gebhart/patrepeval huggingface dataset:
Failure of Immune Homeostasis - The Consequences of Under and Over Reactivity (2005)

The immune system is a tightly regulated network that is able to maintain a balance of immune homeostasis under normal physiological conditions. Normally, when challenged with foreign antigen, specific appropriate responses are initiated that are aimed at restoring homeostasis. However under particular circumstances, this balance is not maintained and immune responses either under or over react. Cancer is an example of a situation where the immune response can be inefficient or unresponsive, resulting in uncontrolled growth of the cancer cells. Conversely, when the immune response over-reacts, this can result in conditions such as autoimmunity or pathology following infection. Many drug therapies have been developed that aim to alleviate or prevent such immune disorders and restore immune homeostasis. This review highlights recent advances in immunotherapies, with an emphasis on specific examples in the treatment of cancer, autoimmune disease (multiple sclerosis) and viral infection (respiratory syncytial virus).
Investigating Pressure Wave Impact on a Surrogate Head Model Using Numerical Simulation Techniques (2019)

Abstract There is an urgent need to understand the mechanism leading to mild traumatic brain injury (mTBI) resulting from blast wave impact to the head. The recent conflicts in Iraq and Afghanistan have heightened the awareness of head impact injuries to military personnel resulting from exposure to blast waves [1, 2]. A blast wave generated in air is a by-product of the detonation of an explosive [3]. To date the mechanism resulting in mTBI from primary blast insult is still unclear.
Enzyme in der organischen Synthese (1985)

Enzyme haben als Katalysatoren in der organischen Synthese eine große Zukunft. Bisher sind ihre Anwendungen auf einige industriell in großem Maßstab durchgeführte Hydrolysen sowie die Herstellung zahlreicher Reagentien für Analysen und Synthesen im Laboratoriumsmaßstab beschränkt. Verbesserungen bei der Produktion von Enzymen, die zum einen auf neuen Erkenntnissen der klassischen Mikrobiologie und zum anderen auf ersten erfolgversprechenden Ansätzen der Gentechnologie beruhen, sowie bei ihrer Stabilisierung und Handhabung machen diese Katalysatoren für einen Gebrauch in der organischen Synthese immer attraktiver. Dieser Aufsatz beschreibt den aktuellen Stand auf dem sich schnell entwickelnden Gebiet der enzymkatalysierten organischen Synthese; daneben werden auch die Entwicklungsmöglichkeiten erörtert.
Bilayer metal gate electrodes with tunable work function: Mechanism and proposed model (2010)

A bilayer metal structure has been demonstrated to adjust the gate work function over the Si band gap. The underlying tuning mechanism is believed to be due to metal interdiffusion based on comparison of work function behavior under different anneal conditions. In this paper, we conduct physical characterization on bilayer metal gates and successfully verify that the interdiffusion is the cause of the work function tuning. Furthermore, we find that metal interdiffusion significantly slows down after an initial anneal, resulting in a stable work function. A diffusion model involving the annealing out of fast diffusion paths is proposed to explain the work function results.
Irreversible polarization in donor doped Pb(Zr, Ti)O3 (2001)

Abstract In this paper, the reversible and irreversible polarization contributions in donor doped PbZr0.45Ti0.55O3 are studied. Small signal capacitance measurements under dc-bias are used to measure the reversible contributions. Quasi-static hysteresis measurements are used to obtain the total polarization, i.e., the sum of the reversible and irreversible contributions. The combination of both measurements allows the separation of the reversible and irreversible contributions. For the sub-coercive regime measurements of the Rayleigh coefficient were performed that allow a comparison to theory.
Biological properties and physical map of the genome of a new papovavirus, HD virus (1978)

The superhelical DNA of the HD papovavirus is heterogeneous and consists of two discrete size classes with molecular weights of 3.45 X 10(6) and 3.25 X 10(6). Both size classes of DNA are encapsidated into HD virion particles. Their relative intracellular amounts differ, depending on the cell system. Vero-76 carrier cultures in which HD virus was detected contain both size classes of DNA, with the larger molecules prevailing by a factor of 10. Five clonal lines derived from Vero-76 cell cultures contain exclusively the larger DNA. On the other hand, after cocultivation of Vero-76 with CV-1 cells for several passages, minicircular DNA is accumulated such that both size classes are synthesized in equal amounts. Any of the originally viral DNA-producing cell lines may, upon subcultivation, cease yielding virus. The RITA cell line of Cercopithecus aethiops origin is the only cell line among numerous ones tested which upon infection permits the establishment of a one-step growth cycle. However, between 6 and 8 days after infection, viral DNA synthesis is discontinued, and a persistent viral infection cannot be established. Physical maps of the genomes were constructed, and it could be shown that the smaller, minicircular DNA had originated from the larger DNA as the result of a deletion. The sequences missing in the minicircular DNA are confined to the relative map position 0.15 to 0.21.
Introduction to the Special Section on USENIX ATC 2019 (2020)

No abstract available.
A Balanced Parallel Distributed Sorting Implemented with PGX.D. (2016)

Sorting has been one of the most challenging studied problems in different scientific researches. Although many techniques and algorithms have been proposed on the theory of having efficient parallel sorting implementation, however achieving desired performance on different types of the architectures with large number of processors is still a challenging issue. Maximizing parallelism level in applications can be achieved by minimizing overheads due to load imbalance and waiting time due to memory latencies. In this paper, we present a distributed sorting algorithm implemented in PGX.D, a fast distributed graph processing system, which outperforms the Spark's distributed sorting implementation by around 2x-3x by hiding communication latencies and minimizing unnecessary overheads. Furthermore, it shows that the proposed PGX.D sorting method handles dataset containing many duplicated data entries efficiently and always results in keeping balanced workloads for different input data distribution types.
Xenogeneic assessment of mitochondrial bioenergetic impairment induced by CSF from MS patients (P2.369) (2017)

To assess whether intrinsic and extrinsic factors modulating neuronal bioenergetics might underlie mechanisms of progression in patients with primary (PPMS) and secondary progressive multiple sclerosis (SPMS)
Intelligent sound source localization for dynamic environments (2009)

As robotic technology plays an increasing role in human lives, ¿robot audition¿, human-robot communication, is of great interest, and robot audition needs to be robust and adaptable for dynamic environments. This paper addresses sound source localization working in dynamic environments for robots. Previously, noise robustness and dynamic localized sound selection have been enormous issues for practical use. To correct the issues, a new localization system ¿Selective Attention System¿ is proposed. The system has four new functions: localization with Generalized EigenValue Decomposition of correlation matrices for noise robustness(¿Localization with GEVD¿), sound source cancellation and focus (¿Target Source Selection¿), human-like dynamic Focus of Attention (¿Dynamic FoA¿), and correlation matrix estimation for robotic head rotation (¿Correlation Matrix Estimation¿). All are achieved by the dynamic design of correlation matrices. The system is implemented into a humanoid robot, and the experimental validation is successfully verified even when the robot microphones move dynamically.
RNAi-mediated rheostat for dynamic control of AAV-delivered transgenes (2023)

Adeno-associated virus (AAV)-based gene therapy could be facilitated by the development of molecular switches to control the magnitude and timing of expression of therapeutic transgenes. RNA interference (RNAi)-based approaches hold unique potential as a clinically proven modality to pharmacologically regulate AAV gene dosage in a sequence-specific manner. We present a generalizable RNAi-based rheostat wherein hepatocyte-directed AAV transgene expression is silenced using the clinically validated modality of chemically modified small interfering RNA (siRNA) conjugates or vectorized co-expression of short hairpin RNA (shRNA). For transgene induction, we employ REVERSIR technology, a synthetic high-affinity oligonucleotide complementary to the siRNA or shRNA guide strand to reverse RNAi activity and rapidly recover transgene expression. For potential clinical development, we report potent and specific siRNA sequences that may allow selective regulation of transgenes while minimizing unintended off-target effects. Our results establish a conceptual framework for RNAi-based regulatory switches with potential for infrequent dosing in clinical settings to dynamically modulate expression of virally-delivered gene therapies.
Inertially-induced secondary flow in microchannels (2011)

We report a novel technique to passively create strong secondary flows at moderate to high flow rates in microchannels, accurately control them and finally, due to their deterministic nature, program them into microfluidic platforms. Based on the flow conditions and due to the presence of the pillars in the channel, the flow streamlines will lose their fore-aft symmetry. As a result of this broken symmetry the fluid is pushed away from the pillar at the center of the channel (i.e. central z-plane). As the flow needs to maintain conservation of mass, the fluid will laterally travel in the opposite direction near the top and bottom walls. Therefore, a NET secondary flow will be created in the channel cross-section which is depicted in this video. The main platform is a simple straight channel with posts (i.e. cylindrical pillars - although other pillar cross-sections should also function) placed along the channel. Channel measures were 200 \mum\times50 \mum, with pillars of 100 \mum in diameter. Positioning the pillars in different locations within the cross-section of the channel will result in induction of different secondary flow patterns, which can be carefully engineered. The longitudinal spacing of the pillars is another design parameter (600 \mum spacing was used for this video). The device works over a wide range (moderate to high) flow rates. We used 150 \muL/min in this experiment. The device has 3 inlets where a dye stream is co-flowed between two water streams. In this video, one can see the effect of the net secondary flow created by inertia in the microchannel by visualizing the cross-section of the fluorescently labeled stream. Confocal images are sequentially taken at the inlet and after 49 consecutive pillars.
Passive Seismic Monitoring to Optimize Hydraulic Fracturing Treatments: Lessons Learned from our American Cousins (2010)

North American shale-gas recovery efforts are quite large, while the extent of such unconventional gas reserves in Europe is largely unknown. Some tests of gas shale formations have recently been carried out with good success in various basins (e.g., Germany’s Lower Saxony, Vienna Basin, southern Sweden, etc.) The development of Europe’s gas resources will take years and may benefit from lessons learned in North America. Firstly production from unconventional shale formations (e.g., Barnett, Fayetteville, Marcellus, Woodford, etc.) has been enabled by modern well log evaluation techniques and completion methods. These are particularly important since stress anisotropy strongly influences fracture system development. Secondly, it is critical to monitor the initiation and evolution of hydraulically-induced fracture systems. Currently almost all predictive models used by reservoir and production engineers to estimate recovery in stimulated wells are based on assumptions that naturally lead to oversimplified fracture geometry. Microseismic monitoring enables reservoir engineers and geoscientists to understand the development of hydraulically-induced fracture systems as well as naturally pre-existing fracture networks in four dimensions.
Waveguide shape control and loss properties of light-induced self-written (LISW) optical waveguides (2002)

We show the feasibility of automatic waveguide formation by means of the self-trapping effect of multimode optical fiber irradiation into a photopolymerizing resin. By using a graded-index multimode optical fiber, we experimentally obtained a straight waveguide of over 20 mm in length. It is shown that its growth properties, such as waveguide shape and diameter, depend on the propagation modal distribution along the optical fiber used for the waveguide formation. Moreover, an all-solid polymer optical waveguide that relies on the selective photopolymerization proceeding into the photopolymerizing resin mixture is also demonstrated. We call this type of waveguide a light-induced self-written optical waveguide. The measured propagation loss in the waveguide is 1.0 dB/cm or less for the wavelength range 0.8/spl sim/1.0 /spl mu/m. The proposed technology is capable of eliminating both costly lenses and the need for an alignment system from optical waveguide devices.
Full-chip-model-based correction of flare-induced linewidth variation (2004)

Scattered light in optical lithography, also known as flare, has been shown to cause potentially significant linewidth variation at low-k1 values. The interaction radius of this effect can extend essentially from zero to the full range of a product die and beyond. Because of this large interaction radius the correction of the effect can be very computation-intensive. In this paper, we will present the results of our work to characterize the flare effect for 65nm and 90nm poly processes, model that flare effect as a summation of gaussian convolution kernels, and correct it within a hierarchical model based OPC engine. Novel methods for model based correction of the flare effect, which preserve much of the design hierarchy, is discussed. The same technique has demonstrated the ability to correct for long-range loading effects encountered during the manufacture of reticles.
Challenge (2002)

Interoperability among a group of devices, applications, and services is typically predicated on those entities having some degree of prior knowledge of each another. In general, they must be written to understand the type of thing with which they will interact, including the details of communication as well as semantic knowledge such as when and how to communicate. This paper presents a case for "recombinant computing" -- a set of common interaction patterns that leverage mobile code to allow rich interactions among computational entities with only limited a priori knowledge of one another. We have been experimenting with a particular embodiment of these ideas, which we call Speakeasy. It is designed to support ad hoc, end user configurations of hardware and software, and provides patterns for data exchange, user control, discovery of new services and devices, and contextual awareness.
Effect of boundary reflection on helix backward wave oscillator (2003)

Summary form only given, as follows. The operation of the PASOTRON (Plasma-assisted slow-wave oscillators) is studied in the BWO regime. The absence of the guiding magnetic field in this device allows for the 3D motion of beam electrons. Recent studies showed the possibility of obtaining high efficiency up to 50 %. This was realized due to not only 3D motion but also due to properly optimized reflections from the slow wave structure ends in the experiment. The effect of the boundary reflection on the PASOTRON BWO is investigated theoretically. A stationary solution for the backward wave field amplitude is obtained in a self-consistent treatment of the wave excitation in the helix BWO with beam electrons 3D motion inside. The device electron efficiency and the oscillation frequency were obtained given a certain boundary reflection coefficient. At each value of the reflection coefficient, a number of different modes can be excited depending on the beam current. The efficiency of each of these modes was calculated. The results of this study can be used to increase the device efficiency, through adjusting the boundary reflection coefficient to the proper value.
Insights into Mechanisms of Antibody-Mediated Immunity from Studies with Cryptococcus neoformans (2005)

At first glance Cryptococcus neoformans appears an unlikely microbe to provide a new understanding of mechanisms of antibody-mediated immunity (AMI), because it is a facultative intracellular fungal pathogen for which the role of naturally acquired AMI in host defense is uncertain. However, numerous studies have now established that certain antibodies (Abs) against C. neoformans are protective in certain hosts. Studies with Abs to C. neoformans have provided new insights into AMI and generated new precedents with implications for other pathogens. The following concepts have emerged: 1) susceptibility to C. neoformans may be related to qualitative and quantitative aspects of the Ab response; 2) protective monoclonal Abs can be generated against pathogens even when the role of humoral immunity is uncertain; 3) Abs to C. neoformans mediate protection by immunomodulatory effects, thereby linking Ab efficacy to the overall host immune response; 4) Ab efficacy is critically dependent on fine specificity, which in turn is affected by immunoglobulin variable region usage, somatic mutation and constant region usage; 5) the efficacy of passive Ab therapy is a function of Ab dose and infecting innoculum, with lack of efficacy at the extremes of Ab concentration; 6) Ab-mediated toxicity resulting from antigen-Ab complex-induced release of platelet activating factor is isotype dependent. Observations with C. neoformans have stimulated a reappraisal of the role of humoral immunity for other pathogens and highlighted the limitations in current methods of assessing the role of Ab in host defense.
In vitro and in vivo efficacy and toxicity comparison between ApoGossypol and Gossypol, Bcl-2 antagonists (2008)

4387 Altered expression of Bcl-2-family proteins plays central roles in apoptosis dysregulation in cancer and leukemia, promoting malignant cell expansion and contributing to chemoresistance. In this study, we compared the toxicity and efficacy in mice of natural product (+)Gossypol and its semi-synthetic derivative (+)ApoGossypol and the purified (+) and (-) enantiomers of this compound, All of these compounds were shown to bind anti-apoptotic Bcl-2-family proteins with similar affinities, based on competitive BH3 peptide displacement assays and NMR-based chemical shift mapping experiments. Comparisons of growth inhibitory and cytotoxic activity of (+)Gossypol and (+)ApoGossypol using the NCI panel of 60 tumor cell lines, as well as cultured lymphoma cell lines and primary leukemia cells suggested that Gossypol and ApoGossypol have overlapping but non-identical cytotoxic mechanisms. Daily oral dosing studies showed that mice tolerate doses of ApoGossypol 2-4-times higher than Gossypol. Hepatotoxicity and gastrointestinal toxicity represented the major adverse activities of Gossypol, with ApoGossypol far less toxic. Efficacy was tested in transgenic mice in which Bcl-2 is over-expressed in B-cells, resembling low-grade follicular lymphoma in humans. In vitro, Bcl-2-expressing B-cells from transgenic mice were more sensitive to cytotoxicity induced by ApoGossypol than Gossypol, with LD50 values of 3-5 µM and 7.5-10 µM, respectively. In vivo, using the maximum tolerated dose of Gossypol (60 µmoles/kg) for sequential daily dosing (daily x 5 days x 3 weeks), ApoGossypol displayed superior activity to Gossypol in terms of reducing splenomegaly and reducing B-cell counts in spleens of Bcl-2 transgenic mice. At higher doses (120 µmole/kg), at which ApoGossypol but not Gossypol is tolerated, ApoGossypol showed even greater in vivo activity, reducing spleen weight by 40 ± 14% (p
Hepatic stellate cell hypertrophy is associated with metabolic liver fibrosis (2020)

Hepatic fibrosis is a major consequence of chronic liver disease such as non-alcoholic steatohepatitis which is undergoing a dramatic evolution given the obesity progression worldwide, and has no treatment to date. Hepatic stellate cells (HSCs) play a key role in the fibrosis process, because in chronic liver damage, they transdifferentiate from a "quiescent" to an "activated" phenotype responsible for most the collagen deposition in liver tissue. Here, using a diet-induced liver fibrosis murine model (choline-deficient amino acid-defined, high fat diet), we characterized a specific population of HSCs organized as clusters presenting simultaneously hypertrophy of retinoid droplets, quiescent and activated HSC markers. We showed that hypertrophied HSCs co-localized with fibrosis areas in space and time. Importantly, we reported the existence of this phenotype and its association with collagen deposition in three other mouse fibrosis models, including CCl<sub>4</sub>-induced fibrosis model. Moreover, we have also shown its relevance in human liver fibrosis associated with different etiologies (obesity, non-alcoholic steatohepatitis, viral hepatitis C and alcoholism). In particular, we have demonstrated a significant positive correlation between the stage of liver fibrosis and HSC hypertrophy in a cohort of obese patients with hepatic fibrosis. These results lead us to conclude that hypertrophied HSCs are closely associated with hepatic fibrosis in a metabolic disease context and may represent a new marker of metabolic liver disease progression.
Crosstalk Limiting Schedulers in AWG Based Optical Switches (2010)

Optical switching fabrics are gaining interest as in multi Terabit switching devices; the advantages over their electronic equivalents are mainly their information density and power consumption. Arrayed Waveguide Gratings (AWGs) are promising optical devices proposed by the academic and industrial community to build optical switching fabrics. Because of their wavelength routing property, AWGs allow wavelength reuse over different ports introducing in-band crosstalk which strongly limits scalability of AWG-based backplanes. However, this effect can be mitigated or even completely avoided by means of proper scheduling algorithms. In this paper, we present several modified scheduling algorithms which limit the effect of coherent crosstalk in AWG-based switching fabrics and achieve good performance in terms of throughput and delay.
Communications systems for handicapped (1985)

2nd Surgical Clinic, University Vienna Bioengineering Laboratory, Van Swieten-Gasse 1, 1090 Vienna, Austria