gebhart/patrepeval huggingface dataset:
Automated staining analysis in digital cytopathology and applications (2022)

The progress of digital pathology in recent years has been an opportunity for the development of automated image analysis algorithms for quantitative measurements and computer aided diagnosis. With those new methods comes the need for high staining quality and reproducibility, as image analysis tools are typically more sensible to slight stain variations than trained pathologists. This article presents a method for the automated analysis of cytology slides stains specifically adapted to the challenges encountered in digital cytopathology. In particular, the variety of cell types in cytology slides, the 3D distribution of the cellular material, the presence of superposed cells and the need for independent analysis of sub-cellular compartments are addressed. The proposed method is applied to the quantification of staining variations for quality control, resulting from changes in the staining protocol such as reagent immersion time or a reagent change. Another demonstrated application is the selection of staining protocol parameters that maximize the visible details in nucleus. Finally the analysis pipeline is also used to compare different stain normalization algorithms on digital cytology slides. Code available at: https://gitlab.com/vitadx/articles/automated_staining_analysis.
National Institutes of Health State-of-the-Science Conference Statement: Preventing Alzheimer Disease and Cognitive Decline (2010)

The National Institute on Aging and the Office of Medical Applications of Research of the National Institutes of Health convened a State-of-the-Science Conference on 26-28 April 2010 to assess the available scientific evidence on prevention of cognitive decline and Alzheimer disease. This article provides the panel's assessment of the available evidence.
Evaluating anaerobic soil disinfestation and other biological soil management strategies for open-field tomato production in Florida (2018)

Abstract In the search for alternative practices to chemical soil fumigation (CSF), anaerobic soil disinfestation (ASD) has proven to be a promising tool for soil-borne pest management and crop production improvement. The ASD treatment with composted poultry litter (CPL) and molasses (M, a labile carbon source) was identified as an effective approach for a biologically based soil disinfestation system in tomato ( Solanum lycopersicum L.) production in Florida. However, environmental and food-safety concerns are associated with animal manure-based amendments, which led to the exploration of composted yard waste (CYW) as a potential substitute for CPL in ASD application. In this study, field trials were conducted in Citra and Immokalee, FL to examine the effects of ASD using CYW, CPL and M compared with a commercially available microbial amendment system on root-knot nematodes, weeds, fruit yield and quality of fresh-market tomato. Treatments included (1) ASD with CPL (11 Mg ha −1 ) and M (6.9 m 3 ha −1 ) (ASD0.5), (2) ASD with CYW (26.9 Mg ha −1 ) and M (CYW1 + M), (3) ASD with CYW (13.5 Mg ha −1 ) and M (CYW0.5 + M), (4) Soil Symphony Amendment (SSA), (5) CYW (26.9 Mg ha −1 ) alone (CYW1) and (6) a combination of CYW1 + SSA, in comparison with (7) untreated control and (8) CSF (Pic-Clor 60 at 224 kg ha −1 ). Cumulative soil anaerobiosis was greater in ASD0.5 compared with all the other treatments. The root-knot nematode gall index ratings on the tomato crop were significantly lower in CSF, ASD0.5, CYW1 + M and CYW0.5 + M than untreated control in Citra. Although CYW1 and SSA alone had a moderately suppressive effect on weed coverage and root-knot nematodes, their positive impact on crop performance was limited when used alone. ASD0.5, CYW1 + M and CSF had significantly higher marketable and total fruit yields than untreated control in both locations, while all treatments showed promising results in the Immokalee trial in comparison with untreated control. In general, few differences in major fruit quality attributes were found. Although using CYW in ASD was not as effective as CPL in creating soil anaerobic conditions, the enhanced crop performance in CYW1 + M and CYW0.5 + M suggests the potential of using CYW as an alternative source of organic amendment in combination with M to achieve benefits similar to those obtained with CPL-based ASD.
Relationship of Surface Tension, Oxygen Partial Pressure, and Temperature for Molten Iron (2011)

Surface tension of molten iron was measured under reducing gas atmosphere of Ar–He–5 vol % H2 by an oscillating droplet method using electromagnetic levitation. The temperature dependence of surface tension did not exhibit a linear relationship but revealed a peculiar kink at around 1810 K, due to competition between the temperature dependence of oxygen partial pressure and that of the oxygen adsorption equilibrium constant. We successfully derived the surface tension of molten iron as functions of both oxygen partial pressure and temperature. Furthermore, the standard enthalpy and entropy for oxygen adsorption reaction on molten iron were also estimated.
Apparent Renal Cell Carcinomas in Tuberous Sclerosis Are Heterogeneous (1998)

Renal epithelial tumors (carcinoma and oncocytoma) have been reported with higher a frequency than expected in patients with the tuberous sclerosis complex. However, the recent identification of a monotypic, epithelioid variant of angiomyolipoma, closely simulating renal cell carcinoma, has cast doubt on the real frequency of carcinoma. Immunohistochemical analysis with a panel of antibodies, including melanogenesis marker HMB45, can discriminate between carcinoma and carcinoma-like angiomyolipoma. We studied five tumors previously reported as carcinoma and found that only one of them showed an immunohistochemical phenotype indicative of an epithelial tumor (Ker+, HMB45-). Three tumors exhibited a phenotype compatible with the monotypic epithelioid variant of angiomyolipoma (HMB45+, Ker-), and two of the three patients died of metastatic disease. The last patient had unusual clinical features, and the tumor was positive both for HMB45 and keratin. It is concluded that (1) renal cell carcinoma is less common in tuberous sclerosis complex than previously believed, (2) some cases called renal cell carcinoma probably represent a monotypic, epithelioid variant of angiomyolipoma, and (3) epithelioid angiomyolipoma is a potentially malignant tumor with invasion and metastases. These findings indicate that all reported renal carcinomas in tuberous sclerosis complex, therefore, must be reevaluated.
Monitoring annealing via CO_2 laser heating of defect populations on fused silica surfaces using photoluminescence microscopy (2010)

Photoluminescence (PL) microscopy and spectroscopy under 266 nm and 355 nm laser excitation are explored as a means of monitoring defect populations in laser-modified sites on the surface of fused silica and their subsequent response to heating to different temperatures via exposure to a CO(2) laser beam. Laser-induced temperature changes were estimated using an analytic solution to the heat flow equation and compared to changes in the PL emission intensity. The results indicate that the defect concentrations decrease significantly with increasing CO(2) laser exposure and are nearly eliminated when the peak surface temperature exceeds the softening point of fused silica (approximately 1900K), suggesting that this method might be suitable for in situ monitoring of repair of defective sites in fused silica optical components.
Ultrastructure of Streptococcus pneumoniae after exposure to xylitol (2004)

This study demonstrates further that xylitol has a harmful effect on pneumococci. The observed changes in the polysaccharide capsule and the cell wall of pneumococci could affect the adherence and virulence of pneumococci, explaining the good clinical efficacy of xylitol in the prevention of acute otitis media.
ChemInform Abstract: Catalytic Enantioselective Synthesis of Prostaglandin E1 Methyl Ester Using a Tandem 1,4‐Addition—Aldol Reaction to a Cyclopentene‐3,5‐dione Monoacetal. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Estimating the Number and Distribution of the Neighbors in an Underwater Communication Network (2008)

Here we present a procedure for estimating the number and distribution of neighbors (nodes withindirect transmission range) with a specified accuracy for an underwater communication network (UCN). The capture effect can degrade the performance of a neighbor-counting procedure, so our estimation procedure is based on a property that is not affected by the capture effect. The procedure for estimating the neighbor's distribution is derived with the help of the capture effect. The two procedures are carried out concurrently. The time taken for estimation is independent of the number of neighbors and the procedure is therefore suitable for networks of all sizes. We further show by a performance and sensitivity analysis that the procedure of estimating the distribution is robust and is applicable to both UCNs and terrestrial communications networks (TCNs).
Muscle fiber hypertrophy in response to 6 weeks of high-volume resistance training in trained young men is largely attributed to sarcoplasmic hypertrophy (2019)

Cellular adaptations that occur during skeletal muscle hypertrophy in response to high-volume resistance training are not well-characterized. Therefore, we sought to explore how actin, myosin, sarcoplasmic protein, mitochondrial, and glycogen concentrations were altered in individuals that exhibited mean skeletal muscle fiber cross-sectional area (fCSA) hypertrophy following 6 weeks of high-volume resistance training. Thirty previously resistance-trained, college-aged males (mean ± standard deviation: 21±2 years, 5±3 training years) had vastus lateralis (VL) muscle biopsies obtained prior to training (PRE), at week 3 (W3), and at week 6 (W6). Muscle tissue from 15 subjects exhibiting PRE to W6 VL mean fCSA increases ranging from 320-1600 μm2 was further interrogated using various biochemical and histological assays as well as proteomic analysis. Seven of these individuals donated a VL biopsy after refraining from training 8 days following the last training session (W7) to determine how deloading affected biomarkers. The 15 fCSA hypertrophic responders experienced a +23% increase in mean fCSA from PRE to W6 (p<0.001) and, while muscle glycogen concentrations remained unaltered, citrate synthase activity levels decreased by 24% (p<0.001) suggesting mitochondrial volume decreased. Interestingly, repeated measures ANOVAs indicated that p-values approached statistical significance for both myosin and actin (p = 0.052 and p = 0.055, respectively), and forced post hoc tests indicated concentrations for both proteins decreased ~30% from PRE to W6 (p<0.05 for each target). Phalloidin-actin staining similarly revealed actin concentrations per fiber decreased from PRE to W6. Proteomic analysis of the sarcoplasmic fraction from PRE to W6 indicated 40 proteins were up-regulated (p<0.05), KEGG analysis indicated that the glycolysis/gluconeogenesis pathway was upregulated (FDR sig. <0.001), and DAVID indicated that the following functionally-annotated pathways were upregulated (FDR value <0.05): a) glycolysis (8 proteins), b) acetylation (23 proteins), c) gluconeogenesis (5 proteins) and d) cytoplasm (20 proteins). At W7, sarcoplasmic protein concentrations remained higher than PRE (+66%, p<0.05), and both actin and myosin concentrations remained lower than PRE (~-50%, p<0.05). These data suggest that short-term high-volume resistance training may: a) reduce muscle fiber actin and myosin protein concentrations in spite of increasing fCSA, and b) promote sarcoplasmic expansion coincident with a coordinated up-regulation of sarcoplasmic proteins involved in glycolysis and other metabolic processes related to ATP generation. Interestingly, these effects seem to persist up to 8 days following training.
Epitaxy: A Chemical Route to Monolithic Integration of Crystalline Oxides on Semiconductors (Adv. Mater. Interfaces 8/2014) (2014)

A chemical route to crystalline oxide growth on semiconductors is demonstrated. As J. G. Ekerdt and co-workers report in article 1400081, the direct deposition of crystalline SrTiO3 on Ge is achieved through atomic layer deposition. This work is a significant milestone for the monolithic integration of crystalline oxides on semiconductors, with wide-reaching potential for advanced electronic applications.
Optimal delay estimation in a multiple sensor array having spatially correlated noise (2005)

The estimation of time-of-arrival differences for signals from a single source or target arriving at multiple sensors enables target location. Herein noises are taken to have equal spatial correlation for all sensor pairs. Resulting estimators are shown to be reasonable and reduce to previously derived estimators where noises are independent.
The Web as a Jungle (2015)

Given a large collection of co-evolving online activities, such as searches for the keywords "Xbox", "PlayStation" and "Wii", how can we find patterns and rules? Are these keywords related? If so, are they competing against each other? Can we forecast the volume of user activity for the coming month? We conjecture that online activities compete for user attention in the same way that species in an ecosystem compete for food. We present ECOWEB, (i.e., Ecosystem on the Web), which is an intuitive model designed as a non-linear dynamical system for mining large-scale co-evolving online activities. Our second contribution is a novel, parameter-free, and scalable fitting algorithm, ECOWEB-FIT, that estimates the parameters of ECOWEB. Extensive experiments on real data show that ECOWEB is effective, in that it can capture long-range dynamics and meaningful patterns such as seasonalities, and practical, in that it can provide accurate long-range forecasts. ECOWEB consistently outperforms existing methods in terms of both accuracy and execution speed.
Tensile Contact Etch Stop Nitride for nMOS Performance Enhancement: Influence of the Film Morphology (2006)

Abstract not Available.
Effect of Tetracyclines on the Dynamics of Formation and Destructuration of β2-Microglobulin Amyloid Fibrils (2010)

The discovery of methods suitable for the conversion in vitro of native proteins into amyloid fibrils has shed light on the molecular basis of amyloidosis and has provided fundamental tools for drug discovery. We have studied the capacity of a small library of tetracycline analogues to modulate the formation or destructuration of β2-microglobulin fibrils. The inhibition of fibrillogenesis of the wild type protein was first established in the presence of 20% trifluoroethanol and confirmed under a more physiologic environment including heparin and collagen. The latter conditions were also used to study the highly amyloidogenic variant, P32G. The NMR analysis showed that doxycycline inhibits β2-microglobulin self-association and stabilizes the native-like species through fast exchange interactions involving specific regions of the protein. Cell viability assays demonstrated that the drug abolishes the natural cytotoxic activity of soluble β2-microglobulin, further strengthening a possible in vivo therapeutic exploitation of this drug. Doxycycline can disassemble preformed fibrils, but the IC(50) is 5-fold higher than that necessary for the inhibition of fibrillogenesis. Fibril destructuration is a dynamic and time-dependent process characterized by the early formation of cytotoxic protein aggregates that, in a few hours, convert into non-toxic insoluble material. The efficacy of doxycycline as a drug against dialysis-related amyloidosis would benefit from the ability of the drug to accumulate just in the skeletal system where amyloid is formed. In these tissues, the doxycycline concentration reaches values several folds higher than those resulting in inhibition of amyloidogenesis and amyloid destructuration in vitro.
Divergent roles for NK-2 class homeobox genes in cardiogenesis in flies and mice (1998)

Recent evidence suggests that cardiogenesis in organisms as diverse as insects and vertebrates is controlled by an ancient and evolutionarily conserved transcriptional pathway. In Drosophila, the NK-2 class homeobox gene tinman (tin) is expressed in cardiac and visceral mesodermal progenitors and is essential for their specification. In vertebrates, the tin homologue Nkx2-5/Csx and related genes are expressed in early cardiac and visceral mesodermal progenitors. To test for an early cardiogenic function for Nkx2-5 and to examine whether cardiogenic mechanisms are conserved, we introduced the mouse Nkx2-5 gene and various mutant and chimeric derivatives into the Drosophila germline, and tested for their ability to rescue the tin mutant phenotype. While tin itself strongly rescued both heart and visceral mesoderm, Nkx2-5 rescued only visceral mesoderm. Other vertebrate 'non-cardiac' NK-2 genes rescued neither. We mapped the cardiogenic domain of tin to a unique region at its N terminus and, when transferred to Nkx2-5, this region conferred a strong ability to rescue heart. Thus, the cardiac and visceral mesodermal functions of NK-2 homeogenes are separable in the Drosophila assay. The results suggest that, while tin and Nkx2-5 show close functional kinship, their mode of deployment in cardiogenesis has diverged possibly because of differences in their interactions with accessory factors. The distinct cardiogenic programs in vertebrates and flies may be built upon a common and perhaps more ancient program for specification of visceral muscle.
Molecule model for deeply bound and broad kaonic nuclear clusters (2011)

A molecule model is proposed for the description of the properties of the kaonic nuclear cluster (KNC) anti-KNN with the structure N(ant-KN)_(I = 0) and quantum numbers I(J^P) = 1/2(0^-), the large binding energy B^(\exp)_(anti-KNN) = 103(6) MeV and the width Gamma^(\exp)_(anti-KNN) = 118(13) MeV, observed recently by the DISTO Collaboration. The theoretical values of the binding energy B^(th)_(anti-KNN) = 118 MeV, the width Gamma^(th)_(anti-KNN) = 142 MeV of the KNC anti-KNN and the density n_(anti-KNN) = 2.71 n_0, where n_0= 0.17 fm^(-3) is the normal nuclear density, reproduce well the large experimental values. They are calculated with the trial harmonic oscillator wave functions by using chiral Lagrangians, accounting for all self-energy terms, contributing to the masses of the kaonic nuclear clusters (anti-KN)_(I = 0) and anti-KNN. In addition the high Lambda*p sticking probability in the pp reaction at the kinetic energy T_p = 2.85 GeV of the incident proton is explained.
Particle manipulation with acoustic waves based on Hertz-Mindlin mechanics (2022)

Ultrasound noncontact particle manipulation (vibrotransportation) is of interest for a number of industrial applications: delivery of solid agents for defect healing, noninvasive excretion of undesirable particles, micromachine technology, and sorting of particles. It is known that a particle on a substrate can be moved by a combined action of acoustic waves and friction. A traditional theory describing the effect considers a particle as a material point capable of moving only against the wave, i.e., in a direction opposite to the wave propagation direction. Here, we use another approach based on Hertz-Mindlin mechanics in which a particle represents a deformable body whereas a zone of its contact with the substrate has a certain structure including evolving regions of stick and slip. The friction dynamics of the Hertz-Mindlin system with a mass comprises different regimes, including a consistent motion in a desired direction (not only the one opposite to the direction of wave propagation but also the one oriented like the wave), which allows a more elaborate manipulation or positioning of the particles. The presented numerical tool treats the problem of a particle on a substrate being moved by Rayleigh waves. We demonstrate various regimes in which steady movement is observed or not, depending on excitation parameters and particle inertia.
Optimal Capital Management in Banking (2008)

Vascular insufficiency and alterations in normal retinal perfusion are among the major factors for the pathogenesis of various sight-threatening ocular diseases, such as diabetic retinopathy, hypertensive retinopathy, and possibly glaucoma. Therefore, retinal microvascular preparations are pivotal tools for physiological and pharmacological studies to delineate the underlying pathophysiological mechanisms and to design therapies for the diseases. Despite the wide use of mouse models in ophthalmic research, studies on retinal vascular reactivity are scarce in this species. A major reason for this discrepancy is the challenging isolation procedures owing to the small size of these retinal blood vessels, which is ~ ≤ 30 µm in luminal diameter. To circumvent the problem of direct isolation of these retinal microvessels for functional studies, we established an isolation and preparation technique that enables ex vivo studies of mouse retinal vasoactivity under near-physiological conditions. Although the present experimental preparations will specifically refer to the mouse retinal arterioles, this methodology can readily be employed to microvessels from rats.
The Enantioface-Differentiating Hydrogenation of the C=O Double Bond with Asymmetrically Modified Raney Nickel. XXXIX. Repeated Uses of the Catalyst in the Hydrogenation of 2-Alkanones (1987)

Abstract The durability of tartaric acid-sodium bromide-modified Raney nickel in the hydrogenation of 2-octanone was investigated. A remarkable lowering of the optical yield was observed in the repeated use of the catalyst. A lack of sodium ions in the reaction system was found to be the origin of this phenomenon. The addition of sodium ions to the reaction mixture was useful for attaining high optical yields in the repeated uses of the catalyst.
3D Simulation of an Accessible Biomedical Lab (2014)

29th Annual International Technology and Persons with Disabilities Conference Scientific/Research Proceedings, San Diego, 2014
Activation of the adenovirus major late promoter by transcription factors MAZ and Sp1 (1997)

Multiple binding sites for the transcription factors MAZ and Sp1 within the adenovirus type 5 major late promoter have been identified by DNase I protection studies. In the proximal region of the promoter, both MAZ and Sp1 interact with GC-rich sequences flanking the TATA box. Two MAZ binding sites are centered at -18 and -36 relative to the transcriptional initiation site. Sp1 bound only to the -18 GC-rich sequence. Several sites of interaction were also evident in the distal region of the promoter. Both MAZ and Sp1 interacted with a sequence centered at -166, and MAZ bound weakly to an additional site centered at -130. Overexpression of MAZ or Sp1 activated expression from the major late promoter in transient expression assays. Mutational analysis of the GC-rich sequences in the major late promoter suggested that a primary target of MAZ activation is the GC-rich sequences flanking the TATA sequence, whereas Sp1 requires the distal GC-rich sequence elements to stimulate gene expression. This activation is enhanced by the adenovirus E1A protein, and evidence for interaction between E1A and both transcription factors was obtained by using an immunoprecipitation assay. Activation by MAZ and Sp1 also was observed in transfection studies using the complete adenovirus type 5 genome as the target. Increased levels of late mRNA from both the L1 and L5 regions were observed when MAZ or Sp1 expression plasmids were transfected with viral DNA. Unexpectedly, activation of the major late promoter by MAZ and Sp1 was detected irrespective of whether the viral DNA could replicate.