gebhart/patrepeval huggingface dataset:
Detection of high risk patients in chronic myelogenous leukemia by DNA-image cytometry. (1991)

Peripheral blood smears from the time of diagnosis of 64 patients with chronic myelogenous leukemia (CML) in chronic phase were restained according to Feulgen. Nuclear DNA content of at least 100 myeloblasts and promyelocytes was measured by interactive DNA-cytometry using a TV-image analysis system, combined with an automated microscope. From the resulting DNA values the DNA parameters stemline ploidy, stemline shoulder fraction and "proliferative" fraction, which reflect cytogenetic and cell kinetic characteristics of CML, were derived. Each of these DNA parameters identified subgroups with a significantly different survival time and duration of chronic phase. Indicators for a good prognosis were a near-diploid stemline ploidy (median survival time 49 v. 26 months), a low percentage of nuclei in the stemline shoulder fraction (45 v. 28 months) and a high "proliferative" fraction (45 v. 23 months). Independently of clinical and hematological features, the DNA-cytometric parameters yielded additional prognostic information both in the univariate and multivariate analysis.
Essential fatty acids and sleep: mini-review and hypothesis (1998)

The neurochemical basis of sleep mechanisms (onset and maintenance) is still controversial although the phenomenon itself is known to be mediated by more than a single molecule. The list of suggested endogenous sleep substances is rather long, and there is no single 'sleep center' identified in the brain. The role of fatty acids, and essential fatty acids in particular, has been ignored in sleep research. This review proposes an integration of the current knowledge about the effects of fatty acids in sleep neurochemistry, wherein fatty acids are seen to exert a direct effect on neuronal membrane structure or indirectly on the dynamics of biochemical compounds (complex lipids, prostaglandins, neurotransmitters, amino acids, interleukins) necessary for the initiation and maintenance of sleep.
501 Vibration characteristics of intentional mistuned bladed disk system (2004)

It is known that, not only mistuning in bladed disk system affect forced response but also it can change the flutter margin. The characteristics of the flutter and the forced response of mistimed bladed disk system are investigated by using sensitivity analysis. The effects of the circumferential wave number of mistuning pattern upon the sensitivities of eigenvalues (natural frequencies and modal damping) and maximum forced responses are discussed. It is shown that the circumferential wave number with maximum sensitivity plays an important role in intentional mistuned system.
Purification and characterization of UV endonucleases I and II from murine plasmacytoma cells (1989)

Three endonucleases from murine plasmacytoma cells that specifically nick DNA which was heavily irradiated with ultraviolet (UV) light were resolved by Sephacryl S-200 column chromatography. Two of these, UV endonucleases I and II, were purified extensively. UV endonuclease I appears to be a monomeric protein with a molecular mass of 43 kDa; UV endonuclease II has an S value of 2.9 S, with a corresponding molecular mass estimated at 28 kDa. Both enzymes act as a class I AP endonuclease, cleaving phosphodiester bonds via a beta-elimination mechanism, so as to form an unsaturated deoxyribose at the 3' terminus. Both have thymine glycol DNA glycosylase activity and their substrate specificities generally appear to be overlapping but not identical. UV endonuclease I acts on both supercoiled and relaxed DNAs, whereas II acts only on supercoiled DNA. Both enzymes are active in EDTA, but have different optima for salt, pH, and Triton X-100. Each enzyme is also present in cultured diploid human fibroblasts.
Imaging Molecular Pathways: Reporter Genes (2012)

Molecular imaging is a rapidly advancing field that allows cancer biologists to look deeper into the complex inner workings of tumor cells, or whole tumors, in a non-invasive manner. In this review, we will summarize some recent advances that enable investigators to study various important biological processes in tumors in vivo. We will discuss novel imaging approaches that allow investigators to visualize and quantify molecular pathways, such as receptor tyrosine kinase activation, hypoxia signal transduction, apoptosis, and DNA double-strand breaks. Select examples of these applications will be discussed. Because of the limited scope of this review, we will only focus on natural reporters, such as bioluminescence and fluorescent proteins.
Density functional study for optical properties of blue silicate phosphor: BaCa2MgSi2O8 (2013)

A density functional calculation is performed to investigate optical properties of blue silicate phosphor, BaCa2MgSi2O8:Eu (BCMS:Eu). The optical absorption and emission processes are discussed based on electronic band structures and density of states. Our calculation indicates that hybridization of the wave function plays an important role for nonradiative migration of electrons and holes. Our results also explain adequately the luminescence feature of BCMS which exhibits two components of blue emission from Eu ion substituted for Ba and Ca site. In addition, it is shown that the structural relaxation around Eu ion does work effectively to describe appropriately the difference of crystal field strength between Ba and Ca sites in BCMS host.
Review of the phenomenon of fluidization and its numerical modelling techniques (2015)

The paper introduces the phenomenon of fluidization as a process. Fluidization occurs when a fluid (liquid or gas) is pushed upwards through a bed of granular material. This may make the granular material to behave like a liquid and, for example, keep a level meniscus on a tilted container, or make a lighter object float on top and a heavier object sink to the bottom. The behavior of the granular material, when fluidized, depends on the superficial gas velocity, particle size, particle density, and fluid properties resulting in various regimes of fluidization. These regimes are discussed in detail in the paper. This paper also discusses the application of fluidized beds from its early usage in the Winkler coal gasifier to more recent applications for manufacturing of carbon nano-tubes. In addition, Geldart grouping based on the range of particle sizes is discussed. The minimum fluidization condition is defined and it is demonstrated that it may be registered slightly different when particles are being fluidized or de-fluidized. The paper presents discussion on three numerical modelling techniques: the two fluid model, unresolved fluid-particle model and resolved fluid particle model. The two fluid model is often referred to Eulerian-Eulerian method of solution and assumes particles as well as fluid as continuum. The unresolved and resolved fluid-particle models are based on Eulerian-Lagrangian method of solution. The key difference between them is the whether to use a drag correlation or solve the boundary layer around the particles. The paper ends with the discussion on the applicability of these models.
Electric Field Stimulation of Bipolar Cells in a Degenerated Retina—A Theoretical Study (2010)

Subretinal implants are the subject of clinical investigation for their ability to evoke useful visual sensations in blind individuals via electrical stimulation of the diseased retina. We investigated the spatial characteristic of the retinal polarization obtained by electric field stimulation through a subretinally located monopolar electrode array and bipolar electrode array. By combining electric potential simulation through a boundary element method with a segmented cell model, we computed the membrane voltage at the axon terminal of the bipolar cells as a function of the axon length (50-110 microm) and the electrode diameter. We found that short OFF bipolar cells are predominantly addressed by small bipolar electrodes (diameter between 60 and 100 microm) and by using a short duration ( < 150 micros) of the stimulating voltage pulse. Long ON cells are best addressed by large monopolar electrodes (diameter > 100 microm) and a long pulse duration ( > 150 micros). However, the low selectivity of the electric field stimulation with regard to the cell length does not enable the individual depolarization of long OFF cells and short ON cells. When the stimulation must take place at multiple retinal sites simultaneously, the bipolar electrode arrays allow for higher spatial modulation of the polarization of the axon terminal than the monopolar arrays.
Partial depletion of sarcoplasmic reticulum calcium does not prevent calcium sparks in Rat Ventricular myocytes (1997)

1. The exact nature of calcium sparks in the heart remains highly controversial. We sought to determine whether calcium sparks arise from a single or multiple calcium release channels/ ryanodine receptors in the sarcoplasmic reticulum (SR). If their genesis involves a calcium-coupled recruitment of multiple channels, calcium sparks might be abolished by a modest depletion of SR calcium (because of the decrease in unitary calcium flux and hence a decrease in the gain of local calcium-induced calcium release). If, on the other extreme, calcium sparks are produced despite severe SR depletion, the single-channel origin will be preferred. 2. Spontaneous calcium sparks were studied in rat ventricular myocytes using confocal microscopy and the fluorescent calcium probe fluo-3. A computer algorithm was developed to count and measure objectively calcium sparks in linescan images. 3. Thapsigargin (25-150 nM) depleted caffeine-releasable SR calcium by up to 64%, in a dose- and time-dependent manner, without altering the resting cytosolic calcium level. During SR depletion, calcium sparks were robustly observed, albeit at reduced frequency (> or = 30% of control) and amplitude (> or = 60% of control). 4. Due to the reduced detectability of small sparks against noise background, the observed data would overestimate reduction in spark frequency but underestimate amplitude reduction. After correction for this detection bias, we found that the spark frequency was independent of SR load, whereas the amplitude was proportional to load. 5. We conclude that, although spark amplitude depends on SR filling status, the frequency of spark generation is independent of SR calcium load, and therefore independent of the local calcium release rate. This implies that sparks are single-channel events, or collective events that are well above threshold for local regeneration. Additionally, our results suggest that intraluminal SR calcium, at normal or low loads, does not play a major role in the regulation of on-gating of the ryanodine receptor.
Bioinspired Synthesis of Mesoporous Gold-silica Hybrid Microspheres as Recyclable Colloidal SERS Substrates (2017)

Noble metal nanostructures have been intensively investigated as active substrates for surface-enhanced Raman spectroscopy (SERS) from visible to near-IR wavelengths. However, metal nanoparticle-based SERS analysis in solutions is very challenging due to uncontrollable and irreproducible colloid aggregation. Here we report the templated synthesis of porous gold-silica hybrid microspheres and their application as reusable colloidal SERS substrates. Mesoporous polymer microspheres are synthesized and used as templates for the synthesis of non-aggregated gold nanoparticles, followed by polydopamine-mediated silicification to fabricate mesoporous gold-silica hybrid microspheres. The mesoporous hybrid particles detect crystal violet in the order of 10<sup>-8</sup> M and provide the structural durability of the immobilized gold nanoparticles, allowing them to be recycled for repeated SERS analyses for analytes in a solution with the similar sensitivity. This work suggests that the mesoporous gold-silica hybrid microspheres are attractive SERS substrates in terms of reusability, sensitivity, and stability.
Purification of Six Human Vitamin K-Dependent Proteins in a Single Chromatographic Step Using Immunoaffinity Columns1 (1986)

The major human vitamin K-dependent proteins were purified from plasma using immunoadsorbents made with antibodies specific for each protein. Monoclonal antibodies to Factor VII, Factor IX, Factor X, Protein C, and Protein S were prepared from mice immunized with isolated vitamin K-dependent antigens. Purified monoclonal antibodies and a purified burro polyclonal anti-prothrombin immunoglobulin were individually coupled to Sepharose and used in a tandem series of columns to purify each of the vitamin K-dependent proteins from eluates of barium citrate precipitates of plasma. The proteins were eluted from the columns by sodium thiocyanate and retained functional activity following dialysis. Prothrombin, Factor VII, Factor IX, Factor X and Protein C were essentially homogeneous as judged by NaDodSO4-PAGE; Protein S was isolated as a Protein S-C4b binding protein complex. These results indicate the utility of monoclonal antibody immunoadsorbents for purifying the human vitamin K-dependent proteins and represent a considerable simplification over other purification schemes.
Observed f Immunosuppression Related Complications in Hand Tx Recipients From 2 to 15 Years Post Tx. (2014)

Purpose: Hand transplant recipients are counseled on the risks of systemic immunosuppression (IS). The information is based on solid organ transplantation where recipients have morbidity at the time of transplant. Here we review IS related complications in 8 VCA patients focusing on renal changes, lipids, blood glucose and hypertension. Methods/Results: Eight hand tx recipients were reviewed, seven of whom are now 2 to 15 years post transplant (Range 282 to 5475 days, mean follow up 2105 days). We compared serum creatinine, blood glucose, HDL and LDL to IS levels and time post transplant. All patients received induction, and are maintained on Prograf with either Rapamycin or MMF, with prednisone as clinical course indicates. Currently 4 are weaned off steroids. When creatinine is plotted vs. time post transplant, six of the eight patients show minimal increases in creatinine. This is especially evident in patient 1, who was a type I diabetic at the time of transplant.Figure: No Caption available.Two patients had an increase in creatinine over time, which may be related to weight gain and pre-existing conditions. The average level of prograf did not correlate with serum creatinine. Patient 1, 2, 4,6, 7 and 8 had overall average trough levels of prograf of 10.0, 11.5, 9.0, 11.6, 9.4 and 7.9 respectively. Patient 3 and 5 had average Prograf levels of 10.3, and 8.2. Analysis of blood sugar levels and lipids also suggest that patient lifestyle and aging may contribute significantly to these changes. Summary: Changes over time in serum creatinine, blood sugar and lipids of our hand transplant recipients may be influenced by factors other than IS. At the time of submission, all patients have a creatinine between 0.9 and 1.3. Conclusion: The number of VCA recipients is still tiny. However, the data in these eight recipients suggest that complications of IS in the absence of lifestyle or other risk factors have not resulted in significant morbidity to date in this patient population.
Sensitive biomarkers to Alzheimer's disease progression in longitudinal MRI from deep learning (2020)

Abstract Background In clinical trials of disease‐modifying treatments of Alzheimer’s disease (AD), the measure of hippocampus volume change from longitudinal MRI is a well‐studied biomarker of disease progression. However, even the most sensitive longitudinal MRI measures can be confounded by the presence of motion and susceptibility artifacts. We hypothesize that deep learning can be used to differentiate MRI changes due to biological factors (tissue loss) from changes due to artifact and other non‐biological factors, leading to novel biomarkers that are more sensitive to longitudinal change that can accurately evaluate disease progression. Method 357 subjects (142 training, 215 test) with 3‐8 longitudinal T1‐weighted MRI scans (0.5 to 5.5 years) were selected from ADNI2/GO (Table 1), including cognitively normal (CN), amyloid negative (A‐) older adults, preclinical AD (A+ controls), and A+ patients with early and late mild cognitive impairment (eMCI, lMCI). For each subject, pairs of scans were rigidly registered and trimmed around the hippocampal region. A 3D convolutional neural network (CNN3D) (He et al., 2015) was trained to detect the correct temporal order of arbitrarily ordered input pairs from the same subject and for two pairs of same‐subject images as input, to detect which pair had a longer interscan interval (Figure 1). The successful detection of the temporal order of scans would suggest that the network can capture only time‐induced biological change and ignore non‐biological factors that are independent of time. The results were compared to ALOHA, a deformation‐based morphometry algorithm for quantifying hippocampal change (Das et al., 2012). Result CNN3D extracted the temporal order of MRI scans much more accurately than ALOHA (Table 2, 3) and the CNN3D‐derived longitudinal change measure was more sensitive than ALOHA in differentiating healthy aging (A‐ CN) and preclinical AD (A+ CN) (Figure 2). CNN3D can also detect change in a shorter period of time (Figure 3). Conclusion CNN3D inferred the temporal order of longitudinal MRI scans, suggesting its ability to pinpoint true biological changes that correlate with time better than registration‐based approaches. Deep‐learning‐based MRI change detection may emerge as a more powerful disease progression biomarker for disease‐modifying clinical trials in AD.
Wireless Broadcast Using Network Coding (2009)

Traditional approaches to reliably transmit information over an error-prone network employ either forward error correction (FEC) or retransmission techniques. In this paper, we propose some network coding schemes to reduce the number of broadcast transmissions from one sender to multiple receivers. The main idea is to allow the sender to combine and retransmit the lost packets in a certain way so that with one transmission, multiple receivers are able to recover their own lost packets. For comparison, we derive a few theoretical results on the bandwidth efficiency of the proposed network coding and traditional automatic repeat-request (ARQ) schemes. Both simulations and theoretical analysis confirm the advantages of the proposed network coding schemes over the ARQ ones.
Nonlinear Cost Estimates at Completion Adjusted with Risk Contingency (2016)

Forecasting the final cost with Earned Value Management (EVM) and managing contingency budgets during the project execution have been traditionally considered as two separate streams of project management research. In an attempt to combine the two areas for the purpose of reflecting the risk impact on the cost forecast, this paper presents a cost estimate at completion (CEAC) methodology adjusted with risk contingency. The proposed method is a refined Earned Schedule (ES) based nonlinear CEAC model modified with a new parameter representing the S-shaped contingency consumption as a portion of the project budget at completion. The model is validated on eight construction projects and its estimates’ accuracy and stability with a varying contingency parameter value in the early, middle, and late stages are evaluated. The cost–schedule-risk relationship represented in the model is a contribution to creating a stronger connection between EVM and contingency cost management theories through capturing the interconnected dynamics between a cost baseline and contingency accounts of ongoing projects. As a practical implication, the model is a tool for integrating the contingency consumption into nonlinear CEAC models for accurate and stable cost forecasting especially during the early and middle stages of project execution.
Comparison of Salivary IgA Secretion Rate Collected by the Aspiration Method and Swab Method (2013)

Salivary immunoglobulin A (IgA) is used as an immunity marker, as saliva can be easily collected, noninvasively with little stress. However, several saliva collection methods can be used. Our comparison between samples collected using different methods demonstrated that the salivary IgA secretion rate in samples collected using an aspiration method was significantly correlated with that in samples collected using a swab method. Moreover, the significant circadian variation in salivary IgA secretion rate in the aspirated saliva suggested that the aspiration method does not suppress salivary IgA secretion rate variability compared with the swab method. Therefore, the aspiration method should be considered as the preferable saliva collection method.
An efficient computational technique for time-fractional modified Degasperis-Procesi equation arising in propagation of nonlinear dispersive waves (2020)

In this paper, an efficient hybrid numerical scheme which is based on a joint venture of the q-homotopy analysis method and Sumudu transform is applied to investigate the time-fractional modified Degasperis-Procesi (DP) equation. The present study considers the Caputo fractional derivative. The fractional order modified DP model is very important and plays a great role in study of ocean engineering and science. The proposed scheme provides a beautiful opportunity for proper selection of the auxiliary parameter ℏ and the asymptotic parameter ρ ( ≥ 1) to handle mainly the differential equations of nonlinear nature. The offered scheme produces the solution in the shape of a convergent series in a large admissible domain which is helpful to regulate the region of convergence of a series solution. The proposed work computes the approximate analytical solution of the fractional modified DP equation systematically and also presents graphically the variation of the obtained solution for diverse values of the fractional parameter β.
Effects of color spaces to the cell segmentation in histopathological images (2016)

With the progressive development of the computer-aided diagnosis (CAD) systems, analysis of high resolution histopathological images has become more easier. In the proposed study, the effects of different color spaces used in various studies in the literature are investigated for the discrimination of cellular structures from background in histopathological images. For this purpose, performances of k-means, fuzzy c-means and expectation-maximization algorithms are compared in different color spaces. In the experimental results section, different segmentation accuracy metrics are presented in comparative manner.
Antiviral properties of trans-δ-viniferin derivatives against enveloped viruses (2023)

Over the last century, the number of epidemics caused by RNA viruses has increased and the current SARS-CoV-2 pandemic has taught us about the compelling need for ready-to-use broad-spectrum antivirals. In this scenario, natural products stand out as a major historical source of drugs. We analyzed the antiviral effect of 4 stilbene dimers [1 (trans-δ-viniferin); 2 (11',13'-di-O-methyl-trans-δ-viniferin), 3 (11,13-di-O-methyl-trans-δ-viniferin); and 4 (11,13,11',13'-tetra-O-methyl-trans-δ-viniferin)] obtained from plant substrates using chemoenzymatic synthesis against a panel of enveloped viruses. We report that compounds 2 and 3 display a broad-spectrum antiviral activity, being able to effectively inhibit several strains of Influenza Viruses (IV), SARS-CoV-2 Delta and, to some extent, Herpes Simplex Virus 2 (HSV-2). Interestingly, the mechanism of action differs for each virus. We observed both a direct virucidal and a cell-mediated effect against IV, with a high barrier to antiviral resistance; a restricted cell-mediated mechanism of action against SARS-CoV-2 Delta and a direct virustatic activity against HSV-2. Of note, while the effect was lost against IV in tissue culture models of human airway epithelia, the antiviral activity was confirmed in this relevant model for SARS-CoV-2 Delta. Our results suggest that stilbene dimer derivatives are good candidate models for the treatment of enveloped virus infections.