gebhart/patrepeval huggingface dataset:
Ionization Efficiency (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Activator of Ca2+ -transport in the lens (1984)

It has been hypothesized that an activator of Ca-ATPase co-exists with Ca-ATPase in the mouse lens. Though the Ca-ATPase activity could be measured from mouse lens homogenate, its activity could not be determined in individual soluble and insoluble fractions. The Ca-ATPase activity, however, could be detected when an activator of this enzyme such as calmodulin was added to the lens insoluble fraction. This enzyme in the lens insoluble fraction was activated also by addition of soluble fraction. The Ca-ATPase in homogenate was inhibited by chlorpromazine and N-(6-amino-hexyl)-5-chloro-1-naphthalenesulfonamide (W-7), which are calmodulin antagonists. When the mouse lens was incubated with W-7, the degree of the lens opacification increased in relation to W-7 concentration.
Applying population-based threshold models to quantify and improve seed quality attributes (2022)

Achieving rapid and uniform stand establishment in crops requires a combination of high-quality seeds and appropriate environmental conditions. In particular, temperature and soil moisture (or water potential) are the major factors influencing germination in the field. In this chapter, we focus on the application of population-based threshold (PBT) models to characterize seed germination time courses and how environmental and technological inputs influence them. Viewing seed quality as a product of the behavior of populations of individual seeds is critical for understanding the causes and consequences of poor performance. Quantitatively characterizing seed population features enables their use in seed sorting and seed enhancement, and provides phenotypes for use in research, breeding, conservation and restoration. We believe that PBT models are essential tools to enable full utilization of new advances in seed technology to improve seed quality and enable successful stand establishment in agriculture or in natural settings.
Tracking of Individual Cell Cohorts in Asynchronous Saccharomyces cerevisiae Populations (1995)

A novel flow cytometric procedure has been developed with the aim to obtain the growth properties of individual Saccharomyces cerevisiae cells in asynchronous culture. The method is based on labeling of the cell surface with FITC-conjugated concanavalin A and detection of the single-cell fluorescence with flow cytometry after cell exposure to growth conditions. Because the formation of new cell wall material in budded cells is restricted to the bud tip, exposure of the stained cells to growth conditions results in three cell types: (i) stained cells, (ii) partially stained cells, and (iii) unstained cells. Analysis of the staining pattern over time permits the determination of the specific growth rate of the cell population, the length of the budded cell cycle phase, and the growth pattern during the cell cycle of newly formed, partially stained daughter cells. The procedure has been tested with yeast cell populations growing at different rates. The data suggest an exponential increase in the size of individual cells during the cell cycle, as reflected by the forward angle light scattering (FALS) signals. It has been found that the apparent single-cell specific cell size growth rates, determined by FALS intensity, are significantly lower than the specific growth rates of the overall population. This could indicate that the tracking of a cohort of cells is significantly perturbed by a distribution of staining levels of daughter cells at cell division and that FALS may not be a good indicator of the cell size.
Removal of SOST or blocking its product sclerostin rescues defects in the periodontitis mouse model (2015)

ABSTRACT Understanding periodontal ligament (PDL) biology and developing an effective treatment for bone and PDL damage due to periodontitis have been longstanding aims in dental medicine. Here, we first demonstrated by cell lineage tracing and mineral double‐labeling approaches that murine PDL progenitor cells display a 2‐ and 3‐fold higher mineral deposition rate than the periosteum and endosteum at the age of 4 weeks, respectively. We next proved that the pathologic changes in osteocytes (Ocys; changes from a spindle shape to round shape with a &gt;50% reduction in the dendrite number/length, and an increase in SOST) are the key pathologic factors responsible for bone and PDL damage in periostin‐null mice (a periodontitis animal model) using a newly developed 3‐dimensional FITC‐Imaris technique. Importantly, we proved that deleting the Sost gene (a potent inhibitor of WNT signaling) or blocking sclerostin function by using the mAb in this periodontitis model significantly restores bone and PDL defects ( n = 4‐5; P &lt; 0.05). Together, identification of the key contribution of the PDL in normal alveolar bone formation, the pathologic changes of the Ocys in periodontitis bone loss, and the novel link between sclerostin and Wnt signaling in the PDL will aid future drug development in the treatment of patients with periodontitis.—Ren, Y., Han, X., Ho, S. P., Harris, S. E., Cao, Z., Economides, A. N., Qin, C., Ke, H., Liu, M., Feng, J. Q. Removal of SOST or blocking its product sclerostin rescues defects in the periodontitis mouse model. FASEB J . 29, 2702‐2711 (2015). www.fasebj.org
Structural Brain Abnormalities in Youth With Psychosis Spectrum Symptoms (2016)

Structural brain abnormalities that have been commonly reported in adults with psychosis are present early in life in youth with PS symptoms and are not due to medication effects. Future longitudinal studies could use the presence of such abnormalities in conjunction with clinical presentation, cognitive profile, and genomics to predict risk and aid in stratification to guide early interventions.
All-optical signal Processing and applications within the esprit project DO/spl I.bar/ALL (2005)

This paper reviews the work performed under the European ESPRIT project DO/spl I.bar/ALL (Digital OpticAL Logic modules) spanning from advanced devices (semiconductor optical amplifiers) to all-optical modules (laser sources and gates) and from optical signal processing subsystems (packet clock recovery, optical write/store memory, and linear feedback shift register) to their integration in the application level for the demonstration of nontrivial logic functionality (all-optical bit-error-rate tester and a 2/spl times/2 exchange-bypass switch). The successful accomplishment of the project's goals has opened the road for the implementation of more complex ultra-high-speed all-optical signal processing circuits that are key elements for the realization of all-optical packet switching networks.
Study of Z boson production in pPb collisions at $\sqrt {s_{NN}} = 5.02$ TeV (2016)

The production of Z bosons in pPb collisions at sqrt(s[NN])=5.02 TeV is studied by the CMS experiment via the electron and muon decay channels. The inclusive cross section is compared to pp collision predictions, and found to scale with the number of elementary nucleon-nucleon collisions. The differential cross sections as a function of the Z boson rapidity and transverse momentum are measured. Though they are found to be consistent within uncertainty with theoretical predictions both with and without nuclear effects, the forward-backward asymmetry suggests the presence of nuclear effects at large rapidities. These results provide new data for constraining nuclear parton distribution functions.
Rough-Sea Deghosting Using Vertical Particle Velocity Field Approximations (2002)

P086 ROUGH-SEA DEGHOSTING USING VERTICAL PARTICLE VELOCITY FIELD APPROXIMATIONS Abstract TAGE RØSTEN 1 LASSE AMUNDSEN 1 JOHAN ROBERTSSON 2 and ED KRAGH 3 1 Statoil Research Centre Trondheim Norway 2 WesternGeco Product Technology Centre Oslo Norway 3 Schlumberger Cambridge Research Cambridge United Kingdom Two related methods for receiver ghost correction that can be applied to towed streamer data in rough-sea environments are compared. The two methods called method I (see Robertsson and Kragh 2001) and method II use different approximations for the vertical component of the particle velocity. Both methods take advantage of dense spatial sampling distance and require that
Highlights of the IEEE ISSCC 2014 Processors, Digital, Memory, Biomedical &amp; Next-Generation Systems Technologies, and Imagers, MEMS, Medical &amp; Displays Sessions (2014)

The 31 papers in this special issue were originally presented at the IEEE International Solid-State Circuits Conference (ISSCC), held in San Francisco, CA, USA, on February 9-13, 2014.
A novel immune competent murine hypertrophic scar contracture model: A tool to elucidate disease mechanism and develop new therapies (2014)

Hypertrophic scar (HSc) contraction following burn injury causes contractures. Contractures are painful and disfiguring. Current therapies are marginally effective. To study pathogenesis and develop new therapies, a murine model is needed. We have created a validated immune-competent murine HSc model. A third-degree burn was created on dorsum of C57BL/6 mice. Three days postburn, tissue was excised and grafted with ear skin. Graft contraction was analyzed and tissue harvested on different time points. Outcomes were compared with human condition to validate the model. To confirm graft survival, green fluorescent protein (GFP) mice were used, and histologic analysis was performed to differentiate between ear and back skin. Role of panniculus carnosus in contraction was analyzed. Cellularity was assessed with 4',6-diamidino-2-phenylindole. Collagen maturation was assessed with Picro-sirius red. Mast cells were stained with Toluidine blue. Macrophages were detected with F4/80 immune. Vascularity was assessed with CD31 immune. RNA for contractile proteins was detected by quantitative real-time polymerase chain reaction (qRT-PCR). Elastic moduli of skin and scar tissue were analyzed using a microstrain analyzer. Grafts contracted to ∼45% of their original size by day 14 and maintained their size. Grafting of GFP mouse skin onto wild-type mice, and analysis of dermal thickness and hair follicle density, confirmed graft survival. Interestingly, hair follicles disappeared after grafting and regenerated in ear skin configuration by day 30. Radiological analysis revealed that panniculus carnosus doesn't contribute to contraction. Microscopic analyses showed that grafts show increase in cellularity. Granulation tissue formed after day 3. Collagen analysis revealed increases in collagen maturation over time. CD31 stain revealed increased vascularity. Macrophages and mast cells were increased. qRT-PCR showed up-regulation of transforming growth factor beta, alpha smooth muscle actin, and rho-associated protein kinase 2 in HSc. Tensile testing revealed that human skin and scar tissues are tougher than mouse skin and scar tissues.
Effect of Flow and Surface Conditions on Human Lymphocyte Isolation Using Microfluidic Chambers (2004)

Phenotypically pure subpopulations of lymphocytes can provide valuable insights into the immune response to injury and disease. The isolation of these subpopulations presents unique challenges, particularly when preprocessing incubation to attach fluorescent or antibody tags is to be minimized. This paper examines the separation of T and B lymphocytes from mixtures using microfluidic chambers coated with antibodies, focusing on flow conditions and surface chemistry. The adhesion of both cell types decreases as shear stress increases irrespective of the surface chemistry. The incorporation of poly(ethylene glycol) chains along with the antibodies on the chamber surface is shown to significantly improve the reproducibility of cell adhesion and is thus an important part of the overall system design. Furthermore, this technique is shown to be an effective way of isolating highly pure subpopulations of lymphocytes from model mixtures, even when the target cell concentration is low.
Effect of Glucose—Insulin—Potassium Infusion on Mortality in Critical Care Settings: A Systematic Review and Meta‐Analysis (2009)

This study seeks to measure the treatment effect of glucose-insulin-potassium (GIK) infusion on mortality in critically ill patients. A systematic review of randomized controlled trials is conducted, comparing GIK treatment with standard care or placebo in critically ill adult patients. The primary outcome variable is mortality. Two authors independently extract data and assess study quality. The primary analysis is based on the random effects model to produce pooled odds ratios (ORs) with 95% confidence intervals (CIs). The search yields 1720 potential publications; 23 studies are included in the final analysis, providing a sample of 22,525 patients. The combined results demonstrate no heterogeneity (P=.57, I2=0%) and no effect on mortality (OR=1.02; 95% CI, 0.93-1.11) with GIK treatment. No experimental studies of shock or sepsis populations are identified. This meta-analysis finds that there is no mortality benefit to GIK infusion in critically ill patients; however, study populations are limited to acute myocardial infarction and cardiovascular surgery patients. No studies are identified using GIK in patients with septic shock or other forms of circulatory shock, providing an absence of evidence regarding the effect of GIK as a therapy in patients with shock.
Colloid structural forces in thin liquid films (2007)

In recent years the interest in non-DLVO forces has continuously increased because of their tremendous importance for dispersion stability. Colloid structural forces appear when thin liquid films are formed from concentrated suspension of monodisperse particles (micelles, latex particles, proteins). At low particle volume fraction these oscillatory forces degenerate into the depletion attraction. We propose simple semiempirical formulas describing the oscillatory structural force and energy. Their comparison with available experimental data and theoretical calculations shows a good agreement. Depending on the conditions (particle size, concentration, charge, etc.) the oscillatory structural forces may stabilize or destablize the thin films and dispersions (emulsions, suspensions). The role of different factors such asd temperature, electrolyte, and micelle concentrations, etc., are treated in a unified way and can be explained by the change of the effective particle volume fraction.
On observing shape from defocused images (2003)

Accommodation cues are measurable properties of an image that are associated with a change of the geometry of the imaging device. To what extent can three-dimensional shape be reconstructed using accommodation cues alone? This question is fundamental to the problem of reconstructing "shape from focus" (SFF) and "shape from defocus" (SFD) for applications in microscopy, image restoration (de-blurring) and visualization. We address it by studying the observability of accommodation cues in an analytical framework that is independent of the imaging device.
Designable Size Exclusion Chromatography Columns Based on Dendritic Polymer-Modified Porous Silica Particles (2003)

Dendritic polymer-modified porous silica particles prepared by a poly(amidoamine) (PAMAM) dendrimer synthesis reaction were characterized by elementary analysis (EA) and size exclusion chromatography (SEC). EA demonstrated the successful alternate growth of dendritic layers on the particles. The phased growth of polymer moieties by cascade reactions filled mesopores on the silica particles and decreased the exclusion limit molecular weight (Mlim) step by step. The density of the dendritic polymer moieties was affected by the reaction conditions, such as reaction time, temperature, and generation. The mesopore size on the particles, indicated as Mlim, was controlled by the grafting ratio, which could be adjusted by the reaction conditions. Furthermore, the elution behaviors of SEC standard samples with a Mw lower than the Mlim were governed by the local microstructure of the dendritic polymer moieties on the silica particles, most notably by polymer density. It was found that the local microstructure of the dendritic polymer moieties could also be controlled by the reaction conditions.
Hardware Implementation of Dynamic Synapse Neural Networks for Acoustic Sound Recognition (2006)

Identification of acoustic signals in noisy environments remains one of the most difficult of signal processing problems, and is a major obstacle to the high degree of accuracy and speed needed to identify suspicious sounds in high-security, high-safety environments. Given that pattern recognition involves fast identification of a set of fundamental features, the essence of the sound recognition problem is the competing needs for both high-dimensionality representations (necessary for accurate discrimination) and a reasonably limited feature space (necessary for rapid identification). We have previously developed an acoustic recognition capability using a novel biologically based Dynamic Synapse Neural Network (DSNN) technology. The DSNN based technology has been demonstrated to classify target sounds with a high degree of accuracy, even in high noise conditions. We have also developed an efficient training algorithm for DSNNs. In this paper we focus on extending the acoustic recognition capability of DSNNs to a hardware implementation and applying the new hardware (acoustic SENTRI) to the problem of gunshot recognition. SENTRI is based on Texas instrument TMS320C6713 DSK and a custom designed data acquisition board. An array of four microphones is attached to the board for sound input. A Time Delay Estimation algorithm (TDE) is employed for triangulation. In field-testing, the SENTRI classifies and localizes over 90% of the trained-for sounds. Performance for firecracker, starter pistol, 9mm, and 44 caliber, explosion / firing sounds was also tested.
An automated method for discriminating aneugen- vs. clastogen-induced micronuclei. (1998)

A flow cytometric (FCM) procedure for quantitating micronucleated reticulocytes in mouse peripheral blood samples was evaluated for its ability to discriminate between aneugen- and clastogen-induced micronuclei (MN). In this experiment, BALB/c mice were injected with 0.9% saline, the model clastogen methyl methanesulfonate (100 mg/kg bw) or the aneugen vincristine (0.2 mg/kg bw). Peripheral blood samples were collected 48 hr after injection and were subsequently fixed and stained for flow cytometric analysis. The staining method utilized FITC-conjugated anti-CD71 to differentially label reticulocytes, and the nucleic acid dye propidium iodide to resolve erythrocyte populations with and without micronuclei. The frequency of micronucleated reticulocytes was determined by analyzing 10,000 total reticulocytes per blood sample. A second analysis was performed on each sample whereby the propidium iodide associated fluorescent signals of 250 MN were collected and graphed as a single-parameter histogram. The histogram statistic "median channel" was recorded for each sample and provided a quantitative description of MN distribution according to DNA content. Cumulatively, the results of this study suggest that 1) flow cytometry can be employed to measure the incidence of MN resulting from clastogenic or aneugenic activity, and 2) MN resulting from aneugens can be discriminated from those arising spontaneously or from clastogen treatment based on flow cytometric analysis of DNA content.
Professionel udvikling af naturfagslærere – brikker til et fælles afsæt (2016)

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Variation associated with measurement of retinal vessel diameters at different points in the pulse cycle (2003)

Measurements of large retinal venules is generally less variable than measurements of other retinal vessels. After controlling for pulse point and grader, the largest source of variation is across images. Understanding the components of variability in measuring retinal vessels is important as these techniques are applied in epidemiological studies.
A study of gene expression in the living human brain (2023)

A goal of medical research is to determine the molecular basis of human brain health and illness. One way to achieve this goal is through observational studies of gene expression in human brain tissue. Due to the unavailability of brain tissue from living people, most such studies are performed using tissue from postmortem brain donors. An assumption underlying this practice is that gene expression in the postmortem human brain is an accurate representation of gene expression in the living human brain. Here, this assumption - which, until now, had not been adequately tested - is tested by comparing human prefrontal cortex gene expression between 275 living samples and 243 postmortem samples. Expression levels differed significantly for nearly 80% of genes, and a systematic examination of alternative explanations for this observation determined that these differences are not a consequence of cell type composition, RNA quality, postmortem interval, age, medication, morbidity, symptom severity, tissue pathology, sample handling, batch effects, or computational methods utilized. Analyses integrating the data generated for this study with data from earlier landmark studies that used tissue from postmortem brain donors showed that postmortem brain gene expression signatures of neurological and mental illnesses, as well as of normal traits such as aging, may not be accurate representations of these gene expression signatures in the living brain. By using tissue from large cohorts living people, future observational studies of human brain biology have the potential to (1) determine the medical research questions that can be addressed using postmortem tissue as a proxy for living tissue and (2) expand the scope of medical research to include questions about the molecular basis of human brain health and illness that can only be addressed in living people (e.g., "What happens at the molecular level in the brain as a person experiences an emotion?").
Emerging Disease or Diagnosis? (2012)

Some viral infections may not represent emerging diseases, but improved detection and diagnosis of common diseases.
OBSTRUCTED VEHICLE-TO-VEHICLE CHANNEL MODELING FOR INTELLIGENT VEHICULAR COMMUNICATIONS (2018)

In this paper, we model obstructed vehicle-to-vehicle (V2V) channels for the 5-GHz band through measurement-validated ray-tracing (RT) simulations. To begin, we establish a realistic V2V RT simulator through integrating three key channel features: small-scale structures (e.g. lampposts, traffic signs), handled by their approximate radar cross sections; large-scale structures (such as buildings and ground), calibrating their electromagnetic and scattering parameters; and obstructing vehicle effects via V2V channel measurements. Then, based on extensive RT simulations, the target channels are characterized comprehensively. All the parameters are input into and verified by the 3GPP-like quasi deterministic radio channel generator (QuaDRiGa). By adding the obstructed V2V scenario into standard channel model families, this paper provides a foundation for evaluating intelligent vehicular communications in challenging conditions.