gebhart/patrepeval huggingface dataset:
Heart Rate Recovery After Exercise and Endothelial Function—Two Important Factors to Predict Cardiovascular Events (2005)

An attenuated heart rate recovery immediately after exercise, thought to be a marker of reduced parasympathetic activity, has been demonstrated to be an independent predictor of all-cause mortality in several large-scale studies; however, the mechanisms by which impaired heart rate recovery confers an increased risk of death are not clear. From clinical observation, vagal reactivation was thought to be the major determinant of the decrease in heart rate during the first 30 seconds of recovery, independent of age and the intensity of exercise; however, patients with attenuated heart rate recovery were also shown to have lower exercise workload, shorter exercise duration, lower numbers achieving 90% target heart rate, and even impaired endothelial function. This review focuses on the roles of heart rate recovery and endothelial function in predicting future mortality and their interaction.
Isolation of interstitial fluid from rat mammary tumors by a centrifugation method (2003)

Access to interstitial fluid is of fundamental importance to understand tumor transcapillary fluid balance, including the distribution of probes and therapeutic agents. Tumors were induced by gavage of 9,10-dimethyl-1,2-benzanthracene to rats, and fluid was isolated after anesthesia by exposing tissue to consecutive centrifugations from 27 to 6,800 g. The observed (51)Cr-EDTA (extracellular tracer) tissue fluid-to-plasma ratio obtained from whole tumor or from superficial tumor tissue by centrifugation at 27-424 g was not significantly different from 1.0 (0.92-0.99), suggesting an extracellular origin only. However, fluid collected from excised central tumor parts had a significantly lower ratio (0.66-0.77) for all imposed G forces, suggesting dilution by fluid deriving from a space unavailable for (51)Cr-EDTA. The colloid osmotic pressure in tumor fluid was generally higher than in fluid isolated from the subcutis, attributable to less selective capillaries and impaired lymphatic drainage in tumors. HPLC analysis of tumor fluid showed that low-molecular-weight macromolecules not present in arterial plasma were present in tumor fluid obtained by centrifugation and in venous blood draining the tumor, most likely representing proteins derived from tumor cells. We conclude that low-speed centrifugation may be a simple and reliable method to isolate interstitial fluid from tumors.
Characterizing Sequence Specificity of DNA Binding Proteins by Proximity Ligation (2006)

Proximity ligation is a recently established technique that can provide answers to questions about the concentration, localization, interactions, modifications and functions of proteins. The method enables sensitive protein measurements with a detection limit in the low femtomolar range in complex biological samples. In proximity ligation, the challenge of detecting specific proteins is converted to the analysis of specific DNA sequences. Proximity probes containing oligonucleotide extensions are designed to bind pairwise to target proteins, and to form amplifiable tag sequences upon ligation when brought in proximity. Protocols for the conversion of monoclonal or polyclonal antibodies into proximity probes through the attachment of oligonucleotide sequences are described in the thesis. In addition, the thesis describes the adaptation of the proximity ligation technology for detection of microbial pathogens, analysis of interactions between proteins and nucleic acids, and of inhibition of receptor-ligand interactions. Nucleic acid amplification allows specific detection of pathogens with single-copy sensitivity. There are many circumstances, however, when analysis of pathogen surface antigens or the antibody response can provide increased diagnostic value. Proximity ligation reactions were used to measure numbers of virus and bacteria by detection of viral or bacterial surface proteins. Detection sensitivities similar to those of nuclear acid-based detection reactions were achieved directly in infected samples for a parvovirus and for an intracellular bacterium. Biological processes are orchestrated by interactions of proteins with molecules in their environment, and investigations of interactions between proteins and other biomolecules are thus of great importance. Protocols were established for very specific and sensitive homogeneous-phase analysis of interactions between proteins and specific nucleic acid sequences. Finally, the proximity ligation mechanism was used to monitor interactions between VEGF-A and two of its receptors, VEGFR-1 and VEGFR-2, and to characterize the effects of agents disrupting this interaction.
Blackleg and soft rot of potatoes (1990)

PP-903; This circular provides information on the symptoms, cause and diseases management of blackleg and soft rot of potatoes
Design of a predictive targeting error simulator for MRI-guided prostate biopsy (2010)

Multi-parametric MRI is a new imaging modality superior in quality to Ultrasound (US) which is currently used in standard prostate biopsy procedures. Surface-based registration of the pre-operative and intra-operative prostate volumes is a simple alternative to side-step the challenges involved with deformable registration. However, segmentation errors inevitably introduced during prostate contouring spoil the registration and biopsy targeting accuracies. For the crucial purpose of validating this procedure, we introduce a fully interactive and customizable simulator which determines the resulting targeting errors of simulated registrations between prostate volumes given user-provided parameters for organ deformation, segmentation, and targeting. We present the workflow executed by the simulator in detail and discuss the parameters involved. We also present a segmentation error introduction algorithm, based on polar curves and natural cubic spline interpolation, which introduces statistically realistic contouring errors. One simulation, including all I/O and preparation for rendering, takes approximately 1 minute and 40 seconds to complete on a system with 3 GB of RAM and four Intel Core 2 Quad CPUs each with a speed of 2.40 GHz. Preliminary results of our simulation suggest the maximum tolerable segmentation error given the presence of a 5.0 mm wide small tumor is between 4-5 mm. We intend to validate these results via clinical trials as part of our ongoing work.
Multivariate classification of pulp NIR spectra for end-product properties using discrete wavelet transform with orthogonal signal correction (2014)

Natural material variations uncorrelated with physical properties of fibre networks hinder the development of robust calibration models by which to predict paper properties from on-line near-infrared (NIR) spectra of production pulps.
Integrin α v β 3 mediates rotavirus cell entry (2000)

Rotavirus strains differ in their need for sialic acid (SA) for initial binding to the cell surface; however, the existence of a postattachment cell receptor, common to most, if not all, rotavirus strains, has been proposed. In the present study, antibodies to the alpha(v) and beta(3) integrin subunits, and the alpha(v)beta(3) ligand, vitronectin, efficiently blocked the infectivity of the SA-dependent rhesus rotavirus RRV, its SA-independent variant nar3, and the neuraminidase-resistant human rotavirus strain Wa. Vitronectin and anti-beta(3) antibodies, however, did not block the binding of virus to cells, indicating that rotaviruses interact with alpha(v)beta(3) at a postbinding step, probably penetration. This interaction was shown to be independent of the tripeptide motif arginine-glycine-aspartic acid present in the natural ligands of this integrin. Transfection of CHO cells with alpha(v)beta(3) genes significantly increased their permissiveness to all three rotavirus strains, and the increment of virus infectivity was reverted by incubation of these cells either with antibodies to beta(3) or with vitronectin. These findings implicate alpha(v)beta(3) integrin as a cellular receptor common to neuraminidase-sensitive and neuraminidase-resistant rotaviruses, and support the hypothesis that this integrin could determine, at least in part, the cellular susceptibility to rotaviruses.
ÁGUA NO SOLO E CONVENIÊNCIA DE IRRIGAÇÃO DO ABACAXIZEIRO NO LITORAL NORTE DO RIO GRANDE DO SUL (1999)

Buscando subsídios para manejar o solo, de modo a maximizar a infiltração e o armazenamento de água, e avaliar se e quando a irrigação é recomendada para o abacaxizeiro cultivado no litoral norte do Rio Grande do Sul, foram usados dados de evapotranspiração (1980-1990) e temperatura (1956-1999) e o comportamento da precipitação (1931-1960), na Estação de Pesquisa e Produção de Maquiné - RS, foi comparado com as condições em que a irrigação é recomendada. No mesmo local, de agosto/1997 a outubro/1999, foi conduzido ensaio em solo franco- argiloso (Brunizem Avermelhado: Vila) e determinado em diferentes datas (28/08/97; 19/11/97; 18/12/97; 4/03/98; 18/ 05/99; 18/08/99), nas parcelas principais, o efeito de técnicas de preparo do solo (convencional, cultivo em faixas e plantio direto) e, nas subparcelas, as técnicas de plantio (sulco e chuço), sobre a umidade gravimétrica do solo. O preparo do solo e a técnica de plantio não afetaram a umidade gravimétrica do solo. Em Maquiné - RS, a precipitação anual (1659 mm) e as mensais de janeiro-173 mm, fevereiro-190 mm, março-178 mm, agosto-149 mm, setembro-167 mm, outubro-137 mm e dezembro-146 mm são maiores do que aquela tida como ideal para o abacaxizeiro (1000 -1500 mm/ ano ou 125 mm/mês), sendo, também, superior à. evapotranspiração (1091 mm/ano) nos onze meses do ano. Estes valores, comparados com as condições em que a irrigação é recomendada, indicam que, naquela região, o abacaxizeiro não precisaria ser irrigado. Porém, em algumas circunstâncias, pode ser necessário fazê-la, como no período de maior crescimento e demanda de água pela cultura (outubro a junho), especialmente nos meses de novembro-dezembro e abril-maio, que são os mais secos.
Effects of treatment intensification with hydroxyurea in HIV-infected patients with virologic suppression (2001)

Switching to IDV + ddI + d4T + HU in patients treated with IDV + ZDV + 3TC was associated with a worse outcome, principally because of drug toxicity.
Surgical Anatomy of the Hypoglossal Nerve for Facial Nerve Reconstruction Research in Swine (2014)

The hypoglossal-facial nerve interpositional nerve graft is a strategy for the treatment of facial paralysis.[1] [2] However, the mechanisms of double/dual innervation[2] and end-to-side neurorrhaphy[1] and the neural supercharge concept[2] remain unclear. To investigate these mechanisms, large animal models are necessary. Miniature swine are used as an experimental or preclinical model for facial surgery, including mandibular reconstruction,[3] distraction osteogenesis,[4] and face transplantation,[5] because the anatomical structure and size of miniature swine are similar to those in humans[6] [7] and because it is a suitable model for surgical training and the teaching of novel transplantation methods.[6]
Randomized Caches Can Be Pretty Useful to Hard Real-Time Systems (2015)

Cache randomization per se, and its viability for probabilistic timing analysis (PTA) of critical real-time systems, are receiving increasingly close attention from the scientific community and the industrial practitioners. In fact, the very notion of introducing randomness and probabilities in time-critical systems has caused strenuous debates owing to the apparent clash that this idea has with the strictly deterministic view traditionally held for those systems. A paper recently appeared in LITES (Reineke, J. (2014). Randomized Caches Considered Harmful in Hard Real-Time Systems. LITES, 1(1), 03:1-03:13.) provides a critical analysis of the weaknesses and risks entailed in using randomized caches in hard real-time systems. In order to provide the interested reader with a fuller, balanced appreciation of the subject matter, a critical analysis of the benefits brought about by that innovation should be provided also. This short paper addresses that need by revisiting the array of issues addressed in the cited work, in the light of the latest advances to the relevant state of the art. Accordingly, we show that the potential benefits of randomized caches do offset their limitations, causing them to be - when used in conjunction with PTA - a serious competitor to conventional designs.
Supplementary Data from Direct and Indirect Regulators of Epithelial–Mesenchymal Transition–Mediated Immunosuppression in Breast Carcinomas (2023)

&lt;p&gt;This file contains Supplementary Figures 1-8 and Supplementary Tables #1-2&lt;/p&gt;
Chronic cerebral hypoperfusion alters the CypA-EMMPRIN-gelatinase pathway: Implications for vascular dementia (2022)

Chronic cerebral hypoperfusion (CCH) is postulated to underlie multiple pathophysiological processes in vascular dementia (VaD), including extracellular matrix dysfunction. While several extracellular matrix proteins, namely cyclophilin A (CypA), extracellular matrix metalloproteinase inducer (EMMPRIN) and gelatinases (matrix metalloproteinases, MMP-2 and -9) have been investigated in acute stroke, their involvement in CCH and VaD remains unclear. In this study, CypA-EMMPRIN-gelatinase proteins were analysed in a clinical cohort of 36 aged, cognitively unimpaired subjects and 48 VaD patients, as well as in a bilateral carotid artery stenosis mouse model of CCH. Lower CypA and higher EMMPRIN levels were found in both VaD serum and CCH mouse brain. Furthermore, gelatinases were differentially altered in CCH mice and VaD patients, with significant MMP-2 increase in CCH brain and serum, whilst serum MMP-9 was elevated in VaD but reduced in CCH, suggesting complex CypA-EMMPRIN-gelatinase regulatory mechanisms. Interestingly, subjects with cortical infarcts had higher serum MMP-2, while white matter hyperintensities, cortical infarcts and lacunes were associated with higher serum MMP-9. Taken together, our data indicate that perturbations of CypA-EMMPRIN signalling may be associated with gelatinase-mediated vascular sequelae, highlighting the potential utility of the CypA-EMMPRIN-gelatinase pathway as clinical biomarkers and therapeutic targets in VaD.
The Relationship Between a History of High-risk and Destructive Behaviors and COVID-19 Infection: Preliminary Study (2022)

This preliminary study provides insights into how a history of destructive and risky behaviors influences infection susceptibility, offering possible explanations for why some persons may be more susceptible to COVID-19, potentially in relation to reduced adherence to prevention guidelines or not seeking vaccination.
Viscosity Measurements of Two Potential Deepwater Viscosity Standard Reference Fluids at High Temperature and High Pressure (2016)

This paper reports high-pressure viscosity measurements for Krytox GPL 102 lot K2391 and tris(2-ethylhexyl) trimellitate (TOTM). These two viscous liquids have recently been suggested as potential deepwater viscosity standard (DVS) reference fluids for high temperature, high pressure viscosity studies associated with oil production from ultradeep formations beneath the deepwaters of the Gulf of Mexico. The measurements are performed using a windowed, variable-volume, rolling-ball viscometer at pressures between 7 and 242 MPa and temperatures between 314 and 527 K with an expanded uncertainty of 3% at a 95% confidence level. The viscosity results are correlated using an empirical temperature/pressure-dependent function and a modified Vogel–Fulcher–Tammann (VFT) Equation. The present viscosity data for TOTM and Krytox GPL 102 lot K2391 are in good agreement with the available reported data in the literature at lower temperatures and pressures. The viscosity values of TOTM and Krytox GPL 102 lot K2391 are 9.5 mPa·s and 25 mPa·s, respectively, at 473 K and 200 MPa, whereas the desired DVS viscosity value at this condition is 20 mPa·s. Although the viscosity of Krytox GPL 102 lot K2391 is closer to the targeted value, a comparison of the present viscosity results with data obtained for lot K1537 indicates a very large lot-to-lot variation of the viscosity for this polydisperse perfluoropolyether oil, which represents a significant deficiency for a DVS.
Oblique incidence reflection imaging of live cells: improving contrast and image quality with an objective mask (2007)

Dry 40x and 60x microscope objectives were fitted with opaque black masks in order to eliminate reflection and scattering of light off the objective front lens assembly during oblique incidence reflection (OIR) microscopy. The reflection and scattering are shown to induce background glare that leads to degradation in the quality of the OIR images. Mask prototypes were designed and machined to snap onto the spring-loaded retractable front lens assembly of each objective. OIR images of live cells and normalized intensity line profiles are used to demonstrate that, if these alterations to the housing of the objective are implemented, background glare is significantly reduced with the 60x objective, and virtually eliminated with the 40x objective.
A class of linear-phase regular biorthogonal wavelets (1992)

A class of biorthogonal systems leading to linear-phase wavelets is presented. A notable feature of this structure is that the wavelets are derived from a filter bank where the lowpass analysis filter is constrained to be a halfband filter. The authors derive finite impulse response (FIR) biorthogonal solutions from a pair of Lagrange halfband filters. They also consider infinite impulse response (IIR) biorthogonal solutions based on a pair of zero-phase halfband filters derived from Butterworth halfband filters.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Scientific and logistical challenges in designing the CONTROL trial: recombinant factor VIIa in severe trauma patients with refractory bleeding (2009)

Research in acutely hemorrhaging trauma patients presents numerous scientific and ethical challenges. The methodology of the CONTROL study is presented as an example of how some of these challenges can be approached and managed, and of the pitfalls that may arise.
Turnover and Degradation of Mitochondria and Their Proteins (1980)

Very little is known about intracellular protein degradation. We have concentrated on mitochondrial proteins for simplicity. Even this is a complex problem and several mechanisms may be involved. The half-lives of mitochondrial proteins vary widely. Using immunological, autoradiographic (ferritin and iodine) and biochemical techniques we are delineating the extent of intra-mitochondrial protein degradation, lysosomal participation in that degradation, and signals controlling the overall process. As a high yielding dividend of our autoradiographic and immunological experiments it seems possible to clarify such important questions as whether there is a selective inactivation and turnover of mitochondria and their proteins. Calculations of autophagy and vacuoles, the concentration of mitochondrial proteins within lysosomes, as well as key aspects of the initiation and regulation of protein turnover and its elasto-plastic control are presented.
Diazo Coupling Method for Covalent Attachment of Proteins to Solid Substrates (2006)

We describe a process for covalently linking proteins to glass microscope slides and microbeads in a manner that optimizes the reactivity of the immobilized proteins and that is suitable for high-throughput microarray and flow cytometry analysis. The method involves the diazo coupling of proteins onto activated self-assembled monolayers formed from p-aminophenyl trimethoxysilane. Proteins immobilized by this method maintained bioactivity and produced enhanced levels of protein-protein interaction, low background fluorescence, and high selectivity. The binding of immobilized proteins to their specific binding partner was analyzed quantitatively and successfully correlated with solution concentrations. Diazotized surfaces bound more efficiently to proteins containing a hexahistidine tag than those without a his-tag. Moreover, significantly higher reactivity of the immobilized his-tagged proteins was observed on diazotized surfaces than on amine-terminated surfaces. Results suggest that his-tagged proteins are immobilized by reaction of the his-tag with the diazotized surface, thus offering the possibility for preferential orientation of covalently bound proteins.
An Extended Conical Intersection Seam Associated with a Manifold of Decay Paths: Excited-State Intramolecular Proton Transfer in O-Hydroxybenzaldehyde (2008)

O-Hydroxybenzaldehyde (OHBA) is a prototypical photoprotector exhibiting excited-state intramolecular proton transfer (ESIPT). Here we report how its photostability depends on an extended conical intersection seam associated with a manifold of decay paths. Thus, the photoreactivity of OHBA derives from a flat excited-state potential energy surface with barriers of only tenths of electronvolts between the reactant and several conical intersection structures that lead to different products: two isomers of a hydrogen-bonded intersection (HBI) that lead back to the enol reactant or to the tautomerized keto form in its Z conformation; an intersection (ZEI) that mediates the Z-E isomerization of the keto tautomer; and a twisted-pyramidalized one (TPI) that leads to an oxetene adduct. The intersection structures are connected to each other, forming a continuous seam, and the competition between the products depends on where the seam is accessed after the initial excitation. The overall picture must be also valid for the methyl salicylate and salicylic acid analogues of OHBA since it reflects the characteristics reported previously for MS and SA.
The non-invasive serum biomarker soluble Axl accurately detects advanced liver fibrosis and cirrhosis (2017)

Soluble Axl (sAxl) was recently shown to be strongly released into the blood during liver fibrogenesis and hepatocellular carcinoma suggesting sAxl as a biomarker of liver diseases. In this study we are the first to evaluate sAxl in human serum in comparison to Enhanced Liver Fibrosis (ELF) test and transient elastography (TE; Fibroscan) for its value to detect significant (F≥2), advanced fibrosis (F≥3), and cirrhosis (F4) in different liver disease etiologies and healthy controls. To properly determine the diagnostic accuracy of sAxl, a test cohort as well as a validation cohort was employed using liver biopsy as a reference method. Most notably, sAxl was confirmed to be an accurate biomarker of liver fibrosis and cirrhosis. Its accuracy was increased, if total serum albumin was added to build a sAxl/albumin ratio. Thereby an AUC of 0.763, 0.776, 0.826, and 0.832 was achieved corresponding to histological fibrosis stages F≥2, F≥3, F4 with liver biopsy as a reference method, and cirrhosis according to imaging techniques, respectively. With a cut-off of 1.29, a sensitivity, specificity, PPV, and NPV of 78.5%, 80.1%, 44%, 94.9% for the detection of cirrhosis was achieved. In comparison, ELF test and TE showed an AUC of 0.910, and 0.934, respectively, for the detection of cirrhosis. However, performance of TE was not possible in 14.4% of patients and both, ELF™ test and TE bear the disadvantage of high costs. In conclusion, the sAxl/albumin ratio is suggested as an accurate biomarker of liver fibrosis and cirrhosis. Due to its easy applicability and low costs it is suitable as screening parameter for significant to advanced liver fibrosis and cirrhosis, especially if TE is not available or not applicable.