gebhart/patrepeval huggingface dataset:
Biodegradation of kraft lignin by a newly isolated anaerobic bacterial strain, <i>Acetoanaerobium</i> sp. WJDL-Y2 (2015)

Kraft lignin containing effluents discharged from pulp and paper industries causes serious environmental pollution in developing countries. Due to the immense environmental adaptability and biochemical versatility, bacterial ligninolytic potential deserve to be studied for application in effluent treatment of pulp and paper industry. In this study, an anaerobic lignin-degrading bacterium, Acetoanaerobium sp. WJDL-Y2 (accession no. KF176997),was isolated from the sludge of a pulp and paper mill. Strain Y2 can play an important role in treating pulp and paper wastewater, as well as breaking down materials for biofuel and chemical production.
PRELIMINARY STUDY OF SURFACE TREATMENTS FOR PLATINUM ELECTRODES DESIGNED FOR OXIDATION-REDUCTION POTENTIAL DETERMINATIONS IN ACTIVATED SLUDGE (1994)

Platinum electrodes with six different surface treatments (polishing, platinization, polypyrrole, polyurethane, cellulose acetate and Nation) were tested for equilibrium exchange current densities and zero-current potential in treated water and activated sludge. Preliminary results show that platinization and polypyrrole treatment increase electron transfer rates, but polypyrrole film breaks up rapidly in activated sludge; polyurethane and cellulose acetate layers did not prevent fouling (and impaired perfonnance) in activated sludge, but Nation seemed more promising.
Transmission electron microscopy of the sequence of phase formation in the interfacial solid-phase reactions in Ta/Si systems (1997)

The interfacial reaction of Ta thin films on (100) Si was investigated by high-resolution transmission electron microscopy. An amorphous layer was observed at the as-deposited Ta/Si interface. A phase of Ta5Si3 was first found to form at the interface between a Ta overlayer and the amorphous layer after annealing at 560 °C for 1 h. Annealing at 630 °C for 1 h led to the formation of another interlayer due to the outdiffusion of Si between the amorphous layer and Si. The phase in this interlayer transformed from a metastable one to TaSi2 due to annealing at 680 °C for 1 h. The first nucleation of Ta5Si3 at the interface between Ta and the amorphous layer implies that the initially formed amorphous layer has a metal-rich composition close to Ta5Si3. The formation of the interlayer between the amorphous layer and Si prior to the nucleation of TaSi2 was considered as a result of a kinetic constraint to favor the nucleation of TaSi2.
Commentary on ‘In the Beginning’ by Felix Post (2010)

“Felix Post was probably the first dedicated old age psychiatrist anywhere in the world. ‘In the beginning’ is his autobiographical account of the earliest days of old age psychiatry in Britain. Such accounts are valuable primary sources for understanding the development of the specialty. We are now reaching a point in time when our earliest pioneers like Felix Post (1913-2001) and Martin Roth (1917-2006) have died. It is important that we remember the contributions of our teachers from the past who have set the foundations for our specialty, just as Phillipe Pinel, Emil Kraepelin, Sigmund Freud and many others are celebrated for their contributions to the mental well being of mainly younger people. This short chapter by Felix Post has been described as ‘pure Felix’. It characteristically reveals his humility and modesty, and his praise of others, attributing little achievement to himself. A brief biographical note and commentary are therefore warranted to set it in context.”
Structure-activity Relationships for α-Glucosidase Inhibition of Baicalein, 5,6,7-Trihydroxyflavone: the Effect of A-Ring Substitution (2004)

In order to estimate the effects of the A-ring hydroxyl group of baicalein (5,6,7-trihydroxyflavone, 1) on rat intestinal alpha-glucosidase inhibition, flavone, monohydroxyflavones, dihydroxyflavones, and methylated derivatives of 5,6,7-trihydroxyflavone were used for the structure-activity relationship (SAR) study. The importance of the 6-hydroxyl group of baicalein was validated for an exertion of the activity. And also, the tested flavones which lacked a hydroxyl substituent on any of positions 5, 6, or 7, showed no activity. Hence, the 5,6,7-trihydroxyflavone structure was concluded to be crucial for the potent inhibitory activity. In addition, an introduction of electron-withdrawing or electron-donating groups at position 8 of baicalein led to a dramatic decrease for activity, except for 8-fluoro-5,6,7-trihydroxyflavone, which carried a less bulky substituent on position 8. Hence, this result suggested that a sterically bulky substituent on C-8 of baicalein was detrimental for the activity regardless of its electronic nature. Through examining the inhibitory mechanism of baicalein against rat intestinal alpha-glucosidase, it was suggested to be a mixed type inhibition.
Differential Transcriptional Regulation of the Apoal Gene by Retinoic Acid Receptor Homo- and Heterodimers in Yeast (1996)

Several members of the nuclear receptor superfamily including RXR (retinoid X receptor) bind to a specific retinoic acid response element (site A) of the apoAI promoter. However, transcriptional activation of the apoAI gene by different homo- and heterodimeric forms of RXR or RAR (retinoic acid receptors) cannot be evaluated in mammalian cells, which contain endogenous RXR or RAR. In order to circumvent this limitation, we assessed the DNA-binding activities and transcriptional activation of different homo- and heterodimers of these receptors in yeast. Electrophoretic mobility shift assays (EMSA) demonstrated that yeast expressed RARalpha does not bind to site A of the apoAl promoter, whereas binding of RARbeta to site A is ligand-dependent. Both RARalpha and RARbeta form heterodimers with RXRalpha and bind to site A with high affinity. These DNA-binding studies correlate with the transcriptional data, which indicated that RARbeta but not RARalpha activates transcription from site A in response equally well to 9-cis and all-trans retinoic acids. 9-cis RA is a more potent ligand than all-trans RA to activate transcription via RXR/RAR heterodimers. We conclude that this yeast expression system is a useful tool to elucidate the 'transactivation code' for apoAl site A via specific combinations of different homo and heterodimeric versions of RXR and RAR.
Densonucleosis virus purification by ion exchange membranes (2004)

Preparative chromatography is widely used in the downstream purification of biopharmaceutical products. Replacement of resins by membranes as chromatographic supports, overcomes many of the limitations associated with resin-based chromatography such as high-pressure drops, slow processing rates due to pore diffusion and channeling of the feed through the bed. In particular, adsorptive membranes may be ideally suited for virus capture. Virus capture is critical in a number of applications. In gene therapy and vaccine production, large-scale purification of virus vectors is often essential. In the manufacture of biopharmaceuticals, validation of virus clearance is critical. Here results for purification of Aedes aegypti densonucleosis virus (AeDNV) using anion and cation exchange membranes are presented. AeDNV is a non-enveloped, single-stranded mosquito-specific parvovirus. Virus particles are around 20 nm in size. AeDNV could find potential applications in integrated vector-borne disease control programs. In addition, capture of parvovirus for validation of virus clearance in the manufacture of biopharmaceuticals is of commercial importance. By adjusting the pH of the feed stream, AeDNV particles may be adsorbed by both anion and cation exchange membranes. However, strongly basic anion exchange membranes were the most effective in adsorbing AeDNV particles. Adsorption and subsequent elution of AeDNV by anion exchange membranes leads to significant virus concentration. Dynamic and static capacities for anion exchange membranes were similar. Further, a sharp elution curve was obtained suggesting that pore diffusional resistances are insignificant. The adsorption of AeDNV particles by anion exchange membranes may be described by a linear isotherm.
Radiation-force-based estimation of acoustic attenuation using harmonic motion imaging (2012)

Tissue characterization such as attenuation estimation remains challenging but important. Attenuation represents the energy loss during wave propagation through biological tissues, thus affects both therapeutic and diagnostic ultrasound applications. In this study, a novel attenuation estimation approach was developed using radiation-force-based method of Harmonic Motion Imaging (HMI). The HMI set-up comprised of a forcing transducer (fcenter = 4.7 MHz, AM frequency = 25 Hz) in conjunction with a confocal pulse-echo transducer (fcenter = 7.5 MHz), with the former inducing tissue displacement and the latter simultaneously acquiring RF signals. Tissue displacements were estimated from the RF signals using a 1-D cross-correlation method (window size: 1 mm; overlap: 90%). 2D displacement images were obtained through raster-scan (10 × 10 mm2). A linear regression model was applied to the displacements at different depths for calculating attenuation. Gel phantoms with known attenuation (n = 5) (CIRS Inc.) and in vitro canine livers (n = 3) were tested. Results demonstrated that attenuations obtained from the phantoms showed good correlation (R2 ≈ 99%) with the independently obtained values (0.28–1.45 dB/cm/MHz) (13 ± 8% underestimated), while those from the canine liver were 0.32 ± 0.03 dB/cm/MHz, within the normal range reported in the literature (0.28–1.01 dB/cm/MHz) (Duck, Academic Press 1990). Future studies will entail attenuation measurements in pathological tissues and HIFU monitoring.
Curie-temperature enhancement in ferromagnetic semiconductor superlattices (2001)

Curie temperatures in ferromagnetic semiconductor superlattices are calculated self-consistently within mean-field theory and the effective bond orbital model of the superlattice band structure. Assuming a null valence-band offset and a constant average hole density of ${10}^{20}{\mathrm{cm}}^{\mathrm{\ensuremath{-}}3},$ the Curie temperature for a GaAs/GaMnAs ``digital alloy'' superlattice is found to be enhanced over its value in a bulk GaMnAs alloy with the same average Mn fraction. This enhancement results from the formation of a hole potential well, induced by the exchange interactions, in the vicinity of the thin magnetic layer. We further show that much larger enhancements may be possible in structures incorporating an Al(Ga)As nonmagnetic barrier layer having a large valence-band offset relative to GaMnAs. This structure creates a much deeper well that much more effectively confines the hole wave functions to the vicinity of the layers with the high Mn concentrations.
In Vitro Analysis of the Butyrolactone Autoregulator Receptor Protein (FarA) of Streptomyces lavendulae FRI-5 Reveals that FarA Acts as a DNA-Binding Transcriptional Regulator That Controls Its Own Synthesis (1999)

FarA of Streptomyces lavendulae FRI-5 is a specific receptor protein for IM-2, a butyrolactone autoregulator that controls the production of a blue pigment and the nucleoside antibiotics showdomycin and minimycin. Gel shift assays demonstrated that FarA binds to the farA upstream region and that this binding is abolished in the presence of IM-2. The FarA binding sequence was localized by DNase I footprinting to a 28-bp sequence located approximately 70 bp upstream of the farA translational start site. High-resolution S1 nuclease mapping of farA transcripts revealed a putative transcription start site, located at an A residue positioned 64 bp upstream from the farA translation start codon and 4 bp downstream from an Escherichia coli sigma(70)-like -10 recognition region. The FarA-binding sequence overlaps this -10 region and contains the farA transcription initiation site, suggesting that FarA acts as a repressor that, in the absence of IM-2, represses transcription of farA.
Solidification/stabilization of arsenic: Effects of arsenic speciation (1996)

Abstract Chemical identity of arsenic compounds subjected to solidification/stabilization (S/S) is a major factor in determining eventual leachability from the treated material. When several arsenic compounds were treated with portland cement under the same conditions, Toxicity Characteristic Leaching Procedure (TCLP) leachability of arsenic after 28 days of cure ranged from 510 mg/L for arsanilic acid to 1.7 mg/L for sodium arsenate. The arsenic compounds also have major effects on cement hydration reactions, as shown in solid‐state NMR spectra, but there is not a direct correlation between degree of hydration in the matrix and arsenic leachability; indeed, the most leachable arsenic compound studied, arsanilic acid, shows the least effect on cement hydration. A commercial organoarsenic fungicide waste was treated with portland cement alone and in the presence of tetramethylammonium bentonite. Inclusion of the organoclay reduced arsenic leachability by a factor of 5–6.
Slow display (2010)

How can we show our 16 megapixel photos from our latest trip on a digital display? How can we create screens that are visible in direct sunlight as well as complete darkness? How can we create large displays that consume less than 2W of power? How can we create design tools for digital decal application and intuitive-computer aided modeling?
Understanding Polymorphic Phase Transformation Behavior during Growth of Nanocrystalline Aggregates:  Insights from TiO<sub>2</sub> (2000)

To understand the impact of particle size on phase stability and phase transformation during growth of nanocrystalline aggregates we conducted experiments using titania (TiO2) samples consisting of nanocrystalline anatase (46.7 wt %, 5.1 nm) and brookite (53.3 wt %, 8.1 nm). Reactions were studied isochronally at reaction times of 2 h in the temperature range 598−1023 K and isothermally at 723, 853, and 973 K by X-ray diffraction (XRD). A numerical deconvolution method was developed to separate overlapping XRD peaks, and an analytical method for determining phase contents of anatase, brookite, and rutile from XRD data was established. Results show that, in contrast to previous studies, anatase in our samples transforms to brookite and/or rutile before brookite transforms to rutile. Thermodynamic and kinetic analyses further support this conclusion. For general titania samples, the transformation sequence among anatase and brookite depends on the initial particle sizes of anatase and brookite, since particle sizes determine the thermodynamic phase stability at ultrafine sizes. These results highlight extremely important size-dependent behavior that may be expected in other nanocrystalline systems where multiple polymorphs are possible.
Prevalence of Premature Ejaculation: A Global and Regional Perspective (2005)

The effort to determine the global burden of premature ejaculation (PE) has been impeded by the lack of a clear and universally accepted definition of the condition. Current diagnostic criteria are variable and rely, to a large degree, on subjective measurements. Moreover, the absence of a clear consensus on what constitutes a normal ejaculatory latency has impeded research into the prevalence of PE, although evidence is gradually accruing that may make this definition easier. Perception of "normal" ejaculatory latency varies by country and can differ when assessed either by the patient or their partner. Despite these limitations, information from the Global Study of Sexual Attitudes and Behaviors and other sources suggests a global prevalence of PE of approximately 30% across all age groups. The etiology underpinning this prevalence remains to be clarified, but current evidence reflects a shift from psychogenic theories to more neurobiological bases. While elucidation of the etiology of PE will undoubtedly aid the development of more effective therapies, it is clear that, whatever the cause of the condition, it is associated with a significant burden on psychological and overall health.
Variability in reference levels for Deauville classifications applied to lymphoma patients examined with 18F-FDG-PET/CT (2017)

Aim: To develop and validate a convolutional neural network (CNN) based method for automated quantification of reference levels in liver and mediastinum (blood pool) for the Deauville therapy response classification using FDG-PET/CT in lymphoma patients. Methods: CNNs were trained to segment the liver and the mediastinum, defined as the thoracic part of the aorta, in CT images from 81 consecutive lymphoma patients, who had undergone FDG-PET/CT examinations. Trained image readers segmented the liver and aorta manually in each of the CT images and these segmentations together with the CT images were used to train the CNN. After the training process, the CNN method was applied to a separate validation group consisting of six consecutive lymphoma patients (17-82 years, 3 female). First, the liver and mediastinum were automatically segmented in the CT images. Second, voxels in the corresponding FDG-PET images, which were localized in the liver and mediastinum, were selected and the median standard uptake value (SUV) was calculated. The CNN based analysis was compared to corresponding manual segmentations by two experienced radiologists. The Dice index was used to analyse the overlap between the segmentations by the CNN and the two radiologists. A Dice index of 1.00 indicates perfect matching.Results: The mean Dice indices for the comparison between CNN based liver segmentations and those of the two radiologists in the validation group were 0.95 and 0.95. A corresponding comparison between the two radiologists also resulted in a Dice index of 0.95. The mean liver volumes were 1,752ml, 1,757ml and 1,768ml for the CNN and two radiologists, respectively. The median SUV for the liver was on average 1.8 and the differences between median SUV based on CNN and manual segmentations were less or equal to 0.1. The mean Dice indices for the mediastinum were 0.80, 0.83 (CNN vs radiologists) and 0.86 (comparing the two radiologists). The mean mediastinum (aorta) volumes were 147ml, 140ml and 125ml for the CNN andtwo radiologists, respectively. The median SUV for the mediastinum was on average 1.4 and the differences between median SUV based on CNN and manual segmentations were less or equal to 0.14. Conclusion: A CNN based method for automated quantification of reference levels in liver and mediastinum show good agreement with results obtained by experienced radiologists, who manually segmented the CT images. This is a first and promising step towards a completely objective treatment response evaluation in patients with lymphoma based on FDG-PET/CT.
Model predictive control of blood glucose in type I diabetics using subcutaneous glucose measurements (2002)

A constrained model predictive controller is implemented on a simulated type I diabetic patient. A Kalman filter is used to estimate the blood glucose concentration based on a subcutaneous glucose measurement. The model predictive controller returns blood glucose to normoglycemic ranges when subjected to a meal disturbance. The settling time is similar to that of a non-diabetic.
Semisynthetic Versus Real-World Sonar Training Data for the Classification of Mine-Like Objects (2014)

The detection of mine-like objects (MLOs) in sidescan sonar (SSS) imagery continues to be a challenging task. In practice, subject matter experts tediously analyze images searching for MLOs. In the literature, there are many attempts at automated target recognition (ATR) to detect the MLOs. This paper focuses on the classifiers that use computer vision and machine learning approaches. These techniques require large amounts of data, which is often prohibitive. For this reason, the use of synthetic and semisynthetic data sets for training and testing is commonplace. This paper shows how a simple semisynthetic data creation scheme can be used to pretest these data-hungry training algorithms to determine what features are of value. The paper provides real-world testing and training data sets in addition to the semisynthetic training and testing data sets. The paper considers the Haar-like and local binary pattern (LBP) features with boosting, showing improvements in performance with real classifiers over semisynthetic classifiers and improvements in performance as semisynthetic data set size increases.
Fifty years of Monte Carlo simulations for medical physics (2006)

Monte Carlo techniques have become ubiquitous in medical physics over the last 50 years with a doubling of papers on the subject every 5 years between the first PMB paper in 1967 and 2000 when the numbers levelled off. While recognizing the many other roles that Monte Carlo techniques have played in medical physics, this review emphasizes techniques for electron-photon transport simulations. The broad range of codes available is mentioned but there is special emphasis on the EGS4/EGSnrc code system which the author has helped develop for 25 years. The importance of the 1987 Erice Summer School on Monte Carlo techniques is highlighted. As an illustrative example of the role Monte Carlo techniques have played, the history of the correction for wall attenuation and scatter in an ion chamber is presented as it demonstrates the interplay between a specific problem and the development of tools to solve the problem which in turn leads to applications in other areas.
Miniscopes in Gastroenterological Endoscopy - Inspection of the Gallbladder and the Biliary and Pancreatic Duct Systems in Autopsy Specimens (1988)

This report describes a newly available endoscopic system, the purpose of which is to inspect the common bile duct, gallbladder, cystic duct and the pancreatic duct with the aid of retrograde endoscopy. A miniscope examination of the gallbladder was carried out in eight out of ten autopsy specimens, and the entire pancreatic duct was inspected in nine out of ten specimens after successful transpapillary catheterisation. The procedure described in this paper opens up a new diagnostic and therapeutic approach to the gallbladder, biliary tree and the pancreatic duct.