gebhart/patrepeval huggingface dataset:
Unfolding ofPlasmodium falciparumTriosephosphate Isomerase in Urea and Guanidinium Chloride:  Evidence for a Novel Disulfide Exchange Reaction in a Covalently Cross-Linked Mutant (1998)

The conformational stability of Plasmodium falciparum triosephosphate isomerase (TIMWT) enzyme has been investigated in urea and guanidinium chloride (GdmCl) solutions using circular dichroism, fluorescence, and size-exclusion chromatography. The dimeric enzyme is remarkably stable in urea solutions. It retains considerable secondary, tertiary, and quaternary structure even in 8 M urea. In contrast, the unfolding transition is complete by 2.4 M GdmCl. Although the secondary as well as the tertiary interactions melt before the perturbation of the quaternary structure, these studies imply that the dissociation of the dimer into monomers ultimately leads to the collapse of the structure, suggesting that the interfacial interactions play a major role in determining multimeric protein stability. The Cm(urea)/Cm(GdmCl) ratio (where Cm is the concentration of the denaturant required at the transition midpoint) is unusually high for triosephosphate isomerase as compared to other monomeric and dimeric proteins. A disulfide cross-linked mutant protein (Y74C) engineered to form two disulfide cross-links across the interface (13-74') and (13'-74) is dramatically destablized in urea. The unfolding transition is complete by 6 M urea and involves a novel mechanism of dimer dissociation through intramolecular thiol-disulfide exchange.
The effects of vitamin A on cells of innate immunity in vitro (2013)

Retinoid treatment is suggested to promote development of inflammatory bowel disease, although preclinical studies are not supportive. We evaluated the effect of retinoids on cytokine response in in vitro-differentiated human dendritic cells (ivDCs) and macrophages (ivMACs) derived from healthy human donors and in cultured human THP-1 cells. Effect on human intestinal epithelial cell integrity was also assessed. Each cell type was incubated (±lipopolysaccharide [LPS]) with all-trans retinoic acid (ATRA), 13-cis-RA (isotretinoin) and 4-oxo-13-cis-RA. Cytokine analysis was performed by array analysis. Cultured human endothelial colorectal adenocarcinoma (Caco-2) cells were incubated with these retinoids and media analyzed for leakage by spectrofluorometric analysis. ATRA consistently and significantly inhibited LPS-induced release of the pro-inflammatory cytokines tumor necrosis factor, interleukin (IL)-6, macrophage inflammatory protein (MIP)-1α and MIP-1β. All retinoids tested stimulated release of the anti-inflammatory cytokines granulocyte-macrophage colony-stimulating factor and IL-10, and also monocyte chemotactic protein-1, vascular endothelial growth factor and eotaxin-1. Incubation with retinoids did not significantly alter the permeability of Caco-2 monolayers. Pre-treatment of each cell type with retinoids promoted an anti-inflammatory cytokine profile with only minimal effect on intestinal epithelial cell permeability; consistent with in vivo studies.
Observation of many-phonon stimulated Raman scattering and related cascaded nonlinear-laser effects in monoclinic LaBO2MoO4 single crystals (2007)

Large single crystals of the compound LaBO 2 MoO 4 , undoped and doped with Nd 3+ ions, were grown. Their multi-wavelength Stokes and anti-Stokes picosecond generation, nonlinear-laser effects, and neodymium IR luminescence were investigated. We classify these crystals as a promising material for Raman frequency converters and gain medium for solid-state lasers.
BioS: a New Tool for Biopotential Experiments (2007)

BioS (Bio-potential Study), a novel environment for Biopotential analysis is here proposed. It provides the processing of biopotentials of any number of channels distributed with different geometry. It includes several features as data importing, data visualization (1D, 2D, 3D), preprocessing (frequency & saturation filtering, statistical analysis), spatio-temporal processing (power spectrum analysis, nonlinear analysis, independent component analysis both in the spatial and time domain). BioS, also, provides a user-friendly Graphic User Interface designed to allow all user to speed up data analysis experiments.
Using Source Models in Speech Separation (2007)

Discusses work on using ASR models to recognize mixtures and recovering spatial information in reverb.
PUSHING PROPYLENE PRODUCTION (2004)

Human alpha 2-macroglobulin can be reversibly dissociated by Cd2+ at low ionic strength in half-molecules which retain their ability to bind tightly plasmin and chymotrypsin. The steady state kinetic parameters of these proteinases towards chromogenic substrates when bound to half-molecules are not greatly different from those determined for these enzymes linked to whole alpha 2M molecules. Cd2+ can also induce the dissociation of plasmin- and chymotrypsin - alpha 2M complexes into proteinase-alpha 2M half-molecule conjugates. These results, taken with the fact that monomeric units of alpha 2M cannot bind these proteinases, strongly suggest that each active site of alpha 2M consists in a specific arrangement of two monomeric units linked by disulfide bridges.
Prospring in Private Practice (1988)

Cincinnati Center for Improved Communication, John G. Clark. Ph.D.. and Associates, Cincinnati. Ohio
Increased E4 Activity in Mice Leads to Ubiquitin-containing Aggregates and Degeneration of Hypothalamic Neurons Resulting in Obesity (2010)

Obesity has become a serious worldwide public health problem. Although neural degeneration in specific brain regions has been suggested to contribute to obesity phenotype in humans, a causal relationship between these two conditions has not been demonstrated experimentally. We now show that E4B (also known as UFD2a), a mammalian ubiquitin chain elongation factor (E4), induces the formation of intracellular aggregates positive for ubiquitin and the adaptor protein p62 when overexpressed in cultured cells or the brain. Mice transgenic for E4B manifested neural degeneration in association with aggregate formation, and they exhibited functional impairment specifically in a subset of hypothalamic neurons that regulate food intake and energy expenditure, resulting in development of hyperphagic obesity and related metabolic abnormalities. The neural pathology of E4B transgenic mice was similar to that of human neurodegenerative diseases associated with the formation of intracellular ubiquitin-positive deposits, indicating the existence of a link between such diseases and obesity and related metabolic disorders. Our findings thus provide experimental evidence for a role of hypothalamic neurodegeneration in obesity, and the E4B transgenic mouse should prove to be a useful animal model for studies of the relationship between neurodegenerative diseases and obesity.
Quantification of daidzein and furanocoumarin conjugates of Psoralea cinerea L. (Leguminosae) (1997)

1 illus. 2 tables 2 graph.
Increased adenosine A2A receptors in the brain of Parkinson's disease patients with dyskinesias (2004)

Brain adenosine A2A receptors have recently attracted considerable attention because of their interaction with the dopaminergic system and as potential targets for Parkinson's disease pharmacotherapy. Post mortem adenosine A2A receptor mRNA and [3H]SCH 58261- specific binding to adenosine A2A receptor were studied in the brain of Parkinson's disease patients using in situ hybridization and receptor binding autoradiography, respectively. Fourteen levodopa-treated Parkinson's disease patients, of which seven developed dyskinesias and seven did not, were compared with nine controls. Nigrostriatal denervation was similar between dyskinetic and non-dyskinetic Parkinson's disease patients, as assessed with catecholamine concentrations and [125I]RTI-121-specific binding to dopamine transporters. A2A receptor mRNA levels (+129%; P < 0.01) and [3H]SCH 58261-specific binding (+32%, P < 0.01) were increased in the putamen (lateral and medial) of dyskinetic patients compared with controls. The increase of adenosine A2A receptor mRNA in dyskinetic Parkinson's disease patients was also significant compared with non-dyskinetic Parkinson's disease patients (+60%; P < 0.05) in the lateral putamen. Moreover, [3H]SCH 58261-specific binding to adenosine A2A receptors was increased in the external globus pallidus (+24%; P < 0.001) of Parkinson's disease patients compared with controls, regardless of the dyskinesigenic response to levodopa. No change of adenosine A2A receptors was observed in the caudate nucleus, whereas adenosine A2A receptor protein and mRNA levels in the internal globus pallidus were not different from background. These findings suggest that increased synthesis of adenosine A2A receptors in striatopallidal pathway neurons is associated with the development of dyskinesias following long-term levodopa therapy in Parkinson's disease.
Diet Related Courtship Success in the Oriental Fruit Moth, Grapholita molesta (Tortricidae) (1989)

Males reared on artificial diet as larvae or starved as adults contained lower amounts of the behaviourally most active courtship pheromone component ethyl trans-cinnamate, but no difference in mating success between apple-reared and diet-reared males could be demonstrated. -from Authors
Efficient frequency-domain sample selection for recovering limited-support images (2003)

An image whose region of support is smaller than its bounding rectangle can, in principle, be reconstructed from a subset of the Nyquist samples. However, determining such a sampling set that gives a stable reconstruction is a difficult and computationally intensive problem. An algorithm is developed for determining periodic nonuniform sampling patterns that is orders of magnitude faster than existing algorithms. The speedup is achieved by using a sequential selection algorithm and heuristic metrics for the quality of sampling sets that are fast to compute, as opposed to the more rigorous linear algebraic metrics that have been used previously. Simulations show that the sampling sets determined using the new algorithm give image reconstructions that are of accuracy comparable with those determined by other slower algorithms.
HIV-1 variants are archived throughout infection and persist in the reservoir (2020)

The HIV-1 reservoir consists of latently infected cells that persist despite antiretroviral therapy (ART). Elucidating the proviral genetic composition of the reservoir, particularly in the context of pre-therapy viral diversity, is therefore important to understanding reservoir formation and the persistence of latently infected cells. Here we investigate reservoir proviral variants from 13 Zambian acutely-infected individuals with additional pre-therapy sampling for a unique comparison to the ART-naïve quasispecies. We identified complete transmitted/founder (TF) viruses from seroconversion plasma samples, and additionally amplified and sequenced HIV-1 from plasma obtained one year post-infection and just prior to ART initiation. While the majority of proviral variants in the reservoir were most closely related to viral variants from the latest pre-therapy time point, we also identified reservoir proviral variants dating to or near the time of infection, and to intermediate time points between infection and treatment initiation. Reservoir proviral variants differing by five or fewer nucleotide changes from the TF virus persisted during treatment in five individuals, including proviral variants that exactly matched the TF in two individuals, one of whom had remained ART-naïve for more than six years. Proviral variants during treatment were significantly less divergent from the TF virus than plasma variants present at the last ART-naïve time point. These findings indicate that reservoir proviral variants are archived throughout infection, recapitulating much of the viral diversity that arises throughout untreated HIV-1 infection, and strategies to target and reduce the reservoir must therefore permit for the clearance of proviruses encompassing this extensive diversity.
Subcellular Distribution of Mouse Mevalonate Pyrophosphate Decarboxylase (2003)

Mevalonate pyrophosphate decarboxylase (MPD) is considered to be a cytosolic protein. Recently, other groups reported that MPD is mostly located in the peroxisomes. In this study, we examined whether the expression of MPD in mice depends on the proliferation of peroxisomes, and whether MPD is predominantly located in the peroxisomes or the cytosol of mice. No increase in the protein level of MPD was observed in the crude extract of the livers of mice administered with peroxisome proliferative drugs. The result suggests that the expression of MPD is independent of the proliferation of peroxisomes, and may be maintained via a specific regulatory mechanism, different from the regulation of the expression of peroxisome proliferator-activated receptor alpha. When the subcellular distribution of MPD in mouse melanoma (B16F10) cells was examined by cell fractionation, MPD was detected in the cytosol of B16F10 cells, but not in the peroxisomes. In permeabilized B16F10 cells treated with digitonin, which lack cytosolic enzymes, 80% and 20% of MPD, 75% and 25% of lactate dehydrogenase, or 2% and 98% of catalase, existed in the medium and in the cell, respectively. From these results, it indicated that MPD was predominantly located in the cytosol and did not exist in the peroxisomes of B16F10 cells.
Hybrid Analysis of Human Exposure from Base-Station Antennas in Underground Environment (2006)

SUMMARY In this study we have employed an effective technique for dosimetric analyses of base station antennas in an underground environment. The technique combines a ray-tracing method and the finitedifference time-domain (FDTD) method to calculate the specific absorption rate (SAR) in the human body. The ray-tracing method was applied to evaluate the incident fields in relation to the exposed subject in a threedimensional space, while the FDTD method was used to calculate the detailed SAR distributions in the human body. A scenario under an underground passage with the installation of a top-loaded monopole antenna was analyzed to investigate the relationship between the actual antenna exposure and a plane-wave exposure. The results show that the plane-wave exposure overestimated the whole-body average SAR in most cases, although this was not always true for peak SAR. The finding implies not only the usefulness of the present uniform-exposure-based reference level for the whole-body average SAR evaluation but also the necessity of modeling actual underground environment for high-precision local peak SAR
Plasma induced damage on sub-0.5 μm MOSFETs using a CMOS driver as input protection (2002)

Plasma charging effects on a sub-0.5 /spl mu/m CMOS process with 90 /spl Aring/ gate oxide and triple layer metal was studied for plasma induced damage with diode and ESD protection schemes. The n and p channel transistors in a CMOS driver enabled discharging of positive and negative charges using the source-drain region as diodes. This study also showed that the p channel devices are more sensitive to plasma charging than n channels. The diode protection provided to the transistor gate reduced the magnitude of plasma process induced damage, but a large antenna ratio on protected gates was observed to produce measurable shifts in V/sub t/ and I/sub dsat/.
Tendon Xanthomas in Familial Hypercholesterolemia Are Associated With Cardiovascular Risk Independently of the Low-Density Lipoprotein Receptor Gene Mutation (2005)

TX are associated with cardiovascular risk factors and higher CVD, indicating that their detection indicates the need for more aggressive lipid-lowering intervention.
Inspection challenges for triple patterning at sub-14 nm nodes with broadband plasma inspection platforms (2015)

With the continuous shrink of technology nodes, lithography becomes more and more challenging. At 20 nm node, double patterning technology (DPT) was the usual way of achieving the fine device structures. Until EUV is available as a high volume manufacturing (HVM) solution, DPT or triple patterning technology (TPT) will be required to sustain scaling. However, as the industry goes forward with scaling, for sub-14 nm nodes the chip manufacturers are anticipating three or four masks per layer. Exposing the patterns separately allows the spacing or pitch of the structures to be reduced by a factor of two (or more for triple/quadruple patterning) while increasing the metrology and inspection challenges. As with many of the previous geometry shrinks, there will be the usual concerns about yield and reliability. In order to control and predict yield for sub-14 nm nodes we show that design information when integrated with inspection platforms can help predict design weak spots efficiently. It is the purpose of this paper to elucidate some of the inspection challenges and solutions for sub 14nm device structures.
How does exercise intensity and type affect equine distal tarsal subchondral bone thickness? (2007)

Adaptation of osteochondral tissues is based on the strains experienced during exercise at each location within the joint. Different exercise intensities and types may induce particular site-specific strains, influencing osteochondral adaptation and potentially predisposing to injury. Our hypotheses were that patterns of equine distal tarsal subchondral bone (SCB) thickness relate to the type and intensity of exercise, and that high-intensity exercise leads to site-specific increases in thickness. SCB thickness was measured at defined dorsal and plantar locations on magnetic resonance images of cadaver tarsi collected from horses with a history of low [general purpose (n=20) and horse walker (n=6)] or high [elite competition (n=12), race training (n=15), and treadmill training (n=4)] exercise intensity. SCB thickness was compared between sites within each exercise group and between exercise groups. SCB thickness in elite competition and race training, but not treadmill training, was greater than low-intensity exercise. For general purpose horses, lateral SCB thickness was greater than medial throughout. Horse walker exercise led to relatively thicker lateral and medial SCB compared with the midline. Elite competition was associated with increased SCB thickness of the proximal small tarsal bones medially and the distal bones laterally. For race training and treadmill training, there were minimal differences between sites overall, although the lateral aspect was greater than medial, and medial greater than midline at a few sites for race training. In conclusion, different types of high-intensity exercise were associated with different patterns of SCB thickness across the joints from medial to lateral and proximal to distal, indicating that both exercise intensity and type of exercise affect the SCB response at any particular site within the equine distal tarsal joints.
Effect of Non‐Surgical Periodontal Therapy on C‐Telopeptide Pyridinoline Cross‐Links (ICTP) and Interleukin‐1 Levels (2001)

A single episode of non-surgical mechanical therapy did not significantly reduce biochemical markers associated with bone resorption in patients exhibiting chronic periodontitis. Future longitudinal studies are warranted to specifically evaluate the relationship between C-telopeptide pyridinoline cross-links and periodontal disease progression.
Prospective Evaluation of Arthroscopic Stabilization of Acute, Initial Anterior Shoulder Dislocations in Young Athletes (2001)

From March 1992 to November 1998, 57 patients sustained 58 acute, initial, traumatic anterior shoulder dislocations at the United States Military Academy. Six patients selected nonoperative treatment. Three patients underwent primary open repair after diagnostic arthroscopy revealed no Bankart lesion amenable to repair with the bioabsorbable tissue tack. The remaining 48 patients with 49 anterior dislocations were treated with arthroscopic primary repair. There were 45 men and 3 women with an average age of 20 years (range, 17 to 23) and an average follow-up of 37 months (range, 24 to 60). The average Rowe score was 92 (range, 30 to 100). The average single assessment numeric evaluation patient rating was 95.5% (range, 50% to 100%). The average Short Form-36 score (physical function) for the stable shoulders was 99 (range, 95 to 100). Forty-three shoulders remained stable (88%). There were six failures (12%). Factors associated with failure included a history of bilateral shoulder instability, a 2+ sulcus sign, and poor capsulolabral tissue at the time of repair. All patients with stable shoulders returned to their preinjury levels of athletic activity. With follow-up of 5 years, we have observed significantly better results compared with nonoperative treatment in young, active adults at the United States Military Academy.
Placement of PMUs to Enable Bad Data Detection in State Estimation (2006)

As the phasor measurement units (PMUs) start populating the substations, their benefits for different power system application functions are being debated. One of these functions is the bad data processing that is commonly integrated into the state estimation. Bad data detection is closely related to the measurement redundancy in that bad data appearing in critical measurements cannot be detected. Such measurements, however, can be transformed into redundant measurements by adding few PMUs at strategic locations. In this paper, it will be shown that with few extra PMUs, the bad data detection and identification capability of a given system can be drastically improved. Description of the placement algorithm is given, and case studies carried out on different size test systems are presented
Dual-modality Optical Spectroscopy and Optical Coherence Tomography Ablation Catheter for Intraprocedural Assessment of Cardiac Lesion Development (2018)

We report the development of a dual-modal ablation catheter incorporating optical coherence tomography (OCT) and optical spectroscopy (OS) for improved assessment of acute endocardial ablation lesions. Validation is performed in ex vivo and in vivo porcine experimental models.
Dihydropyridine Fluorophores Allow for Specific Detection of Human Antibodies in Serum (2018)

Antigen recognition by antibodies plays an important role in human biology and in the development of diseases. This interaction provides a basis for multiple diagnostic assays and is a guide for treatments. We have developed dihydropyridine-based fluorophores that form stable complexes with double-stranded DNA and upon recognition of the antibodies to DNA (anti-DNA) provide an optical response. The fluorophores described herein have advantageous optical properties compared to those of the currently available dyes making them valuable for research and clinical diagnostics. By studying a series of novel fluorophores, crucial parameters for the design were established, providing the required sensitivity and specificity in the detection of antibodies. Using these DNA-fluorophore complexes in a direct immunofluorescence assay, antibodies to DNA are specifically detected in 80 patients diagnosed with an autoimmune disease, systemic lupus erythematosus. Positivity indicated by emission change of α-(4'-<i>O</i>-methoxyphenyl)-2-furyl dihydropyridine strongly correlates with other disease biomarkers and autoimmune arthritis.
Performance of Colorless, Non-directional ROADMs with Modular Client-side Fiber Cross-connects (2012)

We study the impact of partitioning client-side fiber cross-connects on the blocking performance of colorless, non-directional ROADM based dynamic optical networks. Simulations show that smaller fiber cross-connects (16×16, 48×48) can achieve low blocking.
Regulation of the IgE response (2010)

IgE was the last of the five immunoglobulin classes to be discovered and is the antibody that is responsible for much of human type I allergic disease. This review summarizes recent developments with respect to control of IgE synthesis with an emphasis on Th2 (T helper 2) control and regulation using IgE Fc receptors.