gebhart/patrepeval huggingface dataset:
<b>Use of the complete genome sequence information of <i>Haemophilus influenzae</i> strain Rd to investigate lipopolysaccharide biosynthesis</b> (1996)

The availability of the complete 1.83-megabase-pair sequence of the Haemophilus influenzae strain Rd genome has facilitated significant progress in investigating the biology of H.influenzae lipopolysaccharide (LPS), a major virulence determinant of this human pathogen. By searching the H. influenzae genomic database, with sequences of known LPS biosynthetic genes from other organisms, we identified and then cloned 25 candidate LPS genes. Construction of mutant strains and characterization of the LPS by reactivity with monoclonal antibodies, PAGE fractionation patterns and electrospray mass spectrometry comparative analysis have confirmed a potential role in LPS biosynthesis for the majority of these candidate genes. Virulence studies in the infant rat have allowed us to estimate the minimal LPS structure required for intravascular dissemination. This study is one of the first to demonstrate the rapidity, economy and completeness with which novel biological information can be accessed once the complete genome sequence of an organism is available.
Automated Detection of Non-Informative Frames for Colonoscopy Through a Combination of Deep Learning and Feature Extraction (2019)

Colonoscopy is a standard medical examination used to inspect the mucosal surface and detect abnormalities of the colon. Objective assessment and scoring of disease features in the colon are important in conditions such as colorectal cancer and inflammatory bowel disease. However, subjectivity in human disease assessment and measurement is hampered by interobserver variation and several biases. A computer-aided system for colonoscopy video analysis could facilitate diagnosis and disease severity measurement, which would aid in treatment selection and clinical outcome prediction. However, a large number of images captured during colonoscopy are non-informative, making detecting and removing those frames an important first step in performing automated analysis. In this paper, we present a combination of deep learning and conventional feature extraction to distinguish non-informative from informative images in patients with ulcerative colitis. Our result shows that the combination of bottleneck features in the RGB color space and hand-crafted features in the HSV color space can boost the classification performance. Our proposed method was validated using 5-fold cross-validation and achieved an average AUC of 0.939 and an average F1 score of 0.775.
Pharmacokinetic Profile of a 2-Month Dose Regimen of Aripiprazole Lauroxil: A Phase I Study and a Population Pharmacokinetic Model (2017)

Aripiprazole lauroxil (AL) is a long-acting injectable medication approved for the treatment of schizophrenia. Current AL regimens are 441 mg, 662 mg, and 882 mg administered monthly (every 4 weeks [q4wk]), or 882 mg administered every 6 weeks (q6wk). We examined the feasibility of a 2-month (every 8 weeks [q8wk]) dosing interval of AL in a phase I open-label pharmacokinetic study investigating AL 1064 mg administered q8wk for 24 weeks, followed by 20 weeks of safety and pharmacokinetic measurements (ClinicalTrials.gov ID: NCT02320032). Second, a population pharmacokinetic model (referred to as the 2MPopPK model) was generated using data collected from the present trial, as well as data obtained from earlier studies. The phase I study included patients with schizophrenia or schizoaffective disorder maintained on an oral antipsychotic (n = 140) who were assigned to one of three groups: AL 441 mg q4wk, AL 882 mg q6wk, or AL 1064 mg q8wk, with a total of seven, five, or four injections administered, respectively. No oral aripiprazole lead-in supplementation was administered and patients continued on maintenance oral antipsychotics. Pharmacokinetic samples were collected at various time points during the 24-week study period and the 20-week follow-up period. Plasma concentrations obtained from the phase I study were analyzed using non-compartmental methods. Additionally, the data were combined with data collected from prior studies to develop the 2MPopPK model. Following the final injection of AL in the phase I study, maximum aripiprazole concentrations were achieved 24.4–35.2 days after the last dose and persisted for the duration of the study. The mean C avg,ss values were 125.8 ng/ml, 131.1 ng/ml, and 140.7 ng/ml for the 441 mg q4wk, 882 mg q6wk, and 1064 mg q8wk doses, respectively. The mean elimination half-life of aripiprazole following the last dose was 53.9 days for the 1064 mg dose, 55.1 days for the 882 mg dose, and 57.2 days for the 441 mg dose. The 2MPopPK dataset included 14,524 aripiprazole concentrations from 700 patients with schizophrenia. The duration of absorption of aripiprazole was estimated as 43 days (95% confidence interval [CI] 42–45 days), which was preceded by a 3.2-day lag time (95% CI 3.0–3.5 days) for a total duration of input into the systemic circulation of 46 days following intramuscular administration of AL. Multiple-dose simulations showed that the 1064 mg q8wk regimen provides aripiprazole concentrations within the concentration range associated with 441 mg and 882 mg q4wk doses previously demonstrated to be efficacious in a phase III study. These data from the phase I study and the 2MPopPK model support the suitability of using the AL 1064 mg dose as a 2-month (q8wk) dose interval option for the treatment of schizophrenia.
Optimization of Brillouin optical correlation domain analysis system based on intensity modulation scheme (2006)

We report a novel method to enhance the performance of Brillouin optical correlation domain analysis system based on the intensity modulation of light source. The suppression and the modification of the background noise in Brillouin gain spectrum is experimentally demonstrated with different intensity modulation schemes. In an optimum configuration, the signal to noise ratio is improved more than 40%, which extends the measurable strain limit and leads to the substantial increase of measurement range.
Observation of Nuclear Fusion Driven by a Pyroelectric Crystal. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
The Portable Dynamic Fundus Instrument: Uses in telemedicine and research (1994)

For years ophthalmic photographs have been used to track the progression of many ocular diseases such as macular degeneration and glaucoma as well as the ocular manifestations of diabetes, hypertension, and hypoxia. In 1987 a project was initiated at the Johnson Space Center (JSC) to develop a means of monitoring retinal vascular caliber and intracranial pressure during space flight. To conduct telemedicine during space flight operations, retinal images would require real-time transmissions from space. Film-based images would not be useful during in-flight operations. Video technology is beneficial in flight because the images may be acquired, recorded, and transmitted to the ground for rapid computer digital image processing and analysis. The computer analysis techniques developed for this project detected vessel caliber changes as small as 3 percent. In the field of telemedicine, the Portable Dynamic Fundus Instrument demonstrates the concept and utility of a small, self-contained video funduscope. It was used to record retinal images during the Gulf War and to transmit retinal images from the Space Shuttle Columbia during STS-50. There are plans to utilize this device to provide a mobile ophthalmic screening service in rural Texas. In the fall of 1993 a medical team in Boulder, Colorado, will transmit real-time images of the retina during remote consultation and diagnosis. The research applications of this device include the capability of operating in remote locations or small, confined test areas. There has been interest shown utilizing retinal imaging during high-G centrifuge tests, high-altitude chamber tests, and aircraft flight tests. A new design plan has been developed to incorporate the video instrumentation into face-mounted goggle. This design would eliminate head restraint devices, thus allowing full maneuverability to the subjects. Further development of software programs will broaden the application of the Portable Dynamic Fundus Instrument in telemedicine and medical research.
A new “Logicle” display method avoids deceptive effects of logarithmic scaling for low signals and compensated data (2006)

The Logicle display method provides more complete, appropriate, and readily interpretable representations of data that includes populations with low-to-zero means, including distributions resulting from fluorescence compensation procedures, than can be produced using either logarithmic or linear displays. The method includes a specific algorithm for evaluating actual data distributions and deriving parameters of the Logicle scaling function appropriate for optimal display of that data. It is critical to note that Logicle visualization does not change the data values or the descriptive statistics computed from them.
Estimation of prenatal aorta intima-media thickness from ultrasound examination (2014)

Prenatal events such as intrauterine growth restriction and increased cardiovascular risk in later life have been shown to be associated with an increased intima-media thickness (aIMT) of the abdominal aorta in the fetus. In order to assess and manage atherosclerosis and cardiovascular disease risk in adults and children, in recent years the measurement of abdominal and carotid artery thickness has gained a growing appeal. Nevertheless, no computer aided method has been proposed for the analysis of prenatal vessels from ultrasound data, yet. To date, these measurements are being performed manually on ultrasound fetal images by skilled practitioners. The aim of the presented study is to introduce an automatic algorithm that identifies abdominal aorta and estimates its diameter and aIMT from routine third trimester ultrasonographic fetal data.The algorithm locates the aorta, then segments it and, by modeling the arterial wall longitudinal sections by means of a gaussian mixture, derives a set of measures of the aorta diameter (aDiam) and of the intima-media thickness (aIMT). After estimating the cardiac cycle, the mean diameter and the aIMT at the end-diastole phase are computed.Considering the aIMT value for each subject, the correlation between automatic and manual end-diastolic aIMT measurements is 0.91 in a range of values 0.44-1.10 mm, corresponding to both normal and pathological conditions. The automatic system yields a mean relative error of 19%, that is similar to the intra-observer variability (14%) and much lower that the inter-observer variability (42%).The correlation between manual and automatic measurements and the small error confirm the ability of the proposed system to reliably estimate aIMT values in prenatal ultrasound sequences, reducing measurement variability and suggesting that it can be used for an automatic assessment of aIMT.
Sensorless Velocity Control of Permanent-Magnet (1998)

A sensorless velocity controller for the permanent- magnet synchronous motor is designed using discrete-time re- duced order models. A nonlinear observer estimates rotor posi- tion and velocity from stator current measurements, thus elim- inating the need for shaft-mounted sensors. The observer is based on least-squares optimization, and exploits a piecewise- bilinear representation of the back-emf (speed voltage) func- tion. By smoothly switching from an observer-based closed-loop control to an open-loop control at low velocity, observer ill- conditioning is avoided and reliable operation is achieved under all operating conditions. The new scheme delivers performance comparable to sensor-based closed-loop control, yet requires only a moderate amount of on-line computation. Experimental results provide evidence of the viability and performance of the new scheme.
Biocidal polystyrene beads. IV. Functionalized methylated polystyrene (2004)

Abstract Crosslinked chloromethylated polystyrene beads were reacted with hydantoin and imidazolidinone derivatives to produce functionalized beads which could be rendered biocidal upon reaction with free chlorine or bromine. The biocidal efficacies of the N ‐chlorinated, and in one case, the N ‐brominated polymeric beads against Staphylococcus aureus and Escherichia coli O157:H7 in aqueous suspension have been determined. Synthetic methods and test data have been presented. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 92: 368–372, 2004
The OPI1 gene of Saccharomyces cerevisiae, a negative regulator of phospholipid biosynthesis, encodes a protein containing polyglutamine tracts and a leucine zipper. (1991)

In Saccharomyces cerevisiae, recessive mutations at the OPI1 locus result in constitutively derepressed expression of inositol 1-phosphate synthase, the product of the INO1 gene. Many of the other enzymes involved in phospholipid biosynthesis are also expressed at high derepressed levels in opi1 mutants. Thus, the OPI1 gene is believed to encode a negative regulator that is required to repress a whole subset of structural genes encoding for phospholipid biosynthetic enzymes. In this study, the OPI1 gene was mapped to chromosome VIII and cloned. When transformed into an opi1 mutant, the cloned DNA was capable of complementing the mutant phenotype and restoring correct regulation to the INO1 structural gene. Construction of two opi1 disruption alleles and subsequent genetic analysis of strains bearing these alleles confirmed that the cloned DNA was homologous to the genomic OPI1 locus. Furthermore, the OPI1 gene was found to be nonessential to the organism since mutants bearing the null allele were viable and exhibited a phenotype similar to that of previously isolated opi1 mutants. Similar to other opi1 mutants, the opi1 disruption mutants accumulated INO1 mRNA constitutively to a level 2-3-fold higher than that observed in wild-type cells. The cloned OPI1 gene was sequenced, and translation of the open reading frame predicted a protein composed of 404 amino acid residues with a molecular weight of 40,036. The predicted Opi1 protein contained a well defined heptad repeat of leucine residues that has been observed in other regulatory proteins. In addition, the predicted protein contained polyglutamine residue stretches which have also been reported in yeast genes having regulatory functions. Sequencing of opi1 mutant alleles, isolated after chemical mutagenesis, revealed that several were the result of a chain termination mutation located within the largest polyglutamine residue stretch.
Comparison of subcritical and supercritical Rankine cycles for application to the geopressured geothermal resource (1981)

There are several features unique to the geopressure geothermal resource which narrow the range of power cycle alternatives. The thermodynamic and operating restrictions which appear to favor the application of a supercritical Rankine power cycle utilizing propane for the recovery of thermal energy from the geopressure geothermal resource are described. This power cycle can be integrated into a natural gas recovery scheme that conserves reservoir pressure for brine disposal and produces gas at pipeline pressure.
Hydrodesulfurization of Catalytic Cracked Gasoline. 3. Selective Catalytic Cracked Gasoline Hydrodesulfurization on the Co−Mo/γ-Al<sub>2</sub>O<sub>3</sub> Catalyst Modified by Coking Pretreatment (1998)

The interaction of olefins with the hydrodesulfurization (HDS) catalyst surface was studied by the time course of catalytic cracked gasoline (CCG) HDS on the Co−Mo/γ-Al2O3 catalyst. Olefin hydrogenation activity was decreased drastically in the beginning 30 h. After 75 h of time on stream, to wash the catalyst surface, toluene was flown into the reactor at room temperature and this toluene wash recovered some olefin hydrogenation activity. The oligomers of CCG olefins were found in the effluent of toluene wash. It was suggested that oligomerized and polymerized olefin (coke) selectively deactivated the olefin hydrogenation active site. The possibility of improving the HDS selectivity of Co−Mo/γ-Al2O3 by carbonaceous deposit was investigated for HDS reactions of CCG and model compounds. The catalyst with coking pretreatment after sulfiding showed the higher CCG HDS selectivity than that of the catalyst without coking pretreatment. Thiophene HDS in the presence of diisobutylene or 1-octene was also carried out, and the relative deactivation by the coking pretreatment was in the following order, isoolefin hydrogenation > thiophene HDS > n-olefin hydrogenation. The improvement of CCG HDS selectivity by the coking pretreatment was considered to be caused by the selective deactivation of isoolefin hydrogenation active site.
Novel thermoplastic elastomers. I. Synthesis and characterization of star‐block copolymers of PSt‐b‐PIB arms emanating from cyclosiloxane cores (1998)

The synthesis and characterization of novel thermoplastic elastomers consisting of multiple polystyrene-b-polyisobutylene (PSt-b-PIB) arms emanating from cyclosiloxane cores is described. The synthesis involved the sequential living cationic block copolymerization of styrene (St) and isobutylene (IB), followed by quantitative allylic end-functionalization of the living PSt-b-PIB+ to produce PSt-b-PIBCH2 CHCH2 prearms, and finally linking by hydrosilation of these prearms with SiH-containing cyclosiloxanes (e.g., 2,4,6,8,10,12-hexamethylcyclohexasiloxane, D). Two types of star-blocks, namely primary and higher-order star-blocks, were prepared: Primary star-blocks containing 3–9 PSt-b-PIB arms were obtained by using various cyclosiloxanes (D to D) and a close to exact stoichiometry between the SiH and allyl groups, [SiH]/[CC] ∼ 1, in the essential absence of moisture ([H2O] ∼ 100 ppm). Higher-order star-blocks consisting of 13–24 PSt-b-PIB arms radiating from complex coupled cyclosiloxanes were prepared by the use of SiH/allyl ratios significantly larger than unity ([SiH]/[CC] = 2–3) in the presence of controlled amounts of moisture ([H2O] ∼ 600 ppm). Reaction conditions (temperature, concentration, stoichiometry, solvent nature, catalyst concentration, etc.) for efficient syntheses have been developed. The products were characterized by 200 and 600 MHz 1H-NMR spectroscopy and triple-detector (RI, UV, LLS) GPC. The microstructure of the condensed cores in the higher-order star-blocks was studied by 2D-NMR (HMQC) spectroscopy, and the number of cyclosiloxane rings in the cores (i.e., the content (wt %) of cores in the star-blocks) was determined. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: 2997–3012, 1998
Multiview Image Coding Based on Geometric Prediction (2007)

Many existing multiview image/video coding techniques remove inter-viewpoint redundancy by applying disparity compensation in a conventional video coding framework, e.g., H.264/MPEG-4 AVC. However, conventional methodology works ineffectively as it ignores the special characteristics of inter-viewpoint disparity. In this paper, we propose a geometric prediction methodology for accurate disparity vector (DV) prediction, such that we can largely reduce the disparity compensation cost. Based on the new DV predictor, we design a basic framework that can be implemented in most existing multiview image/video coding schemes. We also use state-of-the-art H.264/MPEG-4 AVC as an example to illustrate how the proposed framework can be integrated with conventional video coding algorithms. Our experiments show proposed scheme can effectively tracks disparity and greatly improves coding performance. Compared with H.264/MPEG-4 AVC codec, our scheme outperforms maximally 1.5 dB when encoding some typical multiview image sequences. We also carry out an experiment to evaluate the robustness of our algorithm. The results indicate our method is robust and can be used in practical applications.
Monolithic Fabrication of EWOD Chips for Picoliter Droplets (2011)

We report monolithic fabrication of parallel-plate electrowetting-on-dielectric (EWOD) chips for digital micro-fluidics of picoliter droplets. Instead of assembling a second substrate to form a top plate-the common practice with all previous parallel-plate EWOD chips-the top plate is surface micromachined as a transparent thin-film membrane that forms a monolithic cavity having a gap height on the order of micrometers with excellent accuracy and uniformity. The membrane is embedded with EWOD driving electrodes and confines droplets against the device substrate to perform digital microfluidic operations. Two main attributes of the monolithic architecture that distinguish it from tradition methods are: (i) it enables excellent control of droplet dimensions down to the micrometer scale, and (ii) it does not require the typical alignment and assembly steps. Basic device functions such as creation and splitting are verified by EWOD actuation of ~100 picoliter droplets surrounded by air or oil inside a 10 μm-high cavity. Additionally, flow focusing of droplets containing 5.3 μm beads demonstrates one example of the utilities afforded by monolithic fabrication.
In-line birefringent fiber polarizer (1984)

Due to the increasing application of high-birefringence polarization-holding fiber in fiber systems, there is a high current interest in fiber polarizers and polarizing fibers.1,2 To date, most discrete fiber polarizers reported have been made with ordinary low-birefringence fiber so that they are not compatible with high-birefringence fiber. Recently, two polarizing fibers have been reported1,2 which utilize high fiber birefringence combined with an appropriate fiber geometry to allow the low-loss propagation of only one linear polarization mode.
Characterization of double-stranded RNA satellites associated with the Trichomonas vaginalis virus (1995)

Three small and distinct satellite double-stranded RNAs (dsRNAs) denoted s1, s1', and s2 were recently described for a Trichomonas vaginalis isolate harboring a dsRNA virus. Since characterization of these satellite dsRNAs might provide insight into the virus replication cycle and virus-host interactions, full-length cDNAs to s1 and s1' dsRNAs were synthesized and sequenced. s1 dsRNA has 688 bp, and s1' dsRNA has 616 bp. A 228-bp open reading frame that begins at nucleotide 37 was detected on a putative sense strand of s1. All satellite RNAs were found associated with RNA-dependent RNA polymerase (RDRP) activity that banded on CsCl gradients. Within carrier trichomonads, satellite RNAs synthesized single-stranded replicative intermediates. An in vitro assay was established to assess replication of satellite RNAs. Transcripts generated from s1 cDNA, for example, served as a template for the viral RDRP. These templates had a polarity similar to that of the replicative intermediate found in the satellite-harboring parasites. Importantly, the recognition of s1 RNA was shown to be specific, since unrelated RNAs did not serve as templates for RDRP under the same experimental conditions. The data indicate that the cDNA of s1 has a specific and essential sequence needed for recognition by the viral RDRP and for subsequent RNA synthesis. Both s1 and s1' have conserved domains, albeit of unproven function, but which may be required for replication.