gebhart/patrepeval huggingface dataset:
Rapid assay for extrachromosomal homologous recombination in monkey cells. (1985)

Most of the recombination assays based on the regeneration of selectable marker genes after transient infection or stable integration of DNA into mammalian cells are time consuming. We have used plasmids containing two truncated but overlapping segments of the neomycin resistance gene to rapidly quantitate and characterize the time course of extrachromosomal homologous recombination of DNA transfected into monkey COS cells. By transiently infecting cells with these recombination substrates, extracting Hirt DNA after 1 to 4 days, and transforming recombination-deficient Escherichia coli, we have shown that recombination between direct repeats occurs at frequencies of 1 to 4%. We have also used Southern blot analysis to directly characterize the recombination of this DNA in COS cells and to demonstrate that double-strand breaks in the region of homology increase recombination frequencies 10- to 50-fold.
The plenacoustic function, sampling and reconstruction (2004)

We study the spatialization of the sound field in a room, in particular the evolution of room impulse responses as a function of their spatial positions. The presented technique allows us to characterize completely the sound field in any arbitrary location if the sound field is known in a certain finite number of positions. Existing techniques usually make use of room models to recreate the sound field present at some point in the space. Our technique simply starts from the measurements of impulse responses at a finite number of positions, and, with this information, the total sound field can be recreated. An analytical solution of the problem is given for different cases of spaces. Further, we determine the number of microphones and the spacing between them needed to reconstruct the sound field perfectly up to a certain temporal frequency. The optimal sampling pattern for the microphone positions is given. Applications are also discussed.
Proline clustering in proteins from synaptic vesicles (1994)

Synaptic vesicle proteins share a specialized and common fate throughout the life cycle of the vesicle, and thus may need to respond to some common signals. It is therefore expected that these proteins will share some common motifs. However, sequence comparison among many of these proteins has not revealed any obvious motifs. Such a motif may be formed by the relative abundance of proline residues, which are not randomly distributed along the sequence but rather are clustered at the cytoplasmatic face of vesicular proteins. We propose that proline clusters serve as structural spacers between functional domains as well as potential target sites for protein-protein interactions. In view of the proline-rich nature of SH3 binding proteins, some of the proline-rich synaptic vesicle proteins may also participate in SH3 binding. Such binding may modulate certain signalling pathways in nerve terminals. Surprisingly, the consensus sequence between the proline clusters of synaptic vesicle proteins is found in a large family of abundant proline-rich proteins of the secretory organelles of the parotid exocrine gland.
Drosophilamusclefunction: Dataset For Drosophila Muscle Function Studies (2015)

This is the data and code at the time of publication of Hatfield et al. in Scientific Reports.
Can Autism be Detected at 18 Months? (1992)

Autism is currently detected only at about three years of age. This study aimed to establish if detection of autism was possible at 18 months of age. We screened 41 18-month-old toddlers who were at high genetic risk for developing autism, and 50 randomly selected 18-month-olds, using a new instrument, the CHAT, administered by GPs or health visitors. More than 80% of the randomly selected 18-month-old toddlers passed on all items, and none failed on more than one of pretend play, protodeclarative pointing, joint-attention, social interest, and social play. Four children in the high-risk group failed on two or more of these five key types of behaviour. At follow-up at 30 months of age, the 87 children who had passed four or more of these key types of behaviour at 18 months of age had continued to develop normally. The four toddlers who had failed on two or more of these key types of behaviour at 18 months received a diagnosis of autism by 30 months.
Low-dose heparin treatment does not inhibit SW480 human colon cancer growth and metastasis in vivo. (1997)

We investigated heparin effects on the biological behavior of SW480 human colon adenocarcinoma cells in vivo. Tumor growth, pathological features, metastatic potential and karyotype, were studied after the twelve week low-dose heparin treatment of nude mice subcutaneously injected with SW480 cells. A non statistically significant increase in tumor growth was observed (0.05 < p < 0.1, compared to the control group). No differences in tumor histology and karyotype were detected. Two of the six heparin-treated animals exhibited an increase in tumor vascularization. Metastasis to the lungs and liver was not inhibited. These results do not support the role of heparin in the prevention of the in vivo growth and metastasis of SW 480 colon cancer cells.
Towards Robust Unsupervised Personal Name Disambiguation (2007)

The increasing use of large open-domain document sources is exacerbating the problem of ambiguity in named entities. This paper explores the use of a range of syntactic and semantic features in unsupervised clustering of documents that result from ad hoc queries containing names. From these experiments, we find that the use of robust syntactic and semantic features can significantly improve the state of the art for disambiguation performance for personal names for both Chinese and English.
A low-voltage low-power wide-range CMOS variable gain amplifier (1998)

In this paper, a compact low-power (LP) low-voltage (LV) metal-oxide-semiconductor-only (MOS-only) variable gain amplifier (VCA) is introduced. This amplifier based on complementary MOS (CMOS) transistors operating in strong inversion is composed of a pseudo-exponential current-to-voltage converter, analog multiplier, and output stage. The gain of the amplifier is controlled exponentially by a novel wide-range pseudo-exponential current-to-voltage converter implemented with two back-to-back connected current mirrors exhibiting superb exponential characteristic. Also, a new LV/LP composite transistor is introduced to increase the input dynamic range of the multiplier. The amplifier is fabricated using a 2-/spl mu/m MOSIS n-well process, and its simulation and measurement results are shown in detail.
Equal numbers of neuronal and nonneuronal cells make the human brain an isometrically scaled‐up primate brain (2009)

The human brain is often considered to be the most cognitively capable among mammalian brains and to be much larger than expected for a mammal of our body size. Although the number of neurons is generally assumed to be a determinant of computational power, and despite the widespread quotes that the human brain contains 100 billion neurons and ten times more glial cells, the absolute number of neurons and glial cells in the human brain remains unknown. Here we determine these numbers by using the isotropic fractionator and compare them with the expected values for a human-sized primate. We find that the adult male human brain contains on average 86.1 +/- 8.1 billion NeuN-positive cells ("neurons") and 84.6 +/- 9.8 billion NeuN-negative ("nonneuronal") cells. With only 19% of all neurons located in the cerebral cortex, greater cortical size (representing 82% of total brain mass) in humans compared with other primates does not reflect an increased relative number of cortical neurons. The ratios between glial cells and neurons in the human brain structures are similar to those found in other primates, and their numbers of cells match those expected for a primate of human proportions. These findings challenge the common view that humans stand out from other primates in their brain composition and indicate that, with regard to numbers of neuronal and nonneuronal cells, the human brain is an isometrically scaled-up primate brain.
.GAMMA.-Lactam analogues of .BETA.-lactam antibiotics. (1991)

In vitro interactions between aztreonam (AZT) and 8 other antibiotics were studied using the agar dilution checkerboard technique against 88 clinical isolates of Escherichia coli, Proteus vulgaris, Serratia marcescens and Pseudomonas aeruginosa. Combinations of AZT with 8 other antibiotics were generally additive or indifferent. Synergism was occasionally seen against S. marcescens or P. aeruginosa with AZT plus isepamicin (ISP). Antagonism was observed only between AZT and latamoxef against P. vulgaris. In a phase-contrast microscopic study, synergistic effects between AZT and aspoxicillin or ISP were confirmed against E. coli 177 and P. aeruginosa 15846. AZT in combination with ISP demonstrated a synergy against experimental urinary tract infection in mice caused by P. aeruginosa 15846. We believe that combinations of several antibiotics with AZT should be considered for initial therapy of infections because synergism and additive action were observed and antagonism was rarely found in our study.
Megakaryocyte and platelet biology: getting your FAKs straight (2008)

In this issue of Blood, Hitchcock and colleagues show that the nonreceptor tyrosine kinase FAK plays a critical role in regulating megakaryocyte maturation and platelet function in vivo.
Global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine and terrestrial ecosystems (2007)

The cycles of the key nutrient elements nitrogen (N) and phosphorus (P) have been massively altered by anthropogenic activities. Thus, it is essential to understand how photosynthetic production across diverse ecosystems is, or is not, limited by N and P. Via a large-scale meta-analysis of experimental enrichments, we show that P limitation is equally strong across these major habitats and that N and P limitation are equivalent within both terrestrial and freshwater systems. Furthermore, simultaneous N and P enrichment produces strongly positive synergistic responses in all three environments. Thus, contrary to some prevailing paradigms, freshwater, marine and terrestrial ecosystems are surprisingly similar in terms of N and P limitation.
Local Differentiation of Sugar Donor Specificity of Flavonoid Glycosyltransferase in Lamiales (2009)

Flavonoids are most commonly conjugated with various sugar moieties by UDP-sugar:glycosyltransferases (UGTs) in a lineage-specific manner. Generally, the phylogenetics and regiospecificity of flavonoid UGTs are correlated, indicating that the regiospecificity of UGT differentiated prior to speciation. By contrast, it is unclear how the sugar donor specificity of UGTs evolved. Here, we report the biochemical, homology-modeled, and phylogenetic characterization of flavonoid 7-O-glucuronosyltransferases (F7GAT), which is responsible for producing specialized metabolites in Lamiales plants. All of the Lamiales F7GATs were found to be members of the UGT88-related cluster and specifically used UDP-glucuronic acid (UDPGA). We identified an Arg residue that is specifically conserved in the PSPG box in the Lamiales F7GATs. Substitution of this Arg with Trp was sufficient to convert the sugar donor specificity of the Lamiales F7GATs from UDPGA to UDP-glucose. Homology modeling of the Lamiales F7GAT suggested that the Arg residue plays a critical role in the specific recognition of anionic carboxylate of the glucuronic acid moiety of UDPGA with its cationic guanidinium moiety. These results support the hypothesis that differentiation of sugar donor specificity of UGTs occurred locally, in specific plant lineages, after establishment of general regiospecificity for the sugar acceptor. Thus, the plasticity of sugar donor specificity explains, in part, the extraordinary structural diversification of phytochemicals.
LES of Gas Exchange in IC Engines (2013)

As engine technologies become increasingly complex and engines are driven to new operating points, understanding transient phenomena is important to ensure reliable engine operation. Unlike Reynolds Averaged Navier-Stokes (RANS) studies that only provide cycle-averaged information, Large Eddy Simulation (LES) studies are capable of simulating cycle-to-cycle dynamics. In this work, a finite difference based structured methodology for LES of IC engines is presented. This structured approach allows for an efficient mesh generation process and provides potential for higher order numerical accuracy. An efficient parallel scalable block decomposition is done to overcome the challenges associated with the low ratio of fluid elements to overall mesh elements. The motion of the valves and piston is handled using a dynamic cell blanking approach and the Arbitrary Lagrangian Eulerian (ALE) method, respectively. Modified three-dimensional Navier-Stokes Characteristic Boundary Conditions (NSCBC) are used in the simulation to prescribe conditions in the manifolds. The accuracy of the simulation framework is validated using various canonical configurations. Flow bench simulations of an axisymmetric configuration and an actual engine geometry are done with the LES methodology. Simulations of the gas exchange in an engine under motored conditions are also performed. Overall, good agreement is obtained with experiments for all the cases. Therefore, this framework can be used for LES of engine simulations. In the future, reactive LES simulations will be performed using this framework.
Improved spinal fusion efficacy by long-term delivery of bone morphogenetic protein-2 in a rabbit model (2011)

The HCPN system showed potential as an effective carrier that might improve the osteogenic efficacy of BMP-2 for spinal fusion.
Electromagnetic fields of electric dipoles embedded in a stratified anisotropic Earth (1989)

Abstract The anisotropy of electrical conductivity in earth formations may be caused by crystal anisotropies of minerals, as well as by minilayers which occur frequently in sedimentary environments. The effects of anisotropy on the propagation of electromagnetic (EM) fields have been studied by many geophysicists. For instance, Kong (1972) and Wait (1981) solved the EM propagation problem for vertically anisotropic layered earths; O'Brien and Morrison (1967), for a horizontally anisotropic multilayer half-space; Chetayev (1960), as well as Reddy and Rankin (1971), for media of dipping anisotropies; and Al'tgauzen (1969), for more complicated anisotropic media with a tensor dielectric constant of five components.
SPOROTRICHOSIS RESPONDING TO FEVER THERAPY (1951)

Sporotrichosis in its localized forms is usually readily susceptible to iodide therapy. However, when widespread involvement of many viscera exists, the therapeutic problem is difficult because of lack of specific antibiotic therapy at the present time and the often-encountered resistance of this disease to iodides. The beneficial effect of fever therapy observed in the patient described opens possibilities of an added therapeutic resource. To our knowledge this observation has not been reported in the literature. REPORT OF CASE J. K., a 40-yr.-old Negro man, was first seen in consultation on the eye ward where he had been admitted on March 6, 1950, for treatment of a recurrent iridocyclitis. He presented at that time an 8 by 10 mm. moist reddish swelling of the third knuckle of the left index finger. There were three or four hard, deep-seated nodules surrounding this region and a series of linear nodules varying in size
Fuel Preprocessor (FPP) for a Solid Oxide Fuel Cell Auxiliary Power Unit (2004)

Auxiliary Power Units (APUs), driven by truck engines, consume over 800 million gallon of diesel fuel while idling. Use of separate SOFC based APUs are an excellent choice to reduce the cost and pollution associated with producing auxiliary power. However, diesel fuel is a challenging fuel to use in fuel cell systems because it has heavy hydrocarbons that can transform into carbon deposits and gums that can block passages and deactivate fuel reformer and fuel cell reactor elements. The work reported herein addresses the challenges associated with the diesel fuel sulfur and carbon producing contaminants in a Fuel Preprocessor (FPP). FPP processes the diesel fuel onboard and ahead of the reformer to reduce its carbon deposition tendency and its sulfur content, thus producing a fuel suitable for SOFC APU systems. The goal of this DOE supported Invention and Innovation program was to design, develop and test a prototype Fuel Preprocessor (FPP) that efficiently and safely converts the diesel fuel into a clean fuel suitable for a SOFC APU system. The goals were achieved. A 5 kWe FPP was designed, developed and tested. It was demonstrated that FPP removes over 80% of the fuel sulfur and over 90% of its carbon residues and it was demonstrated that FPP performance exceeds the original project goals.
Separate information required for nuclear and subnuclear localization: additional complexity in localizing an enzyme shared by mitochondria and nuclei. (1992)

The TRM1 gene of Saccharomyces cerevisiae codes for a tRNA modification enzyme, N2,N2-dimethylguanosine-specific tRNA methyltransferase (m2(2)Gtase), shared by mitochondria and nuclei. Immunofluorescent staining at the nuclear periphery demonstrates that m2(2)Gtase localizes at or near the nuclear membrane. In determining sequences necessary for targeting the enzyme to nuclei and mitochondria, we found that information required to deliver the enzyme to the nucleus is not sufficient for its correct subnuclear localization. We also determined that mislocalizing the enzyme from the nucleus to the cytoplasm does not destroy its biological function. This change in location was caused by altering a sequence similar to other known nuclear targeting signals (KKSKKKRC), suggesting that shared enzymes are likely to use the same import pathway as proteins that localize only to the nucleus. As with other well-characterized mitochondrial proteins, the mitochondrial import of the shared methyltransferase depends on amino-terminal amino acids, and removal of the first 48 amino acids prevents its import into mitochondria. While this truncated protein is still imported into nuclei, the immunofluorescent staining is uniform throughout rather than at the nuclear periphery, a staining pattern identical to that described for a fusion protein consisting of the first 213 amino acids of m2(2)Gtase in frame with beta-galactosidase. As both of these proteins together contain the entire m2(2)Gtase coding region, the information necessary for association with the nuclear periphery must be more complex than the short linear sequence necessary for nuclear localization.
Macrophages retain hematopoietic stem cells in the spleen via VCAM-1 (2015)

Splenic myelopoiesis provides a steady flow of leukocytes to inflamed tissues, and leukocytosis correlates with cardiovascular mortality. Yet regulation of hematopoietic stem cell (HSC) activity in the spleen is incompletely understood. Here, we show that red pulp vascular cell adhesion molecule 1 (VCAM-1)(+) macrophages are essential to extramedullary myelopoiesis because these macrophages use the adhesion molecule VCAM-1 to retain HSCs in the spleen. Nanoparticle-enabled in vivo RNAi silencing of the receptor for macrophage colony stimulation factor (M-CSFR) blocked splenic macrophage maturation, reduced splenic VCAM-1 expression and compromised splenic HSC retention. Both, depleting macrophages in CD169 iDTR mice or silencing VCAM-1 in macrophages released HSCs from the spleen. When we silenced either VCAM-1 or M-CSFR in mice with myocardial infarction or in ApoE(-/-) mice with atherosclerosis, nanoparticle-enabled in vivo RNAi mitigated blood leukocytosis, limited inflammation in the ischemic heart, and reduced myeloid cell numbers in atherosclerotic plaques.
The highly-parallel supercomputers (1980)

As computer processing power has increased over the past three decades, so have demands on computer performance. In the race of computer technology to keep abreast of these demands, more and more attention has been given to parallel hardware organizational techniques. Instruction and data pipelining, instruction overlapping and distributed processing are examples of such techniques.
A Review of Biomarkers for Neurodegenerative Disease: Will They Swing Us Across the Valley? (2017)

Measures of the severity of cognitive impairment or parkinsonism are the usual endpoints in clinical trials for Alzheimer's disease (AD) and Parkinson's disease (PD), but are critically hampered by their lack of disease sensitivity and specificity. Due to the high failure rate of clinical trials, the rate of regulatory approval for efficacious new drugs has stagnated in the past few decades, with the gap between basic science discovery and clinical application metaphorically termed the "Valley of Death". While the causes for this are probably multiple and complex, the usage of biomarkers as surrogate endpoints, particularly when they are molecularly-specific for the disease, has achieved some success in cancer trials, and it is likely that neurodegenerative disease trials would benefit from the same approach. As dementia and parkinsonism are not disease-specific clinical syndromes, both AD and PD trials have been flawed by reliance on clinical diagnosis and clinical endpoints. Clinical improvement has been a requirement for regulatory approval, but molecularly-specific biomarkers should improve both diagnostic accuracy and tracking of disease progression, allowing quicker screening of drug candidates. However, even when a molecularly-specific biomarker is found, such as amyloid imaging for AD, it may not reflect the entire extant molecular disease repertoire and may not serve equally well in the different roles of preclinical detection, diagnostic confirmation and surrogate endpoint, necessitating the usage of two, three or more biomarkers, deployed in series or in parallel.
C O 2 detection using polyethylenimine/starch functionalized AlGaN∕GaN high electron mobility transistors (2008)

Al Ga N ∕ Ga N high electron mobility transistors (HEMTs) functionalized with polyethylenimine/starch were used for detecting CO2 with a wide dynamic range of 0.9%–50% balanced with nitrogen at temperatures from 46to220°C. Higher detection sensitivity to CO2 gas was achieved at higher testing temperatures. At a fixed source-drain bias voltage of 0.5V, drain-source current of the functionalized HEMTs showed a sublinear correlation upon exposure to different CO2 concentrations at low temperature. The superlinear relationship was at high temperature. The sensor exhibited a reversible behavior and a repeatable current change of 32 and 47μA with the introduction of 28.57% and 37.5% CO2 at 108°C, respectively.
Simultaneous Floor Planning and Global Routing for Hierarchical Building-Block Layout (1987)

A new methodology for hierarchical floor planning and global routing for building block layout is presented. Unlike the traditional approach, which separates placement and global routing into two consecutive stages, our approach accomplishes both jobs simultaneously in a hierarchical fashion. The global routing problem is formulated at each level as a series of the minimum Steiner tree problem in a special class of partial 3-trees, which can be solved optimally in linear time. The floor planner with a maximum of five rooms per level has been implemented in the C language, running on a VAX 8650 under 4.3 BSD UNIX. The experimental results on examples with a large number of irregular blocks show that our approach out-performs other well-known deterministic algorithms, and gives results that are comparable to random-based algorithms but with a computing time an order of magnitude less. Due to the unique goal-oriented and pattern-directed features of our floor planner, it accepts specifications for overall aspect ratio and I/O pad positions, thus making our approach suitable for hierarchical design.