gebhart/patrepeval huggingface dataset:
The application of the helicon source to plasma processing (1991)

The results of a study of the mode transitions in the helicon source when used in the geometry required for plasma processing are presented. We find that the basic characteristics of high density (&amp;gt;5×1011 cm−3 in the processing chamber at 500 W) and low plasma potential (∼15 V) are observed in this configuration. The mode transitions can be interpreted in terms of the dispersion relation for the helicon wave. A study of the initial plasma breakdown has also been made and the results have aided in the understanding of the operation of the helicon source during pulsed plasma etching.
Late-acting dominant lethal genetic systems and mosquito control (2007)

Conventional SIT induces early-acting (embryonic) lethality, but genetic methods potentially allow the lethal phase to be tailored to the program. For insects with strong density-dependence, we show that lethality after the density-dependent phase would be a considerable improvement over conventional methods. For density-dependent parameters estimated from field data for Aedes aegypti, the critical release ratio for population elimination is modeled to be 27% to 540% greater for early-acting rather than late-acting lethality. Our success in developing a mosquito strain with the key features that the modeling indicated were desirable demonstrates the feasibility of this approach for improved SIT for disease control.
The characterization of soluble amyloid prepared in water (1968)

Amyloid was extracted from the spleen of a patient with primary amyloidosis by homogenizing it at high speed with water after preliminary treatments, first to remove proteins soluble in saline, and then to remove salts. The extracts containing amyloid appeared to be clear at concentrations up to 6 mg/ml of protein. The material gave little sediment on being centrifuged up to 20,000 g for 1 hr, but the protein was sedimented at 100,000 g in 1 hr. The amyloid could be precipitated from the extracts by addition of NaCl to 0.0075 mole/liter or of CaCl(2) to 0.0025 mole/liter. The protein-bound Congo red formed a red precipitate and this property was used to estimate recovery and purity of amyloid during extraction. On electronmicroscopy the isolated amyloid proved to be morphologically pure. It existed either as single filaments measuring 60-80 A in diameter or as large aggregates of these filaments.Freshly isolated amyloid in water sedimented as a single homogeneous peak with an s degrees (20,[unk]) of about 45-50S. On standing, the solution became cloudy and more rapidly sedimenting components appeared. On electrophoresis the material migrated as a homogeneous peak towards the anode. The protein had an amino acid composition different from that of all known serum proteins. It was rich in acidic amino acids and had little cysteine and methionine and no hydroxyproline. The total content of carbohydrate was less than 2%.
Interaction of primitive human myeloid and lymphoid progenitors with the marrow microenvironment. (1994)

Primitive human hematopoietic progenitors containing a high proportion of long-term culture-initiating cells (LTCICs) are found in the 34+DR- fraction of bone marrow mononuclear cells (BMMNCs). These progenitors adhere selectively to the 33/66-kD binding domain of fibronectin and to the FN-CHII binding site, unlike more committed progenitors, which adhere less selectively to fibronectin components. These differences in adhesion to stromal components may explain selective homing and release of progenitors at varying levels of differentiation from the marrow compartment. In additional studies, we demonstrate that cultivation of primitive progenitors in a stroma noncontact long-term culture allows both differentiation of primitive progenitors and conservation of LTCICs. These observations (1) demonstrate that expansion of primitive progenitors does not require stromal contact, (2) shed light on the regulatory role of stroma in myeloid differentiation, and (3) suggest strategies for both ex vivo myeloid progenitor expansion and retrovirus gene insertion. Finally, we demonstrate that a natural killer cell population can be derived from primitive hematopoietic progenitors in a modified long-term culture model. Our findings suggest an important role for marrow stroma in lymphoid differentiation from primitive progenitors and in expression of CD2, a lymphoid marker ordinarily associated with passage of T-lymphocyte progenitors through the thymus.
O2–05–04: Tau–based immunotherapy for dementia (2006)

Immunotherapies that target the Aβ peptide in AD have consistently resulted in amyloid clearance and cognitive improvements in mouse studies, and this effect is likely mediated by antibodies. Despite the setbacks associated with the initial human clinical trials, promising preliminary findings have emerged. These include reduction in amyloid burden and cognitive stabilization. Refinement of this approach is currently underway. Another important target in AD is the neurofibrillary tangles which correlate well with the degree of dementia. Histological analysis in AD brains and mouse models indicate that Aβ and tau pathologies are likely synergistic. Hence, targeting both pathologies at the same time may be more effective. Also, Aβ immunotherapy does not reduce tau aggregates in AD or mouse models, showing the importance of developing a separate tangle–targeting therapy. Clearance of extracellular tangles may reduce associated pathology, and numerous reports of neuronal uptake of antibodies suggest that intracellular tangles and pre–tangles may also be affected. To examine the effect of tau–based active immunotherapy targeting pathological tau conformers in transgenic P301L mice that develop neurofibrillary tangles and associated sensorimotor abnormalities. Homozygous P301L mice received intraperitoneal injections of a phospho–tau peptide derivative in alum adjuvant (n=12) or adjuvant only (n=13), starting at 2 months. Tau–specific immunoglobulin titers were determined and at 5 months their brains were processed for tau biochemistry and histology. A separate group of vaccinated mice (n=12) and controls (n=12) received injections from 2 months and were tested on various sensorimotor tasks (rotarod, traverse beam, locomotor activity) at 5 months. These animals will be retested periodically and their brains subsequently analyzed. The vaccine elicited a robust tau–specific antibody response, associated with a reduction in aggregated tau (47%; p<0.04) in the brain but soluble tau levels were unaltered, compared to the control group. The immunized animals performed better than the controls on the rotarod (p<0.02) and the traverse beam (p<0.001), and attained greater speed (Vmax) in the locomotor task (p<0.01). Histological evaluation is underway. Active immunization with a phospho–tau derivative peptide reduces brain levels of aggregated tau and slows the progression of tangle–related behavioral phenotype.
Parallel Distributed Processing (1987)

What makes people smarter than computers? These volumes by a pioneering neurocomputing group suggest that the answer lies in the massively parallel architecture of the human mind. They describe a new theory of cognition called connectionism that is challenging the idea of symbolic computation that has traditionally been at the center of debate in theoretical discussions about the mind. The authors' theory assumes the mind is composed of a great number of elementary units connected in a neural network. Mental processes are interactions between these units which excite and inhibit each other in parallel rather than sequential operations. In this context, knowledge can no longer be thought of as stored in localized structures; instead, it consists of the connections between pairs of units that are distributed throughout the network. Volume 1 lays the foundations of this exciting theory of parallel distributed processing, while Volume 2 applies it to a number of specific issues in cognitive science and neuroscience, with chapters describing models of aspects of perception, memory, language, and thought.
Peptide nucleic acids : protocols and applications (2004)

1. An Introduction to PNA, P.E. Nielsen and M. Egholm 2. PNA Synthesis by Boc Chemistry, T. Koch 3. Synthesis of PNA Oligomers by Fmoc Chemistry, R. Casale, I.S. Jensen, and M. Egholm 4. Thermodynamics of PNA Interactions, T. Ratilainen, A. Holmen and B. Norden 5. Peptide Nucleic Acid Targeting of Double-Stranded DNA, T. Bentin, H.J. Larsen, and P.E. Nielsen 6. PNA Beacons and Fluoroprobes, B. Datta, M. Wang, and B.A. Armitage 7. Vector Tagging Via PNA, A.G. Rebuffat, A.G. Bernasconi and B.M. Frey 8. PCR Clamping, H. Orum 9. PNA Directed Genome Rare Cutting: New Developments, M.D. Frank-Kamenetskii and Vadim V. Demidov 10. PNA Openers for Duplex DNA: Basic Facts, Fine Tuning and Emerging Applications, V.V. Demidov 11. Combined Use of PNA and DNA for Fluorescence In Situ Hybridization (FISH), K.V. Nielsen, S. Muller, T. Svenstrup Poulsen, S. Gabs, A. Schonau 12. Production of PNA-Arrays for Nucleic Acid Detection, A. Jacob, O. Brandt, S. Wurtz, A. Stephan, M. Schnolzer and J.D. Hoheisel 13. PNA Antisense in Eukaryotic Systems, D.R. Corey 14. Antisense Effects in Escherichia coli, L. Good, R. Dryselius and P.E. Nielsen
HLA-DQA2 and HLA-DQB2 Genes Are Specifically Expressed in Human Langerhans Cells and Encode a New HLA Class II Molecule (2012)

The precise role of human epidermal Langerhans cells (LCs) in immune response is highly controversial. While studying the gene expression profile of these cells, we were intrigued to identify the HLA-DQB2 gene as potentially expressed in LCs. Despite a strong evolutionary conservation of their sequences, the concomitant expression of the poorly polymorphic HLA-DQA2/HLA-DQB2 genes, paralogous to the HLA-DQA1/HLA-DQB1 genes, has never been detected in any cell type. We confirmed by RT-PCR that the HLA-DQA2 and -DQB2 genes are both expressed in LCs, but not in monocyte-derived dendritic cells, or in blood CD1c(+) or plasmacytoid dendritic cells. The presence of the HLA-DQβ2 chain in LCs could be demonstrated by Western blotting, whereas immunofluorescence revealed its localization in early endosomes. As in the case of other HLA class II molecules, the HLA-DQα2 and -DQβ2 chains formed heterodimers that had to associate with the invariant chain to reach endosomal compartments. HLA-DQα2/β2 heterodimers were expressed at the cell surface, where they could mediate staphylococcal superantigen stimulation of T cells. Interestingly, HLA-DQα2 and HLA-DQβ1 chains formed mixed heterodimers which efficiently left the endoplasmic reticulum. These observations strongly suggest that the poorly polymorphic HLA-DQA2 and -DQB2 genes should be considered to be of immunological importance. The HLA-DQα2/β2 molecules could influence the complexity of the repertoire of Ags presented by LCs.
Static Analysis of Executables to Detect Malicious Patterns (2006)

Malicious code detection is a crucial component of any defense mechanism. In this paper, we present a unique viewpoint on malicious code detection. We regard malicious code detection as an obfuscation-deobfuscation game between malicious code writers and researchers working on malicious code detection. Malicious code writers attempt to obfuscate the malicious code to subvert the malicious code detectors, such as anti-virus software. We tested the resilience of three commercial virus scanners against code-obfuscation attacks. The results were surprising: the three commercial virus scanners could be subverted by very simple obfuscation transformations! We present an architecture for detecting malicious patterns in executables that is resilient to common obfuscation transformations. Experimental results demonstrate the efficacy of our prototype tool, SAFE (a static analyzer for executables).
Age-Related Changes in the Accommodation Mechanism (1996)

Presbyopia is caused by changes in the visco-elastic properties of the lens or the choroid or both. Far-to-near (FN) accommodation dynamics are dominated by the properties of the lens, whereas near-to-far (NF) accommodation dynamics depend on the properties of the lens as well as the choroid. The aim of this study was to gain more insight into the cause of presbyopia by analyzing how FN and NF accommodation dynamics change as a function of age. Changes in axial lens thickness during accommodation were measured in vivo using continuous ultrasonographic biometry. The measurements were analyzed with the use of a biomechanical model of the mechanism of accommodation. Fitting the model to the responses yields time constants of FN and NF accommodation. The time constants FN and NF increase with age at an approximately equal rate: 7 ms/year (+/- 1.8 SEM) and 6 ms/year (+/- 1.6 SEM), respectively. This result supports a lenticular cause of presbyopia. In addition, estimations of the lens damping coefficients at different ages are given for the first time: the damping coefficient of the lens increases 20-fold between 15 and 55 years of age.
Selenocysteine: the 21st amino acid (1991)

Great excitement was elicited in the field of selenium biochemistry in 1986 by the parallel discoveries that the genes encoding the selenoproteins glutathione peroxidase and bacterial formate dehydrogenase each contain an in-frame TGA codon within their coding sequence. We now know that this codon directs the incorporation of selenium, in the form of selenocysteine, into these proteins. Working with the bacterial system has led to a rapid increase in our knowledge of selenocysteine biosynthesis and to the exciting discovery that this system can now be regarded as an expansion of the genetic code. The prerequisites for such a definition are co-translational insertion into the polypeptide chain and the occurrence of a tRNA molecule which carries selenocysteine. Both of these criteria are fulfilled and, moreover, tRNASec even has its own special translation factor which delivers it to the translating ribosome. It is the aim of this article to review the events leading to the elucidation of selenocysteine as being the 21st amino acid.
A scalable chip set for MPEG2 real-time encoding (2002)

This is a description of an architecture for video compression based on the MPEG2 (MP@ML) standard. The chip set is comprised of 3 different devices. The architecture is scalable, and real-time MPEG2 systems could be built with one, two or all three chip solutions. The encoder includes an on-chip processor for programming options, and provides direct connections to external DRAM and SRAM.
Performance of Dual-Polarization QPSK for Optical Transport Systems (2009)

The emergence of capable semiconductor processes has allowed digital signal processing to extend the application range of high-capacity optical systems. We report the performance of polarization multiplexed (or dual-polarization) quadrature phase-shift keying at 40 and 100 Gb/s.
Temperature-insensitive fiber Bragg grating accelerometer (2003)

A cantilever beam and fiber Bragg grating is used to measure acceleration. The cantilever induces strain on the grating, resulting in a Bragg wavelength modification that is subsequently detected. The output signal is insensitive to temperature variations and for a temperature change from -20/spl deg/C to 40/spl deg/C, the output signal fluctuated less than 5% without any temperature compensation schemes. Because the accelerometer does not utilize expensive and complex demodulation techniques, it is potentially cost effective. For the experimental system, a linear output range of 8 g could be detected.
Rodent nerve-muscle cell culture system for studies of neuromuscular junction development: Refinements and applications (2000)

Understanding of vertebrate neuromuscular junction (NMJ) development has been advanced by experimentation with cultures of dissociated embryonic nerve and skeletal muscle cells, particularly those derived from Xenopus and chick embryos. We previously developed a rodent (rat) nerve-muscle coculture system that is characterized by extensive induction of acetylcholine receptor (AChR) aggregation at sites of axonal contact with myotubes (Dutton et al., 1995). In this article, we report modifications of this culture system and examples of its application to the study of NMJ development: (1) We describe improved methods for the enrichment of myoblasts to give higher yields of myotubes with equal or greater purity. (2) We demonstrate lipophilic dye labeling of axons in cocultures by injection of dye into neuron aggregates and show the feasibility of studying the growth of living axons on myotubes during synapse formation. (3) We describe the preparation of a better-defined coculture system containing myotubes with purified rat motoneurons and characterize the system with respect to axon-induced AChR aggregation. (4) We demonstrate dependence of the pattern of axon-induced AChR aggregation on muscle cell species, by the use of chick-rat chimeric co-cultures. (5) We provide evidence for the role of alternatively-spliced agrin isoforms in synapse formation by using single cell RT-PCR with neurons collected from co-cultures after observation of axon-induced AChR aggregation. Microsc. Res. Tech. 49:26-37, 2000. Published 2000 Wiley-Liss, Inc.
Fractal modeling of time-series data (1989)

Linear fractal interpolation provides a meam of constructing a function which is continuous, passes through a given set of interpolation points and uses affine transformations fo: the iterated function system. The resulting interpolatiok function is self-affine and may have non-integer dimension. In this paper, we develop an algorithm for determining the parameters needed for linear fractal interpclation so that a fractal function will closely match a given function. Thm method of modeling is applied to image contours of mountains and results indicate that this data is well-modeled with fractal interpolation.
Isolated limb perfusion for melanoma: Effectiveness and toxicity of cisplatin compared with that of melphalan and other drugs (1992)

In patients with advanced or recurrent melanoma confined to a limb, hyperthermic isolated limb perfusion (ILP) with melphalan produces complete remission in 35-40% of cases and partial remission in a further 35-40%. Mild or moderate limb toxicity is usual, but severe toxic reactions in the limb sometimes occur. After preliminary reports suggested that cisplatin administered by ILP was even more effective than melphalan yet less toxic, a study was undertaken to further assess the value of hyperthermic ILP with cisplatin in the management of limb melanoma. Ten patients were treated. The procedure failed to eliminate melanoma in the limb in 5 of the 6 who received therapeutic ILPs for recurrent disease, and recurrence developed in 2 of the 4 patients who received prophylactic ILPs. Toxicity in the perfused limbs was unacceptably high, with 2 of the 10 patients having severe reactions, one necessitating amputation. We conclude from the results of this study and from a review of literature that neither cisplatin nor any other drug or drug combination so far used for ILP in melanoma patients achieves results which are clearly superior to those achieved with melphalan. Studies are currently in progress investigating double perfusion protocols, new strategies with regional hyperthermia, and the administration by ILP of biological response modifiers such as tumor necrosis factor and interferon. However, for the present, hyperthermic ILP with melphalan remains the treatment most likely to be successful in eliminating or controlling advanced or recurrent melanoma in a limb.
Aptamers Chemistry: Chemical Modifications and Conjugation Strategies (2019)

Soon after they were first described in 1990, aptamers were largely recognized as a new class of biological ligands that can rival antibodies in various analytical, diagnostic, and therapeutic applications. Aptamers are short single-stranded RNA or DNA oligonucleotides capable of folding into complex 3D structures, enabling them to bind to a large variety of targets ranging from small ions to an entire organism. Their high binding specificity and affinity make them comparable to antibodies, but they are superior regarding a longer shelf life, simple production and chemical modification, in addition to low toxicity and immunogenicity. In the past three decades, aptamers have been used in a plethora of therapeutics and drug delivery systems that involve innovative delivery mechanisms and carrying various types of drug cargos. However, the successful translation of aptamer research from bench to bedside has been challenged by several limitations that slow down the realization of promising aptamer applications as therapeutics at the clinical level. The main limitations include the susceptibility to degradation by nucleases, fast renal clearance, low thermal stability, and the limited functional group diversity. The solution to overcome such limitations lies in the chemistry of aptamers. The current review will focus on the recent arts of aptamer chemistry that have been evolved to refine the pharmacological properties of aptamers. Moreover, this review will analyze the advantages and disadvantages of such chemical modifications and how they impact the pharmacological properties of aptamers. Finally, this review will summarize the conjugation strategies of aptamers to nanocarriers for developing targeted drug delivery systems.
Distinct Profiles of Cytotoxic Granules in Memory CD8 T Cells Correlate with Function, Differentiation Stage, and Antigen Exposure (2009)

Cytotoxic CD8 T cells exert their antiviral and antitumor activity primarily through the secretion of cytotoxic granules. Degranulation activity and cytotoxic granules (perforin plus granzymes) generally define CD8 T cells with cytotoxic function. In this study, we have investigated the expression of granzyme K (GrmK) in comparison to that of GrmA, GrmB, and perforin. The expression of the cytotoxic granules was assessed in virus-specific CD8 T cells specific to influenza virus, Epstein-Barr virus (EBV), cytomegalovirus (CMV), or human immunodeficiency virus type 1 (HIV-1). We observed a dichotomy between GrmK and perforin expression in virus-specific CD8 T cells. The profile in influenza virus-specific CD8 T cells was perforin(-) GrmB(-) GrmA(+/-) GrmK(+); in CMV-specific cells, it was perforin(+) GrmB(+) GrmA(+) GrmK(-/+); and in EBV- and HIV-1-specific cells, it was perforin(-/+) GrmB(+) GrmA(+) GrmK(+). On the basis of the delineation of memory and effector CD8 T cells with CD45RA and CD127, the GrmK(+) profile was associated with early-stage memory CD8 T-cell differentiation, the perforin(+) GrmB(+) GrmA(+) profile with advanced-stage differentiation, and the GrmB(+) GrmA(+) Grmk(+) profile with intermediate-stage differentiation. Furthermore, perforin and GrmB but not GrmA and GrmK correlated with cytotoxic activity. Finally, changes in antigen exposure in vitro and in vivo during primary HIV-1 infection and vaccination modulated cytotoxic granule profiles. These results advance our understanding of the relationship between distinct profiles of cytotoxic granules in memory CD8 T cells and function, differentiation stage, and antigen exposure.