gebhart/patrepeval huggingface dataset:
Mechanism of Transcription Activation at the <i>comG</i> Promoter by the Competence Transcription Factor ComK of <i>Bacillus subtilis</i> (2004)

ABSTRACT The development of genetic competence in Bacillus subtilis is regulated by a complex signal transduction cascade, which results in the synthesis of the competence transcription factor, encoded by comK . ComK is required for the transcription of the late competence genes that encode the DNA binding and uptake machinery and of genes required for homologous recombination. In vivo and in vitro experiments have shown that ComK is responsible for transcription activation at the comG promoter. In this study, we investigated the mechanism of this transcription activation. The intrinsic binding characteristics of RNA polymerase with and without ComK at the comG promoter were determined, demonstrating that ComK stabilizes the binding of RNA polymerase to the comG promoter. This stabilization probably occurs through interactions with the upstream DNA, since a deletion of the upstream DNA resulted in an almost complete abolishment of stabilization of RNA polymerase binding. Furthermore, a strong requirement for the presence of an extra AT box in addition to the common ComK-binding site was shown. In vitro transcription with B. subtilis RNA polymerase reconstituted with wild-type α-subunits and with C-terminal deletion mutants of the α-subunits was performed, demonstrating that these deletions do not abolish transcription activation by ComK. This indicates that ComK is not a type I activator. We also show that ComK is not required for open complex formation. A possible mechanism for transcription activation is proposed, implying that the major stimulatory effect of ComK is on binding of RNA polymerase.
Effect of dissolution and intermetallic formation on the reliability of FC joints (1998)

The dissolution processes and subsequent intermetallic reactions between high tin solder bump alloys and Cu‐ or Ni‐based UBM‐metallisations were investigated both theoretically and experimentally. The results showed that when the Cu UBM layer is used together with eutectic or higher Sn‐based solder alloys the dissolution of Cu and the rate of the Cu 6 Sn 5 formation is too high for reliable interconnections. On the contrary, Ni provides feasible solution for UBM/high tin solder applications. Although there is strong chemical interaction between nickel and high Sn solder bump alloys, the dissolution and subsequent Ni 3 Sn 4 layer growth rates are very low. Thus, a thin Ni layer can sustain interactions with high Sn liquid as well as solid solders during high temperature use. On the basis of the results obtained flip chip bonding with Ni‐based UBM structures provides a viable interconnection solution for reliable fine‐pitch applications.
Label-free separation of leukocyte subpopulations using high throughput multiplex acoustophoresis (2019)

Multiplex separation of mixed cell samples is required in a variety of clinical and research applications. Herein, we present an acoustic microchip with multiple outlets and integrated pre-alignment channel to enable high performance and label-free separation of three different cell or particle fractions simultaneously at high sample throughput. By implementing a new cooling system for rigorous temperature control and minimal acoustic energy losses, we were able to operate the system isothermally and sort suspensions of 3, 5 and 7 μm beads with high efficiencies (>95.4%) and purities (>96.3%) at flow rates up to 500 μL min-1 corresponding to a throughput of ∼2.5 × 106 beads per min. Also, human viable white blood cells were successfully fractionated into lymphocytes, monocytes and granulocytes with high purities of 96.5 ± 1.6%, 71.8 ± 10.1% and 98.8 ± 0.5%, respectively, as well as high efficiencies (96.8 ± 3.3%, 66.7 ± 3.2% and 99.0 ± 0.7%) at flow rates up to 100 μL min-1 (∼100 000 cells per min). By increasing the flow rate up to 300 μL min-1 (∼300 000 cells per min) both lymphocytes and granulocytes were still recovered with high purities (92.8 ± 1.9%, 98.2 ± 1 .0%), whereas the monocyte purity decreased to 20.9 ± 10.3%. The proposed isothermal multiplex acoustophoresis platform offers efficient fractionation of complex samples in a label-free and continuous manner at thus far unreached high sample throughput rates.
Single and Dual Panel LC Projection Systems (2005)

This chapter contains sections titled: Introduction Generic Color Sequential Single Panel Reflective LC System Example Single Panel Color Sequential Systems Two-panel Systems Commercialized Single Panel Projection Systems Based on Spatial Color Separation
Effect of potassium channel modulators in mouse forced swimming test (1999)

1. The effect of intracerebroventricular (i.c.v.) administration of different potassium channel blockers (tetraethylammonium, apamin, charybdotoxin, gliquidone), potassium channel openers (pinacidil, minoxidil, cromakalim) and aODN to mKv1.1 on immobility time was evaluated in the mouse forced swimming test, an animal model of depression. 2. Tetraethylammonium (TEA; 5 microg per mouse i.c.v.), apamin (3 ng per mouse i.c.v.), charybdotoxin (1 microg per mouse i.c.v.) and gliquidone (6 microg per mouse i.c.v.) administered 20 min before the test produced anti-immobility comparable to that induced by the tricyclic antidepressants amitriptyline (15 mg kg(-1) s.c.) and imipramine (30 mg kg(-1) s.c.). 3. By contrast pinacidil (10-20 microg per mouse i.c.v.), minoxidil (10-20 microg per mouse i.c.v.) and cromakalim (20-30 microg per mouse i.c.v.) increased immobility time when administered in the same experimental conditions. 4. Repeated administration of an antisense oligonucleotide (aODN) to the mKv1.1 gene (1 and 3 nmol per single i.c.v. injection) produced a dose-dependent increase in immobility time of mice 72 h after the last injection. At day 7, the increasing effect produced by aODN disappeared. A degenerate mKv1.1 oligonucleotide (dODN), used as control, did not produce any effect in comparison with saline- and vector-treated mice. 5. At the highest effective dose, potassium channels modulators and the mKv1.1 aODN did not impair motor coordination, as revealed by the rota rod test, nor did they modify spontaneous motility as revealed by the Animex apparatus. 6. These results suggest that modulation of potassium channels plays an important role in the regulation of immobility time in the mouse forced swimming test.
Rauschanteil im Lesesignal (1966)

Der Abtastvorgang sei kurz näher betrachtet : Liegt jedes Bildelement unter der Grenze der Auflösbarkeit für unser Auge, so bedeutet Gleichheit des durchgelassenen Lichtstromintegrals auch dieselbe Stufe in der Grauskala ; wir empfinden die verglichenen Halbtöne als gleiche Leuchtdichtewerte der betreffenden Elementarflächen. Denn was wir messen bzw. visuell bewerten, ist jeweils das Mittel, gebildet aus Partiallichtströmen, die zwischen den von Toner verschiedener Partikelgröße in streuender Verteilung bedeckten Stellen des Bildelements den transparenten Träger durchdringen. In einer dauernden oder mindestens 1/25 sec währenden Projektion des Bildes tritt dann für unser Auge kein Rauschen ein; es empfindet eben nur Mittelwerte.
Determination of frequency of T cells expressing the T cell‐specific serine proteinase 1 (TSP‐1) reveals two types of L3T4<sup>+</sup> T lymphocytes (1988)

TSP-1 is a murine T cell-specific serine proteinase which is exclusively expressed in activated but not in resting T lymphocytes. Among T lymphocyte clones tested so far the enzyme was found to be associated with all Ly-2+ but only with a fraction of L3T4+ lines. Here we have applied a limiting dilution system to determine the frequency of precursor cells of resting L3T4+ and Ly-2+ lymphocytes which can be induced in vitro by antigen/lectin to express TSP-1. T cell subsets were either positively enriched by flow cytofluorometry cell sorting or by negative selection using monoclonal antibodies and complement. Following stimulation of lymphocytes in vitro, individual microwells were tested for growth by visual examination and for the TSP-1 protein/enzyme by analyzing cell lysates using either a specific rabbit anti-TSP-1 antiserum and/or the chromogenic model peptide substrate H-D-Pro-Phe-Arg-p-nitroanilide. Moreover, a large panel of L3T4+ and Ly-2+ T lymphocyte clones generated from primary cultures were similarly investigated. In some cell cultures the presence of TSP-1 was also tested on the mRNA level using a TSP-1-specific oligonucleotide probe. The data show that the majority, if not all, of antigen/lectin-induced-Ly-2+ T cells expressed TSP-1. In contrast, only 12%-27% of the growing lectin or antigen-reactive L3T4+ lymphocytes were positive for the enzyme. Studies performed in parallel with L3T4+ and Ly-2+ lymphocyte populations sensitized in bulk culture showed that under these conditions similar levels of TSP-1-specific mRNA and enzyme activity are detected in both subsets. The finding of primary L3T4+ T lymphocyte clones with distinct patterns of TSP-1 production provides evidence for the existence of two types of L3T4+ effector cells with different functional capacities. The data also suggest a cooperation between distinct L3T4+ lymphocytes for induction of optimal TSP-1 activity in L3T4+ T cells.
ScribbleSup: Scribble-Supervised Convolutional Networks for Semantic Segmentation (2016)

Large-scale data is of crucial importance for learning semantic segmentation models, but annotating per-pixel masks is a tedious and inefficient procedure. We note that for the topic of interactive image segmentation, scribbles are very widely used in academic research and commercial software, and are recognized as one of the most userfriendly ways of interacting. In this paper, we propose to use scribbles to annotate images, and develop an algorithm to train convolutional networks for semantic segmentation supervised by scribbles. Our algorithm is based on a graphical model that jointly propagates information from scribbles to unmarked pixels and learns network parameters. We present competitive object semantic segmentation results on the PASCAL VOC dataset by using scribbles as annotations. Scribbles are also favored for annotating stuff (e.g., water, sky, grass) that has no well-defined shape, and our method shows excellent results on the PASCALCONTEXT dataset thanks to extra inexpensive scribble annotations. Our scribble annotations on PASCAL VOC are available at http://research.microsoft.com/en-us/um/ people/jifdai/downloads/scribble_sup.
Glutamate Metabolism in Major Depressive Disorder (2014)

Research on novel treatments for major depressive disorder focuses quite deeply on glutamate function, and this research would benefit from a brain-imaging technique that precisely quantified glutamate function. Signs of a specific form of glutamate-related dysfunction that could be targeted by novel therapies were found using novel, state-of-the-art techniques to address this issue.
Laser-Etched Designs for Molding Hydrogel-Based Engineered Tissues (2017)

Rapid prototyping and fabrication of elastomeric molds for sterile culture of engineered tissues allow for the development of tissue geometries that can be tailored to different in vitro applications and customized as implantable scaffolds for regenerative medicine. Commercially available molds offer minimal capabilities for adaptation to unique conditions or applications versus those for which they are specifically designed. Here we describe a replica molding method for the design and fabrication of poly(dimethylsiloxane) (PDMS) molds from laser-etched acrylic negative masters with ∼0.2 mm resolution. Examples of the variety of mold shapes, sizes, and patterns obtained from laser-etched designs are provided. We use the patterned PDMS molds for producing and culturing engineered cardiac tissues with cardiomyocytes derived from human-induced pluripotent stem cells. We demonstrate that tight control over tissue morphology and anisotropy results in modulation of cell alignment and tissue-level conduction properties, including the appearance and elimination of reentrant arrhythmias, or circular electrical activation patterns. Techniques for handling engineered cardiac tissues during implantation in vivo in a rat model of myocardial infarction have been developed and are presented herein to facilitate development and adoption of surgical techniques for use with hydrogel-based engineered tissues. In summary, the method presented herein for engineered tissue mold generation is straightforward and low cost, enabling rapid design iteration and adaptation to a variety of applications in tissue engineering. Furthermore, the burden of equipment and expertise is low, allowing the technique to be accessible to all.
Structural basis for neutralization of hepatitis A virus informs a rational design of highly potent inhibitors (2019)

Hepatitis A virus (HAV), an enigmatic and ancient pathogen, is a major causative agent of acute viral hepatitis worldwide. Although there are effective vaccines, antivirals against HAV infection are still required, especially during fulminant hepatitis outbreaks. A more in-depth understanding of the antigenic characteristics of HAV and the mechanisms of neutralization could aid in the development of rationally designed antiviral drugs targeting HAV. In this paper, 4 new antibodies-F4, F6, F7, and F9-are reported that potently neutralize HAV at 50% neutralizing concentration values (neut50) ranging from 0.1 nM to 0.85 nM. High-resolution cryo-electron microscopy (cryo-EM) structures of HAV bound to F4, F6, F7, and F9, together with results of our previous studies on R10 fragment of antigen binding (Fab)-HAV complex, shed light on the locations and nature of the epitopes recognized by the 5 neutralizing monoclonal antibodies (NAbs). All the epitopes locate within the same patch and are highly conserved. The key structure-activity correlates based on the antigenic sites have been established. Based on the structural data of the single conserved antigenic site and key structure-activity correlates, one promising drug candidate named golvatinib was identified by in silico docking studies. Cell-based antiviral assays confirmed that golvatinib is capable of blocking HAV infection effectively with a 50% inhibitory concentration (IC50) of approximately 1 μM. These results suggest that the single conserved antigenic site from complete HAV capsid is a good antiviral target and that golvatinib could function as a lead compound for anti-HAV drug development.
A New Reference Correlation for the Viscosity of Methanol (2006)

A new reference-quality correlation for the viscosity of methanol is presented that is valid over the entire fluid region, including vapor, liquid, and metastable phases. To describe the zero-density viscosity with kinetic theory for polar gases, a new expression for the collision integral of the Stockmayer potential is introduced. The initial density dependence is based on the Rainwater–Friend theory. A new correlation for the third viscosity virial coefficient is developed from experimental data and applied to methanol. The high-density contribution to the viscosity is based on the Chapman–Enskog theory and includes a new expression for the hard-sphere diameter that is a function of both temperature and density. The resulting correlation is applicable for temperatures from the triple point to 630K at pressures up to 8GPa. The estimated uncertainty of the resulting correlation (with a coverage factor of 2) varies from 0.6% in the dilute-gas phase between room temperature and 630K, to less than 2% for the liquid phase at pressures up to 30MPa at temperatures between 273 and 343K, 3% for pressures from 30to100MPa, 5% for the liquid from 100to500MPa, and 10% between 500MPa and 4GPa. At very high pressures, from 4to8GPa, the correlation has an estimated uncertainty of 30% and can be used to indicate qualitative behavior.
Low complexity hardware implementation of reciprocal fractional motion estimation for H.264/AVC in mobile applications (2009)

Motion estimation, one of the most effective modules in H.264/AVC, constitutes 60%-90% of encoding time and computation. Close to %45 of this computation belongs to Fractional Motion Estimation (FME) which has to perform a time consuming half-pixel and quarter-pixel interpolation. In addition, interpolation is a major challenge for hardware implementation in real time, specially in mobile applications where processing and battery power is limited. Several modified sub-pixel accuracy search methods have been proposed in the literature in order to reduce the complexity of interpolation. The reciprocal method has been proposed to reduce the CPU encoding time for a software implementation of an H.264 encoder on personal computers. In this paper, the hardware implementation of the reciprocal method is evaluated and its PSNR performance and hardware cost are compared to that of a simplified Rate-Distortion Optimization (RDO) process. Simulation results indicate that using reciprocal FME with enabled RDO has less computational cost and better PSNR performance than using the conventional FME with disabled RDO.
Differentiation of <i>Aspergillus ustus</i> Strains by Random Amplification of Polymorphic DNA (2002)

The sodium dodecyl sulfate-polyacrylamide gel electrophoresis patterns of water-soluble proteins and the randomly amplified polymorphic DNA (RAPD) patterns of whole-cell lysates from 21 Aspergillus ustus isolates, including 11 reference strains and 10 patient and environmental strains from one hospital, were investigated. All isolates showed identical protein patterns. The RAPD assay discriminated between all reference strains. Comparison of hospital isolates showed identical RAPD patterns in some of the patient and environmental isolates. The data indicate that the RAPD technique is useful for fingerprinting A. ustus.
Experimental Studies on Anisotropic Thermoelectric Properties and Structures of n-Type Bi<sub>2</sub>Te<sub>2.7</sub>Se<sub>0.3</sub> (2010)

The peak dimensionless thermoelectric figure-of-merit (ZT) of Bi(2)Te(3)-based n-type single crystals is about 0.85 in the ab plane at room temperature, which has not been improved over the last 50 years due to the high thermal conductivity of 1.65 W m(-1) K(-1) even though the power factor is 47 x 10(-4) W m(-1) K(-2). In samples with random grain orientations, we found that the thermal conductivity can be decreased by making grain size smaller through ball milling and hot pressing, but the power factor decreased with a similar percentage, resulting in no gain in ZT. Reorienting the ab planes of the small crystals by repressing the as-pressed samples enhanced the peak ZT from 0.85 to 1.04 at about 125 degrees C, a 22% improvement, mainly due to the more increase on power factor than on thermal conductivity. Further improvement is expected when the ab plane of most of the small crystals is reoriented to the direction perpendicular to the press direction and grains are made even smaller.
Antigenic structure of human hepatitis A virus defined by analysis of escape mutants selected against murine monoclonal antibodies (1992)

We examined the antigenic structure of human hepatitis A virus (HAV) by characterizing a series of 21 murine monoclonal-antibody-resistant neutralization escape mutants derived from the HM175 virus strain. The escape phenotype of each mutant was associated with reduced antibody binding in radioimmunofocus assays. Neutralization escape mutations were identified at the Asp-70 and Gln-74 residues of the capsid protein VP3, as well as at Ser-102, Val-171, Ala-176, and Lys-221 of VP1. With the exception of the Lys-221 mutants, substantial cross-resistance was evident among escape mutants tested against a panel of 22 neutralizing monoclonal antibodies, suggesting that the involved residues contribute to epitopes composing a single antigenic site. As mutations at one or more of these residues conferred resistance to 20 of 22 murine antibodies, this site appears to be immunodominant in the mouse. However, multiple mutants selected independently against any one monoclonal antibody had mutations at only one or, at the most, two amino acid residues within the capsid proteins, confirming that there are multiple epitopes within this antigenic site and suggesting that single-amino-acid residues contributing to these epitopes may play key roles in the binding of individual antibodies. A second, potentially independent antigenic site was identified by three escape mutants with different substitutions at Lys-221 of VP1. These mutants were resistant only to antibody H7C27, while H7C27 effectively neutralized all other escape mutants. These data support the existence of an immunodominant neutralization site in the antigenic structure of hepatitis A virus which involves residues of VP3 and VP1 and a second, potentially independent site involving residue 221 of VP1.
Some corrosion failure mechanisms of AMTEC cells (1997)

Simulated models of four existing types of alkali metal thermoelectric converter (AMTEC) devices were chosen for this study. Each cell model was analyzed to determine whether metal is dissolved by sodium from cell materials and is deposited in regions that can degrade performance of the cell. Results of the study show that each cell model has at least one failure mode caused by dissolution of metal from the AMTEC surfaces.
Skeletonization: A Technique for Trimming the Fat from a Network via Relevance Assessment (1988)

This paper proposes a means of using the knowledge in a network to determine the functionality or relevance of individual units, both for the purpose of understanding the network's behavior and improving its performance. The basic idea is to iteratively train the network to a certain performance criterion, compute a measure of relevance that identifies which input or hidden units are most critical to performance, and automatically trim the least relevant units. This skeletonization technique can be used to simplify networks by eliminating units that convey redundant information; to improve learning performance by first learning with spare hidden units and then trimming the unnecessary ones away, thereby constraining generalization; and to understand the behavior of networks in terms of minimal rules.
Intelligent hearing aids: The next revolution (2016)

The first revolution in hearing aids came from nonlinear amplification, which allows better compensation for both soft and loud sounds. The second revolution stemmed from the introduction of digital signal processing, which allows better programmability and more sophisticated algorithms. The third revolution in hearing aids is wireless, which allows seamless connectivity between a pair of hearing aids and with more and more external devices. Each revolution has fundamentally transformed hearing aids and pushed the entire industry forward significantly. Machine learning has received significant attention in recent years and has been applied in many other industries, e.g., robotics, speech recognition, genetics, and crowdsourcing. We argue that the next revolution in hearing aids is machine intelligence. In fact, this revolution is already quietly happening. We will review the development in at least three major areas: applications of machine learning in speech enhancement; applications of machine learning in individualization and customization of signal processing algorithms; applications of machine learning in improving the efficiency and effectiveness of clinical tests. With the advent of the internet of things, the above developments will accelerate. This revolution will bring patient satisfactions to a new level that has never been seen before.