gebhart/patrepeval huggingface dataset:
Culture Conditions Affect Cardiac Differentiation Potential of Human Pluripotent Stem Cells (2012)

Human pluripotent stem cells (hPSCs), including human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs), are capable of differentiating into any cell type in the human body and thus can be used in studies of early human development, as cell models for different diseases and eventually also in regenerative medicine applications. Since the first derivation of hESCs in 1998, a variety of culture conditions have been described for the undifferentiated growth of hPSCs. In this study, we cultured both hESCs and hiPSCs in three different culture conditions: on mouse embryonic fibroblast (MEF) and SNL feeder cell layers together with conventional stem cell culture medium containing knockout serum replacement and basic fibroblast growth factor (bFGF), as well as on a Matrigel matrix in mTeSR1 medium. hPSC lines were subjected to cardiac differentiation in mouse visceral endodermal-like (END-2) co-cultures and the cardiac differentiation efficiency was determined by counting both the beating areas and Troponin T positive cells, as well as studying the expression of OCT-3/4, mesodermal Brachyury T and NKX2.5 and endodermal SOX-17 at various time points during END-2 differentiation by q-RT-PCR analysis. The most efficient cardiac differentiation was observed with hPSCs cultured on MEF or SNL feeder cell layers in stem cell culture medium and the least efficient cardiac differentiation was observed on a Matrigel matrix in mTeSR1 medium. Further, hPSCs cultured on a Matrigel matrix in mTeSR1 medium were found to be more committed to neural lineage than hPSCs cultured on MEF or SNL feeder cell layers. In conclusion, culture conditions have a major impact on the propensity of the hPSCs to differentiate into a cardiac lineage.
JPEG2000 encoder for reducing tiling artifacts and accelerating the coding process (2004)

This paper proposes novel techniques for reducing tiling artifacts and encoding time which are two of the largest problems with the JPEG2000 encoder. The proposed method detects tiling artifacts during the coding process and reduces them automatically using tile-boundary adaptive post-quantization. It also provides a higher speed JPEG2000 coding process. This accelerated performance was obtained by predicting the truncation points using the entropy of wavelet transform coefficients prior to the arithmetic coding. This encoding method also requires no additional processing in the decoder. In the experiment, it was subjectively confirmed that tiling artifacts were greatly reduced and that the coding process was considerably accelerated.
Nicotine Modulation of In Vitro Human Gingival Fibroblast β1 Integrin Expression (2002)

Our results suggest that nicotine may induce an altered compartmentalization process in which beta1 integrin molecules are produced, but are not appropriately transferred to the membrane. Nicotine effects on cellular protein synthesis and its modulation of beta1 integrin expression may impair gingival fibroblast ability to adhere to and communicate with one another and with the extracellular matrix, which could impair wound healing and/or exacerbate periodontal disease.
Implications of the Phylogenetic Distribution of Polyphenol Oxidase in Plants (1995)

A limited phylogenetic survey of the distribution of polyphenol oxidase (PPO: EC 1.10.3.2) was conducted in order to determine if this enigmatous enzyme is present in all plants groups or in only certain phylogenetic lines. Evidence for presence of the enzyme was gathered via enzyme assays using various recognized substrates and through the use a heterologous DNA sequence from the PPO of Vicia faba in DNA hybridization experiments and in polymerase chain reaction amplification of conserved sequence within the gene. Enzyme assays showed PPO activity in members of all eukaryotic groups tested, albeit at low levels in some groups, including green algae, mosses, and gymnosperms. DNA hybridization experiments showed varying degrees of signal strength obtained on the dot blots. This could mean limited homology between Vicia probe and target DNA or different copy number in the target DNA. Amplification experiments using primers for a 111 base pair region of the Vicia copper A binding region yielded 111 base pair products in all members of all phylogenetic groups tested. These data strongly suggest the presence of active PPO in all photosynthetic organisms more advanced than cyanophytes. This, along with data from studies with PPO-less mutants, implies some essential function of the enzyme in plants.
Thermoelectric polymer films with a significantly high Seebeck coefficient and thermoelectric power factor obtained through surface energy filtering (2020)

Coating with Rhodamine 101 can significantly enhance the Seebeck coefficient of PEDOT:PSS, and surface energy filtering is proposed to be the reason for this effect.
Repression vs. activation of<i>MOX</i>,<i>FMD</i>,<i>MPP1</i>and<i>MAL1</i>promoters by sugars in<i>Hansenula polymorpha</i>: the outcome depends on cell's ability to phosphorylate sugar (2012)

A high-throughput approach was used to assess the effect of mono- and disaccharides on MOX, FMD, MPP1 and MAL1 promoters in Hansenula polymorpha. Site-specifically designed strains deficient for (1) hexokinase, (2) hexokinase and glucokinase, (3) maltose permease or (4) maltase were used as hosts for reporter plasmids in which β-glucuronidase (Gus) expression was controlled by these promoters. The reporter strains were grown on agar plates containing varied carbon sources and Gus activity was measured in permeabilized cells on microtitre plates. We report that monosaccharides (glucose, fructose) repress studied promoters only if phosphorylated in the cell. Glucose-6-phosphate was proposed as a sugar repression signalling metabolite for H. polymorpha. Intriguingly, glucose and fructose strongly activated expression from these promoters in strains lacking both hexokinase and glucokinase, indicating that unphosphorylated monosaccharides have promoter-derepressing effect. We also show that maltose and sucrose must be internalized and split into monosaccharides to exert repression on MOX promoter. We demonstrate that at yeast growth on glucose-containing agar medium, glucose-limitation is rapidly created that promotes derepression of methanol-specific promoters and that derepression is specifically enhanced in hexokinase-negative strain. We recommend double kinase-negative and hexokinase-negative mutants as hosts for heterologous protein production from MOX and FMD promoters.
Fate of intravenously administered squalene and plant sterols in human subjects (2001)

We have studied metabolism of plant sterols and squalene administered intravenously in the form of lipid emulsion mimicking chylomicrons (CM). The CM-like lipid emulsion was prepared by dissolving squalene in commercially available Intralipid. The emulsion was given as an intravenous bolus injection of 30 ml containing 6.3 mg of cholesterol, 1.9 mg of campesterol, 5.7 mg of sitosterol, 1.6 mg of stigmasterol, 18.1 mg of squalene, and 6 g of triglycerides in six healthy volunteers. Blood samples were drawn from the opposite arm before and serially 2.5 -180 min after the injections. The decay of CM squalene, plant sterols, and triglycerides was monoexponential. The half-life of CM squalene was 74 +/- 8 min, that of campesterol was 37 +/- 5 min (P < 0.01 from squalene), and those of sitosterol, stigmasterol, and triglycerides were 17 +/- 2, 15 +/- 1, and 17 +/- 2 min, respectively (P < 0.01 from squalene and campesterol). The CM squalene concentration still exceeded the baseline level 180 min after injection (P = 0.02), whereas plant sterols and triglycerides returned to the baseline level between 45 and 120 min after injection. The half-lives of squalene and campesterol were positively correlated with their fasting CM concentrations. In addition, VLDL squalene, campesterol, and triglyceride concentrations, VLDL, LDL, and HDL sitosterol concentrations, as well as VLDL and LDL stigmasterol concentrations were increased significantly. Cholesterol concentrations increased in VLDL (P < 0.05), but were unchanged in CM after injection. These data suggest that squalene clearance occurs more slowly than that of plant sterols and triglycerides from CM, and that squalene is more tightly associated with triglyceride-rich lipoproteins than are plant sterols in injected CM-like emulsions.
Dynamic Hashing: Adaptive Metadata Management for Petabyte-scale File Systems ⁄ (2004)

In a petabyte-scale file system, metadata access performance and scalability will significantly affect the whole system’s performance and scalability. We present a new approach called Dynamic Hashing (DH) for metadata management. DH introduces the RELAB (RElative LoAd Balancing) strategy to adjust the metadata distribution when the workload changes dynamically. Elasticity strategy is proposed to support the MDS cluster changes. WLM (Whole Lifecycle Management) strategy is presented to find hot spots in the file system efficiently and reclaim replicas for these hot spots when necessary. DH combines these strategies and Lazy Policies borrowed from the Lazy Hybrid (LH) metadata management together to form an adaptive, high-performance and scalable metadata management technique.
Our Year of Remote Reference: COVID19’s Impact on Reference Services and Librarians (2021)

After a full year of providing fully remote library reference due to the COVID-19 pandemic campus closures, this exploratory study looks at reference practices of libraries, and librarian response to those practices, at a large, urban, public university. This article focuses on the impact COVID-19 had on reference services themselves, as well as the perceptions of those who provide them.
Electric and magnetic phenomena observed before the volcano-seismic activity in 2000 in the Izu Island Region, Japan (2002)

Significant anomalous changes in the ultra low frequency range (approximately 0.01 Hz) were observed in both geoelectric and geomagnetic fields before the major volcano-seismic activity in the Izu Island region, Japan. The spectral intensity of the geoelectric potential difference between some electrodes on Niijima Island and the third principal component of geomagnetic field variations at an array network in Izu Peninsula started to increase from a few months before the onset of the volcano-seismic activity, culminating immediately before nearby magnitude 6 class earthquakes. Appearance of similar changes in two different measurements conducted at two far apart sites seems to provide information supporting the reality of preseismic electromagnetic signals.
Towards 3D object maps for autonomous household robots (2007)

This paper describes a mapping system that acquires 3D object models of man-made indoor environments such as kitchens. The system segments and geometrically reconstructs cabinets with doors, tables, drawers, and shelves, objects that are important for robots retrieving and manipulating objects in these environments. The system also acquires models of objects of daily use such glasses, plates, and ingredients. The models enable the recognition of the objects in cluttered scenes and the classification of newly encountered objects. Key technical contributions include (1) a robust, accurate, and efficient algorithm for constructing complete object mod els from 3D point clouds constituting partial object views, (2) feature-based recognition procedures for cabinets, tables, and other task-relevant furniture objects, and (3) automatic inference of object instance and class signatures for objects of dally use that enable robots to reliably recognize the objects in cluttered and real task contexts. We present results from the sensor-based mapping of a real kitchen.
When Will You Arrive? Estimating Travel Time Based on Deep Neural Networks (2018)

Estimating the travel time of any path (denoted by a sequence of connected road segments) in a city is of great importance to traffic monitoring, route planning, ridesharing, taxi/Uber dispatching, etc. However, it is a very challenging problem, affected by diverse complex factors, including spatial correlations, temporal dependencies, external conditions (e.g. weather, traffic lights). Prior work usually focuses on estimating the travel times of individual road segments or sub-paths and then summing up these times, which leads to an inaccurate estimation because such approaches do not consider road intersections/traffic lights, and local errors may accumulate. To address these issues, we propose an end-to-end Deep learning framework for Travel Time Estimation called DeepTTE that estimates the travel time of the whole path directly. More specifically, we present a geo-convolution operation by integrating the geographic information into the classical convolution, capable of capturing spatial correlations. By stacking recurrent unit on the geo-convoluton layer, our DeepTTE can capture the temporal dependencies simultaneously. A multi-task learning component is given on the top of DeepTTE, that estimates the travel time of both the entire path and each local path simultaneously during the training phase. The extensive experiments on two large-scale datasets shows our DeepTTE significantly outperforms the state-of-the-art methods.
Advances In Plasma Enhanced Thin Film Deposition (1989)

Plasma enhanced chemical vapor deposition has been used in the semiconductor industry for device passivation and interlayer dielectric applications. The primary function of the glow discharge has been to decompose the reactants to allow lower deposition temperatures. However, in addition to reducing the deposition temperature, RF plasmas can be used to control film stress, improve step coverage and conformality, and obtain exceptional uniformity and process control. Moreover, process induced defects (hillocks, particulates and pinholes) can be greatly reduced by using high rate localized deposition and in situ reactor cleaning. Examples discussed include the deposition of doped and undoped Si0<sub>2</sub>/ SiN and TEOS oxides.
Blind Image Deconvolution by Automatic Gradient Activation (2016)

Blind image deconvolution is an ill-posed inverse problem which is often addressed through the application of appropriate prior. Although some priors are informative in general, many images do not strictly conform to this, leading to degraded performance in the kernel estimation. More critically, real images may be contaminated by nonuniform noise such as saturation and outliers. Methods for removing specific image areas based on some priors have been proposed, but they operate either manually or by defining fixed criteria. We show here that a subset of the image gradients are adequate to estimate the blur kernel robustly, no matter the gradient image is sparse or not. We thus introduce a gradient activation method to automatically select a subset of gradients of the latent image in a cutting-plane-based optimization scheme for kernel estimation. No extra assumption is used in our model, which greatly improves the accuracy and flexibility. More importantly, the proposed method affords great convenience for handling noise and outliers. Experiments on both synthetic data and real-world images demonstrate the effectiveness and robustness of the proposed method in comparison with the state-of-the-art methods.
Cotton Planting Date: Yield, Seedling Survival, and Plant Growth (2009)

New cultivars, changes in technology and production practices, and climate change may have altered the optimal planting time for cotton ( Gossypium hirsutum L.) in the midsouthern United States. A field experiment was conducted from 2002 through 2005 on Gigger silt loam to define planting date (PD) effects on selected cotton cultivars. Six cultivars in 2002 (Deltapine DP555BR and Delta Pearl, Phytogen PHY355, SureGrow SG215BR and SG821, and Stoneville ST4892BR) and eight cultivars in 2003 through 2005 (DP555BR, DeltaPearl, PSC355, DP444BR, Fibermax FM960BR, PHY410RR, ST4892BR, and ST5599BR) were planted on or near eight PDs (25 March; 5, 15, and 25 April; 5, 15, and 25 May; and 5 June). Data were collected on seedling emergence, plant height, main stem node number, nodes above white flower, lint percentage, lint yield, fiber properties, soil and air temperature, rainfall, and photosynthetically active radiation (PAR). Planting date and cultivar affected most measured variables, and although there were some significant PD × Cultivar interactions, these were very small in relation to the main effects. Low soil temperature, few heat units, and rainfall combined to reduce seedling survival at early PD to <15%. For lint yield, the optimal PD was earlier than in previous studies and the highest average yield (1700 kg ha −1 ) was produced from a PD between 15 April and 5 May. Cotton planted at a PD later than 5 May did not benefit from recent changes and improvements in technology and, therefore, incurred yield declines similar to those reported in the 1970s.
An Approach To Correlate The Statistical-Based Lorenz Method, As A Way Of Measuring Heterogeneity, With Kozeny-Carman Equation (2017)

Dealing with carbonate reservoirs can be mind-boggling for the reservoir engineers due to various digenetic processes that cause a variety of properties through the reservoir. A good estimation of the reservoir heterogeneity which is defined as the quality of variation in rock properties with location in a reservoir or formation, can better help modeling the reservoir and thus can offer better understanding of the behavior of that reservoir. Most of reservoirs are heterogeneous formations whose mineralogy, organic content, natural fractures, and other properties vary from place to place. Over years, reservoir engineers have tried to establish methods to describe the heterogeneity, because heterogeneity is important in modeling the reservoir flow and in well testing. Geological methods are used to describe the variations in the rock properties because of the similarities of environments in which different beds have deposited in. To illustrate the heterogeneity of a reservoir vertically, two methods are generally used in petroleum work: Dykstra-Parsons permeability variations (V) and Lorenz coefficient (L) that are reviewed briefly in this paper. The concept of Lorenz is based on statistics and has been used in petroleum from that point of view. In this paper, we correlated the statistical-based Lorenz method to a petroleum concept, i.e. Kozeny-Carman equation and derived the straight line plot of Lorenz graph for a homogeneous system. Finally, we applied the two methods on a heterogeneous field in South Iran and discussed each, separately, with numbers and figures. As expected, these methods show great departure from homogeneity. Therefore, for future investment, the reservoir needs to be treated carefully.
What determines the strength of noncovalent association of ligands to proteins in aqueous solution? (1993)

Free energy perturbation methods using molecular dynamics have been used to calculate the absolute free energy of association of two ligand-protein complexes. The calculations reproduce the significantly more negative free energy of association of biotin to streptavidin, compared to N-L-acetyltryptophanamide/alpha-chymotrypsin. This difference in free energy of association is due to van der Waals/dispersion effects in the nearly ideally performed cavity that streptavidin presents to biotin, which involves four tryptophan residues.
COVID-19 and tuberculosis (2020)

On March 11, 2020, the WHO declared that coronavirus disease 2019 (COVID-19) can be characterized as a pandemic based on the alarming levels of spread and severity and on the alarming levels of inaction. COVID-19 has received worldwide attention as emergency, endangering international public health and economic development. There is a growing body of literatures regarding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as well as COVID-19. This review will focus on the latest advance of epidemiology, pathogenesis, and clinical characteristics about COVID-19. Meanwhile, tuberculosis (TB) remains the leading representative respiratory tract communicable disease threatening public health. There are limited data on the risk of severe disease or outcomes in patients with concurrence of TB and COVID-19. Nevertheless, co-infection of some virus would aggravate TB, such as measles. And tuberculosis and influenza co-infection compared with tuberculosis single infection was associated with increased risk of death in individuals. This review will also introduce the characteristics about the concurrence of TB and emerging infectious diseases to provide a hint to manage current epidemic.
β‐Substituierte Enamine, 12. Mitt. N‐Aryl‐2‐nitro‐ und N‐Aryl‐2‐chlor‐2‐nitro‐enamine (1977)

Abstract 1‐Chlor‐1‐nitro‐aceton ( 4 ), gewonnen durch Einwirkung son Sulfurylchlorid auf Nitroaceton ( 2 ), ist eine beständige Substanz, die in Gegenwart von Alkali in 1‐Chlor‐1‐isonitroso‐aceton ( 9 ) übergeht und mit Diazomethan unter Bildung von 1‐Chlor‐1‐methoximino‐aceton ( 8 ) reagiert. Anilin spaltet 4 unter Bildung von Acetanilid und Chlor‐nitromethan, jedoch gelingt in Gegenwart von Titantetrachlorid die Kondensation zu 1‐Chlor‐1‐nitro‐2‐phenylamino‐propen ( 3a ). Man kann auch Nitroaceton ( 2 ) zunächst mit primären aromatischen Aminen zu β‐Nitroenaminen 1 kondensieren, die durch Einwirkung von N‐Chlorsuccinimid in N‐Aryl‐2‐chlor‐2‐nitro‐enamine 3 zu überführen sind.
Simultaneous Saccharification and Fermentation of Highly Digestible Variety of Grain Sorghum for Ethanol Production (2007)

The simultaneous saccharification and fermentation of corn and different varieties of grain sorghum (i.e. high digestible and low digestible) were carried out using commercially available alpha amylase and glucoamylase enzymes and Saccharomyces cerevisiea yeast. The hydrolysis and fermentation conditions, such as enzyme, yeast and substrate concentrations, pH and temperature in all the runs were similar so that the ethanol yield will just be dependent on the starch digestibility. Among the three substrates, the highest ethanol concentration was obtained from the highly digestible sorghum. The study revealed that the high yielding sorghum cultivars with modified endosperm matrices can be used as an alternative for corn and can be optimized as a substrate for low energy input ethanol production. Since the food consumption demand for sorghum is lower compared to corn, the new variety of highly digestible grain sorghum has a great potential for ethanol fermentation, especially in semi-arid region. Savings in energy and time in this process could be accomplished via saccharification at lower temperature (32oC) concurrent with the fermentation process. The fermentation system needs to be optimized to ensure that there is no shortage of reducing sugars during the entire fermentation process.