gebhart/patrepeval huggingface dataset:
The ins and outs of programmed cell death during <i>C. elegans</i> development (1994)

Abstract During the development of the C. elegans hermaphrodite, 131 of the 1090 cells generated undergo programmed cell death. Genetic studies have identified mutations in 14 genes that specifically affect this process. These genes define a genetic pathway for programmed cell death in C. elegans. Two genes, ced-3 and ced-4, are required for cells to undergo programmed cell death, while a third gene, ced-9, protects cells that should live from undergoing programmed cell death. The proteins encoded by ced-3 and ced-9 show significant similarity to proteins that affect programmed cell death in vertebrates, suggesting that the molecular cell death pathway in which ced-3, ced-4, and ced-9 act has been conserved between nematodes and vertebrates.
SSZ‐27: A Small‐Pore Zeolite with Large Heart‐Shaped Cavities Determined by Using Multi‐crystal Electron Diffraction (2019)

The high-silica zeolite SSZ-27 was synthesized using one of the isomers of the organic structure-directing agent that is known to produce the large-pore zeolite SSZ-26 (CON). The structure of the as-synthesized form was solved using multi-crystal electron diffraction data. Data were collected on eighteen crystals, and to obtain a high-quality and complete data set for structure refinement, hierarchical cluster analysis was employed to select the data sets most suitable for merging. The framework structure of SSZ-27 can be described as a combination of two types of cavities, one of which is shaped like a heart. The cavities are connected through shared 8-ring windows to create straight channels that are linked together in pairs to form a one-dimensional channel system. Once the framework structure was known, molecular modelling was used to find the best fitting isomer, and this, in turn, was isolated to improve the synthesis conditions for SSZ-27.
Influence of Layer Structure on Write/Erase Repetition Characteristics of Magneto-Optical Disks (1993)

The relationship between erase-write characteristics or write/erase repetition characteristics and the layer structure of magneto-optical disks, was studied both experimentarily and by computer simulation. For tri-layer structure disks such as Sub./SiNx/TbFeCo/SiNx, an erase power of 11.5 mW is needed to erase a recorded domain, perfectly. The carrier level of tri-layered disks decreases with increasing write/erase repetition cycle. This is due to structure relaxation in the recording film which is caused by heating above a maximum temperature of 350°C.A quadri-layer structure is studied which has a thinner recording layer and a metal layer, whose thermal conductivity is low. With this structure, the carrier level decreases after repeated write/erase processes. As the maximum temperature on the recording film is higher than 370°C, there is also structure relaxation in the recording film. When Al, whose conductivity is large, was used as the metal layer, the number of the write/erase repetition cycles was increased and there was no structure relaxation when the maximum temperature was lower than 300°C. The disk incorporating this structure has a large carrier to noise ratio. Using these results, the disk structure was optimized. After repetition of erase and write, C/N did not change. This disk has high reliability against thermal resistance.
VISIDEP (TM): Visual Image Depth Enhancement By Parallax Induction (1984)

The usual descriptions of depth perception have traditionally required the simultaneous presentation of disparate views presented to separate eyes with the concomitant demand that the resulting binocular parallax be horizontally aligned. Our work suggests that the visual input information is compared in a short-term memory buffer which permits the brain to compute depth as it is normally perceived. However, the mechanism utilized is also capable of receiving and processing the stereographic information even when it is received monocularly or when identical inputs are simultaneously fed to both eyes. We have also found that the restriction to horizontally displaced images is not a necessary requirement and that improvement in image acceptability is achieved by the use of vertical parallax. Use of these ideas permit the presentation of three-dimensional scenes on flat screens in full color without the encumbrance of glasses or other viewing aids.
Poly(β-L-malic acid) production by diverse phylogenetic clades of <i>Aureobasidium pullulans</i> (2011)

Poly(β-L-malic acid) (PMA) is a natural biopolyester that has pharmaceutical applications and other potential uses. In this study, we examined PMA production by 56 strains of the fungus Aureobasidium pullulans representing genetically diverse phylogenetic clades. Thirty-six strains were isolated from various locations in Iceland and Thailand. All strains from Iceland belonged to a newly recognized clade 13, while strains from Thailand were distributed among 8 other clades, including a novel clade 14. Thirty of these isolates, along with 26 previously described strains, were examined for PMA production in medium containing 5% glucose. Most strains produced at least 4 g PMA/L, and several strains in clades 9, 11, and 13 made 9-11 g PMA/L. Strains also produced both pullulan and heavy oil, but PMA isolated by differential precipitation in ethanol exhibited up to 72% purity with no more than 12% contamination by pullulan. The molecular weight of PMA from A. pullulans ranged from 5.1 to 7.9 kDa. Results indicate that certain genetic groups of A. pullulans are promising for the production of PMA.
A Synthesizable IP Core for DVB-S2 LDPC Code Decoding (2005)

The new standard for digital video broadcast DVB-S2 features low-density parity-check (LDPC) codes as their channel coding scheme. The codes are defined for various code rates with a block size of 64800 which allows a transmission close to the theoretical limits. The decoding of LDPC is an iterative process. For DVB-S2 about 300000 messages are processed and reordered in each of the 30 iterations. These huge data processing and storage requirements are a real challenge for the decoder hardware realization, which has to fulfill the specified throughput of 255 Mbit/s for base station applications. In this paper we show, to the best of our knowledge, the first published IP LDPC decoder core for the DVB-S2 standard. We present a synthesizable IP block based on ST Microelectronics 0.13 /spl mu/m CMOS technology.
Activation of a neurofilament kinase, a tau kinase, and a tau phosphatase by decreased ATP levels in nerve growth factor-differentiated PC-12 cells. (1995)

Brain pathology in Alzheimer disease and in aged controls shows hyperphosphorylation of tau and of neurofilament proteins. Roder and Ingram [Roder, H.M. & Ingram, V.M. (1991) J. Neurosci. 11, 3325-3343 and Roder, H.M., Eden, P.A. & Ingram, V.M. (1993) Biochem. Biophys. Res. Commun. 193, 639-647] previously reported that the brain protein kinase PK40erk can hyperphosphorylate both tau and neurofilaments and interestingly, is strongly inhibited by ATP uncomplexed with Mg2+. We now report that the mitochondrial uncoupler carbonyl cyanide p-trifluoro-methoxyphenylhydrazone decreases ATP levels in rat pheochromacytoma (PC-12) cells differentiated with nerve growth factor and activates a neurofilament kinase, a tau kinase, and, unexpectedly, a tau phosphatase--either PP1 or PP2A. Such aberrant modulation of protein phosphorylation patterns could be the common biochemical basis for senile dementia and for Alzheimer disease and could explain the late-onset etiology of both conditions.
1.5.4 Time‐Expanded Decision Networks: A Framework for Designing Evolvable Complex Systems (2007)

Abstract This paper describes the concept of Time‐Expanded Decision Networks (TDN), a new methodology to design and analyze flexibility in large‐scale complex systems. This includes a preliminary application of the methodology to the design of Heavy Lift Launch Vehicles for NASA's space exploration initiative. Synthesizing concepts from Decision Theory, Real Options Analysis, Network Optimization, and Scenario Planning, TDN provides a holistic framework to quantify the value of system flexibility, analyze development and operational paths, and identify designs which can allow managers and systems engineers to react more easily to exogenous uncertainty. TDN consists of five principle steps, which can be implemented as a software tool: 1. Design a set of potential system configurations 2. Quantify switching costs to create a “static network” that captures the difficulty of switching among these configurations 3. Create a time‐expanded decision network by expanding the static network in time, including chance and decision nodes 4. Evaluate minimum cost paths through the network under plausible operating scenarios 5. Modify the set of initial design configurations to exploit high‐leverage switches and repeat the process to convergence. Results can inform decisions about how and where to embed flexibility in order to enable system evolution along various development and operational paths.
Design-based metrology: advanced automation for CD-SEM recipe generation (2005)

The procedure for properly implementing OPC for a new technology node or chip design involves multiple steps: selection of the RET (resolution enhance technique), selection of design rules, OPC Model Building, OPC Verification, CD control quantification (across chip, reticle, wafer, focus, exposure, etc), calibration of Optical Rule Checks (ORC), and other verification steps. Many of these steps require up to thousands of wafer measurements, and while state-of-the-art CD-SEM tools provide automated metrology for production, manually creating a CD recipe with thousands of unique sites is extremely tedious and error-prone. This places a practical limit on both the quality and number of measurements that can be acquired during the technology development and qualification period. At the same time, the number of measurements required to qualify a new reticle design has increased drastically due to the growing complexity of RET and diminishing tolerances. To meet this challenge, a direct and automated link from the design systems to the process metrology tools is needed. Novel methodologies must also be developed to enable automated generation of teh recipe from the design inputs and to translate the flood of metrology results into information that can improve the design, mask data processing, or the patterning process. To facilitate this two-way data flow, a new framework has been created enabling true Design-Based Metrology (DBM), and an application named OPC-Check has been developed to operate within this framework. This DBM framework provides the common language and interface that facilitates the direct transfer of desired measurement locations from teh design to the metrology tool. This link is a critical element in Design for Manufacturability (DFM) efforts, a central theme in many presentations at Microlithography 2005. This article discusses the significant benefits of the tight integration of design and process metrology for OPC implementation in a new technology node, and provides some examples of the novel OPC-Check application as currently implemented at AMD SDC with Applied Materials CD-SEM tools.
Materials Behavior and Manufacturing Aspects of High Pressure Combustion Driven Compaction P/M Components (2004)

This paper provides an overview of materials behavior and manufacturing aspects of P/M parts fabricated by high pressure Combustion Driven Compaction (CDC) at UTRON.[24-29] This unique compaction method has several advantages such as net-shaping, improved surface finish/quality, amenability to simple or complex geometries, suitability for single or multilayered materials, reduced processing time (e.g., ms) compared to traditional rapid prototyping techniques, little or no post-machining, and improved process flexibility. Select results of CDC processed Aluminum alloys, Stainless Steel 316L (SS316L), Copper and dissimilar combination of SS316L/Copper under optimum process conditions will be presented and discussed. The structure/property characteristics include microstructures, surface roughness/quality and mechanical properties. The potential commercial uses [1-37] of high pressure compaction CDC technology include a wide range of applications such as vacuum seals [15], x-ray targets, cryogenic parts, accelerator/RF microwave components [18-27, 31, 34-36], computer hard disk drive accessories such as read/write heads, engine parts such as valves/valve seats, pushrods, high temperature nozzle liner parts/heat sinks, electrical/electromagnetic parts such as contacts/commutator rings/brushes, tooling inserts, advanced magnets [37], high performance gears, bearings, welding electrodes, and wear/corrosion resistant tribological components.
Development of Novel CD138 Antigen-Specific Peptide Capable of Eliciting Myeloma-Specific Cytotoxic T Lymphocytes Response. (2005)

Abstract Multiple myeloma (MM) is characterized by the accumulation of mature plasma cells in the bone marrow. Despite progress in treatment, the disease still remains incurable, therefore novel therapeutic approaches are required to achieve better treatment. Development of peptide-based immunotherapies against specific tumor-associated antigens offers an attractive approach that may lead to tumor-targeted cellular therapy in MM patients. CD138 (Syndecan-1) is an unique target expressed on the surface of MM cells and normal plasma cells with very limited other distribution or expression. CD138 has been reported to play an important role in myeloma cell survival and, infact, is used to purify MM cells in laboratory experiments. The purpose of this study was to develop immunogenic peptides derived from CD138 antigen for the induction of antigen-specific cytotoxic T lymphocytes (CTLs) against MM. We have identified an immunogeneic HLA-A2-specific CD138 peptide that is capable of inducing MM specific-CTLs. To induce the specific CTLs, HLA-A2-positive normal human T lymphocytes were stimulated with autologous dendritic cells or T2 cells pulsed with the CD138 peptide. The generated CTLs showed a distinct phenotype consisting of 67% of CD69+/CD45RO+ and 1% of CD45RA+/CCR7+ T cells, characteristic of effector memory cell population. A significant (p < 0.05) increase in T cell proliferation and IFN-g secretion were observed by the CTLs following restimulation with HLA-A2+/CD138+ MM cells. The CTLs displayed HLA-A2-restricted CD138-specific cytotoxic activity against MM cell, demonstrated as 76% and 86% cytotoxicity at Effector:Target ratios of 20:1 or 60:1, respectively. The MM cell-specific cytotoxicity was confirmed in “cold” target inhibition assays using HLA-A2.1+/CD138+ MM cells as “cold” inhibitor, demonstrated 25% and 39% reduction in cytotoxicity when incubated with cold inhibitors at E:T ratios of 20:1 or 60:1, respectively. A distinct CD138 peptide-specific tetramer+/CD8+ population was also confirmed. Taken together, these data demonstrate the efficacy of the immunogenic CD138 peptide in inducing a cellular immune response in MM for future clinical application.
Antitumor Agents From Bohemic Acid Complex, III. The Isolation of Marcellomycin, Musettamycin, Rudolphomycin, Mimimycin, Collinemycin, Alcindoromycin, and Bohemamine (1980)

Six anthracycline antitumor agents, marcellomycin, musettamycin, rudolphomycin, alcindoromycin, collinemycin, and mimimycin, have now been isolated from bohemic acid complex. This has been achieved by classical column chromatography with Sephadex LH-20 and ammonia-neutralized silica and by analytical and prepatative hplc techniques with normal phase systems containing aqueous ammonia.
Shift register multi-phase clock based downsampled floating tap DFE for serial links (2014)

This paper proposes a power/area efficient method for realizing a class of downsampled floating tap decision feedback equalization (DFE) architectures for serial links. The architectures offer significant complexity and power reduction over a standard floating tap DFE architecture with minimal performance loss. A shift register multi-phase clock based design in 28 nm CMOS is implemented for operation at 28.05 Gb/s. At 28.05 Gb/s, the designed downsampled architecture dissipates only 67% of the power of the corresponding standard architecture operating at 17 Gb/s. At the lower 17 Gb/s speed, the downsampled architecture dissipates only 45% of the power of the standard architecture.
Localization of functionally important epitopes within the second C-type domain of coagulation factor V using recombinant chimeras. (1994)

Coagulation factor V, an integral component of the prothrombinase complex, possesses two C-type domains at the carboxyl-terminal end of the molecule. Homologous C-type domains are present in factor VIII as well as several non-coagulation proteins. Deletion of the second C-type domain of factor V results in the loss of procoagulant activity and the ability to bind phosphatidylserine. We now report the effect of substitution of all or a portion of the C2 domain of factor V with the corresponding regions of factor VIII or the human breast carcinoma protein BA46. Substitution of the entire domain with a heterologous C2 domain does not restore significant procoagulant activity, although smaller, exon-size substitutions do result in chimeras with partial activity (approximately 10% of factor Va). Using chimeras with partial substitutions, we determined that the amino-terminal region of the domain is involved in binding to phosphatidylserine. In contrast, the central region of the domain is not involved in phosphatidylserine binding, but an antibody binding at or near this site inhibits procoagulant activity, suggesting that this region is involved in a separate function. Lastly, the molecular basis for the light chain doublet, which is important in the expression of full procoagulant activity, is located within the carboxyl-terminal region of the C2 domain.
Hyper-inducible expression system for streptomycetes (2004)

Streptomycetes produce useful enzymes and a wide variety of secondary metabolites with potent biological activities (e.g., antibiotics, immunosuppressors, pesticides, etc.). Despite their importance in the pharmaceutical and agrochemical fields, there have been no reports for practical expression systems in streptomycetes. Here, we developed a "P(nitA)-NitR" system for regulatory gene expression in streptomycetes based on the expression mechanism of Rhodococcus rhodochrous J1 nitrilase, which is highly induced by an inexpensive and safe inducer, epsilon-caprolactam. Heterologous protein expression experiments demonstrated that the system allowed suppressed basal expression and hyper-inducible expression, yielding target protein levels of as high as approximately 40% of all soluble protein. Furthermore, the system functioned in important streptomycete strains. Thus, the P(nitA)-NitR system should be a powerful tool for improving the productivity of various useful products in streptomycetes.
An xml index advisor for DB2 (2008)

XML database systems are expected to handle increasingly complex queries over increasingly large and highly structured XML databases. An important problem that needs to be solved for these systems is how to choose the best set of indexes for a given workload. We have developed an XML Index Advisor that solves this XML index recommendation problem and is tightly coupled with the query optimizer of the database system. We have implemented our XML Index Advisor for DB2. In this demonstration we showcase the new query optimizer modes that we added to DB2, the index recommendation process, and the effectiveness of the recommended indexes.
Robust and Efficient Distributed Compression for Cloud Radio Access\n Networks (2012)

This work studies distributed compression for the uplink of a cloud radio\naccess network where multiple multi-antenna base stations (BSs) are connected\nto a central unit, also referred to as cloud decoder, via capacity-constrained\nbackhaul links. Since the signals received at different BSs are correlated,\ndistributed source coding strategies are potentially beneficial, and can be\nimplemented via sequential source coding with side information. For the problem\nof compression with side information, available compression strategies based on\nthe criteria of maximizing the achievable rate or minimizing the mean square\nerror are reviewed first. It is observed that, in either case, each BS requires\ninformation about a specific covariance matrix in order to realize the\nadvantage of distributed source coding. Since this covariance matrix depends on\nthe channel realizations corresponding to other BSs, a robust compression\nmethod is proposed for a practical scenario in which the information about the\ncovariance available at each BS is imperfect. The problem is formulated using a\ndeterministic worst-case approach, and an algorithm is proposed that achieves a\nstationary point for the problem. Then, BS selection is addressed with the aim\nof reducing the number of active BSs, thus enhancing the energy efficiency of\nthe network. An optimization problem is formulated in which compression and BS\nselection are performed jointly by introducing a sparsity-inducing term into\nthe objective function. An iterative algorithm is proposed that is shown to\nconverge to a locally optimal point. From numerical results, it is observed\nthat the proposed robust compression scheme compensates for a large fraction of\nthe performance loss induced by the imperfect statistical information.\nMoreover, the proposed BS selection algorithm is seen to perform close to the\nmore complex exhaustive search solution.\n
Electric Power Generation Using Buoyancy-Induced Vortices (2017)

Thermally-stratified air layers over solar-heated ground are exploited for scalable, low-cost power generation by the deliberate formation of intense buoyancy-induced vertical columnar vortices. Such vortices entrain the ground-heated air layer in regions with high surface solar heating rates, and convert the (gravitational) potential energy into “solar-induced wind” with significant kinetic energy. Unlike naturally occurring “dust devil” vortices, these columnar vortices are deliberately triggered and anchored. Each vortex is sustained by continuous entrainment of ground-heated air through an azimuthal array of stationary ground-mounted vertical vanes. Electric power is generated by using the rotational and vertical air motions within the columnar vortex to drive a vertical-axis turbine. Meter-scale laboratory experiments have demonstrated the nucleation, anchoring, and sustainment of strong, buoyancy-driven vortices centered within an azimuthal array of stationary vertical vanes above a controlled thermal ground plane. Outdoor tests of a meter-scale prototype have demonstrated autonomous start-up, formation, anchoring, and sustainment of a buoyancy-induced vortex generated solely by absorbed solar energy.
Uniform-Diameter Single-Walled Carbon Nanotubes Catalytically Grown in Cobalt-Incorporated MCM-41 (2003)

Single-walled carbon nanotubes of uniform diameter were grown in cobalt-substituted MCM-41 molecular sieves templated with C12 and C16 alkyl chains to result in pore diameters of 2.6 and 3.3 nm, respectively. The narrow diameter distribution of the tubes grown was probed by Raman, UV−visible, and NIR spectroscopy, as well as by high-resolution transmission electron microscopy. Tube diameters have been observed to vary with the size of the Co clusters formed during carbon deposition, as measured by extended X-ray absorption fine structure (EXAFS). It is proposed that the diameter of the carbon nanotubes grown in MCM-41 catalysts is controlled by the size of the metallic clusters formed in the template. Because MCM-41 catalysts of different pore diameter form Co clusters of different sizes, this mechanism can be exploited to grow carbon nanotubes of uniform, preselected diameters.