gebhart/patrepeval huggingface dataset:
Process Control of an Alternating Aerobic‐Anoxic Sequencing Batch Reactor for Nitrogen Removal via Nitrite (2008)

Abstract Nitrogen removal via nitrite is a novel technology and is becoming popular for engineering applications since it results in a saving of the aeration energy required for nitritation and external carbon sources for denitritation. An alternating aerobic‐anoxic (AAA) operational pattern was applied in a sequencing batch reactor (SBR) process to improve the nitrogen removal efficiency and achieve partial nitrification via nitrite from industrial wastewater with influent alkalinity deficiencies. The results showed that the online monitoring of the pH‐time variations during nitrification could indicate if the alkalinity was sufficient and when the ammonia nitrogen was completely oxidized. Under conditions of deficient influent alkalinity, the AAA process reduced the external alkalinity and the carbon sources addition and improved the effluent quality with ammonia nitrogen concentration below the detection limits. Half of the alkalinity previously consumed during aerobic nitrification could be recovered during the subsequent anoxic denitrification period. If the cycles of alternating aerobic/anoxic were repeated more than twice, the first nitrification cycle was stopped when the pH decreased by 0.4–0.5. The middle nitrification was terminated when the pH decreased by 0.8–1.0, and the final nitrification duration was controlled by the dissolved oxygen (DO) breakpoint and ammonia valley on the pH profile. Each anoxic time‐scale for denitrification was determined by the nitrate knee on the oxidation‐reduction potential (ORP) profile and the nitrate apex on the pH profiles. In comparison to the conventional SBR process, the AAA process with a real‐time control strategy resulted in an improved nitrogen removal efficiency of greater than 97 % under conditions of deficient influent alkalinity. Moreover, nitrogen removal via nitrite was achieved with a nitrite accumulation rate above 95 %.
Connexin expression and gap junctional intercellular communication in human squamous cell carcinoma of the head and neck (2006)

The data presented have relevance to our ongoing investigations of gap-junction mediated bystander effects in SCCHN and are being expanded to investigations on actual SCCHN tumor specimens.
Selective targeting of gene products with the megakaryocyte platelet factor 4 promoter. (1991)

We have used the 1.1 kilobases of the 5' upstream region of the platelet factor four (PF4) gene coupled to the prokaryotic beta-galactosidase gene to generate two lines of transgenic mice that express this construct. Studies of blood, bone marrow, spleen, and thymus reveal that platelets are the only circulating blood cells and megakaryocytes are the only hematopoietic precursor cells that possess the prokaryotic enzyme. The lack of transgene expression in brain, heart, intestine, kidney, liver, lung, and skeletal muscle was established by in situ staining of tissue sections as well as kinetic assay of tissue homogenates. These data suggest that this domain of the PF4 promoter contains most, if not all, of the tissue-specific region of the gene. Unexpectedly, the adrenal gland exhibits approximately 2% of the levels of beta-galactosidase possessed by megakaryocytes and the distribution of the prokaryotic enzyme corresponds to the location of mineralocorticoid-secreting cells. This result implies that either the PF4 gene is transcribed at low levels in specialized adrenal cells or that these specialized endocrine cells possess trans-acting factors similar to those that control the megakaryocyte promoter. The selective high-level expression of transgenes linked to the PF4 promoter should allow us to augment or suppress the in vivo levels of critical components in megakaryocytes and platelets and subsequently ascertain the effects of these modifications.
Final results of a phase I study of liposome encapsulated SN-38 (LE-SN38): Safety, pharmacogenomics, pharmacokinetics, and tumor response (2005)

2017 Background: The prodrug irinotecan is converted into its active moiety, SN-38, with wide interpatient variability, due in part to differential expression of cellular carboxylesterases responsible for prodrug hydrolysis. The enzyme UDP-glucuronosyltransferase 1A1 (UGT1A1) detoxifies SN-38 by metabolizing it to SN-38 glucuronide. Polymorphisms in the UGT1A1 promoter lead to decreased expression of the enzyme and are associated with increased risk of irinotecan toxicity. Methods: This was a multi-center, dose-escalation study of Liposome Encapsulated SN-38 (LE-SN38) in patients with advanced cancer. To examine whether toxicities and appropriate dose levels might differ with UGT1A1*28 genotype, patients were stratified prospectively. LE-SN38 was infused intravenously over 90 minutes every 21 days until disease progression or unacceptable toxicity occurred. Tumor progression was monitored radiographically after every 2 cycles. Results: Enrollment is complete; 75 patients were treated with LE-SN38. Screened patients had genotype frequencies of 42.4% homozygous wild-type (WT/WT), 45.1% heterozygous (WT/*28), 10.9% homozygous variant (*28/*28), and 1.6% other. Across all genotypes the most frequent adverse events were fatigue, nausea, anorexia, diarrhea, and vomiting. Importantly, diarrhea was generally mild and self-limiting, and no late onset diarrhea was reported. DLTs of neutropenia/febrile neutropenia in WT/WT patients at 40 mg/m2 resulted in an MTD of 35 mg/m2. No DLTs occurred in *28/*28 patients; accrual was halted at 20 mg/m2 before the MTD was reached. PK results showed that *28/*28 patients had 2- to 3-fold greater drug exposure than WT/*28 or WT/WT patients at the same doses. Stable disease (≥4 cycles) was observed in 37% of patients. Conclusions: LE-SN38 was well tolerated in all patients, with no reported acute/delayed diarrhea. The MTD was not reached for *28/*28 patients. An MTD of 35 mg/m2 LE-SN38 was found for WT/WT patients. Since WT/WT and WT/*28 patients did not appear to exhibit clinically significant differences in safety or PK profiles, this dose will be evaluated in both groups in a Phase II study of patients with colon cancer. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration NeoPharm
[MRT of the knee joint cartilage using 3D volume imaging in combination with a fast image processor]. (1989)

From the knees of healthy persons and cadavers 2D-spin-echo-sequences were compared to 3D-gradient-echo-sequences (FLASH, FISP). We were able to show that 3D-volume-imaging, combined with image processing on a fast computer, is superior to 2D-spin-echo-imaging. The advantages are: slice thickness lower than 1 mm, secondary reconstruction in any desired plane, good contrast between intraarticular fluid, the meniscus and the hyaline cartilage. For the practical application of 3D-volume-imaging resulting in multiple images the secondary reconstruction and post processing of the large numbers of images with an image processing computer is necessary.
In vivo protein complex topologies: Sights through a cross‐linking lens (2012)

Proteins are a remarkable class of molecules that exhibit wide diversity of shapes or topological features that underpin protein interactions and give rise to biological function. In addition to quantitation of abundance levels of proteins in biological systems under a variety of conditions, the field of proteome research has as a primary mission the assignment of function for proteins and if possible, illumination of factors that enable function. For many years, chemical cross-linking methods have been used to provide structural data on single purified proteins and purified protein complexes. However, these methods also offer the alluring possibility to extend capabilities to complex biological samples such as cell lysates or intact living cells where proteins may exhibit native topological features that do not exist in purified form. Recent efforts are beginning to provide glimpses of protein complexes and topologies in cells that suggest continued development will yield novel capabilities to view functional topological features of many proteins and complexes as they exist in cells, tissues, or other complex samples. This review will describe rationale, challenges, and a few success stories along the path of development of cross-linking technologies for measurement of in vivo protein interaction topologies.
Synthesis and Characterization of Oligodeoxynucleotides Containing Formamidopyrimidine Lesions and Nonhydrolyzable Analogues (2002)

Oligodeoxynucleotides containing formamidopyrimidine lesions and C-nucleoside analogues at defined sites were prepared by solid-phase synthesis and in some cases enzymatic ligation. Formamidopyrimidine lesions were introduced as dinucleotides to prevent rearrangement to their pyranose isomers. Oligodeoxynucleotides containing single diastereomers of C-nucleoside analogues of Fapy.dA were introduced by using the respective phosphoramidites. The formamidopyrimidine lesions reduce the T(M) of dodecamers relative to their unmodified nucleotide counterparts when opposite the nucleotide proper base-pairing partner. However, duplexes containing Fapy.dG-dA mispairs melt significantly higher than those comprised of dG-dA. All duplexes containing Fapy.dA-dX or its C-nucleoside analogue melt lower than the respective complexes containing dA-dX. Studies of the alkaline lability of oligodeoxynucleotides containing formamidopyrimidine lesions indicate that Fapy.dA is readily identified as an alkali-labile lesion with use of piperidine (1.0 M, 90 degrees C, 20 min), but Fapy.dG is less easily identified in this manner.
Routing stability in congested networks (2000)

Loss of the routing protocol messages due to network congestion can cause peering session failures in routers, leading to route flaps and routing instabilities. We study the effects of traffic overload on routing protocols by quantifying the stability and robustness properties of two common Internet routing protocols, OSPF and BGP, when the routing control traffic is not isolated from data traffic. We develop analytical models to quantify the effect of congestion on the robustness of OSPF and BGP as a function of the traffic overload factor, queueing delays, and packet sizes. We perform extensive measurements in an experimental network of routers to validate the analytical results. Subsequently we use the analytical framework to investigate the effect of factors that are difficult to incorporate into an experimental setup, such as a wide range of link propagation delays and packet dropping policies. Our results show that increased queueing and propagation delays adversely affect BGP's resilience to congestion, in spite of its use of a reliable transport protocol. Our findings demonstrate the importance of selective treatment of routing protocol messages from other traffic, by using scheduling and utilizing buffer management policies in the routers, to achieve stable and robust network operation.
DST sequences, highly conserved among plant SAUR genes, target reporter transcripts for rapid decay in tobacco. (1993)

DST elements are highly conserved sequences located in the 3' untranslated regions (UTRs) of a set of unstable soybean transcripts known as the small auxin-up RNAs (SAURs). To test whether DST sequences could function as mRNA instability determinants in plants, a model system was developed to facilitate the direct measurement of mRNA decay rates in stably transformed cells of tobacco. Initial experiments established that the chloramphenicol acetyltransferase (CAT) and beta-glucuronidase (GUS) transcripts degraded with similar half-lives in this system. In addition, their decay kinetics mirrored the apparent decay kinetics of the corresponding transcripts produced in transgenic plants under the control of a regulated promoter (Cab-1). The model system was then used to measure the decay rates of GUS reporter transcripts containing copies of the DST sequence inserted into the 3'UTR. An unmodified CAT gene introduced on the same vector served as the internal reference. These experiments and a parallel set utilizing a beta-globin reporter gene demonstrated that a synthetic dimer of the DST sequence was sufficient to destabilize both reporter transcripts in stably transformed tobacco cells. The decrease in transcript stability caused by the DST sequences in cultured cells was paralleled by a coordinate decrease in transcript abundance in transgenic tobacco plants. The implications of these results for the potential function of DST sequences within the SAUR transcripts are discussed.
A context‐free grammar‐driven, one‐pass HMM‐based continuous speech recognition method (1994)

Abstract This paper describes a frame synchronous continuous speech recognition algorithm using a context‐free grammar and its evaluation. A frame‐synchronous parsing algorithm for context‐free grammar based on the top‐down strategy is used for the prediction of successive words. The parsing process is incorporated into the one‐pass search algorithm with the dynamical expansion of a finite‐state automaton. Of course, since the number of the states becomes large, the beam search method should be used in the prediction and in pruning unreliable candidate branches from the search space. By using the proposed algorithm, a sentence recognition rate of 90 percent in a speaker adaptation mode is obtained while the conventional system based on word spotting and lattice parsing algorithm obtained 80.7 percent for the task of perplexity 10.
Protective Efficacy of DNA Vaccines Encoding Outer Membrane Protein A and OmpK36 of Klebsiella pneumoniae in Mice (2010)

The immunogenicity of DNA vaccines expressing outer membrane proteins as antigens was evaluated in this study. DNA vaccines consisting of vector pVAX1 expressing either outer membrane protein A or OmpK36 were injected into mice by either the intradermal or the intramuscular route. Antibodies elicited were shown to be specifically reactive to OmpA and OmpK36 by immunoblotting. The immunoglobulin G (IgG) antibodies elicited by both vaccines included IgG1, IgG2a, IgG2b, and IgG3. Immunized mice exhibited a predominance of IgG1 over IgG2a, therefore indicating a stronger humoral response. Mice receiving either of the DNA vaccines produced high levels of interleukin-12 (IL-12) and IL-10 and low levels of gamma interferon, suggesting the induction of a mixed Th1 and Th2 response. Sera from DNA vaccine-immunized mice had significantly higher opsonic activity in opsonophagocytic assays than did sera from the control mice. The level of protection afforded by pOmpK36 DNA injected intradermally into mice was the highest. These results suggest that both OmpA and OmpK36 are excellent candidates for use in future studies of vaccination against infections caused by Klebsiella pneumoniae. This is the first study which established the efficacy of protection afforded by DNA vaccines based on outer membrane proteins against K. pneumoniae infections.
Incorporation of homologous and heterologous proteins into the envelope of Moloney murine leukemia virus (1994)

The efficiencies with which homologous and heterologous proteins are incorporated into the envelope of Moloney murine leukemia virus (M-MuLV) have been analyzed by utilizing a heterologous, Semliki Forest virus-driven M-MuLV assembly system and quantitative pulse-chase assays. Homologous M-MuLV spike protein was found to be efficiently incorporated into extracellular virus particles when expressed at a relatively low density at the plasma membrane. In contrast, efficient incorporation of heterologous proteins (the spike complex of Semliki Forest virus and a cytoplasmically truncated mutant of the human transferrin receptor) was observed only when these proteins were expressed at high densities at the cell surface. These results imply that homologous and heterologous proteins are incorporated into the M-MuLV envelope via two distinct pathways.
Neuron Specificity of the Neurofilament Light Promoter in Transgenic Mice Requires the Presence of DNA Unwinding Elements (1995)

Three reporter genes, the chloramphenicol acetyltransferase (CAT), the lacZ, and the intronless NF-L DNA, were used to test the activity of the proximal promoter region (-292 bp) of the human neurofilament light (hNF-L) gene in transgenic mice. Surprisingly, the hNF-L/CAT construct was highly sensitive to position effect, and its expression was found at low levels in several tissues of adult transgenic mice (Beaudet, L., Charron, G., Houle, D., Tretjakoff, I. Peterson, A., and Julien, J.-P. (1992) Gene (Amst.) 116, 205-214). In contrast, the hNF-L/lacZ or the hNF-L/intronless constructs were expressed exclusively in the nervous system during embryonic development and in adult animals. The DNA sequences analysis of the different reporter genes revealed the presence of matrix attachment regions (MARs) within the 3'-untranslated regions of all three transgenes. DNA unwinding elements were found within the MARs of lacZ and hNF-L gene constructs but not in the CAT gene construct. When this element was removed from the lacZ construct, expression of the hNF-L/lacZ transgene became susceptible to position effect and was no longer tissue-specific. These results indicate that DNA unwinding elements are essential for position effect independence conferred by MARs to the hNF-L basal promoter.
The unique signal concept for detonation safety in nuclear weapons (1993)

The purpose of a unique signal (UQS) in a nuclear weapon system is to provide an unambiguous communication of intent to detonate from the UQS information input source device to a stronglink safety device in the weapon in a manner that is highly unlikely to be duplicated or simulated in normal environments and in a broad range of ill-defined abnormal environments. This report presents safety considerations for the design and implementation of UQSs in the context of the overall safety system.
Mapping of B-cell epitopes on the outer membrane P2 porin protein of Haemophilus influenzae by using recombinant proteins and synthetic peptides (1991)

The P2 protein of Haemophilus influenzae type b has a porin activity and is the most abundant protein in the outer membrane. We have employed fusion protein constructs and synthetic peptides along with monoclonal antibodies to map B-cell epitopes in this protein. A linear, surface-exposed epitope was identified between residues 158 and 174. A second surface-exposed epitope was identified near the carboxy-terminal end of the protein (residues 319 to 341). Two additional B-cell epitopes were identified. One was localized between residues 28 and 55, whereas the other was located between residues 148 and 174. These epitopes were not present on the surface of intact H. influenzae cells. Thus, four distinct immunogenic and antigenic regions on the P2 protein have been identified.
Unsupervised query categorization using automatically-built concept graphs (2009)

Automatic categorization of user queries is an important component of general purpose (Web) search engines, particularly for triggering rich, query-specific content and sponsored links. We propose an unsupervised learning scheme that reduces dramatically the cost of setting up and maintaining such a categorizer, while retaining good categorization power. The model is stored as a graph of concepts where graph edges represent the cross-reference between the concepts. Concepts and relations are extracted from query logs by an offline Web mining process, which uses a search engine as a powerful summarizer for building a concept graph. Empirical evaluation indicates that the system compares favorably on publicly available data sets (such as KDD Cup 2005) as well as on portions of the current query stream of Yahoo! Search, where it is already changing the experience of millions of Web search users.
Three Parallel Quorum-Sensing Systems Regulate Gene Expression in Vibrio harveyi (2004)

In a process called quorum sensing, bacteria communicate using extracellular signal molecules termed autoinducers. Two parallel quorum-sensing systems have been identified in the marine bacterium Vibrio harveyi. System 1 consists of the LuxM-dependent autoinducer HAI-1 and the HAI-1 sensor, LuxN. System 2 consists of the LuxS-dependent autoinducer AI-2 and the AI-2 detector, LuxPQ. The related bacterium, Vibrio cholerae, a human pathogen, possesses System 2 (LuxS, AI-2, and LuxPQ) but does not have obvious homologues of V. harveyi System 1. Rather, System 1 of V. cholerae is made up of the CqsA-dependent autoinducer CAI-1 and a sensor called CqsS. Using a V. cholerae CAI-1 reporter strain we show that many other marine bacteria, including V. harveyi, produce CAI-1 activity. Genetic analysis of V. harveyi reveals cqsA and cqsS, and phenotypic analysis of V. harveyi cqsA and cqsS mutants shows that these functions comprise a third V. harveyi quorum-sensing system that acts in parallel to Systems 1 and 2. Together these communication systems act as a three-way coincidence detector in the regulation of a variety of genes, including those responsible for bioluminescence, type III secretion, and metalloprotease production.
Super-resolution image reconstruction: a technical overview (2003)

A new approach toward increasing spatial resolution is required to overcome the limitations of the sensors and optics manufacturing technology. One promising approach is to use signal processing techniques to obtain an high-resolution (HR) image (or sequence) from observed multiple low-resolution (LR) images. Such a resolution enhancement approach has been one of the most active research areas, and it is called super resolution (SR) (or HR) image reconstruction or simply resolution enhancement. In this article, we use the term "SR image reconstruction" to refer to a signal processing approach toward resolution enhancement because the term "super" in "super resolution" represents very well the characteristics of the technique overcoming the inherent resolution limitation of LR imaging systems. The major advantage of the signal processing approach is that it may cost less and the existing LR imaging systems can be still utilized. The SR image reconstruction is proved to be useful in many practical cases where multiple frames of the same scene can be obtained, including medical imaging, satellite imaging, and video applications. The goal of this article is to introduce the concept of SR algorithms to readers who are unfamiliar with this area and to provide a review for experts. To this purpose, we present the technical review of various existing SR methodologies which are often employed. Before presenting the review of existing SR algorithms, we first model the LR image acquisition process.