gebhart/patrepeval huggingface dataset:
Plasma functionalization of poly(vinyl alcohol) hydrogel for cell adhesion enhancement (2013)

Tailoring the interface interactions between a biomaterial and the surrounding tissue is a capital aspect to consider for the design of medical devices. Poly(vinyl alcohol) (PVA) hydrogels present suitable mechanical properties for various biological substitutes, however the lack of cell adhesion on their surface is often a problem. The common approach is to incorporate biomolecules, either by blending or coupling. But these modifications disrupt PVA intra- and intermolecular interactions leading therefore to a loss of its original mechanical properties. In this work, surface modification by glow discharge plasma, technique known to modify only the surface without altering the bulk properties, has been investigated to promote cell attachment on PVA substrates. N2/H2 microwave plasma treatment has been performed, and the chemical composition of PVA surface has been investigated. X-ray photoelectron and Fourier transform infrared analyses on the plasma-treated films revealed the presence of carbonyl and nitrogen species, including amine and amide groups, while the main structure of PVA was unchanged. Plasma modification induced an increase in the PVA surface wettability with no significant change in surface roughness. In contrast to untreated PVA, plasma-modified films allowed successful culture of mouse fibroblasts and human endothelial cells. These results evidenced that the grafting was stable after rehydration and that it displayed cell adhesive properties. Thus plasma amination of PVA is a promising approach to improve cell behavior on contact with synthetic hydrogels for tissue engineering.
Log-Based Pore Volume Compressibility Prediction—A Deepwater GoM Case Study (2005)

Abstract Pore Volume Compressibility (PVC) is one of the most important parameters for proceeding with project sanctioning. An accurate estimation of pore volume compressibility of reservoir rocks is essential for compaction evaluation, reservoir drive determination, reserves estimates, reservoir pressure maintenance, casing collapse analyses, and production forecasting. This information is then used in modeling the reservoir and calculating the economic value of the project. Thus, obtaining credible indications of this value early in the well evaluation process is invaluable. Unfortunately, this data is usually required long before a conventional core can be obtained and mechanical rock properties measured. Furthermore, cores are only available at discrete points along the wellbore requiring the data to be extrapolated to the missing sections. To accommodate the need for this data early in the project and to circumvent the short comings of core-based information gaps in the wellbore, a cost effective approach that utilizes common wireline data is used to obtain a continuous profile of the pore volume compressibility with depth shortly after wireline logging operations have concluded. The method employs a log-based mechanical property program that simulates triaxial loading to obtain static elastic moduli as well as rock strength. The resulting rock mechanical properties are then converted into their uniaxial strain equivalents and used to determine the pore volume compressibility. The process is repeated for several drawdown stages with the condition that the deformations are contained within elastic limits. This yields the complete reservoir compaction trend as a function of reservoir depletion. The log-based model was recently validated by comparing with lab-derived results from an offset well in deepwater Gulf of Mexico. The results indicate that the uniaxial pore volume compressibility obtained from the log-based method matches well with the results obtained in the laboratory. This fact suggests that the log-based approach should be utilized with a high degree of confidence to determine the PVC in the absence of core data, insufficient depth coverage of the cores, and/or to validate the core results.
Direct digital frequency synthesis of low-jitter clocks (2002)

The development of communication systems in the past years has increased the necessity to synthesize very accurate clocks. For example, in Digital Television (DTV) an audio data stream must be inserted into a video data stream, which implies that we must synchronize the audio clock with the video clock. According to one digital audio standard, the audio clock frequency is 5,6448 MHz, and with the PAL digital television standard, the video clock frequency is 35.46895 MHz. In this case, the division ratio is 112896/709379. Other division ratios are required with other DTV standards such as NTSC, SECAM or HDTV, and with other digital audio standard frequencies. Direct Digital Synthesis (DDS) is a popular technique that can be used to derive the audio frequency from the video frequency used as clock. A critical component of a DDS is its phase accumulator, which controls the DDS output frequency. The limited number of bits in the phase accumulator reduces its precision and its ability to express divide ratios defined with large integers. This will produce a phase error that accumulates with time to produce a low-band jitter in the output signal, which is particularly harmful when the output clock is used for synchronization purposes. This paper reviews some circuits found in the literature, which could be used to reduce the phase error given by a phase accumulator, and it presents a new phase correction technique which can give better results in terms of jitter, and which simplify design and implementation of practical DDS circuits.
Colour Image Transformations of Wireline Logs as a Medium for Sedimentary Profile Analysis (1988)

ABSTRACT Spontaneous potential and gamma-ray log profiles of sandstone-shale sequences express variations in shale content and indicate trends in relative grain size. The generalized log shapes of sandstone units are widely used as diagnostic aids in the recognition of depositional environments. The conventional method of shape characterization is highly qualitative, as is reflected in its terminology of and cylinder. In a new approach, the log curve derivatives are transformed to a colour image that gives immediate expression to curve shapes. A compound colour log strip is generated by assigning the colours green and red to the first and second derivatives. The basic shape descriptions of bell, funnel and cylinder are matched by distinctive dominant colour motifs, which can be recognized on the colour image. Since log shapes occur at all scales and in compound hierarchies, the colour processing is applied as a multiple pass procedure, using windows of increasing dimension. Cubic polynomial filters are run for each window size to extract smoothed values and the first two derivatives. The resultant colour image is a spectrogram that is sensitive to log shape at a variety of scales. LA TRANSFORMATION DE DIAGRAPHIES EN IMAGES DE COULEUR ET L'UTILISATION DE CES DERNIERES COMME MOYEN D'ANALYSE DE PROFILS SEDIMENTAIRES RESUME Les diagraphies par potentiel spontane et par rayons gamma de sequences gres/schiste refletent des variations dans la teneur en schiste et indiquent des tendances dans la granulometrie relative. Les formes generalisees des diagraphies de couches de gres sont frequemment utilisees comme guide dans l'identification des milieux sedimentaires. La methode conventionnelle qui consiste en l'identification des formes est tres qualitative, comme l'indiquent des termes tels que entonnoir et cylindre. Dans une nouvelle approche, les derivees des courbes diagraphiques sont transformees en une image de couleur qui exprime immediatement les formes des courbes. Une bande diagraphique composee en couleur est produite en assignant les couleurs vertes et rouges aux premieres et aux secondes derivees. La description des formes de base, c'est-a-dire la cloche, l'entonnoir et le cylindre est appareillee a des motifs distinctifs de couleurs dominantes, qui peuvent etre reconnus sur les images de couleur. Puisque les formes des courbes diagraphiques se retrouvent a toutes les echelles et en hierarchies composees, le developement des couleurs est une procedure a passages multiples, utilisant des fenetres aux dimensions croissantes. Des filtres cubiques polynomiaux sont employes pour chaque grandeur de fenetre afin d'en retirer des valeurs arrondies et les deux premieres derivees. L'image en couleur qui resulte est un spectrogramme qui est sensible a la forme des courbes de diagraphie a toute une gamme d'echelles. Traduit par Marc Charest
Effects of Maxwell‐Wagner polarization on soil complex dielectric permittivity under variable temperature and electrical conductivity (2006)

The presence of free charges and numerous discontinuities separating liquid, gas, and solid phases in partially saturated soils give rise to Maxwell‐Wagner polarization that may significantly affect bulk dielectric permittivity measurements. Evidence suggests a complex interplay shaping the response of low‐frequency (<100 MHz) dielectric permittivity to changes in ambient temperature and amount of ionic charges present in a wet soil. Model calculations based on the Maxwell‐Wagner‐Brugermann‐Hanai (MWBH) theory are supported by direct measurements using a network analyzer, showing an increase in soil bulk dielectric permittivity with increasing temperature and with higher bulk electrical conductivity at low frequency range (<100 MHz). Beyond a certain frequency the decrease in permittivity of free water becomes dominant and results in a decrease in soil bulk dielectric permittivity with increasing temperature. The value of this crossover frequency can be predicted as a function of solution electrical conductivity (EC) as confirmed in limited tests. The dielectric permittivity inferred from TDR waveform travel time analysis is not significantly influenced by the low frequency range of the dielectric spectrum. In contrast, dielectric permittivity sensors operating at frequencies lower than 100 MHz are likely to show significant sensitivity to factors affecting the Maxwell‐Wagner effect (temperature and electrical conductivity), hence requiring special care in measurement interpretation.
Comparison of Analytic Algorithms for Detecting Glaucomatous Visual Field Loss (1991)

The sensitivity and specificity of alternate analytic strategies for recognizing glaucomatous visual field loss from automated threshold perimetry (C-30-2 test of the Humphrey Field Analyzer) were compared among one eye each of 106 patients with glaucoma and 249 normal subjects. Algorithms included commercially available global indexes and cross-meridional differences (Statpac 1 and Statpac 2), as well as cross-meridional and cluster analyses that were developed independently for natural history studies and clinical trials. The sensitivity of most algorithms was high, except for those that used only diffuse loss as an indicator of abnormality. Specificity was acceptably high for all algorithms. Subjects who failed to meet the manufacturer's standard for reliability had much reduced specificity, but sensitivity was also affected. Algorithms that were based on any of the alternate definitions of localized reduction in retinal sensitivity performed equally well, which suggests that any of these approaches is useful in searching for glaucomatous visual loss as typified by this database. Availability, familiarity, and convenience may govern the selection of any one analytic approach for use in a particular setting.
Genotypic Differences in Sweet Cherry Fruit Size are Primarily a Function of Cell Number (2007)

Understanding the genetic control of fruit size in sweet cherry ( Prunus avium L.) is critical for maximizing fruit size and profitable fresh market production. In cherry, coordinated cycles of cell division and expansion of the carpel result in a fleshy mesocarp that adheres to a stony endocarp. How these structural changes are influenced by differing genetics and environments to result in differing fruit sizes is not known. Thus, the authors measured mesocarp cell length and cell number as components of fruit size. To determine the relative genotypic contribution, five sweet cherry cultivars ranging from ≈1 to 13 g fresh weight were evaluated. To determine the relative environmental contribution to fruit size, different-size fruit within the same genotype and from the same genotype grown in different environments were evaluated. Mesocarp cell number was the major contributor to the differences in fruit equatorial diameter among the five sweet cherry cultivars. The cultivars fell into three significantly different cell number classes: ≈28 cells, ≈45 cells, and ≈78 cells per radial mesocarp section. Furthermore, mesocarp cell number was remarkably stable and virtually unaffected by the environment as neither growing location nor physiological factors that reduced final fruit size significantly altered the cell numbers. Cell length was also significantly different among the cultivars, but failed to contribute to the overall difference in fruit size. Cell length was significantly influenced by the environment, indicating that cultural practices that maximize mesocarp cell size should be used to achieve a cultivar's fruit size potential.
GENETIC DIVERGENCE AND HYBRID SPECIATION (2007)

Although the evolutionary importance of natural hybridization has been debated for decades, it has become increasingly clear that hybridization plays a fundamental role in the evolution of many plant and animal taxa, sometimes resulting in the formation of entirely new species. Although some hybrid species retain the base chromosome number of their parents, others combine the full chromosomal complements of their progenitors. Hybrid speciation can thus produce two fundamentally different types of evolutionary lineages, yet relatively little is known about the factors influencing ploidy level in hybrid neospecies. We estimated genetic divergence between species pairs that have given rise to homoploid and polyploid hybrid species and found that divergence is significantly greater for the parents of polyploids, even after controlling for potentially confounding factors. Our data thus provide the first direct evidence in support of the notion that the extent of genomic divergence between hybridizing species influences the likelihood of diploid versus polyploid hybrid speciation.
Clonostachys rosea BAFC3874 as a Sclerotinia sclerotiorum antagonist: mechanisms involved and potential as a biocontrol agent (2011)

Clonostachys rosea BAFC3874 may be a good fungal biological control agent against S. sclerotiorum. In addition, we were also able to isolate and identify peptaibols, an unusual family of compounds in this genus of fungi.
Bond Dissociation Energies of the N−H Bond and Rate Constants for the Reaction with Alkyl, Alkoxyl, and Peroxyl Radicals of Phenothiazines and Related Compounds (1999)

The results of a detailed thermodynamic and kinetic investigation on the homolytic reactivity of phenothiazine, phenoxazine, and phenoselenazine, of several substituted phenothiazines, and of related tricyclic aromatic amines are reported. All these compounds give, by hydrogen atom abstraction from the N−H group, persistent aminyl radicals. Equilibration of each of these radicals with the parent amine and a reference compound having an easily abstractable hydrogen allowed us to determine, by using EPR spectroscopy, the N−H Bond Dissociation Energies (BDE) of the amines. These are characterized by low BDE values (in some cases lower than the O−H bond strength of α-tocopherol, i.e 78.3 kcal/mol) and therefore are very good hydrogen atom transfer reagents. To check the efficiency of tricyclic amines as antioxidants and as polymerization inhibitors, absolute rate constants were determined for their reaction with alkyl, alkoxyl, and peroxyl radicals by using competitive techniques in the first two cases and by autoxidation studies under controlled conditions in the last one. All amines have been found to be highly reactive toward these radicals which makes them very good autoxidation and polymerization inhibitors.
Evaluation of Streptococcus Pneumoniae-urinary Antigen Detection kit in Patients with Community Acquired Pneumonia (2002)

We evaluated a new rapid urinary antigen detection kit. NOW Streptococcus pneumoniae (Binax Inc., USA) that detected S. pneumoniae antigen by immunochromatographic membrane assay, with 66 Japanese adult patients of community acquired pneumonia. Twenty-two (33.3%) patients were found to be positive with the kit and S. pneumoniae was isolated from six patients (27.3%) of these 22 patients. S. pneumoniae was not isolated from eight of the 22 patients by blood or sputum culture. Analysis of clinical laboratory data showed that the levels of C-reactive protein (CRP) in the serum were significantly higher in the urine-antigen positive group than those in the urine-antigen negative group. There were no significant difference between the two groups including renal function, urinalysis, clinical symptom, and severity of pneumonia. Our study suggests that more cases of community acquired pneumonia are caused by S. pneumoniae than conventional tests can currently confirm. Since it is not technically complex, does not require equipment, and detects within as quickly as in 15 minutes, the S. pneumoniae urinary antigen kit is useful for rapid diagnosis of community acquired pneumonia in adults.
Variation of lateral doping as a field terminator for high-voltage power devices (1986)

In this brief a new concept for high-voltage planar junctions is presented. The necessary widening of the space-charge region at the junction surface is obtained by implantation through small openings in the oxide mask and subsequent drive-in, leading to a controlled smeared-out dopant distribution. Compared to other planar junctions, this concept also yields a gain in active chip area. Experimental results show the validity of the concept.
Definitions and Theories (1994)

‘Imperialism’ has always been a diffuse and emotive subject, even when there is broad agreement on what is being considered. Recent writings have done little to dispel this problem, and any discussion almost immediately exposes a semantic minefield. Words like ‘political’, ‘social’, ‘cultural’ or ‘economic’ are unavoidable, but, ordinary though they may be, they are difficult to use precisely; the boundaries between the things they describe are rarely clear-cut. Of course, all historians face this problem. Although many solve it to their own satisfaction by labelling themselves ‘political’ or ‘economic’ historians, historians of imperialism cannot specialise in quite the same way. The interest of the subject, as well as its frustrations, lies in the fact that it embraces all these subdivisions. Its study involves historians in attempting both to define and disentangle a wide range of social, political or economic processes, in order to understand their distinct function and perhaps their importance relative to each other. These tasks of identification, disentanglement arid assessment are unavoidably contentious. Even the title of this essay will raise the hackles of at least some readers! However, the problem of definition seems as appropriate a spot as any at which to start.
Iatrogenic Hyperinsulinemia, Not Hyperglycemia, Drives Insulin Resistance in Type 1 Diabetes as Revealed by Comparison With GCK-MODY (MODY2) (2019)

Although insulin resistance consistently occurs with type 1 diabetes, its predominant driver is uncertain. We therefore determined the relative contributions of hyperglycemia and iatrogenic hyperinsulinemia to insulin resistance using hyperinsulinemic-euglycemic clamps in three participant groups (<i>n</i> = 10/group) with differing insulinemia and glycemia: healthy control subjects (euinsulinemia and euglycemia), glucokinase-maturity-onset diabetes of the young (GCK-MODY; euinsulinemia and hyperglycemia), and type 1 diabetes (hyperinsulinemia and hyperglycemia matching GCK-MODY). We assessed the contribution of hyperglycemia by comparing insulin sensitivity in control and GCK-MODY and the contribution of hyperinsulinemia by comparing GCK-MODY and type 1 diabetes. Hemoglobin A<sub>1c</sub> was normal in control subjects and similarly elevated for type 1 diabetes and GCK-MODY. Basal insulin levels in control subjects and GCK-MODY were nearly equal but were 2.5-fold higher in type 1 diabetes. Low-dose insulin infusion suppressed endogenous glucose production similarly in all groups and suppressed nonesterified fatty acids similarly between control subjects and GCK-MODY, but to a lesser extent for type 1 diabetes. High-dose insulin infusion stimulated glucose disposal similarly in control subjects and GCK-MODY but was 29% and 22% less effective in type 1 diabetes, respectively. Multivariable linear regression showed that insulinemia-but not glycemia-was significantly associated with muscle insulin sensitivity. These data suggest that iatrogenic hyperinsulinemia predominates in driving insulin resistance in type 1 diabetes.
Active Serine Involved in the Stabilization of the Active Site Loop in the <i>Humicola </i><i>l</i><i>anuginosa</i> Lipase (1998)

We have investigated the binding properties of and dynamics in Humicola lanuginosa lipase (Hll) and the inactive mutant S146A (active Ser146 substituted with Ala) using fluorescence spectroscopy and molecular dynamics simulations, respectively. Hll and S146A show significantly different binding behavior for phosphatidylcholine (PC) and phosphatidylglycerol (PG) liposomes. Generally, higher binding affinity is observed for Hll than the S146A mutant. Furthermore, depending on the matrix, the addition of the transition state analogue benzene boronic acid increases the binding affinity of S146A, whereas only small changes are observed for Hll suggesting that the active site lid in the latter opens more easily and hence more lipase molecules are bound to the liposomes. These observations are in agreement with molecular dynamics simulations and subsequent essential dynamics analyses. The results reveal that the hinges of the active site lid are more flexible in the wild-type Hll than in S146A. In contrast, larger fluctuations are observed in the middle region of the active site loop in S146A than in Hll. These findings reveal that the single mutation (S146A) of the active site serine leads to substantial conformational alterations in the H. lanuginosa lipase and different binding affinities.
Structural Insights into Endobiotic Reactivation by Human Gut Microbiome-Encoded Sulfatases (2020)

Phase II drug metabolism inactivates xenobiotics and endobiotics through the addition of either a glucuronic acid or sulfate moiety prior to excretion, often via the gastrointestinal tract. While the human gut microbial β-glucuronidase enzymes that reactivate glucuronide conjugates in the intestines are becoming well characterized and even controlled by targeted inhibitors, the sulfatases encoded by the human gut microbiome have not been comprehensively examined. Gut microbial sulfatases are poised to reactivate xenobiotics and endobiotics, which are then capable of undergoing enterohepatic recirculation or exerting local effects on the gut epithelium. Here, using protein structure-guided methods, we identify 728 distinct microbiome-encoded sulfatase proteins from the 4.8 million unique proteins present in the Human Microbiome Project Stool Sample database and 1766 gut microbial sulfatases from the 9.9 million sequences in the Integrated Gene Catalogue. We purify a representative set of these sulfatases, elucidate crystal structures, and pinpoint unique structural motifs essential to endobiotic sulfate processing. Gut microbial sulfatases differentially process sulfated forms of the neurotransmitters serotonin and dopamine, and the hormones melatonin, estrone, dehydroepiandrosterone, and thyroxine in a manner dependent both on variabilities in active site architecture and on markedly distinct oligomeric states. Taken together, these data provide initial insights into the structural and functional diversity of gut microbial sulfatases, providing a path toward defining the roles these enzymes play in health and disease.