gebhart/patrepeval huggingface dataset:
Dominant Active Alleles of <i>RIM101</i>(<i>PRR2</i>) Bypass the pH Restriction on Filamentation of <i>Candida albicans</i> (2000)

Morphological development of the fungal pathogen Candida albicans is profoundly affected by ambient pH. Acidic pH restricts growth to the yeast form, whereas neutral pH permits development of the filamentous form. Superimposed on the pH restriction is a temperature requirement of approximately 37 degrees C for filamentation. The role of pH in development was investigated by selecting revertants of phr2Delta mutants that had gained the ability to grow at acid pH. The extragenic suppressors in two independent revertants were identified as nonsense mutations in the pH response regulator RIM101 (PRR2) that resulted in a carboxy-terminal truncation of the open reading frame. These dominant active alleles conferred the ability to filament at acidic pH, to express PHR1, an alkaline-expressed gene, at acidic pH, and to repress the acid-expressed gene PHR2. It was also observed that both the wild-type and mutant alleles could act as multicopy suppressors of the temperature restriction on filamentation, allowing extensive filamentation at 29 degrees C. The ability of the activated alleles to promote filamentation was dependent upon the developmental regulator EFG1. The results suggest that RIM101 is responsible for the pH dependence of hyphal development.
Increasing the power efficiency of an IEEE802.11a Power Amplifier (2005)

OFDM modulation is extensively used in many applications. However, it also exhibits high peak-to-average power ratios (PAPR) requiring the associated transmit amplifier to have a very large linear region. This linear amplifier does therefore have poor power efficiency. To reduce the PAPR, cupping and filtering was carried out at baseband. This paper investigates the impact that clipping has on the resultant power efficiency and BER. The simulations show that when the input back-off (IBO) dynamically controls the input average power in every OFDM symbol, for a 64-subcarrier QPSK OFDM signal, the power efficiency can be improved by 55% without increasing the bit error rate.
Variation in Yield, Starch, and Protein of Dry Pea Grown Across Montana (2017)

Core Ideas Dry pea yield, protein, and resistant starch varied greatly across Montana. Yield and protein were mainly determined by environments. Resistant starch is controlled by genetics to a great extent. Effects of drought index, growth period, seed size, and seed weight on yield, protein, and starch were analyzed. Pea ( Pisum sativum L.) has long been an important component of the human diet, providing an excellent source of protein. In addition to its protein, pea starch, especially resistant starch (RS), has received an extensive attention in food industries in recent years. We evaluated nine pea cultivars varying in cotyledon color, grain weight, maturity group, and phenology planted at five locations with diverse climatic conditions across Montana in 2013 and 2014 to assess genetic and environmental factors affecting their yield, protein, RS, and total starch (TS). Grain yield varied from 982 to 5951 kg ha −1 , RS content ranged from 5 to 53 g kg −1 , and protein from 159 to 251 g kg −1 . Statistical analysis showed that environment was the most important driving factor in grain yield, protein, and TS determination whereas RS content was mainly determined by cultivar. Drought at all phenological stages reduced pea yield and different cultivars tended to respond differently. Yield was positively correlated with protein, implying a potential to select/breed a cultivar with higher yield and protein. Protein was negatively correlated with TS, thus protein‐ or starch‐type cultivars may be bred for different end users. Compared to other cultivars tested, DS Admiral was the most promising one with above average yield, protein, and RS.
The use of CCD pixel binning in PIV measurements (2009)

In this work, we study the effects of a CCD camera binning option, which increases camera frame rate throughput at the expense of loosing spatial resolution, on the particle image velocimetry measurements. The camera frame rate defines upper bound on a speed of a flow a PIV system can measure. We have carried our experiments on the real images of the 1 mum size fluorescence polystyrene microparticles placed onto a thick quartz glass plate and illuminated with the high-power LED. The in-plane images were captured at various CCD binning factors and the distances between particles were calculated using cross-correlation analysis with a sub-pixel interpolation scheme based on the Gaussian regression. As a result of this study, we show that despite the decrease in the spatial resolution, the advantages of the pixel binning, such as increase in sensitivity and the total full frame rate, can be useful for LED illuminated PIV measurements, especially in laminar fluid flows.
Dissociated glucocorticoids with anti-inflammatory potential repress interleukin-6 gene expression by a nuclear factor-kappaB-dependent mechanism. (1999)

Synthetic glucocorticoids (GCs) remain among the most effective agents for the management of chronic inflammatory diseases. However, major side effects severely limit their therapeutic use. Physiologic and therapeutic activities of GCs are mediated by a nuclear receptor belonging to a superfamily of ligand-inducible transcription factors that, in addition to directly regulating their cognate gene programs, can also mutually interfere with other signaling pathways. We recently identified selective ligands of the glucocorticoid receptor that dissociate transactivation from activator protein 1 transrepression, and most importantly retain in vivo anti-inflammatory activity. To further document the mechanisms of action sustaining the observed in vivo activity, we report here on the interference of dissociated GCs with nuclear factor kappaB (NF-kappaB)-driven gene activation. We show that dissociated GCs repress tumor necrosis factor-induced interleukin-6 gene expression by an NF-kappaB-dependent mechanism, without changing the expression level of inhibitor kappaB. The DNA-binding activity of induced NF-kappaB also remained unchanged after stimulation of cells with the various compounds. Evidence for a direct nuclear mechanism of action was obtained by analysis of cell lines constitutively expressing a fusion protein between the DNA-binding domain of the yeast Gal4 protein and the transactivating p65 subunit of NF-kappaB, which was able to efficiently repress a Gal4-dependent luciferase reporter gene upon addition of the dissociated compounds. We therefore conclude that, in addition to dissociating transactivation from activator protein 1 transrepression, dissociated GCs mediate inhibition of NF-kappaB signaling by a mechanism that is independent of inhibitor kappaB induction.
Ventricular non-compaction a frequently ignored finding? (2007)

The investigation by Kohli and his colleagues1 reveals startling findings. In a population of almost 200 patients referred to a dedicated clinic investigating cardiac failure in the UK, almost one-quarter were found to satisfy the currently accepted diagnostic criteria for ventricular non-compaction, or hypertrabeculation to give the finding its alternative name.2 Significantly, these criteria were also satisfied by five of 60 control subjects, of whom 30 were black, with four of these showing the features of non-compaction. The authors rightly conclude that the current criteria used for diagnosis of non-compaction are too sensitive, particularly amongst the black population. The alternative conclusion is that non-compaction, or hypertrabeculation, is simply a variant of normal maturation of the ventricular myocardium, with only the most severe forms producing a pathological entity. Both interpretations beg the question as to why the entity is now being recognized with such frequency, having come to clinical attention as recently as 1990.3

It is also the case that examples of what we would now call non-compaction were recognized prior to the important study of Chin et al. 3 Dusek and his colleagues,4 in 1975, are usually credited with being the first to describe ‘spongy myocardium’, but most of the hearts they described had associated congenital malformations, and not all would … 

*Corresponding author. Tel: +44 20 7905 2295, Fax: +44 20 7905 2324. Email: r.anderson{at}ich.ucl.ac.uk
Large, Tunable Liquid Crystal Pretilt Achieved by Enhanced Out-of-Plane Reorientation of Azodye Thin Films (2020)

In-plane, or azimuthal, photo-reorientation of azodye films using polarized exposure makes them promising alignment layers for a host of liquid crystal (LC) applications beyond displays including beam steering, q-plates, liquid crystal elastomer origami, and control of active matter. Out-of-plane, or polar, reorientation of azodye films, which dictates the liquid crystal pretilt, has received far less attention. Spatial control over the full polar and azimuthal orientation enables the generation of complex patterns that have broad interests and applications. In this paper, we describe an enhanced out-of-plane reorientation in Brilliant Yellow films utilizing a two-step exposure and demonstrate a liquid crystal pretilt angle that is tunable over a range of 0–33° with the associated anchoring strength of the alignment layer being unaffected by the inclusion of a pretilt. We report an order of magnitude increase in both amplitude and tunability of the pretilt angle in terms of previous results for single photoalignment films. This is a significant result for liquid crystal applications because it offers a simple, scalable, single-component solution with the potential to provide three-dimensional (3-D) patternability of the LC director at the surface.
The Northfield Experiments (1992)

The Northfield Experiments took place at Hollymoor Hospital, Northfield, Birmingham, during World War II. The first experiment was conducted by Bion & Rickman. The second evolved gradually; many people contributed to its success, including Foulkes, Main and Bridger. The experiments were an important landmark in the evolution of theory and practice in group psychotherapy and in the therapeutic community movement. They were not carried out solely as responses to the need for mass treatment of neurotic disorders among army personnel; antecedent factors, the theoretical orientation of the practitioners and the nature of army life were equally important. The two experiments differed in pace and in recognition of the needs of higher-order systems, particularly the military hierarchy. They shared many underlying concepts, including responsibility to society, the therapeutic use of groups (including the hospital community) and an emphasis on process. Lessons learned at Northfield remain relevant to the practice of psychiatry today.
Sir John Soane's House and Museum model (1997)

This paper describes a model of Sir John Soane's House and Museum which was executed as an independent study during the authors' Third Year at Yale University School of Architecture. Having visited the building independently of each other and having returned with a similar mystified curiosity, they initiated the project as an attempt to further understand the house by developing an analytical method of representation specific to it. The model was constructed from drawings prepared by the authors which synthesised information from available published documentation and drawings obtained from the Soane Museum Library.
Context dependent language model adaptation (2008)

Language models (LMs) are often constructed by building multiple component LMs that are combined using interpolation weights.By tuning these interpolation weights, using either perplexity or discriminative approaches, it is possible to adapt LMs to a particular task.In this work, improved LM adaptation is achieved by introducing context dependent interpolation weights.An important part of this new approach is obtaining robust estimation.Two schemes for this are described.The first is based on MAP estimation, where either global interpolation weights are used as priors, or context dependent interpolation priors obtained from the training data.The second scheme uses class based contexts to determine the interpolation weights.Both schemes are evaluated using unsupervised LM adaptation on a Mandarin broadcast transcription task.Consistent gains in perplexity using context dependent, rather than global, weights are observed as well as reductions in character error rate.
Deletions in the hepatitis B virus small envelope protein: effect on assembly and secretion of surface antigen particles (1992)

The small envelope S protein of hepatitis B virus carrying the surface antigen has the unique property of mobilizing cellular lipids into empty envelope particles which are secreted from mammalian cells. We studied the biogenesis of such particles using site-directed mutagenesis. In this study, we describe the effect of deletions in the N-terminal hydrophobic and hydrophilic domains of the S protein. Whereas short overlapping deletions of hydrophilic sequences flanking the first hydrophobic domain were tolerated, larger deletions of the same sequences were not. Conversely, the hydrophilic region preceding the second hydrophobic domain was not permissive for even short deletions. Deletion of part or all of the first hydrophobic domain also completely blocked secretion, confirming that the entire apolar region serves an essential function. Most of the secretion-defective deletion mutants still entered the secretory pathway and translocated at least the second hydrophilic domain across the membrane of the endoplasmic reticulum. These mutants appeared to remain arrested in a membrane-associated configuration in the endoplasmic reticulum or the cis-Golgi compartment but preserved their capacity for oligomerization with the wild-type S protein. While secretion of wild-type S protein was specifically blocked by the formation of intracellularly retained mixed envelope aggregates, secretion of an unrelated protein (interleukin 9) was completely unaffected.
Interleukin-6 Is a Useful Marker for Early Prediction of the Severity of Acute Pancreatitis (1997)

Twelve patients with acute pancreatitis admitted to our department between January 1993 and December 1994 were studied prospectively and classified into two groups (severe group, five patients; mild group, seven patients), according to the criteria for grading severity of acute pancreatitis proposed by the Research Committee for Intractable Diseases of the Pancreas, Japanese Ministry of Health and Welfare (1990). To evaluate markers for early estimation of the severity of acute pancreatitis, we measured serum changes in various parameters. In the severe group interleukin-6 (IL-6) levels were increased significantly 5, 24, 72, and 120 h after the onset (p < 0.01), compared with the mild group. C-reactive protein (CRP), thrombin antithrombin III, and alpha 2-plasmin inhibitor plasmin complex levels were significantly increased only at the 72-h time point. Peak values of interleukin-8 (IL-8) and soluble human E selectin were observed at 5 and 72 h, respectively, after the onset. There was a significant correlation between IL-6 at 5 h and both pancreatic secretory trypsin inhibitor (r = 0.85) and CRP (r = 0.94) at 72 h. We therefore conclude that IL-6 is a useful marker for assessment of the severity of acute pancreatitis in its early stages.
Chemical modification of porcine kidney aminopeptidase P indicates the involvement of two critical histidine residues (1996)

Aminopeptidase P (AP-P), purified to homogeneity from porcine kidney membranes, was completely inactivated by treatment with 0.2 mM diethylpyrocarbonate (DEP) at pH 7.0. Treatment of the modified enzyme with 20 mM hydroxylamine resulted in recovery of AP-P activity. The differential absorption of native and modified AP-P at 240 mm showed that DEP modified two histidyl residues per mol of AP-P. The substrates, bradykinin(1-5) and Gly-Pro-Hyp, and also the inhibitor, apstatin, could protect against DEP inactivation. These results suggest that histidine residues are critical for AP-P activity.
Optical Constants of Cubic GaN, AlN, and AlGaN Alloys (2000)

We have used spectroscopic ellipsometry to investigate, for the first time, the optical constants of cubic GaN, AlN, and AlGaN alloy epitaxial layers grown by molecular beam epitaxy. The refractive indices of cubic AlGaN were found to decrease with increasing Al content, as expected from the empirical observation that the refractive index decreases with increasing direct bandgap energy. In the transparent wavelength region, the refractive indices of cubic AlGaN with lower Al contents are somewhat larger than those of hexagonal modifications, while with higher Al contents, the refractive indices of cubic AlGaN and hexagonal AlGaN are almost equal. We also found that the direct bandgap energies of cubic AlGaN show a parabolic dependence on the Al content.
Induced Pluripotent Stem Cells: To Model, To Treat (2011)

The development of the ability to convert somatic cells into induced pluripotent stem cells (iPSCs) through expression of a small combination of transcription factors is a major breakthrough in the field of stem cell research. It has raised the possibilities of providing personalized cells for the study and treatment of numerous human diseases. In recent years, iPSCs have been derived from patients of a large variety of disorders. Here, the progresses that has been made in establishing iPSC-based disease models and the potentials of iPSC technology for personalized medicine, drug discovery and cell therapy are reviewed. The challenges from iPSC technology are also briefly discussed.
Quantifying the impact of learning algorithm parameter tuning (2006)

The impact of learning algorithm optimization by means of parameter tuning is studied. To do this, two quality attributes, sensitivity and classification performance, are investigated, and two metrics for quantifying each of these attributes are suggested. Using these metrics, a systematic comparison has been performed between four induction algorithms on eight data sets. The results indicate that parameter tuning is often more important than the choice of algorithm and there does not seem to be a trade-off between the two quality attributes. Moreover, the study provides quantitative support to the assertion that some algorithms are more robust than others with respect to parameter configuration. Finally, it is briefly described how the quality attributes and their metrics could be used for algorithm selection in a systematic way.
Magnetic colloid mediated recovery of cadmium ions from an aqueous solution using a flow-through hybrid field-gradient device (2002)

A flow-through hybrid magnetic field gradient device that uses polymer-coated magnetic particles as a mobile solid affinity phase was developed for the removal of cadmium ions from an aqueous solution. The device consists of a horizontal glass tube rotating about its axis, with repeating hybrid magnetic units positioned along the outside of the tube. Two arrangements for the magnetic units were used. In the first configuration, four hybrid pairs were distributed axially—each pair consisted of an alternating current carrying solenoid, followed by four azimuthally distributed permanent magnets that rotate with the chamber. In the second configuration, all four solenoids were placed first, followed by the four sets of four azimuthally distributed permanent magnets. The polymer-coated (ion exchange resin) magnetic particles and the cadmium-ion containing solution flow concurrently through the tube. The azimuthally flowing alternating current in the solenoid introduces axial and radial forces as well as a torque on the magnetic particles, permitting more contact between the particles and the surrounding solution, and allowing cadmium ions to absorb efficiently on to the particle surfaces. The particles are then immobilized on the chamber walls, while the depleted cadmium solution flows through the end of the tube. The 1–10 μm diameter magnetic particles with iron oxide nanoparticles embedded within a quaternary ammonium cellulose matrix (MagaCell-Q, Cortex Biochem, San Leandro, CA) at a starting concentration of 0.5 mg particles/mL were used as the mobile solid support. The feed consisted of a 10.0 mg/L cadmium sulfate solution, at a flow rate of 35 mL/min. The depleted cadmium solution was collected and used as feed for a second stage, where it contacted with a fresh batch of magnetic particles. This was repeated for a third stage. For the first arrangement, the Cd(II) concentration at the exit of the third stage dropped to 0.97 mg/L. The second configuration produced a final Cd(II) concentration of 0.68 mg/L. For the first arrangement, three stage processing resulted in an overall ∼90% w/w cadmium removal, and the second configuration removed ∼94% of the original cadmium ions. While the specific system studied here consists of removal of cadmium ions from an aqueous solution, the general principle of magnetic colloidal separation using this flow-through device can be exploited for other environmental and biotechnological applications where large volumes of sample must be processed with high capture efficiency.
Identification and Characterization of a Novel Microsomal Enzyme with Glutathione-dependent Transferase and Peroxidase Activities (1997)

5-Lipoxygenase activating protein (FLAP), leukotriene-C4 (LTC4) synthase, and microsomal glutathione S-transferase II (microsomal GST-II) are all members of a common gene family that may also include microsomal GST-I. The present work describes the identification and characterization of a novel member of this family termed microsomal glutathione S-transferase III (microsomal GST-III). The open reading frame encodes a 16.5-kDa protein with a calculated pI of 10.2. Microsomal GST-III has 36, 27, 22, and 20% amino acid identity to microsomal GST-II, LTC4 synthase, microsomal GST-I, and FLAP, respectively. Microsomal GST-III also has a similar hydrophobicity pattern to FLAP, LTC4 synthase, and microsomal GST-I. Fluorescent in situ hybridization mapped microsomal GST-III to chromosomal localization 1q23. Like microsomal GST-II, microsomal GST-III has a wide tissue distribution (at the mRNA level) and is predominantly expressed in human heart, skeletal muscle, and adrenal cortex, and it is also found in brain, placenta, liver, and kidney tissues. Expression of microsomal GST-III mRNA was also detected in several glandular tissues such as pancreas, thyroid, testis, and ovary. In contrast, microsomal GST-III mRNA expression was very low (if any) in lung, thymus, and peripheral blood leukocytes. Microsomal GST-III protein was expressed in a baculovirus insect cell system, and microsomes from Sf9 cells containing either microsomal GST-II or microsomal GST-III were both found to possess glutathione-dependent peroxidase activity as shown by their ability to reduce 5-HPETE to 5-HETE in the presence of reduced glutathione. The apparent Km of 5-HPETE was determined to be approximately 7 microM for microsomal GST-II and 21 microM for microsomal GST-III. Microsomal GST-III was also found to catalyze the production of LTC4 from LTA4 and reduced glutathione. Based on these catalytic activities it is proposed that this novel membrane protein is a member of the microsomal glutathione S-transferase super family, which also includes microsomal GST-I, LTC4 synthase, FLAP, and microsomal GST-II.
Studies on the taxonomy of the Myxobacterales II. Polyangium and the demise of the Sorangiaceae (1970)

The order Polyangiaceae is redefined to include only those myxobacters with cylindrical cells, It includes all organisms formerly included in the Sorangiaceae and the genera Chondromyces and Synangium. A new family, the Cystobacteraceae, type species Cystobacter fuscus (Polyangium fuscum), is erected for sporangial myxobacters with tapered vegetative cells. It includes the genera Stigmatella and Podangium in addition to Cystobacter.