gebhart/patrepeval huggingface dataset:
Passaging HuES Human Embryonic Stem Cell-lines with Trypsin. (2006)

In this video we demonstrate how our lab routinely passages HuES human embryonic stem cell lines with trypsin. Human embryonic stem cells are artifacts of cell culture, and tend to acquire karyotypic abnormalities with high population doublings. Proper passaging is essential for maintaining a healthy, undifferentiated, karyotypically normal HuES human embryonic stem cell culture. First, an expanding culture is washed in PBS to remove residual media and cell debris, then cells are overlaid with a minimal volume of warm 0.05% Trypsin-EDTA. Trypsin is left on the cells for up to five minutes, then cells are gently dislodged with a 2mL serological pipette. The cell suspension is collected and mixed with a large volume of HuES media, then cells are collected by gentle centrifugation. The inactivated trypsin media mixture is removed, and cells resuspended in pre-warmed HuES media. An appropriate split ratio is calculated (generally 1:10 to 1:20), and cells re-plated onto a 1-2 day old plate containing a monolayer of irradiated mouse embryonic fibroblast feeder cells. The newly seeded HuES culture plate is left undisturbed for 48 hrs, then media is changed every day thereafter. It is important not to trpsinize down to a single cell suspension, as this increases the risk of introducing karyotypic abnormalities.
Evidence for an Abrupt Transition between SiO<sub>2</sub> and SiC from EELS and <i>Ab Initio</i> Modelling (2019)

Electron energy loss spectroscopy (EELS) and ab initio simulations are combined in this study to produce an atomistic interpretation of the interface morphology in lateral 4H-SiC / SiO 2 MOSFETs with deposited gate oxides. This allows the question of interface abruptness, and the presence the postulated SiO x C y interlayer to be explored for a subset of devices with deposited oxides. From comparison between EELS and ab initio calculation the interfaces considered are best described as abrupt, but stepped, transitioning without any of the carbon excess or SiO x C y interlayer that have been described for other devices observed.
Novel Approach for Metallic Surface-Initiated Atom Transfer Radical Polymerization Using Electrografted Initiators Based on Aryl Diazonium Salts (2005)

This paper reports on the preparation of poly(methyl methacrylate) (PMMA), poly(n-butyl acrylate) (PBA), and polystyrene (PS) brushes at the surface of conducting materials that were modified by the electrochemical reduction of a brominated aryl diazonium salt BF4-, +N2-C6H4-CH(CH3)-Br (D1). The grafted organic species -C6H4-CH(CH3)-Br was found to be very effective in initiating atom transfer radical polymerization (ATRP) of vinyl monomers. This novel approach combining diazonium salts and ATRP allowed PMMA, PBA, and PS brushes to be grown from the surface of iron electrodes. The polymer films were characterized in terms of their chemical structure by infrared reflection absorption spectroscopy and X-ray photoelectron spectroscopy. Atomic force microscopy studies indicated that the polymer brushes are densely packed. Contact angle measurements of water drops on PS and PMMA brushes were 88.1 +/- 2.0 and 70.3 +/- 2.1 degrees, respectively, which is consistent with the published wettability data for the corresponding polymer sheets.
A New Approach to Simulate Transient Heat Transfer Within the Discrete Element Method (2008)

The scope of this paper is to demonstrate the ability of a radial temperature model for spherical particles to allow for the calculation of the thermal behavior of granular assemblies with large particle numbers using Discrete Element simulations. The model efficiently accounts for inner particle heat transfer and is based on an analytical solution of the differential equation of heat conduction for a solid spherical particle with time and radius as independent parameters. It avoids the high computational costs of a numerical solution as well as the shortcoming of the assumption of uniform temperature profiles. To account for conduction due to multiple particle-particle or particle-wall contacts, each particle is divided into segments. Contact heat transfer on the particle scale is analyzed, comparisons with numerical solutions of Siu and Lee [1] for a contact of two spheres and a contact of a sphere with a wall were made for the adjustment and verification of the model. Results of a Discrete Element simulation using the radial temperature model for spheres stirred by moving walls are presented.
Ferritin nanoparticles as magnetic resonance reporter gene (2009)

Dynamic imaging of gene expression in live animals is among the exciting challenges of molecular imaging. To achieve that, one of the approaches is to use reporter genes that encode for the synthesis of easily detectable products. Such reporter genes can be designed to be expressed under the control of the regulatory elements included in a promoter region of a gene of interest, thus allowing the use of the same reporter gene for the detection of multiple genes. The most commonly used reporter genes include the firefly light-generating enzyme luciferase and the green fluorescent protein detectable by bioluminescence and fluorescence optical imaging, respectively. Over the last years a number of studies demonstrated the ability to use the iron-binding protein ferritin as a reporter gene that allows the detection of gene expression by magnetic resonance imaging (MRI). MRI provides high spatial resolution and soft tissue contrast for deep tissues along with a large arsenal of functional and anatomical contrast mechanisms that can be correlated with gene expression, and can potentially be translated into clinical use.
GATE simulation of a new design of pinhole SPECT system for small animal brain imaging (2017)

Small animal SPECT imaging has gained an increased interest over the past decade since it is an excellent tool for developing new drugs and tracers. Therefore, there is a huge effort on the development of cost-effective SPECT detectors with high capabilities. The aim of this study is to simulate the performance characteristics of new designs for a cost effective, stationary SPECT system dedicated to small animal imaging with a focus on mice brain. The conceptual design of this SPECT system platform, Stationary Small Animal SSA-SPECT, is to use many pixelated CsI:TI detector modules with 0.4 mm x 0.4 mm pixels in order to achieve excellent intrinsic detector resolution where each module is backed by a single pinhole collimator with 0.3 mm hole diameter. In this work, we present the simulation results of four variations of the SSA-SPECT platform where the number of detector modules and FOV size is varied while keeping the detector size and collimator hole size constant. Using the NEMA NU-4 protocol, we performed spatial resolution, sensitivity, image quality simulations followed by a Derenzo-like phantom evaluation. The results suggest that all four SSA-SPECT systems can provide better than 0.063% system sensitivity and &amp;lt; 1.5 mm FWHM spatial resolution without resolution recovery or other correction techniques. Specifically, SSA-SPECT-1 showed a system sensitivity of 0.09% in combination with 1.1 mm FWHM spatial resolution.
Pulsed-DC Electrophoretic Deposition (EPD) of Aqueous Alumina Suspension for Controlling Bubble Incorporation and Deposit Microstructure (2009)

Electrophoretic deposition (EPD) from aqueous suspension generally forms deposit containing incorporated bubbles because of evolution of gases at electrodes due to electrolysis of water. We have demonstrated here that application of pulsed voltage /current instead of continuous DC enables controlling the amount of bubble incorporation and obtain bubble-free deposits during EPD of aqueous suspension. The yield and bubble incorporation decreased progressively with decrease in size of the applied pulse. A characteristic band of deposition window was found in the plot of voltage/current vs. pulse width within which smooth and bubble-free deposits are obtained. The window is wider at low applied voltages/currents than at higher voltages/currents implying that it is more easier to control the pulsed EPD at lower applied voltages and/currents. No deposition occurred below the window whereas deposits with incorporated bubbles formed above the window. Suppression of bubbles with decreasing pulse size was attributed to decrease in the amount of hydrogen evolved per pulse and verified by monitoring the gain in weight of palladium (Pd) electrode used as cathode during electrolysis of water.
The Online Survey: An Efficient And Effective Means Of Engineering Graduate Student Assessment (2020)

A survey is a potent tool for assessing student needs and concerns to improve an engineering graduate program as demonstrated by recent, documented survey studies conducted in an environmental engineering graduate program. We extended the work done in prior studies employing paper surveys by conducting an online student assessment for the first time in the program history. With regard to survey design and analysis methods, we mostly adopted the methods established in the prior studies.
KlebSeq, a Diagnostic Tool for Surveillance, Detection, and Monitoring of Klebsiella pneumoniae (2016)

Health care-acquired infections (HAIs) kill tens of thousands of people each year and add significantly to health care costs. Multidrug-resistant and epidemic strains are a large proportion of HAI agents, and multidrug-resistant strains of Klebsiella pneumoniae, a leading HAI agent, have caused an urgent public health crisis. In the health care environment, patient colonization by K. pneumoniae precedes infection, and transmission via colonization leads to outbreaks. Periodic patient screening for K. pneumoniae colonization has the potential to curb the number of HAIs. In this report, we describe the design and validation of KlebSeq, a highly informative screening tool that detects Klebsiella species and identifies clinically important strains and characteristics by using highly multiplexed amplicon sequencing without a live-culturing step. We demonstrate the utility of this tool on several complex specimen types, including urine, wound swabs and tissue, and several types of respiratory and fecal specimens, showing K. pneumoniae species and clonal group identification and antimicrobial resistance and virulence profiling, including capsule typing. Use of this amplicon sequencing tool to screen patients for Klebsiella carriage could inform health care staff of the risk of infection and outbreak potential. KlebSeq also serves as a model for next-generation molecular tools for public health and health care, as expansion of this tool can be used for several other HAI agents or applications.
Neurogenomic signatures of spatiotemporal memories in time-trained forager honey bees (2011)

Honey bees can form distinct spatiotemporal memories that allow them to return repeatedly to different food sources at different times of day. Although it is becoming increasingly clear that different behavioral states are associated with different profiles of brain gene expression, it is not known whether this relationship extends to states that are as dynamic and specific as those associated with foraging-related spatiotemporal memories. We tested this hypothesis by training different groups of foragers from the same colony to collect sucrose solution from one of two artificial feeders; each feeder was in a different location and had sucrose available at a different time, either in the morning or afternoon. Bees from both training groups were collected at both the morning and afternoon training times to result in one set of bees that was undergoing stereotypical food anticipatory behavior and another that was inactive for each time of day. Between the two groups with the different spatiotemporal memories, microarray analysis revealed that 1329 genes were differentially expressed in the brains of honey bees. Many of these genes also varied with time of day, time of training or state of food anticipation. Some of these genes are known to be involved in a variety of biological processes, including metabolism and behavior. These results indicate that distinct spatiotemporal foraging memories in honey bees are associated with distinct neurogenomic signatures, and the decomposition of these signatures into sets of genes that are also influenced by time or activity state hints at the modular composition of this complex neurogenomic phenotype.
Beiträge zur Chemie des Bors. VIII. Über Die Einwirkung von Schwefel auf Alkaliboranate (1961)

Abstract Lithiumboranat reagiert mit Schwefel in Ätherlösung unter Wasserstoffentwicklung zu Lithiumsulfid und der Verbindung LiB 3 S 2 H 6 . In Abwesenheit eines Lösungsmittels erhält man aus Schwefel und den Alkaliboranaten oberhalb von 200°C Alkalimetathioborate MeBS 2 .
PAK5, a New Brain-Specific Kinase, Promotes Neurite Outgrowth in N1E-115 Cells (2002)

We have characterized a new member of the mammalian PAK family of serine/threonine kinases, PAK5, which is a novel target of the Rho GTPases Cdc42 and Rac. The kinase domain and GTPase-binding domain (GBD) of PAK5 are most closely related in sequence to those of mammalian PAK4. Outside of these domains, however, PAK5 is completely different in sequence from any known mammalian proteins. PAK5 does share considerable sequence homology with the Drosophila MBT protein (for "mushroom body tiny"), however, which is thought to play a role in development of cells in Drosophila brain. Interestingly, PAK5 is highly expressed in mammalian brain and is not expressed in most other tissues. We have found that PAK5, like Cdc42, promotes the induction of filopodia. In N1E-115 neuroblastoma cells, expression of PAK5 also triggered the induction of neurite-like processes, and a dominant-negative PAK5 mutant inhibited neurite outgrowth. Expression of activated PAK1 caused no noticeable changes in these cells. An activated mutant of PAK5 had an even more dramatic effect than wild-type PAK5, indicating that the morphologic changes induced by PAK5 are directly related to its kinase activity. Although PAK5 activates the JNK pathway, dominant-negative JNK did not inhibit neurite outgrowth. In contrast, the induction of neurites by PAK5 was abolished by expression of activated RhoA. Previous work has shown that Cdc42 and Rac promote neurite outgrowth by a pathway that is antagonistic to Rho. Our results suggest, therefore, that PAK5 operates downstream to Cdc42 and Rac and antagonizes Rho in the pathway, leading to neurite development.
Impacts of long-term CPAP therapy on fatty liver in male OSA patients with abdominal obesity (2014)

Background: The evidences for significant relationships between obstructive sleep apnoea (OSA) and fatty liver is gradually accumulating. However, placebo-controlled studies in OSA patients with mild fatty liver reported that several months of continuous positive airway pressure (CPAP) therapy did not improve fatty liver. On the other hand, the strong causal factor of fatty liver is abdominal obesity, the central factor of metabolic syndrome. The aim of this study is to evaluate the changes in liver fat accumulation (LFA) of OSA patients with abdominal obesity and developed fatty liver after longer-term CPAP therapy. Methods: The participants were 61 male OSA patients who had started CPAP between 2008 and 2010 and had abdominal obesity (waist circumference ≥ 85 cm; Japanese criterion) at the time. At the follow-up examination, the data from abdominal computed tomography (CT), fasting blood tests and CPAP memory cards were collected. LFA was determined as an average CT value of liver. Visceral fat accumulation and subcutaneous fat accumulation were also measured. Results: The average age, BMI and LFA at the baseline, and the average period and daily usage time of CPAP were 57.2 y, 28.6 kg/m 2 , 49.7 HU, 31.3 M, and 4.8 h/d, respectively. In the entire group, LFA did not change during the CPAP therapy. On the other hand, in those who had developed fatty liver (CT value of liver &amp;lt; 50 HU) at the baseline, LFA decreased after the CPAP in spite of stable BMI, visceral and subcutaneous fat accumulation, and other metabolic conditions. Conclusion: Long-term CPAP may contribute to improvement of fatty liver in OSA patients with abdominal obesity and developed fatty liver.
Towards an Understanding of the Value of Cooperation in Uncertain World (2011)

Recent work has provided tantalizing hints that small amounts of cooperation may actually hurt a group's performance rather than help it. In this paper, we take a systematic look at the value of cooperation. Using a simple cooperative task where agents can act effectively individually but where high levels of cooperation will intuitively lead to better behavior, we investigated when and how cooperation helped overall performance. We systematically varied properties of the environment, e.g., the amount of uncertainty, and how much of what sort of cooperation the agents would perform, e.g., information sharing, resource allocation etc. Our experimental results show that, even if communication were free, and while typically coordination helps the team, under some circumstances, the team may be better off not coordinating at all than coordinating a little bit. We show that the level of uncertainty the agents face and their initial understandings of the environment determine whether a small amount of coordination is useful.
Lixiviation Effects In Glass Polishing (1989)

From our glass polishing process of precision optics we know that its physical-chemical nature frequently leads to a complex interaction of several parameters determining the process and the resulting quality. Surface analysis using SIMS and WDX prove that surface and sharp edge polishing of integrated optics chips has to be watched critically in order to obtain useful parts in a reproducible manner.
Antibodies to nonhistone nuclear antigens and antilymphocyte antibodies among children and adults with systemic lupus erythematosus and their relatives. (1984)

Antibodies to nonhistone nuclear antigens are found with increased frequency in the serum of patients with systemic lupus erythematosus (SLE) and their first degree relatives. We measured the prevalence of ANA and antibodies against DNA, RNP, Sm, SSA, and SSB as well as antilymphocyte antibodies (ALA) in the serum of 24 patients with childhood onset SLE and 94 of their first degree relatives and compared the prevalence of these same antibodies in 8 patients with adult onset SLE and 33 of their first degree relatives. Antibodies against DNA, RNP, and Sm occurred more frequently in the serum of adult onset SLE patients. Among the first degree relatives ALA occurred more frequently in the sera of relatives of patients with childhood onset SLE, and parental antibodies to SSA were associated with the occurrence of childhood onset SLE in 3/24 cases. Since antibodies to SSA have been shown to be related to neonatal SLE their possible relationship to childhood SLE requires further study.
Serum C-reactive Protein Change after Extracorporeal Shock Wave Lithotripsy (1995)

The purpose of this study was to evaluate the tissue effect of extracorporeal shock wave lithotripsy (ESWL), based on changes in serum C-reactive protein (CRP) levels. Forty-eight patients received 51 treatments of ESWL for 36 renal and 15 ureteral stones. Shock waves were applied by Siemens Lithostar-II unit with mean 3508 impulses (range 874 to 4000) and with mean voltage 17.2 KV (range 15.3 to 18.9). Patients who were treated with ESWL for urinary stones were evaluated by serum CRP level before ESWL, immediately after, then six hours, one day and one week after ESWL. Two-way analysis of variance (ANOVA) was used to compare the changes in serum CRP levels. The post-ESWL CRP levels increased, ranging from 38% to 65% in all the group studies. But statistically, there was no significant change in serum CRP levels among these groups. To conclude, ESWL did not cause significant tissue damage, according to evaluation of CRP level.
Shifted Pixel Method for Through-Wall Radar Imaging (2012)

The current approach for accurate localization of targets behind walls using radar involves coupling of wall properties estimation and target location estimation. This involves the solution of a transcendental equation using approximations over several iterations. A new approach for through-wall target localization proposed in this paper which decouples the through-wall localization problem into the following three separate components: 1) physical properties of the wall, 2) analytic solution of target location; and 3) numerical approach to pixel interpolation. In this way, the target location can be calculated using simple algorithms without the need to solve complicated transcendental equations. Both wall properties and a more accurate numerical method for pixel interpolation can be dealt with independently to improve the accuracy of target location estimation.
Careful what you wish for - Risk mitigation for unplanned behaviors in distributed diagnostic software systems (2007)

There are several efforts underway to standardize interfaces between software components responsible for various elements of system test and diagnosis. Frameworks currently being defined by the DoD ARI and ATML Consortium seek to define data exchange interfaces across application boundaries with the goals of creating distributed information systems that will realize efficiencies of scale through the reuse of information. This paper makes the case that engineering common sense be applied to minimize the risk associated with ad hoc distributed system design to acceptable levels and realize the expected benefits. This demands that one must gain a sufficient level of understanding of the archetypical information elements within each of the distributed components, the relation of these elements across distributed components, and the transformations that occur as information flows between distributed system components. This understanding can be provided by treating the development of the proposed distributed system as an analytical engineering exercise to understand and model fundamental system component relationships and interactions.
Finding the Event Structure of Neuronal Spike Trains (2020)

Neurons in sensory systems convey information about physical stimuli in their spike trains. In vitro, single neurons respond precisely and reliably to the repeated injection of the same fluctuating current, producing regions of elevated firing rate, termed events. Analysis of these spike trains reveals that multiple distinct spike patterns can be identified as trial-to-trial correlations between spike times (Fellous, Tiesinga, Thomas, & Sejnowski, 2004). Finding events in data with realistic spiking statistics is challenging because events belonging to different spike patterns may overlap. We propose a method for finding spiking events that uses contextual information to disambiguate which pattern a trial belongs to. The procedure can be applied to spike trains of the same neuron across multiple trials to detect and separate responses obtained during different brain states. The procedure can also be applied to spike trains from multiple simultaneously recorded neurons in order to identify volleys of near-synchronous activity or to distinguish between excitatory and inhibitory neurons. The procedure was tested using artificial data as well as recordings in vitro in response to fluctuating current waveforms.