critical to the acidizing job, and the degree to which it is stable dictates how successful the job will be. This work aims to experimentally study the factors which contribute to create a stable emulsion by conducting thermal stability and rheology tests. These factors include mixing means (magnetic stirrer &amp; high-power mixer), emulsifier concentration (up to 1.5vol%), mixing speed (up to 1500 rpm), addition rate of acid phase to diesel one (separatory funnel &amp; syringe pump). Moreover, the emulsified acid is prepared using 15wt% HCl and diesel. The volume ratio of acid-to-diesel is 70:30. And, all of the thermal stability tests are conducted at 120°C in a heating oven. Furthermore, the apparent viscosity is measured at different temperatures and supported by droplet size distribution. The results show that emulsifier concentration and mixing speed have significant effect when the emulsion is prepared using magnetic stirrer; however, this effect diminishes when the mixing means is a high-power mixer. Interestingly, the addition rate plays a key role on the stability; even a small difference as 0.5 mL/minute would result in changing the behavior of the emulsion at 120°C. Also, the results confirm that the smaller the droplet size of an emulsion, the more viscous it becomes. Furthermore, temperature increase results in emulsion degradation. This study offers a unique way to look at emulsified acids and addresses factors that have never been addressed before. The novelty of this study is the comprehensive knowledge it brings about the factors affecting the stability of HCl emulsion. It helps to better understand HCl emulsion and how it works. Hence, production engineers can design and conduct acidizing jobs seamlessly.
Cytoscape: the network visualization tool for GenomeSpace workflows (2014)

Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013.
Characterising the effect of large‐scale model resolution upon calculated OH production using MOZAIC data (2002)

The coarse spatial resolution of large‐scale models can be a significant source of error in calculating grid cell averaged rates of physical processes. We investigate here the influence of resolution in the case of chemical reactions. We use high resolution MOZAIC ozone and water vapour data to characterise the effects of unresolved structures on model‐calculated production of the hydroxyl radical (OH) in the upper troposphere/lower stratosphere region. The statistical analysis of MOZAIC data indicates that, on average, large‐scale models may overestimate OH production by 5% to 20% for resolutions ranging from ∼200 to ∼800 km respectively. This systematic bias is found to be most significant in the tropopause region.
Quantifying the Impact of Chronic Ischemic Injury on Clinical Outcomes in Acute Stroke With Machine Learning (2020)

Acute stroke is often superimposed on chronic damage from previous cerebrovascular events. This background will inevitably modulate the impact of acute injury on clinical outcomes to an extent that will depend on the precise anatomical pattern of damage. Previous attempts to quantify such modulation have employed only reductive models that ignore anatomical detail. The combination of automated image processing, large-scale data, and machine learning now enables us to quantify the impact of this with high-dimensional multivariate models sensitive to individual variations in the detailed anatomical pattern. We introduce and validate a new automated chronic lesion segmentation routine for use with non-contrast CT brain scans, combining non-parametric outlier-detection score, Zeta, with an unsupervised 3-dimensional maximum-flow, minimum-cut algorithm. The routine was then applied to a dataset of 1,704 stroke patient scans, obtained at their presentation to a hyper-acute stroke unit (St George's Hospital, London, UK), and used to train a support vector machine (SVM) model to predict between low (0-2) and high (3-6) pre-admission and discharge modified Rankin Scale (mRS) scores, quantifying performance by the area under the receiver operating curve (AUROC). In this single center retrospective observational study, our SVM models were able to differentiate between low (0-2) and high (3-6) pre-admission and discharge mRS scores with an AUROC of 0.77 (95% confidence interval of 0.74-0.79), and 0.76 (0.74-0.78), respectively. The chronic lesion segmentation routine achieved a mean (standard deviation) sensitivity, specificity and Dice similarity coefficient of 0.746 (0.069), 0.999 (0.001), and 0.717 (0.091), respectively. We have demonstrated that machine learning models capable of capturing the high-dimensional features of chronic injuries are able to stratify patients-at the time of presentation-by pre-admission and discharge mRS scores. Our fully automated chronic stroke lesion segmentation routine simplifies this process, and utilizes routinely collected CT head scans, thereby facilitating future large-scale studies to develop supportive clinical decision tools.
Génome Québec & Montreal Heart Institute Pharmacogenomics Centre: a translational pharmacogenomics platform – from R&D to the clinic (2008)

The Génome Québec and Montreal Heart Institute Pharmacogenomics Centre (Montreal, Canada), created in 2006, is a translational pharmacogenomics platform whose main objectives are to conduct pharmacogenomics research, provide pharmacogenomics services to the academic, biotechnology and pharmaceutical sectors, and integrate pharmacogenomics solutions into the healthcare system. The Centre has brought together a multidisciplinary team of researchers with expertise in genomics, bioinformatics and clinical trial research. All the Centre's clinical research studies are supported by the Centre's unique Good Laboratory Practice facility framework, which has the ability to perform pharmaceutical clinical trials and deliver clinical diagnostics under the highest standards. The Centre has successfully leveraged its experience and expertise in technology development and pharmacogenomics clinical trial work to attract funding and collaborative partnerships in both the public and private sectors.
Spatial coherence of nonlinear dynamics in a semiconductor experiment (1993)

For the case of an experimental semiconductor system, it is shown how different dynamical states that range from periodicity to hyperchaos are connected to distinct spatial patterns developing inside the sample. Collective synchronization of subsystems gives rise to low-dimensional periodic states, whereas the interaction of spatially localized oscillation centers leads to quasiperiodicity and ordinary chaos as well as higher-dimensional chaotic dynamics.
A Pilot Study Investigating Changes in the Human Plasma and Urine NAD+ Metabolome During a 6 Hour Intravenous Infusion of NAD+ (2019)

Accumulating evidence suggests that active maintenance of optimal levels of the essential pyridine nucleotide, nicotinamide adenine dinucleotide (NAD+) is beneficial in conditions of either increased NAD+ turnover or inadequate synthesis, including Alzheimer's disease and other neurodegenerative disorders and the aging process. While studies have documented the efficacy of some NAD+ precursors such as nicotinamide riboside (NR) in raising plasma NAD+, no data are currently available on the fate of directly infused NAD+ in a human cohort. This study, therefore, documented changes in plasma and urine levels of NAD+ and its metabolites during and after a 6 h 3 μmol/min NAD+ intravenous (IV) infusion. Surprisingly, no change in plasma (NAD+) or metabolites [nicotinamide, methylnicotinamide, adenosine phosphoribose ribose (ADPR) and nicotinamide mononucleotide (NMN)] were observed until after 2 h. Increased urinary excretion of methylnicotinamide and NAD+ were detected at 6 h, however, no significant rise in urinary nicotinamide was observed. This study revealed for the first time that: (i) at an infusion rate of 3 μmol/min NAD+ is rapidly and completely removed from the plasma for at least the first 2 h; (ii) the profile of metabolites is consistent with NAD+ glycohydrolase and NAD+ pyrophosphatase activity; and (iii) urinary excretion products arising from an NAD+ infusion include NAD+ itself and methyl nicotinamide (meNAM) but not NAM.
DNA sequence homology betweenattB-related sites ofCorynebacterium diphtheriae, Corynebacterium ulcerans, Corynebacterium glutamicum, and theattP side of Î³-Cornephage (1990)

Chromosomal restriction fragments of Corynebacterium ulcerans and C. diphtheriae, containing an integration site for corynephages of the β family, show homology on Southern blots. Homologous DNA in also found in the soil isolate C. glutamicum, although this strain is not susceptible to gb-corynephages. Three of these DNA fragments, one for each bacterial strain, and a fragment of γ-corynephage DNA previously shown to contain the phage integration site, were cloned and sequenced. Alignment of the 3 bacterial sequences shows a very high degreee of homology in a stretch of ca 120 nucleotides, whereas the rest of the sequences is generally non-homologous. Within this common bacterial portion, a segment of ca. 96 nucleotides (core sequence) is also highly homologous to the plague sequence. The first half (ca. 50 bp) of the core sequence is identical in all aligned sequences whereas the second half, which is largely occupied by a stem-and-loop structure, contains point mutations peculiar to each clone. The described sequences are likely to be involved in phage integration/excision processes.
427 RECOVERY OF SPERMATOGENESIS AFTER ANDROGEN-PROGESTIN THERAPY. (2006)

<h3>Context</h3> Male hormonal contraceptive methods are approaching market. Factors predicting the reversibility of these methods have not been systematically examined. <h3>Objective</h3> To determine the time and potential modulating covariables required for sperm density to recover to normal after androgen or androgen-progestin therapy sufficient for contraceptive purposes and to characterize other semen parameters as sperm density recovers. <h3>Design</h3> An integrated multivariate stepwise and best-subset Cox proportional hazards analysis of all published studies of at least 3 months9 treatment duration. Individual subject, not just summary, data were directly collected from individual investigators concerning studies published 1990-2005, which assessed subjects monthly until sperm density recovered to normal (to 20 M/mL). <h3>Setting</h3> 29 separate studies spanning the globe. <h3>Participants</h3> 1,549 normal (by physical, blood, and semen exam) men aged 19-51 years of predominantly Caucasian (two-thirds) or Asian (one-third) descent. This represents 1,283.5 patient years of treatment and 705 patient years of recovery and includes &gt; 97% of all the published data. <h3>Intervention(s)</h3> Men were treated with testosterone (T) with or without progestin for 3 to 18 months. <h3>Results</h3> Sperm density recovered to normal after 3.4 (3.2-3.5 95% CI) months in 50% of all subjects (Kaplan-Meier). Slower recovery occurred with very prolonged treatment, Caucasian ethnicity, and with longer-acting T preparations. For a typical male, aged 35 years of Caucasian descent, treated for 1 year with intramuscular T undecanoate, the median recovery time was 4.6 (4.1-5.0) months. These times were 4.1 (3.9-4.6), 5.3 (4.9-6.3), and 3.0 (2.8-3.6), months if the male was of Asian descent, treated for 1.5 years, or treated with T enanthate, respectively. Faster recovery was predicted by greater age, faster suppression of spermatogenesis, higher baseline sperm density, and lower baseline blood LH; however, although significant, these adjusted-effect sizes were small. From multivariate model analyses, the probability of recovery within 6, 12, 16, and 24 months was 67 (61-72), 90 (85-93), 96 (92-98), and 100%, respectively. Recovery to lower sperm thresholds (3 M/mL and 10 M/mL) tracked recovery to 20 M/mL and sperm morphology and motility closely followed recovery of sperm density. <h3>Conclusion</h3> We have identified important predictors and quantified expected probabilities of recovery. This is critical for the utilization of male hormonal contraceptive regimens.
Covalently crosslinked graphene oxide membranes by esterification reactions for ions separation (2015)

We present a method to prepare covalently crosslinked graphene oxide (GO) membranes with adjustable intersheet spacing by esterification reactions, using dicarboxylic acids, diols or polyols as the crosslinker and hydrochloric acid as the catalyst.