gebhart/patrepeval huggingface dataset:
Mining the web to create minority language corpora (2001)

The Web is a valuable source of language specific resources but the process of collecting, organizing and utilizing these resources is difficult. We describe CorpusBuilder, an approach for automatically generating Web-search queries for collecting documents in a minority language. It differs from pseudo-relevance feedback in that retrieved documents are labeled by an automatic language classifier as relevant or irrelevant, and this feedback is used to generate new queries. We experiment with various query-generation methods and query-lengths to find inclusion/exclusion terms that are helpful for retrieving documents in the target language and find that using odds-ratio scores calculated over the documents acquired so far was one of the most consistently accurate query-generation methods. We also describe experiments using a handful of words elicited from a user instead of initial documents and show that the methods perform similarly. Experiments applying the same approach to multiple languages are also presented showing that our approach generalizes to a variety of languages.
Characterization of spatial patterns of flow within the reperfused myocardium by myocardial contrast echocardiography. Implications in determining extent of myocardial salvage. (1993)

MCE revealed striking temporal heterogeneity in the spatial distribution of myocardial perfusion during postischemia reflow and either significantly underestimated or did not correlate with infarct size during reperfusion. Because of abnormalities in coronary vascular reserve specific to infarcted tissue, MCE in conjunction with intravenous dipyridamole depicted, in vivo, the actual topography of the infarct with remarkable accuracy.
Biosynthesis and Properties of Poly(3-hydroxybutyrate-co-3-hydroxyalkanoates) by Recombinant Strains of Pseudomonas sp. 61-3 (2000)

Pseudomonas sp. 61-3 (phbC::tet) strain, which is a phbCPs-disrupted mutant, accumulated a random copolymer consisting of (R)-3-hydroxybutyrate (3HB) and (R)-medium-chain-length 3-hydroxyalkanoate (3HA) units of 6-12 carbon atoms, but the 3HB fraction in the copolymer was less than 50 mol %, resulting in the formation of an amorphus polymer. Therefore, the genes encoding beta-ketothiolase (PhbARe) and NADPH-dependent acetoacetyl-CoA reductase (PhbBRe) from Ralstonia eutropha were expressed under the control of promoters for Pseudomonas sp. 61-3 pha locus or R. eutropha phb operon together with the phaC1Ps gene (PHA synthase 1 gene) from Pseudomonas sp. 61-3 in the phbCPs-disrupted mutant. The recombinant strains synthesized P(3HB-co-3HA) copolymers with very high 3HB compositions (up to 94 mol %) from glucose. The number-average molecular weights of P(3HB-co-3HA) were in the range of 349 x 10(3) to 605 x 10(3). The structure and physical properties of P(3HB-co-3HA) copolymers were characterized by 1H- and 13C-NMR spectrometry, differential scanning calorimetry, and mechanical tensile measurement. P(94% 3HB-co-3HA) copolymer was demonstrated to have good physical properties and to be a flexible material with moderate toughness, similar to low-density polyethylene.
THE FATE OF BACTERIA WITHIN PHAGOCYTIC CELLS (1963)

The intraleucocytic fate of a variety of P(32)- and C(14)-labeled bacteria has been studied in both polymorphonuclear leucocytes and macrophages. Both cell types brought about extensive degradation of bacterial lipids, nucleic acids, and proteins. Intracellular breakdown was primarily dependant upon the composition of the ingested particle rather than on the type or source of the phagocyte. Evidence is presented for the reincorporation of bacterial constituents into leucocyte lipid. More than 50 per cent of the acid-soluble degradation products of P(32)-labeled bacteria appear as inorganic phosphate. Bacterial RNA is degraded more readily than DNA. Following phagocytosis, labeled bacteria lose their pool of small molecular weight intermediates. This is followed by the degradation of acid-insoluble constituents. The majority of bacterial breakdown products are then excreted by the leucocyte and appear in the medium. Heat-killed bacteria were more readily broken down than viable organisms. Only small amounts of C(14)-labeled bacteria were completely oxidized by leucocytic enzymes to C(14)O(2). Acid extracts of polymorphonuclear leucocyte granules, which were highly bactericidal, liberated the acid-soluble constituents of labeled bacteria but did not significantly degrade bacterial macromolecules.
CD24 mediates rolling of breast carcinoma cells on P‐selectin (1998)

P-selectin mediates rolling of neutrophils and other leukocytes on activated endothelial cells and platelets through binding to P-selectin glycoprotein ligand-1 (PSGL-1). Certain PSGL-1 negative tumor cell lines can bind P-selectin under static conditions through the GPI-linked surface mucin, CD24, but the physiological significance of this interaction and whether it can occur under flow conditions is not known. Here, we show that CD24+ PSGL-1- KS breast carcinoma cells attach to and roll on recombinant P-selectin under a continuous wall shear stress, although at a lower density and higher velocity than CD24+ PSGL-1+ cells, such as HL-60. Adding excess soluble CD24 or removing CD24 from the cell surface with phosphatidylinositol-phospholipase C (PI-PLC) significantly reduced KS cell rolling on P-selectin. The ability of KS cells to roll on P-selectin was positively correlated with the CD24 expression level. Comparison with three other CD24+ cell lines established that expression of sialyl-Lewis(x) antigen was also necessary for CD24-mediated rolling on P-selectin. CD24 purified from KS cells supported rolling of P-selectin transfectants, but not L-selectin transfectants. Finally, KS cells rolled on vascular endothelium in vivo in a P-selectin-dependent manner. Together our data show that CD24 serves as a ligand for P-selectin under physiological flow conditions. Interaction of tumor cells with P-selectin via CD24 may be an important adhesion pathway in cancer metastasis.
Hypoxia Post-translationally Activates Iron-regulatory Protein 2 (1999)

Iron-regulatory proteins 1 and 2 (IRP1 and IRP2) are RNA-binding proteins that post-transcriptionally regulate the expression of mRNAs that code for proteins involved in the maintenance of iron and energy homeostasis. Here we show that hypoxia differentially regulates the RNA binding activities of IRP1 and IRP2 in human 293 and in mouse Hepa-1 cells. In contrast to IRP1, where hypoxic exposure decreases IRP1 RNA binding activity, hypoxia increases IRP2 RNA binding activity. The hypoxic increase in IRP2 RNA binding activity results from increased IRP2 protein levels. Cobalt, which mimics hypoxia by activation of hypoxia-inducible factor 1 (HIF-1), also increases IRP2 protein levels; however, cobalt-induced IRP2 lacks RNA binding activity. Addition of a reductant to cobalt-treated extracts restored IRP2 RNA binding activity. Hypoxic activation of IRP2 is not because of an increase in transcriptional activation by HIF-1, because IRP2 accumulates in Hepa-1 cells lacking a functional HIF-1beta subunit, nor is it because of an increase in IRP2 mRNA stability. Rather, our data indicate that hypoxia increases IRP2 levels by a post-translational mechanism involving protein stability. Differential regulation of IRP1 and IRP2 during hypoxia may regulate specific IRP target mRNAs whose expression is required for hypoxic adaptation. Furthermore, these data imply mechanistic parallels between the hypoxia-induced post-transcriptional regulation of IRP2 and HIF-1alpha.
“Receptor free” inner filter effect based universal sensors for nitroexplosive picric acid using two polyfluorene derivatives in the solution and solid states (2018)

Two "receptor-free" blue fluorescent conjugated polymers (CPs) of fluorene namely 9,9-bis(6-bromohexyl)-2-phenyl-9H-fluorene (PF1) and 9,9-bis(6-bromohexyl)-9H-fluorene (PF2) were synthesized using Suzuki cross coupling polymerization and oxidative coupling polymerization methods in high yields and well characterized by gel permeable chromatography, NMR, UV-vis, fluorescence and time-resolved photoluminescence (TRPL) spectroscopy. Both CPs explicitly recognized nitroexplosive picric acid (PA) and displayed a fluorescence quenching response in solution and on a solid support via the Inner Filter Effect (IFE) mechanism. Both CPs were highly selective and sensitive towards PA with high quenching constant values (K<sub>sv</sub>) of 5.1 × 10<sup>4</sup> M<sup>-1</sup> and 5.0 × 10<sup>4</sup> M<sup>-1</sup> and remarkably low limit of detection (LOD) values of 110 nM and 219 nM. Contact mode detection of PA was also accomplished using economical and transportable fluorescent paper test strip devices for on-site sensing, which detect a minimum of 22.9 femtograms of PA. The IFE mechanism for PA sensing (or for other analytes) is an interesting concept that can detect PA by just having blue fluorescence. Therefore, careful experiments for IFE correction were performed herein for PA detection to observe ∼77% suppression efficiency due to the IFE. These studies provide fundamentally important information on the IFE based mechanism for the detection of various analytes.
Structure and putative function of a murine epididymal retinoic acid-binding protein (mE-RABP). (1998)

Vitamin A is required to maintain the epididymal epithelium. In this report, the characterization and putative functions of a murine epididymal retinoic acid-binding protein (mE-RABP) that is secreted into the lumen from the mid-/distal caput epididymidis are discussed. The amino acid sequence analysis of the mE-RABP preprotein shows that mE-RABP is the mouse orthologue of the rat epididymal secretory protein I (ESPI). These proteins belong to the lipocalin superfamily and bind to active retinoids but not to retinol. Therefore, we propose that mE-RABP may function as an extracellular retinoid carrier-protein involved in the paracrine regulation of epididymal function by retinoids.
A Network of Multi-tasking Proteins at the DNA replication Fork Preserves Genome Stability (2005)

To elucidate the network that maintains high fidelity genome replication, we have introduced two conditional mutant alleles of DNA2, an essential DNA replication gene, into each of the approximately 4,700 viable yeast deletion mutants and determined the fitness of the double mutants. Fifty-six DNA2-interacting genes were identified. Clustering analysis of genomic synthetic lethality profiles of each of 43 of the DNA2-interacting genes defines a network (consisting of 322 genes and 876 interactions) whose topology provides clues as to how replication proteins coordinate regulation and repair to protect genome integrity. The results also shed new light on the functions of the query gene DNA2, which, despite many years of study, remain controversial, especially its proposed role in Okazaki fragment processing and the nature of its in vivo substrates. Because of the multifunctional nature of virtually all proteins at the replication fork, the meaning of any single genetic interaction is inherently ambiguous. The multiplexing nature of the current studies, however, combined with follow-up supporting experiments, reveals most if not all of the unique pathways requiring Dna2p. These include not only Okazaki fragment processing and DNA repair but also chromatin dynamics.
Methods for Mitigating IP Network Packet Loss in Realtime Audio Streaming Applications (2014)

Increasingly Internet protocol (IP)-based networks are being used for transport of realtime broadcast quality audio. IP networks provide clear benefits of cost and flexibility over circuit-switched networks. However, IP networks can have impairments that must be mitigated in order to realize the quality of service that broadcasters are accustomed to with circuit-switched networks. Among these impairments, packet loss poses the toughest challenge. In many non-realtime applications, transport protocols such as transmission control protocol (TCP) or reliable user datagram protocol (UDP) can be used to retransmit lost packets. However, for realtime media streaming applications that are delay-sensitive and where multicasting is used, such protocols cannot be used. Therefore, techniques used for packet loss mitigation have to minimize delay and work in unidirectional network paths. The challenge faced as we encounter different packet loss patterns in real networks is that the effectiveness of the mitigation techniques depends upon the model these packet losses follow. This paper first shows how packet losses in real networks can be modeled. The results of the effectiveness of different mitigation techniques are then shown, using these models and how they can be cascaded to provide for a scalable method to mitigate varying levels of packet loss.
Scoring Users’ Privacy Disclosure Across Multiple Online Social Networks (2017)

Users in online social networking sites unknowingly disclose their sensitive information that aggravate the social and financial risks. Hence, to prevent the information loss and privacy exposure, users need to find ways to quantify their privacy level based on their online social network data. Current studies that focus on measuring the privacy risk and disclosure consider only a single source of data, neglecting the fact that users, in general, can have multiple social network accounts disclosing different sensitive information. In this paper, we investigate an approach that can help social media users to measure their privacy disclosure score (PDS) based on the information shared across multiple social networking sites. In particular, we identify the main factors that have impact on users privacy, namely, sensitivity and visibility, to obtain the final disclosure score for each user. By applying the statistical and fuzzy systems, we can specify the potential information loss for a user by using obtained PDS. Our evaluation results with real social media data show that our method can provide a better estimation of privacy disclosure score for users having presence in multiple online social networks.
A simple procedure to improve the surface passivation for single molecule fluorescence studies (2015)

The single-molecule fluorescence technique is becoming a general and mature tool to probe interactions and dynamics of biomolecules with ultra high precision and accuracy. However, nonspecific adsorption of biomolecules to the flow cells remains a major experimental riddle for the study of many complex biological systems, especially those exhibiting low binding affinity and presenting with weakly populated intermediates. Many novel surface passivation methods have been introduced to reduce nonspecific interactions. Here, we present an effective and inexpensive method to significantly reduce nonspecific binding of biomolecules in conventional poly (ethylene glycol) (PEG)-based surface passivation protocols, without additional exogenous effects. In particular, we propose a simple 10 min Tween-20 treatment for the PEG passivated surface, which could further increase the hydrophilicity of the surface and thus promote passivation efficacy by about 5 to 10 times. We anticipate that this new procedure will find broad practical applications and extend the current reaches of single-molecule fluorescence studies.
Solid phase extraction on microfluidic devices (2000)

A microfabricated device with C18-coated channels was used to demonstrate on-chip solid phase extraction. Sample solutions containing a neutral dye were enriched and eluted in less than 4 min. Distinct elution peaks with good signal-to-noise ratios were obtained even for highly dilute samples. The gain in concentration estimated from the enrichment and elution volumes was 80-fold. ©2000 John Wiley & Sons, Inc. J Micro Sep 12: 93–97, 2000
Water‐soluble Aliphatic Polyesters: Poly(malic acid)s (2002)

Abstract Introduction Historical Outline Poly(malic acid) from Natural Sources Poly(malic acid) by Chemical Synthesis Chemical Structures Occurrence Poly(malic acid) from Natural Sources Poly(β‐malic acid) by Chemical Synthesis Functions Analysis Physicochemical Properties Chemistry Physiology Biochemistry Degradation and Biodegradation Production Applications Outlook and Perspectives Patents
N,N‐Dialkyl‐4‐[(8‐azabicyclo [3.2.1]‐oct‐3‐ylidene)phenylmethyl]benzamides, Potent, Selective δ Opioid Agonists. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Characterization of Distinct Molecular Signatures in Myeloproliferative Diseases with the JAK2V617F Mutation and Wild Type JAK2. (2005)

Abstract The recently discovered JAK2V617F mutation provides a critical insight into the molecular pathogenesis of polycythemia vera and other myeloproliferative diseases (MPD). However, the mutations present in patients with wild type JAK2 have not been discovered, and the precise molecular consequences of JAK2 mutation have not been elucidated. We employed gene expression profiling to characterize the molecular phenotype of cells with the JAK2V617F mutation, to identify a distinct signature in cells without JAK2 mutations, and to refine a molecular taxonomy of MPDs. Using purified neutrophils from 70 patients with myeloproliferative diseases and 11 unaffected individuals, we performed gene expression profiling using oligonucleotide microarrays, sequencing of the JAK2 gene, quantitative genotyping by mass spectrometry and allele-specific quantitative PCR, and X-inactivation clonality assays. To reduce the confounding influence of normal neutrophils that are admixed with cells bearing disease-causing mutations, we examined the gene expression profiles of samples in which greater than 80% of JAK2 alleles bear the V617F mutation. PRV1, a previously identified marker of polycythemia vera, was powerfully overexpressed in neutrophils with a homozygous JAK2 mutation. In addition, cells with the JAK2 mutation had increased expression of a set of kinases, including JAK2, and decreased expression of a set of phosphatases. Cells that rely on JAK2 activation for clonal dominance may therefore derive a selective advantage from increased expression of the JAK2 gene. We next examined samples that have high clonality, and therefore relatively few normal neutrophils, but do not have a mutation in the JAK2 gene. These samples have a markedly different gene expression profile and overexpress a distinct set of kinases. The kinases overexpressed in cells with wild type JAK2 are candidates for further mutational analysis and are potential therapeutic targets. Utilizing these signatures and unsupervised analytical algorithms, the samples cluster according to their mutational status and the percentage of normal neutrophils in the sample. Our data demonstrate that the gene expression profiles of MPD samples are not uniform regardless of JAK2 genotype, implying that samples with and without JAK2 mutations have not activated the same pathway via alternative mechanisms. Moreover, we have identified a common signature in samples without JAK2 mutations that meets significance, indicating that one or a small number of mutations may play a critical role in these cells. Genotype and gene expression analyses are defining a molecular classification of myeloproliferative diseases with subtypes that have distinct therapeutic targets.
Miniature fiber optic pressure and temperature sensors (2005)

New miniature extrinsic Fabry-Perot interferometric (MEFPI) optical fiber sensors with a size of 125&#956;m in diameter are presented, which are ideal for applications where the operation space is highly restricted. The temperature sensor can work up to 800°C with a sensitivity of 0.46nm/°C. The pressure sensor exhibited a sensitivity of about 0.36nm/psi. The sensitivities of the pressure and temperature sensor can be controlled with high precision during fabrication. In addition, their Fabry-Perot cavity lengths can be controlled with a resolution of several nanometers, which provides excellent flexibility in sensor design and signal demodulation. The sensors are composed entirely of fused silica, which is very reliable, biocompatible, corrosion resistant and immune to electromagnetic interference (EMI).
Harsh Environments Minimally Invasive Optical Sensing Technique For Extreme Temperatures: 1000 °C And Approaching 2500 °C (2005)

To the best of our knowledge, for the first time is designed and demonstrated a single crystal Silicon Carbide (SiC)-based minimally invasive smart optical sensor suited for harsh environments and temperatures reaching 2500 °C. The novel sensor design is based on an agile wavelength source, instantaneous single wavelength interferometry, full optical power cycle data acquisition, free-space targeted laser beam, multiple single crystal thick SiC optical frontend chips, and multi-wavelength signal processing for unambiguous temperature measurements to form a fast and distributed smart optical sensor system. Experiments conducted using a 1550 nm eye safe band tunable laser and a 300 micron coating-free thick SiC chip demonstrate temperature sensing from room temperature to 1000 °C with a measured 1.3 °C resolution. Applications for the proposed sensor include use in fossil fuel-based power systems, aerospace/aircraft systems, satellite systems, deep space exploration systems, and drilling and oil mining industries.
Nucleotide sequence ofkatF ofEscherichia colisuggestsKatF protein is a novel σ transcription factor (1989)

The katF gene of Escherichia coli has been sequenced revealing a 1086 base pair open reading frame from which the sequence of a 362 amino acid protein has been deduced. The direction of transcription of katF was confirmed by expression of the gene cloned in both directions behind a T7 promoter. The KatF protein expressed in vitro migrates with an apparent size of 42 kDa. Comparison of the katF sequence to the sequence of rpoD, which encodes the sigma subunit of RNA polymerase, revealed a 181 bp region with 65% homology and a 38 bp segment that was 87% homologous. A 62 amino acid region of the predicted KatF protein sequence was found to be 85% homologous to the corresponding sequence of sigma 70, including a segment implicated in core polymerase binding. Homology was also observed with the heat shock regulatory protein encoded by htpR.
Disposition of a murine monoclonal antibody vinca conjugate (KS1/4-DAVLB) in patients with adenocarcinomas (1990)

The pharmacokinetics of a murine monoclonal antibody vinca conjugate (KS1/4-DAVLB) was investigated in 13 patients with adenocarcinomas who received single intravenous doses ranging from 40 to 250 mg/m2 and in three patients who were administered 1.5 mg/kg every 48 to 72 hours for up to 15 doses. Five patients in the single-dose study also received 100 microCi of [3H]-KS1/4-DAVLB. Overall mean values for the pharmacokinetic variables were as follows: elimination half-life, 31.5 hours; distribution volume, 4.43 L; and clearance, 0.09 L/hr. KS1/4-DAVLB demonstrated linear elimination kinetics in both the single- and multiple-dose studies. Significant concentrations of KS1/4-DAVLB were noted in a pleural effusion. Ten percent of the radioactive dose was recovered in the urine and 20% in the feces over a 5-day period. Small molecular weight vinca species were detected in the feces but not in the serum.