gebhart/patrepeval huggingface dataset:
Gene expression profiling of cervical cancer and cell line models (2006)

869 Introduction: The main objective of this research was to determine how well cervical cancer cell lines model cervical cancer by using gene expression profiling. Many studies choose one or two cervical cancer cell lines without regard to how well they actually represent tissue. Therefore, the outcome of this research was to characterize nine commonly used cell lines in terms of normal cervical tissue and invasive cervical cancer based on a collection of samples. In addition, several cell lines were cultured in different types of media to investigate media changes and model performance. Finally, several cell lines were also cultured in organotypic environments where they are more phenotypically similar to actual cervical tissue. It was our hypothesis that it is possible to increase the accuracy of cell lines as models of cancer by 1) simply selecting different media, 2) culturing cell lines in an organotypic environment, and 3) selecting primary cell lines obtained from an in vivo source. Methods: Individual cell lines were cultured three times independently to account for biological variation. Biopsies were obtained through various tissue banks. In all samples, total RNA was isolated, mRNA was amplified, and cDNA was generated and hybridized to cDNA microarrays containing 45,000 unique sequences. In each experiment, a universal human reference was used to enable expression profile comparisons among all experiments. Results: In order to identify which cell lines and conditions best model tissue, we compared the gene expression of each cell line and condition to the gene expression of a set of cervical cancers. Better cell line models have more expression overlap with the cancer set and thus have a higher correlation coefficient. Our results indicate that many things can be done to improve the performance of cell lines as models of tissue. Adding more nutrients to the media SiHa cells were cultured in vastly improved their performance in modeling invasive cervical cancer. Culturing cell lines in an organotypic environment also improves their performance as a model. Primary cells obtained from patients were the best models of cervical cancer. However, as obtaining and culturing primary cells is difficult, the next best model would be to use the cell line C4-I. However, despite the fact that some models are better than others, in general expression correlation between cell lines and tissues is low, indicating cell lines are poor models of tissue. Conclusions: In conclusion, selecting appropriate cell lines as models of cervical cancer should not be an arbitrary process. When researching a particular gene, it is not only necessary that the cell line chosen expresses the gene of interest, but we can also move beyond a single gene emphasis and chose a model that more closely represents the tissue of interest. This can be optimized by examining media effects and culturing in an organotypic environment.
Control of Self-Assembly through the Influence of Terminal Hydroxymethyl Groups on the Metal Coordination of Pyrimidine−Hydrazone Cu(II) Complexes (2010)

The synthesis and characterization of 6-hydroxymethylpyridine-2-carboxaldehyde (2-methyl-pyrimidine-4,6-diyl)bis(1-methylhydrazone) (1) is reported. Ligand 1 was designed as a ditopic pyrimidine-hydrazone molecular strand with hydroxymethyl groups attached to the terminal pyridine rings. Coordination of 1 with Cu(ClO(4))(2) x 6 H(2)O or Cu(SO(3)CF(3))(2) x 4 H(2)O in a 1:2 molar ratio resulted in the dinuclear Cu(II) complexes [Cu(2)1(CH(3)CN)(4)](ClO(4))(4) x CH(3)CN (4) and [Cu(2)1(SO(3)CF(3))(2)(CH(3)CN)(2)](SO(3)CF(3))(2) x CH(3)CN (5). X-ray crystallography and (1)H NMR NOESY experiments showed that 1 adopted a horseshoe shape with both pyrimidine-hydrazone (pym-hyz) bonds in a transoid conformation, while 4 and 5 were linear in shape, with both pym-hyz bonds in a cisoid conformation. Coordination of 1 with Cu(ClO(4))(2) x 6 H(2)O or Cu(SO(3)CF(3))(2) x 4 H(2)O in a 1:1 molar ratio resulted in three different bent complexes, [Cu(1H)(ClO(4))(2)](ClO(4)) (6), [Cu(1H)(CH(3)CN)](ClO(4))(3) x 0.5 H(2)O (7), and [Cu1(SO(3)CF(3))](2)(SO(3)CF(3))(2) x CH(3)CN (8), where the pym-hyz bond of the occupied coordination site adopted a cisoid conformation, while the pym-hyz bond of the unoccupied site retained a transoid conformation. Both 6 and 7 showed protonation of the pyridine nitrogen donor in the empty coordination site; complex 8, however, was not protonated. A variety of Cu(II) coordination geometries were seen in structures 4 to 8, including distorted octahedral, trigonal bipyramidal, and square pyramidal geometries. Coordination of the hydroxymethyl arm in the mononuclear Cu(II) complexes 6, 7, and 8 appeared to inhibit the formation of a [2 x 2] grid by blocking further access to the Cu(II) coordination sphere. In addition, the terminal hydroxymethyl groups contributed to the supramolecular structures of the complexes through coordination to the Cu(II) ions and hydrogen bonding.
Micromachined thermally based CMOS microsensors (1998)

An integrated circuit (IC) approach to thermal microsensors is presented. The focus is on thermal sensors with on-chip bias and signal conditioning circuits made by industrial complementary metal-oxide-semiconductor (CMOS) IC technology in combination with post-CMOS micromachining or deposition techniques. CMOS materials and physical effects pertinent to thermal sensors are summarized together with basic structures used for microheaters, thermistors, thermocouples, thermal isolation, and heat sinks. As examples of sensors using temperature measurement, we present micromachined CMOS radiation sensors and thermal converters. Examples for sensors based on thermal actuation include thermal flow and pressure sensors, as well as thermally excited microresonators for position and chemical sensing. We also address sensors for the characterization of process-dependent thermal properties of CMOS materials, such as thermal conductivity, Seebeck coefficient, and heat capacity, whose knowledge is indispensable for thermal sensor design. Last, two complete packaged microsystems-a thermoelectric air-flow sensor and a thermoelectric infrared intrusion detector-are reported as demonstrators.
Selective recruitment of single motor units in human flexor digitorum superficialis muscle during flexion of individual fingers (2005)

Flexor digitorum superficialis (FDS) is an extrinsic multi-tendoned muscle which flexes the proximal interphalangeal joints of the four fingers. It comprises four digital components, each with a tendon that inserts onto its corresponding finger. To determine the degree to which these digital components can be selectively recruited by volition, we recorded the activity of a single motor unit in one component via an intramuscular electrode while the subject isometrically flexed each of the remaining fingers, one at a time. The finger on which the unit principally acted was defined as the 'test finger' and that which flexed isometrically was the 'active' finger. Activity in 79 units was recorded. Isometric finger flexion forces of 50% maximum voluntary contraction (MVC) activated less than 50% of single units in components of FDS acting on fingers that were not voluntarily flexed. With two exceptions, the median recruitment threshold for all active-test finger combinations involving the index, middle, ring and little finger test units was between 49 and 60% MVC (60% MVC being the value assigned to those not recruited). The exceptions were flexion of the little finger while recording from ring finger units (median: 40% MVC), and vice versa (median: 2% MVC). For all active-test finger combinations, only 35/181 units were activated when the active finger flexed at less than 20% MVC, and the fingers were adjacent for 28 of these. Functionally, to recruit FDS units during grasping and lifting, relatively heavy objects were required, although systematic variation occurred with the width of the object. In conclusion, FDS components can be selectively activated by volition and this may be especially important for grasping at high forces with one or more fingers.
Process Analytical Technology (PAT) in Insect and Mammalian Cell Culture Processes: Dielectric Spectroscopy and Focused Beam Reflectance Measurement (FBRM) (2013)

Modern bioprocesses demand for a careful definition of the critical process parameters (CPPs) already during the early stages of process development in order to ensure high-quality products and satisfactory yields. In this context, online monitoring tools can be applied to recognize unfavorable changes of CPPs during the production processes and to allow for early interventions in order to prevent losses of production batches due to quality issues. Process analytical technologies such as the dielectric spectroscopy or focused beam reflectance measurement (FBRM) are possible online monitoring tools, which can be applied to monitor cell growth as well as morphological changes. Since the dielectric spectroscopy only captures cells with intact cell membranes, even information about dead cells with ruptured or leaking cell membranes can be derived. The following chapter describes the application of dielectric spectroscopy on various virus-infected and non-infected cell lines with respect to adherent as well as suspension cultures in common stirred tank reactors. The adherent mammalian cell lines Vero (African green monkey kidney cells) and hMSC-TERT (telomerase-immortalized human mesenchymal stem cells) are thereby cultured on microcarrier, which provide the required growth surface and allow the cultivation of these cells even in dynamic culture systems. In turn, the insect-derived cell lines S2 and Sf21 are used as examples for cells typically cultured in suspension. Moreover, the FBRM technology as a further monitoring tool for cell culture applications has been included in this chapter using the example of Drosophila S2 insect cells.
Properties of Cu(II) and Ni(II) Sulfides Prepared by Coprecipitation in Aqueous Solution (1999)

Among semiconductors, metal sulfides are very interesting materials that may be used for solar energy conversion arrangements. We prepared a series of CuxNi1-xS powders, where x = 0.05, 0.20, 0.50, and 0.80, by spontaneous precipitation. Various stoichiometries of Cu(NO3)2, Ni(NO3)2, and (NH4)2S solutions at 25 °C and pH 2.50, at conditions in which the aqueous solutions were supersaturated with respect to CuS and NiS, yielded precipitates corresponding to intermediate mixed sulfides. The appearance of new peaks in the powder X-ray diffraction spectra suggested the formation of new phases. Measurements of the resistance of the bulk solids as a function of temperature for the preparations with x = 0.05, 0.20, and 0.50 showed a decrease with increasing temperature. A hysteresis was found upon thermal cycling of the sulfide preparations, possibly due to changes in the solid state that affect the energy bands of the semiconductors. The Cu and Ni sulfide preparations with x = 0.80 showed metallic behavior. All preparations were highly charged when suspended in aqueous media, and the electrical charge was found to depend strongly on the activity of copper ion in solutions equilibrated with the solid phase. Finally, current potential curves of electrodes prepared from the precipitated sulfides under constant illumination gave values for the open circuit potential as high as 0.868 V, with 0.119 mA for the photocurrent and 0.58 for the field factor. These values are encouraging for the potential application of these materials in cells for the conversion of solar into electric energy.
Energy efficiency analysis of a C-RAN with distance—Based power control (2017)

Reducing the global energy consumption is an important goal of fifth generation (5G) networks. The cloud-radio access network (C-RAN) along with power control mechanism can potentially offer the much sought after relief in energy consumption by enabling centralized processing. In this paper, a tunable downlink distance-based power control mechanism is considered and its effects on network-level coverage probability, along with energy efficiency (EE) of C-RAN are studied. Finding from analysis based on stochastic geometry reveals that distance-based power control can provide up to a seven-fold increase in the EE of C-RAN without power control. The significance of this finding lies in showing that by carefully tuning the transmit power, interference reduces and the achievable average rate improves, resulting in increased EE.
One contact for every twelve residues allows robust and accurate topology‐level protein structure modeling (2013)

A number of methods have been described for identifying pairs of contacting residues in protein three-dimensional structures, but it is unclear how many contacts are required for accurate structure modeling. The CASP10 assisted contact experiment provided a blind test of contact guided protein structure modeling. We describe the models generated for these contact guided prediction challenges using the Rosetta structure modeling methodology. For nearly all cases, the submitted models had the correct overall topology, and in some cases, they had near atomic-level accuracy; for example the model of the 384 residue homo-oligomeric tetramer (Tc680o) had only 2.9 Å root-mean-square deviation (RMSD) from the crystal structure. Our results suggest that experimental and bioinformatic methods for obtaining contact information may need to generate only one correct contact for every 12 residues in the protein to allow accurate topology level modeling.
An Adenylic Acid-Rich Sequence in Messenger RNA of HeLa Cells and Its Possible Relationship to Reiterated Sites in DNA (1971)

Messenger RNA from HeLa cells contains, as part of the polynucleotide chain, RNase-resistant sequences that are labeled by adenosine but not by uridine. Heterogeneous nuclear RNA also contains adenylate-rich RNase-resistant regions, but in lower proportion than messenger RNA. Hybridization to DNA of (32)P-labeled messenger RNA reveals that some of the adenylate-rich region is included in the rapidly-hybridizing fraction.
THE ROLE OF THE GUT IN MULTIPLE ORGAN FAILURE (MOF) (2006)

The gut is both the instigator and victim of MOF. Our current global hypothesis is that novel therapeutic interventions can modulate gut inflammation and dysfunction related to MOF to improve patient outcome. Project 1 is identifying the key molecular events by which therapeutic interventions differentially modulate protective anti-inflammation over injurious pro-inflammation. In the intensive care unit (ICU) the Clinical Core has standardized shock resuscitation (resus) and identified that crystalloid resus causes problematic gut edema. Project 2 is studying gut edema and its effects on gut function. Project 3 is examing the mechanism by which hypertonic saline resus limits ischemia reperfusion induced gut inflammation. A minority supplement is studying novel adjuncts in this model. In the ICU the Clinical Core has standardized early enteral nutrition (EEN) but has identified that after severe shock EEN can cause devastating nonocclusive bowel necrosis. A K-08 project is investigating how intraluminal nutrients can protect against IR inflammation. Additionally, the Clinical Core has identified that gastroparesis is an obstacle in EEN and that the stomach remains alkinalized in the early postinjury period. Project 4 is studying how sedative doses of ketamine instead of morphine can limit gastric inflammation, alkinalization and gastroparesis. A clinical trial is proposed. A 2nd K08 is studying the role of matrix metalloproteinases in sepsis induced gastric inflammation. In the ICU the Clinical Core has observed that bile reflux contributes to stress gastritis. Project 5 is exploring how novel phospholipids can maintain the hydrophobic barrier which protects against bile reflux induced inflammation. Through collaborative multidisciplinary efforts the UTHMS TRC is improving our basic understanding of how the gut contributes to adverse outcome in critical illness and is providing an environment in which to train the next generation of clinical scientists. NIGMS P50 GM38529, T32GM08792, K08 GM62975, K08 GM070812.
The Mind and Brain of Short-Term Memory (2007)

The past 10 years have brought near-revolutionary changes in psychological theories about short-term memory, with similarly great advances in the neurosciences. Here, we critically examine the major psychological theories (the "mind") of short-term memory and how they relate to evidence about underlying brain mechanisms. We focus on three features that must be addressed by any satisfactory theory of short-term memory. First, we examine the evidence for the architecture of short-term memory, with special attention to questions of capacity and how--or whether--short-term memory can be separated from long-term memory. Second, we ask how the components of that architecture enact processes of encoding, maintenance, and retrieval. Third, we describe the debate over the reason about forgetting from short-term memory, whether interference or decay is the cause. We close with a conceptual model tracing the representation of a single item through a short-term memory task, describing the biological mechanisms that might support psychological processes on a moment-by-moment basis as an item is encoded, maintained over a delay with some forgetting, and ultimately retrieved.
Session 15 overview: Data converter techniques (2013)

Lists the sessions held at the conference proceedings.
Spectrally Tunable and Stable Electroluminescence Enabled by Rubidium Doping of CsPbBr3 Nanocrystals (2019)

Abstract Perovskite nanocrystals exhibit high photoluminescence quantum yields (PLQYs) and tunable bandgaps from ultraviolet to infrared. However, blue perovskite light‐emitting diodes (LEDs) suffer from color instability under applied bias. Developing narrow‐bandwidth deep‐blue emitters will maximize the color gamut of display technologies. Mixed anion approaches suffer from halide segregation that leads to their spectral instability. Here instead, a mixed cation strategy is employed whereby Rb + is directly incorporated during synthesis into CsPbBr 3 nanocrystals. Blue‐emitting perovskite quantum dots (QDs) with stable photoluminescence, PLQYs greater than 60%, tunable emission from 460 to 500 nm, and narrow emission linewidths (&lt;25 nm) are reported. The strategy retains a pure bromine crystal structure resulting in color‐pure stable electroluminescence at operating voltages of up to 10 V, peak external quantum efficiencies (EQEs) of 0.87% and 0.11% for sky‐blue (490 nm), and deep‐blue (464 nm) devices. The sky‐blue devices exhibit the highest combined luminance of 93 cd m −2 at an EQE of 0.75%, the best reported to date of perovskite QD LEDs.
Estimation of dynamic chemoresponsiveness in wakefulness and non-rapid-eye-movement sleep (1995)

We developed a method for quantifying dynamic chemoresponsiveness on the basis of the ventilatory response to pseudorandom binary CO2 stimulation. The dynamic chemoreflex gain (GD) and effective time delay (TDeff) relating breath-to-breath fluctuations in alveolar PCO2 to ventilation were evaluated at frequencies between 0 and 0.05 Hz. Application of the method to simulated "data" showed that estimation errors in GD and TDeff were most likely to be minimized in the range of 0.01-0.03 Hz, corresponding to periodicities of 30-100 s. Estimation of TDeff was generally more susceptible to error than that of GD because of the limited time resolution of the breath-by-breath measurements. In eight awake normal adults, we compared estimates of GD derived from the pseudorandom binary CO2 stimulation test with peripheral and central hypercapnic sensitivities deduced from single-breath and Read rebreathing measurements in the same subject. GD at 0.02 Hz was highly correlated with peripheral hypercapnic sensitivity but poorly correlated with central hypercapnic sensitivity, underscoring the importance of the peripheral chemoreflexes in mediating ventilatory responses to phasic stimuli. Application of the procedure to a different group of 10 healthy volunteers during wakefulness and stage 2 sleep showed decreases in GD in 8 subjects but increases in 2 subjects. However, for the group as a whole, GD and TDeff did not change significantly between wakefulness and sleep. The proposed method may provide information more pertinent to periodic breathing than traditional CO2 response tests do, since the chemoreflex responses to phasic variations in blood gases are likely to be important in determining ventilatory control during sleep.
The Nuclear-Chemical Method of Carbenium and Silylenium Cation Generation.Ab IntioCalculations in Radiochemistry (1998)

The equilibrium geometry and the electronic structure of CH3+, SiH3+ cations formed from MH4 (M = C, Si) molecules by the nuclear-chemical method are calculated with the help of GAUSSIAN 94W program with 6-311G** and 6-31G** basis sets in the framework of RHF and RHF + MP2 methods. The “deformation energies” E = 31 kcal/mol (RHF), E = 29 kcal/mol (RHF + MP2) for CH3+ and E = 24 kcal/mol (RHF), E = 22 kcal/mol (RHF + MP2) for SiH3+ cations are obtained.
Barriers, drivers and challenges for sustainable product recovery and recycling (2009)

There has been a significant growth in research and applications of product recovery and recycling over the last two decades, in particular with the view of recent product take-back legislation which has extended the responsibility of manufacturers to include the recovery and safe disposal of their products. However, at present, the global scale of product recovery applications is significantly disproportional to the total manufacturing output. Hence, to achieve the idealistic goal of 'zero landfill', there is a need to significantly improve and extend both the scale of product recovery activities and the range of manufacturing applications in which such activities have yet to be implemented. This paper examines a range of barriers, drivers and challenges in research and development for the next generation of product recovery initiatives. A range of existing applications and case studies undertaken for the UK market has been used to analyse issues related to: the need for improvement and expansion of current legislation on producer responsibility; product take-back and reverse logistic models for collection of used products; knowledge-based approaches for end-of-life considerations during the design phase; improved technologies and increased automation in pre- and post-fragmentation recycling processes and most importantly, the requirement for sustainable business models for establishing value recovery chains which can be based on the provision of services rather than products. The paper concludes by summarising the results of this analysis to bridge the gap between existing and future sustainable solutions for product recovery.