gebhart/patrepeval huggingface dataset:
Members of the genus Arthrobacter grow anaerobically using nitrate ammonification and fermentative processes: anaerobic adaptation of aerobic bacteria abundant in soil (2003)

Members of the genus Arthrobacter are usually regarded as obligate aerobic bacteria. The anaerobic growth and energy metabolism of two Arthrobacter species were investigated. Arthrobacter globiformis utilized both nitrate ammonification and lactate, acetate and ethanol producing fermentation processes for anaerobic growth. Only nitrate supported anaerobic growth of Arthrobacter nicotianae. Anaerobically induced respiratory nitrate reductase activity was detected in both strains. Neither of the tested strains used the alternative electron acceptors fumarate, dimethylsulfoxide or trimethylamine-N-oxide.
Disaster recovery as a cloud service: economic benefits & deployment challenges (2010)

Many businesses rely on Disaster Recovery (DR) services to prevent either manmade or natural disasters from causing expensive service disruptions. Unfortunately, current DR services come either at very high cost, or with only weak guarantees about the amount of data lost or time required to restart operation after a failure. In this work, we argue that cloud computing platforms are well suited for offering DR as a service due to their pay-as-you-go pricing model that can lower costs, and their use of automated virtual platforms that can minimize the recovery time after a failure. To this end, we perform a pricing analysis to estimate the cost of running a public cloud based DR service and show significant cost reductions compared to using privately owned resources. Further, we explore what additional functionality must be exposed by current cloud platforms and describe what challenges remain in order to minimize cost, data loss, and recovery time in cloud based DR services.
Sp1 and the subfamily of zinc finger proteins with guanine-rich binding sites. (1992)

Structures from the Stone Age can provide unique insights into Late Glacial and Mesolithic cultures around the Baltic Sea. Such structures, however, usually did not survive within the densely populated Central European subcontinent. Here, we ...The Baltic Sea basins, some of which only submerged in the mid-Holocene, preserve Stone Age structures that did not survive on land. Yet, the discovery of these features is challenging and requires cross-disciplinary approaches between archeology and ...
Impurity-Related Excitonic Processes in CaF2 : Sr (2002)

Excitation and emission spectra of CaF2:Sr single crystals with various strontium concentrations have been investigated by the method of luminescence spectroscopy. A new emission band peaking at 4.1 eV has been found and attributed to the radiative decay of excitons trapped near the Sr2+ impurity ions. The same spectral composition has the emission band arising from the recombination of conduction-band electrons with holes localised near Sr2+ ions (VKA(Sr2+) centres). A mechanism of exciton and hole trapping by homologous cation impurities of large ionic radii is suggested. It is concluded, that the doping of CaF2 by strontium leads to the increase in radiation stability of this optical material.
Predicted Packet Padding for Anonymous Web Browsing Against Traffic Analysis Attacks (2012)

Anonymous communication has become a hot research topic in order to meet the increasing demand for web privacy protection. However, there are few such systems which can provide high level anonymity for web browsing. The reason is the current dominant dummy packet padding method for anonymization against traffic analysis attacks. This method inherits huge delay and bandwidth waste, which inhibits its use for web browsing. In this paper, we propose a predicted packet padding strategy to replace the dummy packet padding method for anonymous web browsing systems. The proposed strategy mitigates delay and bandwidth waste significantly on average. We formulated the traffic analysis attack and defense problem, and defined a metric, cost coefficient of anonymization (CCA), to measure the performance of anonymization. We thoroughly analyzed the problem with the characteristics of web browsing and concluded that the proposed strategy is better than the current dummy packet padding strategy in theory. We have conducted extensive experiments on two real world data sets, and the results confirmed the advantage of the proposed method.
An introduction to Pound–Drever–Hall laser frequency stabilization (2001)

This paper is an introduction to an elegant and powerful technique in modern optics: Pound–Drever–Hall laser frequency stabilization. This introduction is primarily meant to be conceptual, but it includes enough quantitative detail to allow the reader to immediately design a real setup, suitable for research or industrial application. The intended audience is both the researcher learning the technique for the first time and the teacher who wants to cover modern laser locking in an upper-level physics or electrical engineering course.
Bispecific antibody and iodine-131-labeled bivalent hapten dosimetry in patients with medullary thyroid or small-cell lung cancer. (1996)

High absorbed dose values were calculated for small MTC recurrences. For SCLC recurrences the values were smaller but in the same range as those obtained by other investigators with the one-step technique in lymphoma.
Nitric oxide regulates oxygen uptake and hydrogen peroxide release by the isolated beating rat heart (1998)

Isolated rat heart perfused with 1.5-7.5 microM NO solutions or bradykinin, which activates endothelial NO synthase, showed a dose-dependent decrease in myocardial O2 uptake from 3.2 +/- 0.3 to 1.6 +/- 0.1 (7.5 microM NO, n = 18, P < 0.05) and to 1.2 +/- 0.1 microM O2.min-1.g tissue-1 (10 microM bradykinin, n = 10, P < 0.05). Perfused NO concentrations correlated with an induced release of hydrogen peroxide (H2O2) in the effluent (r = 0.99, P < 0.01). NO markedly decreased the O2 uptake of isolated rat heart mitochondria (50% inhibition at 0.4 microM NO, r = 0.99, P < 0.001). Cytochrome spectra in NO-treated submitochondrial particles showed a double inhibition of electron transfer at cytochrome oxidase and between cytochrome b and cytochrome c, which accounts for the effects in O2 uptake and H2O2 release. Most NO was bound to myoglobin; this fact is consistent with NO steady-state concentrations of 0.1-0.3 microM, which affect mitochondria. In the intact heart, finely adjusted NO concentrations regulate mitochondrial O2 uptake and superoxide anion production (reflected by H2O2), which in turn contributes to the physiological clearance of NO through peroxynitrite formation.
“Epigenetic Memory” Phenomenon in Induced Pluripotent Stem Cells (2013)

To date biomedicine and pharmacology have required generating new and more consummate models. One of the most perspective trends in this field is using induced pluripotent stem cells (iPSCs). iPSC application requires careful high-throughput analysis at the molecular, epigenetic, and functional levels. The methods used have revealed that the expression pattern of genes and microRNA, DNA methylation, as well as the set and pattern of covalent histone modifications in iPSCs, are very similar to those in embryonic stem cells. Nevertheless, iPSCs have been shown to possess some specific features that can be acquired during the reprogramming process or are remnants of epigenomes and transcriptomes of the donor tissue. These residual signatures of epigenomes and transcriptomes of the somatic tissue of origin were termed "epigenetic memory." In this review, we discuss the "epigenetic memory" phenomenon in the context of the reprogramming process, its influence on iPSC properties, and the possibilities of its application in cell technologies.
Proteins of the Hard Keratins of Echidna, Hedgehog, Rabbit, Ox and Man (1977)

In the accompanying paper it has been shown that two major groups of proteins (low-sulphur and high-sulphur) of ovine wool, horn, and hoof contain similar components although the overall proportions of the groups of proteins and the relative proportions of components within the groups may show significant differences. In the present paper it has been shown for five other species (echidna, hedgehog, rabbit, ox and man) that the hard keratins produced by one animal contain the same groups of protein components but in different relative proportions. The wide apparent differences in the type and relative proportions of the the low-sulphur components which comprise the major constituent proteins of the microfibrils suggest that microfibrils can tolerate a considerable variation in the constituent proteins and still produce functional structures. The low-sulphur protein components are sufficiently well resolved by sodium dodecyl sulphate-polyacrylamide gel electrophoresis to make this procedure potentially useful for animal identification and classification.
LIVER CANCER (2019)

Hepatocellular carcinoma (HCC or hepatoma) is the most common primary liver malignancy. Chronic hepatic inflammation is the major driving factor in the development of HCC. Risk factors vary by regional exposures. As chronic Hepatitis B virus (HBV) infection is the most common risk factor leading to HCC development, HBV vaccination is one option to reduce the risk of HCC, particularly in high-risk areas. Antiviral medications can interrupt the transformation of acute to chronic infection, which ultimately is the primary way to reduce the incidence of HCC. If HCC is a result of cirrhosis, then special consideration is needed in treatment of both diseases since both are potentially life-ending. For this reason, the management of patients with HCC often involves multiple teams including hepatology, radiology (diagnostic and interventional), surgery, medical oncology, nutrition, social work, and drug/alcohol counseling.
Terahertz reflection imaging using Kirchhoff migration (2001)

We describe a new imaging method that uses single-cycle pulses of terahertz (THz) radiation. This technique emulates data-collection and image-processing procedures developed for geophysical prospecting and is made possible by the availability of fiber-coupled THz receiver antennas. We use a simple migration procedure to solve the inverse problem; this permits us to reconstruct the location and shape of targets. These results demonstrate the feasibility of the THz system as a test-bed for the exploration of new seismic processing methods involving complex model systems.
Expression of Bone Morphogenetic Proteins and Receptors in Sarcomas (1999)

Bone morphogenetic proteins, which are capable of inducing mesenchymal tissue to form bone in mammals, have been implicated as important in normal skeletal development. The expression of bone morphogenetic proteins and their receptors were studied in 36 osteosarcoma specimens, six Ewing's sarcomas, 20 synovial sarcomas, and 20 chondrosarcomas by reverse transcriptase-polymerase chain reaction, and the findings were correlated with clinical data. Bone morphogenetic protein-2, and −4 messages were detected in most sarcoma samples. Bone morphogenetic protein-6 expression was detected in 22 of 32 osteosarcomas and seven of eight chondrosarcomas. Bone morphogenetic protein-7 and receptor IB were not detected in sarcoma samples but were detected in three osteosarcoma cell lines and one malignant fibrous histiocytoma cell line. Expression of bone morphogenetic protein receptor II was found in 25 of 36 osteosarcomas, eight of 20 chondrosarcomas, four of six Ewing's sarcomas, and 15 of 20 synovial sarcoma samples. Expression of bone morphogenetic protein type II receptor was found to correlate with metastasis in osteosarcomas, which suggests that the bone morphogenetic protein pathway may participate in tumor aggressiveness or progression. The expression of bone morphogenetic protein receptor II in metastatic synovial sarcoma and dedifferentiated chondrosarcoma lesions also supports this hypothesis. The current study showed that the ligands for bone morphogenetic protein receptors, bone morphogenetic proteins-2, −4, and −6 also are expressed in osteosarcoma and other sarcoma tissues, indicating a potential for autocrine or paracrine growth stimulation in these tumors.
3-Tetrahydrofuran and pyran urethanes as high-affinity P2-ligands for HIV-1 protease inhibitors (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT3-Tetrahydrofuran and pyran urethanes as high-affinity P2-ligands for HIV-1 protease inhibitorsArun K. Ghosh, Wayne J. Thompson, Sean P. McKee, Tien T. Duong, Terry A. Lyle, Jenny C. Chen, Paul L. Darke, Joan A. Zugay, Emilio A. Emini, and Cite this: J. Med. Chem. 1993, 36, 2, 292–294Publication Date (Print):January 1, 1993Publication History Published online1 May 2002Published inissue 1 January 1993https://pubs.acs.org/doi/10.1021/jm00054a015https://doi.org/10.1021/jm00054a015research-articleACS PublicationsRequest reuse permissionsArticle Views351Altmetric-Citations73LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Review of progress in shape-memory polymers (2007)

Shape-memory polymers (SMPs) have attracted significant attention from both industrial and academic researchers due to their useful and fascinating functionality. This review thoroughly examines progress in shape-memory polymers, including the very recent past, achieved by numerous groups around the world and our own research group. Considering all of the shape-memory polymers reviewed, we identify a classification scheme wherein nearly all SMPs may be associated with one of four classes in accordance with their shape fixing and recovering mechanisms and as dictated by macromolecular details. We discuss how the described shape-memory polymers show great potential for diverse applications, including in the medical arena, sensors, and actuators.
Molecular Mechanics Force Fields for Bent Metallocenes of the Type [M(Cp)2Cl2] (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular Mechanics Force Fields for Bent Metallocenes of the Type [M(Cp)2Cl2]Thompson N. Doman, T. Keith Hollis, and B. BosnichCite this: J. Am. Chem. Soc. 1995, 117, 4, 1352–1368Publication Date (Print):February 1, 1995Publication History Published online1 May 2002Published inissue 1 February 1995https://pubs.acs.org/doi/10.1021/ja00109a020https://doi.org/10.1021/ja00109a020research-articleACS PublicationsRequest reuse permissionsArticle Views167Altmetric-Citations46LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
ChemInform Abstract: Synthesis and Antimalarial Activity of Pyrido(3,2‐f)quinoxalines and Their N‐Oxides. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Serum mucin antigens casa and msa in tumors of the breast, ovary, lung, pancreas, bladder, colon, and prostate. A blind trial with 420 patients (1993)

The commercial CASA and MSA assays are reliable and reproducible tests for these tumor markers. In addition to ovarian cancer, CASA is also elevated significantly in many patients with breast, lung, prostate, and bladder cancer and has potential clinical use in patients with these tumors. The use of the MSA assay appears restricted to breast cancer.
ADCT-301, a Pyrrolobenzodiazepine (PBD) Dimer–Containing Antibody–Drug Conjugate (ADC) Targeting CD25-Expressing Hematological Malignancies (2016)

Despite the many advances in the treatment of hematologic malignancies over the past decade, outcomes in refractory lymphomas remain poor. One potential strategy in this patient population is the specific targeting of IL2R-α (CD25), which is overexpressed on many lymphoma and leukemic cells, using antibody-drug conjugates (ADC). ADCT-301 is an ADC composed of human IgG1 HuMax-TAC against CD25, stochastically conjugated through a dipeptide cleavable linker to a pyrrolobenzodiazepine (PBD) dimer warhead with a drug-antibody ratio (DAR) of 2.3. ADCT-301 binds human CD25 with picomolar affinity. ADCT-301 has highly potent and selective cytotoxicity against a panel of CD25-expressing human lymphoma cell lines. Once internalized, the released warhead binds in the DNA minor groove and exerts its potent cytotoxic action via the formation of DNA interstrand cross-links. A strong correlation between loss of viability and DNA cross-link formation is demonstrated. DNA damage persists, resulting in phosphorylation of histone H2AX, cell-cycle arrest in G<sub>2</sub>-M, and apoptosis. Bystander killing of CD25-negative cells by ADCT-301 is also observed. In vivo, a single dose of ADCT-301 results in dose-dependent and targeted antitumor activity against both subcutaneous and disseminated CD25-positive lymphoma models. In xenografts of Karpas 299, which expressed both CD25 and CD30, marked superiority over brentuximab vedotin (Adcetris) is observed. Dose-dependent increases in DNA cross-linking, γ-H2AX, and PBD payload staining were observed in tumors in vivo indicating a role as relevant pharmacodynamic assays. Together, these data support the clinical testing of this novel ADC in patients with CD25-expressing tumors. Mol Cancer Ther; 15(11); 2709-21. ©2016 AACR.
Wireless power domino-resonator systems with noncoaxial axes and circular structures (2011)

In this paper, a general analysis on wireless power domino-resonator systems with noncoaxial axes is presented. The mathematical formulation established can in principle be used to analyze wireless resonator systems with various domino forms. In this study, it is used to analyze and evaluate wireless domino-resonator systems with circular structures because such structures have more than one main power flow paths and have not been analyzed previously. Based on the superposition method, individual power flow paths are analyzed and then their interactions are emerged and explained with vector diagrams. Unlike the resonator pair used by Tesla, it is demonstrated that optimization of the domino systems can be achieved under “nonresonance frequency” operation and optimal load conditions. The shift of the optimal frequency from the resonance frequency is due to the multiple power flow paths. The theoretical results have been favorably verified with practical measurements obtained from two circular systems.
Four Consecutive Serines in the Third Intracellular Loop Are the Sites for β-Adrenergic Receptor Kinase-mediated Phosphorylation and Desensitization of the α2A-Adrenergic Receptor (1995)

During short term agonist exposure, the alpha 2A-adrenergic receptor (alpha 2AAR) undergoes rapid functional desensitization caused by phosphorylation of the receptor by the beta-adrenergic receptor kinase (beta ARK). This signal quenching is similar in nature to that found with a number of G-protein coupled receptors in which agonist-promoted desensitization is due to beta ARK phosphorylation; like these other receptors, the precise molecular determinants of the receptor required for beta ARK phosphorylation are not known. To delineate such a motif in the human alpha 2AAR (alpha 2C10), we constructed six mutated receptors consisting of deletions or substitutions of Ser-296-299 in the EESSSS sequence of the third intracellular loop of the receptor. These were expressed in Chinese hamster ovary and COS-7 cells, and agonist-promoted desensitization and receptor phosphorylation were assessed. Deletion of the EESSSS sequence and substitution of alanine for all four serines resulted in a total loss of phosphorylation and desensitization. Mutant receptors that retained two of the original serines (AASS and SSAA) underwent agonist-promoted phosphorylation of 55 +/- 7% and 57 +/- 8% of the phosphorylation found for wild type alpha 2C10. Additional substitution mutants (SSSA and SAAA) underwent 77 +/- 1% and 27 +/- 4% of wild type phosphorylation, respectively. Thus, substitution of alanine for each additional serine decreased overall phosphorylation as compared with wild type alpha 2C10 by approximately 25%, which is consistent with all 4 serines being phosphorylated. Mutated receptors that only partially phosphorylated (as compared with wild type) failed to undergo agonist-promoted desensitization. Thus, beta ARK-mediated phosphorylation of alpha 2C10 occurs at Ser-296-299 in the third intracellular loop, and this represents the critical step in rapid agonist-promoted desensitization. A number of other G-protein coupled receptors that undergo desensitization have a sequence motif similar to that which we have found for beta ARK-mediated phosphorylation of alpha 2C10, suggesting that these receptors may also be substrates for beta ARK.
X-ray Absorption Studies of Human Matrix Metalloproteinase-2 (MMP-2) Bound to a Highly Selective Mechanism-based Inhibitor (2001)

Malignant tumors express high levels of zinc-dependent endopeptidases called matrix metalloproteinases (MMPs), which are thought to facilitate tumor metastasis and angiogenesis by hydrolyzing components of the extracellular matrix. Of these enzymes, gelatinases A (MMP-2) and B (MMP-9), have especially been implicated in malignant processes, and thus, they have been a target for drugs designed to block their activity. Therefore, understanding their molecular structure is key for a rational approach to inhibitor design. Here, we have conducted x-ray absorption spectroscopy of the full-length human MMP-2 in its latent, active, and inhibited states and report the structural changes at the zinc ion site upon enzyme activation and inhibition. We have also examined the molecular structure of MMP-2 in complex with SB-3CT, a recently reported novel mechanism-based synthetic inhibitor that was designed to be highly selective in gelatinases. It is shown that SB-3CT directly binds the catalytic zinc ion of MMP-2. Interestingly, the novel mode of binding of the inhibitor to the catalytic zinc reconstructs the conformational environment around the active site metal ion back to that of the proenzyme.