gebhart/patrepeval huggingface dataset:
Spectrally Efficient Long-Haul Optical Networking Using 112-Gb/s Polarization-Multiplexed 16-QAM (2009)

We discuss the generation, wavelength-division-multiplexed (WDM) long-haul transmission, and coherent detection of 112-Gb/s polarization-division-multiplexed (PDM) 16-ary quadrature amplitude modulation (16-QAM) at a line rate of 14 Gbaud and spectral efficiencies beyond 4 b/s/Hz. We describe the (off-line) digital signal processing and blind filter adaptation algorithms used in our intradyne receiver and characterize its performance using both simulated and measured 16-QAM waveforms. We measure a required optical signal-to-noise ratio of 20.2 dB (0.1-nm reference bandwidth; 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> bit-error ratio), 3.2-dB off the theoretical limit. We study the effects of finite analog-to-digital converter resolution, laser frequency offset, laser phase noise, and narrowband optical filtering. Our experiments on a 25-GHz WDM grid (4.1-b/s/Hz spectral efficiency) reveal a 1-dB penalty after 7 passes though reconfigurable optical add/drop multiplexers (ROADMs) and an achievable transmission reach of 1022 km of uncompensated standard single-mode fiber. At a spectral efficiency of 6.2 b/s/Hz (16.67-GHz WDM channel spacing) a transmission reach of 630 km is attained.
Direct Binding of Toll-Like Receptor 2 to Zymosan, and Zymosan-Induced NF-κB Activation and TNF-α Secretion Are Down-Regulated by Lung Collectin Surfactant Protein A (2003)

The lung collectin surfactant protein A (SP-A) has been implicated in the regulation of pulmonary host defense and inflammation. Zymosan induces proinflammatory cytokines in immune cells. Toll-like receptor (TLR)2 has been shown to be involved in zymosan-induced signaling. We first investigated the interaction of TLR2 with zymosan. Zymosan cosedimented the soluble form of rTLR2 possessing the putative extracellular domain (sTLR2). sTLR2 directly bound to zymosan with an apparent binding constant of 48 nM. We next examined whether SP-A modulated zymosan-induced cellular responses. SP-A significantly attenuated zymosan-induced TNF-alpha secretion in RAW264.7 cells and alveolar macrophages in a concentration-dependent manner. Although zymosan failed to cosediment SP-A, SP-A significantly reduced zymosan-elicited NF-kappaB activation in TLR2-transfected human embryonic kidney 293 cells. Because we have shown that SP-A binds to sTLR2, we also examined whether SP-A affected the binding of sTLR2 to zymosan. SP-A significantly attenuated the direct binding of sTLR2 to zymosan in a concentration-dependent fashion. From these results, we conclude that 1) TLR2 directly binds zymosan, 2) SP-A can alter zymosan-TLR2 interaction, and 3) SP-A down-regulates TLR2-mediated signaling and TNF-alpha secretion stimulated by zymosan. This study supports an important role of SP-A in controlling pulmonary inflammation caused by microbial pathogens.
Epigenetics in Cancer (2008)

Gene transcription can be activated or inhibited by a reversible modification of the gene; this modification is termed an epigenetic change. This account of epigenetics in cancer reviews the mechanisms and consequences of epigenetic changes in cancer cells and concludes with the implications of these changes for the diagnosis, prognosis, and treatment of cancer.
Mid-Wave Infrared 3D Integral Imaging at Long Range (2013)

Integral imaging is an established method for passive three-dimensional (3D) image formation, visualization, and ranging. The applications of integral imaging include significantly improved scene segmentation and the ability to visualize occluded objects. Past demonstrations of this technique have been mainly conducted over short ranges achievable in the laboratory. In this paper, we demonstrate 3D computational integral imaging for ranges out to 2 km using multiple looks from a single moving mid-wave infrared (MWIR) imager. We also demonstrate 3D visualization of occluded objects at ranges over 200 m. To our knowledge, this paper is the first such demonstration at these ranges and the first example of this technique using a mid wave IR imaging system. In addition to presenting results, we also outline our new approach for overcoming the technical challenges unique to long range applications of integral imaging. Future applications of long range 3D integral imaging may include aerospace, search and rescue, satellite 3D imaging, etc.
Decay-Accelerating Factor Must Bind Both Components of the Complement Alternative Pathway C3 Convertase to Mediate Efficient Decay (2007)

Decay-accelerating factor (DAF; CD55) inhibits the complement (C) cascade by dissociating the multimolecular C3 convertase enzymes central to amplification. We have previously demonstrated using surface plasmon resonance (Biacore International) that DAF mediates decay of the alternative pathway C3 convertase, C3bBb, but not of the inactive proenzyme, C3bB, and have shown that the major site of interaction is with the larger cleavage subunit factor B (Bb) subunit. In this study, we dissect these interactions and demonstrate that the second short consensus repeat (SCR) domain of DAF (SCR2) interacts only with Bb, whereas SCR4 interacts with C3b. Despite earlier studies that found SCR3 to be critical to DAF activity, we find that SCR3 does not directly interact with either subunit. Furthermore, we demonstrate that properdin, a positive regulator of the alternative pathway, does not directly interact with DAF. Extending from studies of binding to decay-accelerating activity, we show that truncated forms of DAF consisting of SCRs 2 and 3 bind the convertase stably via SCR2-Bb interactions but have little functional activity. In contrast, an SCR34 construct mediates decay acceleration, presumably due to SCR4-C3b interactions demonstrated above, because SCR3 alone has no binding or functional effect. We propose that DAF interacts with C3bBb through major sites in SCR2 and SCR4. Binding to Bb via SCR2 increases avidity of binding, concentrating DAF on the active convertase, whereas more transient interactions through SCR4 with C3b directly mediate decay acceleration. These data provide new insights into the mechanisms involved in C3 convertase decay by DAF.
Pharmacokinetics and pharmacodynamics of a human monoclonal anti-FGF23 antibody (KRN23) after ascending single-dose administration in patients with X-linked hypophosphatemia (2014)

Searchable abstracts of presentations at key conferences on calcified tissues ISSN 2052-1219 (online)
Expression of full-length human dystrophin cDNA in mdx mouse muscle by HVJ-liposome injection. (1996)

Duchenne muscular dystrophy (DMD) is an X-linked progressive muscle disorder which is caused by a defect of dystrophin, a 427-kDa muscle cell membrane protein. One of the possible means of DMD therapy is to express the dystrophin gene in patients' muscles. In this study, full length dystrophin cDNA was expressed in mdx (muscular dystrophy model) mouse muscle using the hemagglutinating virus of Japan (HVJ)-liposome method. With the HVJ-liposome method, the lacZ reporter genes were expressed in 50-80% of cultured mdx mouse myoblasts, which suggested its potential usefulness for an in vivo gene study. Three expression vectors containing human full length dystrophin cDNA driven by Rous sarcoma virus (RSV), mouse leukemia virus, or human dystrophin promoters, were used. HVJ-liposomes containing these plasmids were directly injected into mdx mouse quadriceps muscle. The highest efficiency of expression of dystrophin was in 26% of the muscle fibers at the injected site on day 3 after HVJ-liposome injection of the RSV-based vector. The expression was decreased on day 10. The study thus demonstrates the feasibility of full length human dystrophin cDNA transfer and dystrophin expression using HVJ-liposomes in vivo.
Blending Diverse Physical Priors with Neural Networks (2019)

Machine learning in context of physical systems merits a re-examination of the learning strategy. In addition to data, one can leverage a vast library of physical prior models (e.g. kinematics, fluid flow, etc) to perform more robust inference. The nascent sub-field of \emph{physics-based learning} (PBL) studies the blending of neural networks with physical priors. While previous PBL algorithms have been applied successfully to specific tasks, it is hard to generalize existing PBL methods to a wide range of physics-based problems. Such generalization would require an architecture that can adapt to variations in the correctness of the physics, or in the quality of training data. No such architecture exists. In this paper, we aim to generalize PBL, by making a first attempt to bring neural architecture search (NAS) to the realm of PBL. We introduce a new method known as physics-based neural architecture search (PhysicsNAS) that is a top-performer across a diverse range of quality in the physical model and the dataset.
The Molecular Signature of Metastases of Human Hepatocellular Carcinoma (2005)

The current metastasis paradigm suggests that the primary tumor starts off benign but over time slowly acquires changes that provide a few rare cells within the tumor the ability to metastasize. However, this concept has been challenged by several recent studies using the microarray-based approach. We have recently found that the molecular signature of primary hepatocellular carcinoma (HCC) is very similar to that of their corresponding metastases, while it differs significantly in primary HCCs with or without metastasis. Similar findings are also evident in primary cancers of the lung, breast, and prostate. Such a signature can be used to predict the prognosis of HCC patients. Moreover, there are significant differences in the gene expression profiles of liver parenchyma among HCC patients with or without intrahepatic metastases. These findings imply that many of the metastasis-promoting genes are embedded in the primary tumors and that the ability to metastasize may be an inherent quality of the tumor from the beginning. In addition, the condition of liver parenchyma may dictate the intrahepatic metastasis potential, which is consistent with the hypothesis that the degree of viral-hepatitis-mediated liver damage or possibly the genetic makeup of individuals may play an important role in metastasis.
Effect of low level direct current on in vivo tumor growth in hamsters. (1985)

A preliminary study has been carried out on the effect of low level direct current on tumor growth using an experimental tumor model developed from an amelanotic melanoma (T1-4) in the hamster. An inoculum of 2 X 10(6) viable cells was injected s.c. on day 0; on day 7 the tumor-bearing animals were randomly divided into treatment and control groups. On days 7 through 11 inclusive, the treatment group was subjected to electrical current (direct current) at levels from 0.1 to 2.4 mA, for 1 h/day under general anesthesia. Control groups were subjected to the same procedures, with the exception that the electrodes were not connected to the current source. On day 14, the animals were killed and autopsied; their tumors were removed, weighed, and sectioned. Treated tumors decreased in mass (as a percentage of controls) from 89% at 0.1 mA to 2% at 2.4 mA. Increased necrosis of the treated tumors was noted macroscopically and microscopically. On histological examination, it was observed that a thin rim of viable cells remained around the periphery after treatment even at the highest current levels. Similar results were obtained with both stainless steel and platinum-30% iridium electrodes. In separate experiments where the animals were allowed to survive after a treatment period (1 h/day for 5 days at 2.4 mA), the viable cells at the periphery developed into tumors whose mass at 28 days posttreatment averaged only 52% of that of the control tumors. The mechanism of growth reduction is unknown but hyperthermia was shown not to be a factor.
Broadband return-to-zero wavelength conversion and signal regeneration using a monolithically integrated, photocurrent-driven wavelength converter (2006)

Broadband wavelength switching and signal regeneration experiments with 10 Gbit/s return-to-zero signals using a photocurrent-driven wavelength converter (PD-WC) are presented. For wavelength switching using an ideal input signal to the PD-WC, the device generates up to +3.7 dB facet to facet gain and shows &lt;1 dB power penalty in bit error rate measurements. For wavelength switching with a degraded input signal, the PD-WC shows extinction ratio regeneration from 5 to &gt;11 dB, jitter reduction from 35 to 17 ps, significant eyeshape regeneration, and a −2.8 dB power penalty.
Fundamental Principles and Issues of High-speed Piezoactuated Three-legged Motion for Miniature Robots Designed for Nanometer-scale Operations (2005)

One of the important aspects in the development of high-throughput platforms based on a fleet of scientific instruments in the form of miniature wireless robots designed for fast operations at the nanometer-scale, is the conception of an embedded locomotion system capable of fast displacements between two successive locations while being accurate enough to position the robot within the range of the embedded instrument, typically within a few tenths of nanometers. This paper describes not only the fundamental principles of the locomotion method and mechanisms but the main constraints, challenges, and environmental conditions that must be taken into account in the implementation of such a system. Preliminary experimental results show the validity of this approach.
Smart Microgel Capsules from Macromolecular Precursors (2010)

Microgel particles and capsules which consist of multiple layers can be fabricated using droplet microfluidics, but in existing methods, emulsion templating forms layers of dissimilar polarity. In this paper, we fabricate functional microgel capsules that consist of two miscible yet distinct layers. We use microfluidic devices to template micrometer-sized drops that are loaded with prepolymerized precursors and solidify them through a polymer-analogous reaction. This allows the particle morphology to be controlled and prevents pronounced interpenetration of the different layers despite their miscibility. We use polyacrylamide and poly(N-isopropylacrylamide) precursors to form thermoresponsive core-shell microparticles and demonstrate their utility for encapsulation and controlled release applications.
Effect of inactivation ofnuo andackA-pta on redistribution of metabolic fluxes inEscherichia coli (1999)

The nuoA-N gene cluster encodes a transmembrane NADH:ubiquinone oxidoreductase (NDH-I) responsible for coupling redox chemistry to proton-motive force generation. Interactions between nuo and the acetate-producing pathway encoded by ackA-pta were investigated by examining the metabolic patterns of several mutant strains under anaerobic growth conditions. In an ackA-pta strain, the flux to acetate was decreased dramatically, whereas flux to lactate was increased significantly when compared with its parent strain; the fluxes to pyruvate and ethanol also increased slightly. In addition, pyruvate was excreted. A strain carrying the nuo mutation showed metabolic flux distribution similar to the wild type. The ackA-pta-nuo strain showed a different metabolic pattern. It not only exhibited reduced acetate accumulation but also significantly lower ethanol and formate synthesis. Metabolic flux distribution analysis suggests that the excessive carbon flux was redirected at the pyruvate node through the lactate dehydrogenase pathway for lactate formation rather than the pyruvate formate-lyase (PFL) pathway for acetyl-CoA and formate production. The diminished capacity through the formate and ethanol (ADH) pathways was not the result of genetic disruption of functional PFL or ADH production. The introduction of a Bacillus subtilis acetolactate synthase gene returned formate, ethanol, and lactate levels to those of the wild type (ackA(+)pta(+)nuo(+)) strain. Furthermore, transfer of a lactate dehydrogenase mutation yielded a strain producing ethanol as the sole fermentation product. As confirmation of the nuo effect, cultures of the ackA-pta strain, supplemented with an NDH-I inhibitor, produced intermediary levels of flux to ethanol and formate. Mutations in both ackA-pta and nuo are required to significantly reduce the flux through the PFL pathway.
The biology of cell reproduction (1985)

PART I: BIOLOGY 1. The Cell Cycle Phases of the cell cycle Variability of the cell cycle 2. Nondividing Cells G0 cells Terminally differentiated cells 3. Populations of Cells Stem cells Transformed cells 4. Tissue Growth Growth in size Growth in number Doubling time Growth of tumors 5. Synchronization of Cells in the Cell Cycle Methods for synchronizing cells in culture Morphology of cells during the cell cycle PART II: CELL BIOLOGY 6. Temperature-Sensitive Mutants of the Cell Cycle Defining cell cycle mutants Conditional cell cycle mutants The execution point 7. Informational Content of Cells in Different Phases of the Cell Cycle Cell fusion Informational content of S phase cells Informational content of G0-G<small1 cells Premature chromosome condensation 8. Perturbation of the Cell Cycle by Drugs Actinomycin D Cycloheximide Other drugs Monoclonal antibodies 9. Growth in Size and Cell Proliferation Growth in size and cell DNA replication Growth in size and cell division The role of RNA polymerase II PART III: MOLECULAR BIOLOGY 10. The Environmental Signals Growth factors Inhibitory factors 11. Biochemical Events in the Cell Cycle Does the cell cycle exist? Controlling events and prerequisite events G1 and G0 S phase G2 and mitosis 12. Virally-Coded Proteins and Cell Proliferation SV4O and polyoma Adenovirus Other viruses Mechanisms of viral-induced cell DNA replication 13. Genetic Basis of Cell Proliferation Cdc genes in yeasts Retroviral oncogenes Cellular oncogenes Cdc genes in animal cells Some speculations References Index
Alzheimer’s Disease and the Aging Brain (2006)

The frequencies of each of the several types of dementia are enumerated, showing that Alzheimer's disease is present in about 80% of cases. Cerebral changes associated with cognitively normal aging include shrinkage of large cortical neurons but not a significant loss of total neuronal number. Nevertheless, the population density of synapses measured by confocal microscopy does decline significantly in normal aging. The classical lesions of Alzheimer's disease are neuritic plaques and neurofibrillary tangles, and their frequency correlates with declining cognitive measures. Although amyloid is prominent in plaques, it is probably not the agent of destruction. That role seems to be held by Abeta oligomers. The strongest structural correlate with cognitive tests is synapse loss, which is probably caused by Abeta oligopeptides in the terminal axons and dendrites.
Nitric Oxide in Health and Disease of the Nervous System (2008)

Nitric oxide (NO) is an important messenger molecule in a variety of physiological systems. NO, a gas, is produced from L-arginine by different isoforms of nitric oxide synthase (NOS) and serves many normal physiologic purposes, such as promoting vasodilation of blood vessels and mediating communication between nervous system cells. In addition to its physiologic actions, free radical activity of NO can cause cellular damage through a phenomenon known as nitrosative stress. Here, we review the role of NO in health and disease, focusing on its role in function and dysfunction of the nervous system. Substantial evidence indicates that NO plays a key role in most common neurodegenerative diseases, and, although the mechanism of NO-mediated neurodegeneration remains uncertain, studies suggest several possibilities. NO has been shown to modify protein function by nitrosylation and nitrotyrosination, contribute to glutamate excitotoxicity, inhibit mitochondrial respiratory complexes, participate in organelle fragmentation, and mobilize zinc from internal stores. In this review, we discuss and analyze the evidence for each of these mechanisms in different neurodegenerative diseases and propose future directions for research of the role of NO in neurodegeneration.
A Transformative Tool for Minimally Invasive Procedures: Design, Modeling and Real-Time Control of a Polycrystalline Shape Memory Alloy Actuated Robotic Catheter (2009)

Cardiac catheterization is rapidly transforming the diagnosis and treatment of cardiovascular disease. However, the use of catheters is limited to procedures where the target anatomy can be easily accessed via natural vasculature. Robotically controlled catheters have the potential to provide greater access and more precise interaction with internal anatomies. This dissertation presents the development of a shape memory alloy (SMA) actuated robotic catheter: from electromechanical design to the development of novel modeling and control approaches. \n\nThe robotic catheter is fabricated using conventional manufacturing and rapid prototyping. To analyze the transient characteristics of the catheter, a dynamic model is developed. Its bending mechanics are derived using a circular arc model and are experimentally validated. The effects of outer sleeve thickness on heat transfer and transient response characteristics are studied. SMA actuation is described using the Seelecke-Muller-Achenbach model for single-crystal SMA with experimentally determined parameters. Joule heating is used to generate tip deflections, which are measured in real-time using a dual-camera imaging system. The dynamic characteristics of this active catheter system are simulated and validated experimentally. \n\nThe direct extension of the Seelecke-Muller-Achenbach model to a catheter with multiple SMA tendons proves difficult because of the computational cost and inherent inaccuracies of the single-crystal modeling assumptions. Moreover, the requisite variable-step solvers are not suitable to real-time control. To facilitate more accurate modeling and effective real-time control of an SMA catheter with multiple tendons, a new modeling technique based on Hysteretic Recurrent Neural Networks (HRNNs) is proposed. Its efficacy is demonstrated experimentally for two- and three-phase hysteretic systems. The HRNN is extended to three-phase SMA actuation and is shown to accurately capture the polycrystalline stress-strain characteristics of SMA tendons at different temperatures. \n\nA robotic catheter system consisting of four SMA tendons is then decoupled into two planar bending systems, each consisting of a pair of antagonistic SMA tendons. An HRNN model is developed directly from experimental measurements, and is used to develop a feed-forward controller.
A unified learning paradigm for large-scale personalized information management (2005)

Statistical-learning approaches such as unsupervised learning, supervised learning, active learning, and reinforcement learning have generally been separately studied and applied to solve application problems. In this paper, we provide an overview of our newly proposed unified learning paradigm (ULP), which combines these approaches into one synergistic framework. We outline the architecture and the algorithm of ULP, and explain benefits of employing this unified learning paradigm on personalizing information management.