gebhart/patrepeval huggingface dataset:
KNOWS: Kognitiv Networking Over White Spaces (2007)

The Federal Communications Commission (FCC) has announced that it is willing to consider unlicensed operation in the TV broadcast bands. Compared to the ISM bands, this portion of the spectrum has several desirable properties for robust data communications. However, to make efficient use of this spectrum in a way that is non-disruptive to incumbents, there are a number of challenges that must be handled. For example, an unused portion of the spectrum must be found, and it is likely that its availability will vary over time. To address such challenges, we present KNOWS, a cognitive wireless networking system. KNOWS is a hardware-software platform that includes a spectrum-aware Medium Access Control (MAC) protocol and algorithms to deal with spectrum fragmentation. We describe our prototype and present evaluation results obtained from simulating our MAC protocol. We show that in common scenarios KNOWS accomplishes a remarkable 200 % throughput improvement over systems that use a IEEE 802.11 based MAC protocol.
Cloning and analysis of the MNN4 gene required for phosphorylation of N-linked oligosaccharides in Saccharomyces cerevisiae (1996)

The Saccharomyces cerevisiae MNN4 gene, which is involved in mannosylphosphate transfer from GDP-mannose to N-linked oligosaccharide, has been cloned from a lambda phage containing a yeast chromosome XI DNA fragment. The MNN4 ORF encodes a protein of 1178 amino acids. The deduced amino acid sequence shows a topology of type II membrane proteins and has a unique repeated sequence of lysine and glutamic acid at the C-terminus. Disruption and overexpression of MNN4 led to a decrease and increase, respectively, of the mannosylphosphate content in cell wall mannans prepared from both mnn4 and wild type strains. A dramatic decrease of mannosylphosphate occurs in delta mnn4 mutans. The results from genetic and biochemical experiments combine to suggest that Mnn4p is required to mediate mannosylphosphate transfer in both the core and outer chain portions of N-linked oligosaccharides.
Modulating Phagocyte Activation (2000)

Helicobacter pylori (Hp) is a highly successful human pathogen that has colonized the gastric mucosa of approximately half of the world's population. Infection with this gram-negative bacterium induces a state of chronic inflammation that does not resolve the underlying infection and often leads to
gp130-mediated Signal Transduction in Embryonic Stem Cells Involves Activation of Jak and Ras/Mitogen-activated Protein Kinase Pathways (1996)

The leukemia inhibitory factor/interleukin 6 (LIF/IL6) family of cytokines promotes cell type-specific pleiotropic effects by engaging multimeric receptor complexes that share the common affinity converter/signal transducing subunit gp130. While the maintenance of embryonic stem (ES) cell self-renewal is an activity unique to this family of cytokines, the intracellular signaling events mediated by gp130 remain largely unknown. Here we show a rapid and transient increase in the specific activity of the Src-related kinase Hck as well as of the Janus kinases Jak1, Jak2, and Tyk2 following treatment of ES cells with LIF or a combination of IL6 plus a soluble form of the IL6 receptor. Within 2 min of stimulation, we also observed increased tyrosine phosphorylation of SHC, activation of the guanidine nucleotide exchange activity on p21(ras), and an electrophoretic mobility shift of MAP kinase. Functional involvement of Hck and p21(ras) activation in gp130-mediated signaling is supported by the finding that the introduction of constitutively activated Hck or v-Ha-ras partially alleviates the requirement of ES cells for LIF to remain undifferentiated. In contrast, suppression of Jak1 in ES cells by antisense technology increased the amount of LIF required to retain their pluripotentiality. These results are consistent with the notion that gp130-mediated suppression of ES cell differentiation depends on signaling through at least two cascades, namely a p21(ras)-dependent pathway that possibly involves Hck, as well as a Jak kinase-dependent pathway.
Detection of the chromosomal translocation t(11;14) by polymerase chain reaction in mantle cell lymphomas (1994)

The t(11;14)(q13;q32) and its molecular counterpart, BCL1 rearrangement, are consistent features of mantle cell lymphoma (MCL). Rearrangement is thought to deregulate the nearby CCND1 (BCL1/PRAD1) proto-oncogene, a member of the cyclin G1 gene family, and thereby to contribute to tumorigenesis. We and others have previously shown that the BCL1 locus is rearranged in 55% to 60% of MCL patients and that, on chromosome 11, more than 80% of the breakpoints are localized within a 1-kbp DNA segment known as the major translocation cluster (MTC). We have determined the nucleotide sequence for a portion of the MTC region, and constructed chromosome 11-specific oligonucleotides that were in conjunction with a consensus immunoglobulin (Ig) heavy chain joining region (JH) primer used to perform the polymerase chain reaction (PCR) to amplify t(11;14) chromosomal junctional sequences in DNA from 16 MCL patients with breakpoints in the MTC region. 15 of the 16 breakpoints that occurred at the MTC region were amenable to PCR detection. The sizes of the amplified bands, the existence or not of a Sac I site in the PCR products, and nucleotide sequencing of the amplified DNA from four patients showed that the breakpoints share a remarkable tendency to tightly cluster within 300 bp on chromosome 11, some of them occurring at the same nucleotide. On chromosome 14, the breakpoints were localized within the Ig JH. Our findings indicate that a BCL1 rearrangement can be detected using this approach in roughly one half of the MCL patients. This has implications for both the diagnosis and the clinical management of MCL.
Adenovirus E1a proteins repress expression from polyomavirus early and late promoters. (1986)

We have examined the effects of the E1a products of adenovirus types 5 and 12 on the expression of polyomavirus early and late promoters. In cotransfection experiments in HeLa cells, plasmids expressing the E1a region of adenovirus type 5 or 12 repressed both the early and late promoters of polyomavirus, and deletion analysis indicates that the polyomavirus enhancers were the target of the E1a repression. With mutants lacking enhancer sequences, the polyomavirus early promoter but not the late promoter was trans-activated by E1a. Chimeric mutant plasmids with deletions in the regulatory region that contained either the A enhancer or the B enhancer were repressed to the same extent, indicating that E1a can repress both elements. Polyomavirus variant plasmids with rearrangements in the regulatory region conferring activity in embryonal carcinoma stem cells were repressed by E1a as was the wild type, suggesting that the repressor function is quite general. We discuss a model in which the influence of E1a on the transcriptional activity of a gene is the sum of positive and negative effects on promoter and enhancer elements and discuss possible mechanisms of negative regulation of enhancer function.
Signaling pathway of globo-series glycosphingolipids and β1,3-galactosyltransferase V (β3GalT5) in breast cancer (2019)

The globo-series glycosphingolipids (GSLs) SSEA3, SSEA4, and Globo-H specifically expressed on cancer cells are found to correlate with tumor progression and metastasis, but the functional roles of these GSLs and the key enzyme β1,3-galactosyltransferase V (β3GalT5) that converts Gb4 to SSEA3 remain largely unclear. Here we show that the expression of β3GalT5 significantly correlates with tumor progression and poor survival in patients, and the globo-series GSLs in breast cancer cells form a complex in membrane lipid raft with caveolin-1 (CAV1) and focal adhesion kinase (FAK) which then interact with AKT and receptor-interacting protein kinase (RIP), respectively. Knockdown of β3GalT5 disrupts the complex and induces apoptosis through dissociation of RIP from the complex to interact with the Fas death domain (FADD) and trigger the Fas-dependent pathway. This finding provides a link between SSEA3/SSEA4/Globo-H and the FAK/CAV1/AKT/RIP complex in tumor progression and apoptosis and suggests a direction for the treatment of breast cancer, as demonstrated by the combined use of antibodies against Globo-H and SSEA4.
Expression of Mycoplasma pneumoniae antigens in Escherichia coli (1986)

A genomic library of Mycoplasma pneumoniae was generated by using bacteriophage lambda EMBL3 as the vector. Screening of the library for the expression of M. pneumoniae protein antigens with adsorbed anti-M. pneumoniae serum revealed strong reactivity from a third of those clones which contained mycoplasma DNA inserts. Three of the most highly reactive clones were analyzed in detail and found to synthesize discrete mycoplasma proteins. Two carried overlapping fragments of mycoplasma DNA which encoded a protein that was readily detected in Escherichia coli after infection with recombinant bacteriophage. The third clone contained a novel mycoplasma DNA fragment which directed the synthesis of two additional mycoplasma proteins. Further screening of the library with antiserum raised against the major M. pneumoniae adhesin protein P1 (165 kilodaltons [kDa]) yielded one clone which produced an immunologically reactive protein of 140 kDa. Adsorption of anti-P1 serum by this clone selected a population of antibodies that were reactive with M. pneumoniae adhesin P1 (165 kDa). These results demonstrate that immunologically active M. pneumoniae proteins are synthesized in E. coli.
Cystic fibrosis infections: treatment strategies and prospects (2009)

Pseudomonas aeruginosa and Burkholderia cepacia are the two major Gram-negative rods that colonize/infect the lungs of patients with cystic fibrosis (CF). These organisms may cause progressive respiratory failure, although occasionally more rapid infections result in the 'Cepacia' syndrome. Many antibiotics have been used against Pseudomonas and Burkholderia, but once chronic colonization has been established, eradication of these organisms is rare. Drug therapy for CF patients is compromised by a number of bacterial factors that render the infectious agents resistant to antibiotics, including efflux pumps that remove antibiotics, lack of penetration of antibiotics into bacterial biofilms, and changes in the cell envelope that reduce the permeability of antibiotics. Any combination of these mechanisms increases the likelihood of bacterial survival. Therefore, combinations of antibiotics or of antibiotic and nonantibiotic compounds are currently being tested against Pseudomonas and Burkholderia. However, progress has been slow, with only occasional combinations showing promise for the eradication of persistent Gram-negative rods in the airways of CF patients. This review will summarize the current knowledge of CF infections and speculate on potential future pathways to treat these chronic infections.
A bug you like: A framework for automated assignment of bugs (2009)

Assigning bug reports to individual developers is typically a manual, time-consuming, and tedious task. In this paper, we present a framework for automated assignment of bug-fixing tasks. Our approach employs preference elicitation to learn developer predilections in fixing bugs within a given system. This approach infers knowledge about a developer's expertise by analyzing the history of bugs previously resolved by the developer. We apply a vector space model to recommend experts for resolving bugs. When a new bug report arrives, the system automatically assigns it to the appropriate developer considering his or her expertise, current workload, and preferences. We address the task allocation problem by proposing a set of heuristics that support accurate assignment of bug reports to the developers.
Nonlinear control methods for planar carangiform robot fish locomotion (2002)

Considers the design of motion control algorithms for robot fish. We present modeling, control design, and experimental trajectory tracking results for an experimental planar robotic fish system that is propelled using carangiform-like locomotion. Our model for the fish's propulsion is based on quasi-steady fluid flow. Using this model, we propose gaits for forward and turning trajectories and analyze system response under such control strategies. Our models and predictions are verified by experiment.
A simplified acute physiology score for ICU patients (1984)

We used 14 easily measured biologic and clinical variables to develop a simple scoring system reflecting the risk of death in ICU patients. The simplified acute physiology score (SAPS) was evaluated in 679 consecutive patients admitted to eight multidisciplinary referral ICUs in France. Surgery accounted for 40% of admissions. Data were collected during the first 24 h after ICU admission. SAPS correctly classified patients in groups of increasing probability of death, irrespective of diagnosis, and compared favorably with the acute physiology score (APS), a more complex scoring system which has also been applied to ICU patients. SAPS was a simpler and less time-consuming method for comparative studies and management evaluation between different ICUs.
Resolving Intermediate Solution Structures during the Formation of Mesoporous SBA-15 (2006)

The evolution of the solution microstructures during the formation of the hexagonal mesoporous material SBA-15 was studied by direct imaging and freeze-fracture replication cryo-TEM. A reaction mixture was sampled at different times after the addition of tetramethoxyorthosilane (TMOS) to an acidic solution of Pluronic P123 held at 50 degrees C. Solution microstructures were detected by direct imaging cryo-TEM in the time window of 6.5-40 min after the addition of the TMOS (t = 0). The micrographs revealed that the initial spheroidal micelles evolve into threadlike micelles, which become longer and straighter with time. Then bundles with the dimensions similar to those found in the final material appeared, although there was no sign of a hexagonal arrangement up to 40 min. Due to the appearance of a precipitate at 40 min the sample became too viscous, preventing clear observation of its content. To observe the structures present after 40 min, freeze-fracture replication was carried out as well. Such samples were collected also at 22 min and showed the presence of threadlike micelles in agreement with the direct imaging cryo-TEM micrographs. The 2 h samples showed some areas of hexagonal ordered structures, which become very clear at 2 h 50 min. The cryo-TEM measurements were carried out under the same reaction conditions used in earlier in situ EPR experiments, thus allowing us to correlate molecular level events with the microstructure shape evolutions. This showed that the elongation of the micelles is a consequence of a reduction of the polarity and the water content within the micelles due to silicate adsorption and polymerization. Similar experiments were carried out also on SBA-15 prepared with HCl and TMOS at 35 degrees C. The appearance of threadlike micelles, followed by clustering of the TLMs, was observed under these conditions as well, but the reaction rate was faster. This suggests that the observed mechanism for the formation of SBA-15 is general.
PulsON second generation timing chip: enabling UWB through precise timing (2003)

In 1999, Time Domain Corporation (TDC) introduced the first ultra-wideband (UWB) radios using full custom integrated circuits, the PulsON 100 chipset. This paper describes TDC's recently developed second generation precision SiGe timing chip. PulsON time modulated UWB radios are composed of three basic components: (1) a precise timing subsystem; (2) a correlator subsystem (often consisting of multiple correlators); (3) a digital baseband signal processing and system control subsystem. Precise timing is crucial in the design of the PulsON UWB radios. Similar to TDC's earlier T1 chip, the T2 timing generator accurately places pulses within very small windows (100 ns windows for the T1, as small as 50 ns for the T2). These timing chips use a high speed counter to set a coarse delay in 800 ps quantized steps followed by an IQ phase delay circuit that sets a fine delay on top of the course delay to about 3 ps resolution. The T2 positions pulses to an accuracy of better than 3 ps with a jitter of less than 10 ps. The T2 IC, a mixture of analog, digital, and RF functions, operates up to a clock rate of 1.228 GHz, and consumes a maximum of 0.5 W.
What is the Intrinsic Value of the Dow? (1999)

We model the time‐series relation between price and intrinsic value as a cointegrated system, so that price and value are long‐term convergent. In this framework, we compare the performance of alternative estimates of intrinsic value for the Dow 30 stocks. During 1963–1996, traditional market multiples (e.g., B/P, E/P, and D/P ratios) have little predictive power. However, a V/P ratio, where V is based on a residual income valuation model, has statistically reliable predictive power. Further analysis shows time‐varying interest rates and analyst forecasts are important to the success of V. Alternative forecast horizons and risk premia are less important.
Synthesis of the C11-C21 and C13-C21 Fragments of Epothilones from D-Glucose (2000)

Macrolide epothilones 1 and 2, isolated by Höfle et al. from the myxobacterium Sorangium cellulosum, have evoked intensive interest and excitement due to their potent anti-tumor activity.1 Epothilones promote the polymerization of tubulins and stabilize microtubule assembly.2 In this aspect epothilones have almost identical mode of action to that of paclitaxel (Taxol®) and furthermore, are superior to pacli-taxel in retaining activity in multidrug-resistant cells, solu-bility in water, and their easy availability from fermentation. These significant biological properties along with their structural features have prompted synthetic investigation of organic chemists.3 Our synthetic plan toward epothilones A-D (1a-d) com-prises of two pathways as shown in Scheme 1. The first approach implies a key transforamtion of the ring closing
Surface Urban Heat Island Across 419 Global Big Cities (2011)

Urban heat island is among the most evident aspects of human impacts on the earth system. Here we assess the diurnal and seasonal variation of surface urban heat island intensity (SUHII) defined as the surface temperature difference between urban area and suburban area measured from the MODIS. Differences in SUHII are analyzed across 419 global big cities, and we assess several potential biophysical and socio-economic driving factors. Across the big cities, we show that the average annual daytime SUHII (1.5 ± 1.2 °C) is higher than the annual nighttime SUHII (1.1 ± 0.5 °C) (P < 0.001). But no correlation is found between daytime and nighttime SUHII across big cities (P = 0.84), suggesting different driving mechanisms between day and night. The distribution of nighttime SUHII correlates positively with the difference in albedo and nighttime light between urban area and suburban area, while the distribution of daytime SUHII correlates negatively across cities with the difference of vegetation cover and activity between urban and suburban areas. Our results emphasize the key role of vegetation feedbacks in attenuating SUHII of big cities during the day, in particular during the growing season, further highlighting that increasing urban vegetation cover could be one effective way to mitigate the urban heat island effect.
Therapeutic potentials of angiostatin in the treatment of cancer. (1999)

The discovery of specific endothelial inhibitors such as angiostatin and endostatin not only increases our understanding of the functions of these molecules in the regulation of physiological and pathological angiogenesis, but also provides an important therapeutic strategy for cancer treatment. Recent studies have demonstrated that the angiostatin protein significantly suppresses the growth of a variety of tumors in mice. However, the dosages of angiostatin protein used in these animal studies seem to be too high for clinical trials. In addition, repeated injections and long-term treatment with angiostatin are required to reach its maximal antitumor effect. In this article, I will discuss several alternative approaches that may become feasible to move angiostatin therapy from animal experiments into the clinic. In particular, I will emphasize the therapeutic potentials of angiostatin gene therapy and more potent angiogenesis inhibitors that are related to angiostatin.
Molecular mechanisms of action of new xenobiotic immunosuppressive drugs: tacrolimus (FK506), sirolimus (rapamycin), mycophenolate mofetil and leflunomide (1996)

Among all the new immunosuppressive molecules being investigated either preclinically or clinically, four stand out: tacrolimus (FK506), sirolimus (rapamycin), mycophenolate mofetil and leflunomide (and its malononitriloamide analogs). Each drug has distinct mechanisms of immunosuppressive action, and in the past year significant advances have been made in our understanding of the actions of these drugs at the molecular and even atomic levels. Data from recent clinical trials demonstrate that these drugs very effectively suppress graft rejection or autoimmune diseases, validating the pivotal role played by each of their distinct molecular targets in the normal functioning of immune cells.
Copper(II) Complexes of Novel N-Alkylated Derivatives of cis,cis-1,3,5-Triaminocyclohexane. 2. Metal-Promoted Phosphate Diester Hydrolysis (2001)

Aqueous copper(II) N,N‘,N‘ ‘-trimethyl-cis,cis-1,3,5-triaminocyclohexane (Cu(tach-Me3)2+(aq)) promotes the hydrolysis of activated phosphate diesters in aqueous medium at pH 7.2. This complex is selective for cleavage of the phosphate diester sodium bis(p-nitrophenyl) phosphate (BNPP), the rate of hydrolysis of the monoester disodium p-nitrophenyl phosphate being 1000 times slower. The observed rate acceleration of BNPP hydrolysis is slightly greater than that observed for other Cu(II) complexes, such as [Cu([9]aneN3)Cl2] ([9]aneN3 ≡ 1,4,7-triazacyclononane). The rate of hydrolysis is first-order in phosphate ester at low ester concentration and second-order in [Cu(tach-Me3)]2+(aq), suggesting the involvement of two metal complexes in the mechanism of substrate hydrolysis. The reaction exhibits saturation kinetics with respect to BNPP concentration according to a modified Michaelis−Menten mechanism: 2CuL + S ⇌ LCu−S−CuL → 2CuL + products (KM = 12.3 ± 1.8 mM2, kcat = (4.0 ± 0.4) × 10-4 s-1, 50 °C) where CuL ≡ [Cu(tach-Me3)]2+, S ≡ BNPP, and LCu−S−CuL is a substrate-bridged dinuclear complex. EPR data indicate that the dicopper complex is formed only in the presence of BNPP; the active LCu−S−CuL intermediate species then slowly decays to products, regenerating monomeric CuL.