gebhart/patrepeval huggingface dataset:
A comparison of selected force constants derived from ab initioSCF calculations on β‐hydroxyacrolein. Acrolein, performic acid, and formic acid (1981)

Abstract Harmonic force fields have been calculated for the planar hydrogen‐bonded ring conformer of β‐hydroxyacrolein, c C c , which is the most stable, and the chain conformer, c C t , generated by 180° rotation of OH about the CO bond axis. The equilibrium structure obtained using the 4‐31 G basis set with full geometry optimization was employed in each case. Selected force constants for the bonds directly concerned in the formation of the ring from the chain structure, and the increments in going from the one to the other, are compared with the values for the corresponding conformers of performic and formic acids. As the ring size increases from four in trans ‐formic acid, to five in cis – cis ‐performic acid and to six in the c C c conformer of β‐hydroxyacrolein there is a successive increase in the mechanical strength of the hydrogen‐bridging unit. The energy changes for the chain → ring conversion do not follow this progression: performic acid is out of order. But, since a force constant is a localized bond property, whereas the energy changes are determined not only by interactions specific to the hydrogendonor and hydrogen‐acceptor groups but also by interactions involving more distant parts of the molecule, the force constants for the bonds directly concerned in the formation of the hydrogen bridge provide a less ambiguous basis for comparing the strength of the intramolecular hydrogen bonding.
Amino acids critical for the functions of the bovine papillomavirus type 1 E2 transactivator (1996)

The N-terminal domain of the bovine papillomavirus type 1 E2 protein is important for viral DNA replication, for transcriptional transactivation, and for interaction with the E1 protein. To determine which residues of this 200-amino-acid domain are important for these activities, single conservative amino acid substitutions have been generated in 17 residues that are invariant among all papillomavirus E2 proteins. The resulting mutated E2 proteins were tested for the ability to support viral DNA replication, activate transcription, and cooperatively bind to the origin of replication with the E1 protein. We identified five mutated proteins that were completely defective for transcriptional activation and either were defective or could support viral DNA replication at only low levels. However, several of these proteins could still interact efficiently with the E1 protein. In addition, we identified several mutated proteins that were unable to efficiently cooperatively bind to the origin with the E1 protein. Although a number of the mutated proteins demonstrated wild-type activity in all of the functions tested, only 3 out of 17 mutated viral genomes were able to induce foci in a C127 focus formation assay when the mutations were generated in the background of the entire bovine papillomavirus type 1 genome. This finding suggests that the E2 protein may have additional activities that are important for the viral life cycle.
High performance many-to-many intranet screen sharing with DisplayCast (2014)

DisplayCast is a many to many Intranet screen sharing system. Its screen capture mechanism creates a sequence of pixmap images of the screen updates. Prior systems that used a similar approach were designed to operate over constrained wide-area networks and did not exploit the Intranet network conditions to achieve high capture rates. First we empirically analyzed the screen contents for a variety of scenarios. We showed that screen updates were sporadic with long periods of inactivity. When active, screens were updated at far higher rates than was supported by earlier systems. The mismatch was pronounced for interactive scenarios. Even during active screen updates, the number of updated pixels were frequently small. We showed that crucial information can be lost if individual updates were merged. When the available system resources could not support high capture rates, we showed ways in which updates can be effectively collapsed. Next, we investigate compression mechanisms for streaming these updates. Even while using a hardware encoder, lossy compressors such as H.264 were unable to sustain high frame rates. Though Zlib lossless compression operated within the latency and compression rate requirements, the compression efficiency was poor. By analyzing the screen pixels, we developed a practical transformation that significantly improved compression rates. DisplayCast incorporates these observations. It shares the processor and network resources required for screen capture, compression and transmission with host applications whose output needs to be shared. DisplayCast is agile and uses faster processing capability to achieve even higher performance. Our system components operate natively in Windows 7, Mac OS X and iOS and is deployed in a production setting. DisplayCast is released under a New BSD License.
Implementation of the Ficus Replicated File System. (1990)

As we approach nation-wide integration of computer systems, it is clear that file replication will play a key role, both to improve data availability in the face of failures, and to improve performance by locating data near where it will be used. We expect that future file systems will have an extensible, modular structure in which features such as replication can be &amp;quot;slipped in&amp;quot; as a transparent layer in a stackable layered architecture. We introduce the Ficus replicated file system for NFS and show how it is layered on top of existing file systems. The Ficus file system differs from previous file replication services in that it permits update during network partition if any copy of a file is accessible. File and directory updates are automatically propagated to accessible replicas. Conflicting updates to directories are detected and automatically repaired; conflicting updates to ordinary files are detected and reported to the owner. The frequency of communications outages rendering i...
Inhibition of Hypoxia-Inducible Factor Is Sufficient for Growth Suppression of VHL−/− Tumors (2004)

The von Hippel-Lindau tumor suppressor protein (pVHL) is a substrate receptor for the mammalian SCF-2 E3 ubiquitin ligase complex that targets several substrates for ubiquitination and proteasomal degradation. Among these targets are the alpha-regulatory subunits of the hypoxia-inducible factor (HIF). VHL-/- cells constitutively overexpress hypoxia-inducible genes through both transcriptional and posttranscriptional mechanisms and form tumors when injected into nude mice. Reintroduction of pVHL into VHL-/- cell lines restores normal oxygen-dependent regulation of these genes and suppresses tumor formation in the mouse xenograft assay. We report here that short hairpin RNA-mediated inactivation of HIF phenocopies the effects of pVHL reintroduction with respect to decreased expression of hypoxia-inducible genes, decreased ability to promote vascular endothelial cell proliferation in vitro, and tumor growth suppression in vivo. In addition, HIF inactivation abrogated the cellular response to hypoxia, indicating that HIF is the only pVHL target required for this response. These data suggest that deregulation of hypoxia-inducible genes in VHL-/- cells can be attributed mainly to deregulation of HIF and validate HIF as a therapeutic anticancer drug target.
A Convenient and Mild Procedure for the Synthesis of Hydrazones and Semicarbazones from Aldehydes or Ketones under Solvent-free Conditions (1999)

Hydrazone and semicarbazone derivatives are readily prepared from the corresponding aldehydes or ketones, hydrazine derivatives and semicarbazides under solvent-free conditions.
A New Major Seti Project Based on Project Serendip Data and 100,000 Personal Computers (1997)

Abstract We are now developing an innovative SETI project, tentatively named seti@home, involving massively parallel computation on desktop computers scattered around the world. The public will be uniquely involved in a real scientific project. Individuals will download a Screensaver program that will not only provide the usual attractive graphics when their computer is idle, but will also perform sophisticated analysis of SETI data using the host computer. The data are tapped off Project Serendip IV’s receiver and SETI survey operating on the 305-meter diameter Arecibo radio telescope. We make a continuous tape-recording of a 2 MHz bandwidth signal centered on the 21 cm H I line. The data on these tapes are then preliminarily screened and parceled out by a server that supplies small chunks of data (50 sec of 20 kHz bandwidth, a total of 0.25 MB) over the Internet to clients possessing the screen-saver software. After the client computer has automatically analyzed a complete chunk of data (in a much more detailed manner than Serendip normally does) a report on the best candidate signals is sent back to the server, whereupon a new chunk of data is sent out. If 50,000-100,000 customers can be achieved, the computing power will be equivalent to a substantial fraction of a typical supercomputer, and seti@home will cover a comparable volume of parameter space to that of Serendip IV.
Antiproliferative effect of LXR agonists T0901317 and 22(R)-hydroxycholesterol on multiple human cancer cell lines. (2010)

Previously, we and other groups reported that liver X receptor (LXR) agonists T0901317, 22(R)-hydroxycholesterol, and 24(S)-hydroxycholesterol suppressed the proliferation of prostate and breast cancer cells. In this study, we report that T0901317 and 22(R)-hydroxycholesterol treatment inhibited the proliferation of different progression stages of LNCaP human prostate cancer cells, as well as different commonly used human cancer cell lines. Cancer cell lines with higher LXRα mRNA expression were more sensitive to 22(R)-hydroxycholesterol-induced inhibition. T0901317 treatment decreased the percentage of the cell population in S-phase and caused G(1) cell cycle arrest. Overexpression of S-phase kinase-associated protein 2 (Skp2) partially blocked the suppressive effect of T0901317 treatment. Modulating LXR signaling is therefore a potential adjuvant therapy for advanced prostate cancer and other types of cancer.
High-Titer Adeno-Associated Viral Vectors from a Rep/Cap Cell Line and Hybrid Shuttle Virus (1998)

Adeno-associated virus (AAV) is a potential vector for in vivo gene therapy. A critical analysis of its utility has been hampered by methods of production that are inefficient, difficult to scale up, and that often generate substantial quantities of replication-competent AAV. We describe a novel method for producing AAV that addresses these problems. A cell line, called B50, was created by stably transfecting into HeLa cells a rep/cap-containing plasmid utilizing endogenous AAV promoters. Production of AAV occurs in a two-step process. B50 is infected with an adenovirus defective in E2b, to induce Rep and Cap expression and provide helper functions, followed by a hybrid virus in which the AAV vector is cloned in the E1 region of a replication-defective adenovirus. This results in a 100-fold amplification and rescue of the AAV genome, leading to a high yield of recombinant AAV that is free of replication-competent AAV. Intramuscular injection of vector encoding erythropoietin into skeletal muscle of mice resulted in supraphysiologic levels of hormone in serum that was sustained and caused polycythemia. This method of AAV production should be useful in scaling up for studies in large animals, including humans.
Organ-Specific Invertase Deficiency in the Primary Root of an Inbred Maize Line (1991)

An organ-specific invertase deficiency affecting only the primary root system is described in the Oh 43 inbred maize (Zea mays). Invertases (acid and neutral/soluble and insoluble) were assayed in various tissues of hybrid (NK 508) and inbred (Oh 43, W 22) maize lines to determine the basis for an early report that Oh 43 root tips were unable to grow on sucrose agar (27). Substantial acid invertase activity (7.3 to 16.1 micromoles of glucose per milligram of protein per hour) was evident in extracts of all tissues tested except the primary root system of Oh 43. This deficiency was also evident in lateral roots arising from the primary root. In contrast, morphologically identical lateral roots from the adventitious root system had normal invertase levels. These results suggest that ontogenetic origin of root tissues is an important determinant of invertase expression in maize. Adventitious roots (including the seminals) arise above the scutellar node and are, therefore, of shoot origin. The Oh 43 deficiency also demonstrated that invertase activity was not essential for maize root growth. Sucrose synthase was active in extracts from all root apices and theoretically provided the only available avenue for sucrose degradation in primary root tips of Oh 43. The deficiency described here will provide a useful avenue of investigation into the expression and significance of root invertase.
Temperature insensitive measurements of static displacements using a fiber Bragg grating (2003)

We report a chirped fiber Bragg grating transducer for the measurement of acceleration, in which a cantilever beam and fiber Bragg grating are used. The cantilever induces strain on the grating resulting in a Bragg grating wavelength modification that is subsequently detected. The output signal is insensitive to temperature variations and for a temperature change from -20 degrees C to 40 degrees C, the output signal fluctuated less than 5 % without any temperature compensation schemes. Because the accelerometer does not utilize the complex demodulation techniques it is potentially inexpensive. For the experimental system a linear output range of 8 g could be detected.
Inflammatory cytokines enhance the in vivo clonal expansion and differentiation of antigen-activated CD4+ T cells (1997)

Despite the wealth of information on the signals required for T cell activation in vitro, the signals required for the generation of functional Th cells in vivo are poorly understood. We addressed this by directly tracking the behavior of adoptively transferred CD4+ TCR transgenic T cells following Ag administration in vivo. Injection of soluble Ag induced a transient accumulation of Ag-specific T cells in lymphoid tissue. If bacterial LPS was present during this period, enhanced numbers of Ag-specific T cells accumulated, migrated into B cell-rich follicles, and provided help for Ab production. The ability of LPS to enhance the accumulation and follicular migration of Ag-activated T cells was mimicked by the proinflammatory cytokines, TNF-alpha and IL-1, and the capacity of LPS to promote the generation of IFN-gamma-secreting T cells, which provide help for IgG2a production, was mimicked by IL-12. Thus, the in vivo generation of functional Th cells can arise from Ag-dependent clonal expansion in the context of inflammatory cytokines.
Lack of Neointimal Proliferation After Implantation of Sirolimus-Coated Stents in Human Coronary Arteries (2001)

The implantation of sirolimus-coated BX Velocity stents is feasible and safe and elicits minimal neointimal proliferation. Additional placebo-controlled trials are required to confirm these promising results.
Cache-conscious structure layout (1999)

Hardware trends have produced an increasing disparity between processor speeds and memory access times. While a variety of techniques for tolerating or reducing memory latency have been proposed, these are rarely successful for pointer-manipulating programs.This paper explores a complementary approach that attacks the source (poor reference locality) of the problem rather than its manifestation (memory latency). It demonstrates that careful data organization and layout provides an essential mechanism to improve the cache locality of pointer-manipulating programs and consequently, their performance. It explores two placement techniques---clustering and coloring---that improve cache performance by increasing a pointer structure's spatial and temporal locality, and by reducing cache-conflicts.To reduce the cost of applying these techniques, this paper discusses two strategies---cache-conscious reorganization and cache-conscious allocation---and describes two semi-automatic tools---ccmorph and ccmalloc---that use these strategies to produce cache-conscious pointer structure layouts. ccmorph is a transparent tree reorganizer that utilizes topology information to cluster and color the structure. ccmalloc is a cache-conscious heap allocator that attempts to co-locate contemporaneously accessed data elements in the same physical cache block. Our evaluations, with microbenchmarks, several small benchmarks, and a couple of large real-world applications, demonstrate that the cache-conscious structure layouts produced by ccmorph and ccmalloc offer large performance benefits---in most cases, significantly outperforming state-of-the-art prefetching.
Eine neuartige Methode zur Synthese von Spiro[pyrrolidin-3,3′-oxindolen]: katalysierte Ringerweiterung von Cyclopropanen mit Aldiminen (1999)

Die Rolle des bifunktionellen Katalysators ist entscheidend: Das Magnesium-Ion als Lewis-Säure und seine nucleophilen Iodid-Gegenionen wirken zusammen und tragen gemeinsam zur erfolgreichen Ringerweiterung des Cyclopropans 1 mit Aldiminen des Typs 2 bei [Gl. (1)]. Diese Reaktion bietet einen neuartigen Zugang zu Spiro[pyrrolidin-3,3′-oxindolen] 3.
Analyzing BGP policies: methodology and tool (2004)

The robustness of the Internet relies heavily on the robustness of BGP routing. BGP is the glue that holds the Internet together: it is the common language of the routers that interconnect networks or autonomous systems (AS). The robustness of BGP and our ability to manage it effectively is hampered by the limited global knowledge and lack of coordination between autonomous systems. One of the few efforts to develop a globally analyzable and secure Internet is the creation of the Internet routing registries (IRRs). IRRs provide a voluntary detailed repository of BGP policy information. The IRR effort has not reached its full potential because of two reasons: a) extracting useful information is far from trivial, and b) its accuracy of the data is uncertain. In this paper, we develop a methodology and a tool (Nemecis) to extract and infer information from IRR and validate it against BGP routing tables. In addition, using our tool, we quantify the accuracy of the information of IRR. We find that IRR has a lot of inaccuracies, but also contains significant and unique information. Finally, we show that our tool can identify and extract the correct information from IRR discarding erroneous data. In conclusion, our methodology and tool close the gap in the IRR vision for an analyzable Internet repository at the BGP level
Direct Binding of CRKL to BCR-ABL Is Not Required for BCR-ABL Transformation (1997)

CRKL has previously been shown to be a major tyrosine phosphorylated protein in neutrophils of patients with BCR-ABL+ chronic myelogenous leukemia and in cell lines expressing BCR-ABL. CRKL and BCR-ABL form a complex as demonstrated by coimmunoprecipitation and are capable of a direct interaction in a yeast two-hybrid assay. We have mapped the site of interaction of CRKL and BCR-ABL to the amino terminal SH3 domain of CRKL with a proline rich region in the C-terminus of ABL. The proline-rich region was mutated and the effect of this deletion on BCR-ABL transforming function was assayed. Our data show that this deletion does not impair the ability of BCR-ABL to render myeloid cells factor independent for growth. In cells expressing the proline deletion mutation of BCR-ABL, CRKL is still tyrosine phosphorylated and forms a complex with BCR-ABL as demonstrated by coimmunoprecipitation. Our data suggest that the interaction between CRKL and the proline deletion mutant of BCR-ABL is an indirect interaction as CRKL does not interact directly with the proline deletion mutant of BCR-ABL in a gel overlay assay or in a yeast two-hybrid assay. Thus, a direct interaction of CRKL and BCR-ABL is not required for CRKL to become tyrosine phosphorylated by BCR-ABL and suggests that CRKL function may still be required for BCR-ABL function through an indirect interaction.
VLSI architectures for iterative decoders in magnetic recording channels (2001)

VLST implementation complexities of soft-input soft-output (SISO) decoders are discussed. These decoders are used in iterative algorithms based on Turbo codes or Low Density Parity Check (LDPC) codes, and promise significant bit error performance advantage over conventionally used partial-response maximum likelihood (PRML) systems, at the expense of increased complexity. This paper analyzes the requirements for computational hardware and memory, and provides suggestions for reduced-complexity decoding and reduced control logic. Serial concatenation of interleaved codes, using an outer block code with a partial response channel acting as an inner encoder, is of special interest for magnetic storage applications.
The Universality of Bioenergetic Disease: Age‐associated Cellular Bioenergetic Degradation and Amelioration Therapy (1998)

During the present century there has been a dramatic change in life expectancy in advanced societies, now exceeding 80 years. As distinct from life expectancy, life potential is said to be at least 120 years, so that the continuing increase in knowledge has the potential for further major changes in the survival of humans conceivably in the near future. This presentation will be concerned with one aspect of the development of biomedical advances related in part to a concept of an "age-related universality of bioenergetic disease," and its potential amelioration and proposed impact on age-related disease and lifestyle. Aging is a complex biological process associated with a progressive decline in the physiological and biochemical performance of individual tissues and organs, leading to age-associated disease and senescence. Consideration of the progressive accumulation of mitochondrial DNA mutation with age and the tissue/cellular bioenergy decline associated with the aging process has led us to the proposal of a "universality of bioenergetic disease" and the potential for a redox therapy for the condition. This concept envisages that a tissue-bioenergetic decline will be intrinsic to various diseases of the aged and thereby contribute to their pathology, in particular, heart failure, degenerative brain disease, muscle and vascular diseases, as well as other syndromes. The information and concepts embodied in this proposal will be reviewed under the following headings: (1) mitochondrial DNA deletion mutation in some tissue is very extensive and shows mosaicism; (2) age-associated tissue/cellular bioenergy mosaic closely corresponds to the mtDNA profile; (3) cellular bioenergy as a function of mitochondrial bioenergy, glycolysis, and plasma membrane oxidoreductase; (4) redox therapy for the reenergization of cells, tissues, and whole organs. A redox therapy based on coenzyme Q10 has demonstrated profound alteration in heart function of old rats; no significant effect was observed with young rats.
Effect of Combination Therapy with a Novel Bisphosphonate, Minodronate (YM529), and Docetaxel on a Model of Bone Metastasis by Human Transitional Cell Carcinoma (2005)

These studies indicate that combination therapy with minodronate and docetaxel may be beneficial in patients with bone metastasis of human TCC in the urinary tract.
Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies (2008)

When evaluated using different sets of both simulated data and experimental data, Ab-origin outperformed all the other five popular tools in terms of prediction accuracy. The features of batch query and confidence indication of IGHD identification would provide extra help to users. The program is freely available at http://mpsq.biosino.org/ab-origin/supplementary.html.