gebhart/patrepeval huggingface dataset:
Sensitivity study of marine CSEM data for reservoir production monitoring (2008)

Abstract Using numerical and analytical modeling, we assess the feasibility of marine controlled-source electromagnetic (CSEM) data for monitoring the flooding front during water flooding of an oil reservoir. We discuss the ability of time-lapse CSEM data to resolve changes in the electric conductivity small enough to be of interest for monitoring purposes. Measurement and modeling errors are discussed briefly, and analytical calculations comparing time-lapse signals with a certain type of time-lapse modeling errors are performed. Numerical calculations, performed with a volume integral-equation method, are used to study the effect on the electromagnetic (EM) fields of relevant conductivity changes. The numerical investigation includes robustness with respect to survey parameter values, discrimination between different front shapes, and ability to overcome time-lapse error. Simulated signals are found to be strong enough to overtake typical measurement errors and are fairly robust toward perturbations of survey parameters. It is found analytically and numerically that certain modeling errors experience a high degree of time-lapse cancellation.
Functional Diversification of CLAVATA3-Related CLE Proteins in Meristem Maintenance in Rice (2008)

Postembryonic development in plants depends on the activity of the shoot apical meristem (SAM) and root apical meristem (RAM). In Arabidopsis thaliana, CLAVATA signaling negatively regulates the size of the stem cell population in the SAM by repressing WUSCHEL. In other plants, however, studies of factors involved in stem cell maintenance are insufficient. Here, we report that two proteins closely related to CLAVATA3, FLORAL ORGAN NUMBER2 (FON2) and FON2-LIKE CLE PROTEIN1 (FCP1/Os CLE402), have functionally diversified to regulate the different types of meristem in rice (Oryza sativa). Unlike FON2, which regulates the maintenance of flower and inflorescence meristems, FCP1 appears to regulate the maintenance of the vegetative SAM and RAM. Constitutive expression of FCP1 results in consumption of the SAM in the vegetative phase, and application of an FCP1 CLE peptide in vitro disturbs root development by misspecification of cell fates in the RAM. FON1, a putative receptor of FON2, is likely to be unnecessary for these FCP1 functions. Furthermore, we identify a key amino acid residue that discriminates between the actions of FCP1 and FON2. Our results suggest that, although the basic framework of meristem maintenance is conserved in the angiosperms, the functions of the individual factors have diversified during evolution.
Efficient motion-vector-based video search using query by clip (2005)

A simple and efficient motion-vector-based search engine supporting query by clip is presented for indexing and retrieving of videos. We propose a technique to filter and reconstruct noisy motion vectors to improve the fidelity of the motion activity. In addition to the motion features of intensity and direction, a new motion descriptor, named representative spectrum, extracted by a vector quantization expressing the spatial-temporal distribution of motion activity, is introduced for video indexing. A dynamic programming scheme is also utilized to measure the similarity of two videos based on the concept of common subsequence. Furthermore, a 2-step search of similar videos is employed to reduce the computational complexity. The experimental results indicate that the proposed search engine performs well and the obtained recall and precision values are also high enough.
Heterodimerization of Insulin-like Growth Factor Receptor/Epidermal Growth Factor Receptor and Induction of Survivin Expression Counteract the Antitumor Action of Erlotinib (2006)

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) have been used to treat non-small cell lung cancer (NSCLC). However, the overall response rate to EGFR TKIs is limited, and the mechanisms mediating resistance to the drugs are poorly understood. Here, we report that insulin-like growth factor-I receptor (IGF-IR) activation interferes with the antitumor activity of erlotinib, an EGFR TKI. Treatment with erlotinib increased the levels of EGFR/IGF-IR heterodimer localized on cell membrane, activated IGF-IR and its downstream signaling mediators, and stimulated mammalian target of rapamycin (mTOR)-mediated de novo protein synthesis of EGFR and survivin in NSCLC cells. Inhibition of IGF-IR activation, suppression of mTOR-mediated protein synthesis, or knockdown of survivin expression abolished resistance to erlotinib and induced apoptosis in NSCLC cells in vitro and in vivo. Our data suggest that enhanced synthesis of survivin protein mediated by the IGFR/EGFR heterodimer counteracts the antitumor action of erlotinib, indicating the needs of integration of IGF-IR-targeted agents to the treatment regimens with EGFR TKI for patients with lung cancer.
Immunoadjuvant effects of polyadenylic:polyuridylic acids through TLR3 and TLR7 (2007)

Double-stranded RNA (dsRNA) is produced upon viral infection and can activate innate immunity. Polyinosinic:polycytidylic acids [poly(I:C)] is a synthetic mimetic of dsRNA and functions through an endosomal receptor, Toll-like receptor (TLR) 3 or cytosolic receptors. Another type of dsRNA, polyadenylic:polyuridylic acids [poly(A:U)], can also act as an immune adjuvant, but it remains unclear how it exhibits its adjuvant effects. Here, we have characterized the adjuvant effects of poly(A:U). Poly(A:U) could induce both IFN-alpha and IL-12p40 from murine bone marrow dendritic cells (DCs). Poly(A:U)-induced IFN-alpha production depended on a DC subset, plasmacytoid dendritic cell (pDC), and required TLR7. IL-12p40 was also produced by poly(A:U)-stimulated pDC in a TLR7-dependent manner. In addition to pDC, conventional dendritic cell (cDC) also produced IL-12p40 in response to poly(A:U). This IL-12p40 induction resulted from two cDC subsets, CD24(high) cDC and CD11b(high) cDC in a TLR3- and TLR7-dependent manner, respectively. In vivo injection of poly(A:U) with antigen led to clonal expansion of and IFN-gamma production from antigen-specific CD8(+) T cells. Consistent with the in vitro findings, TLR3 and TLR7 were required for the clonal T-cell expansion. Notably, TLR3, rather than TLR7, was critical for generating IFN-gamma-producing CD8(+) T cells. CD8(+) T-cell responses induced by poly(A:U) were independent of type I IFN signaling. Our results demonstrate that poly(A:U) functions as an in vivo immunoadjuvant mainly through TLR3 and TLR7.
Preparation of immobilized L-phenylalanine ammonia-lyase in tubular form for depletion of L-phenylalanine. (1978)

A systematic study on the composition and bonding structure of plasma-assisted ALD Al2O3 films deposited at substrate temperatures between 25 and 400 °C is presented. The composition of the films is determined with Rutherford back scattering (RBS) and elastic recoil detection (ERD). The O/Al atom ratio in the films changes from 2.0 to 1.5 and the mass density increases from 2.6 to 3.1 g/cm3 when increasing the substrate temperature. The hydrogen content decreases with substrate temperature from 13 at.% at 50 °C to less than 1 at.% at 400 °C. Fourier transform infrared spectroscopy shows that the H atoms are predominantly bonded to O atoms, and that the H atoms are effectively removed after annealing at 400 °C. Depth resolved XPS measurements reveal that the atomic concentrations remains constant after annealing. The O1s and Al2p XPS peak positions show that film has different bonding structure at the interface. compared to the bulk. After annealing the bulk of the film shows indications of relaxation whereas the interface is unchanged.
A Compositional Look at the Human Gastrointestinal Microbiome and Immune Activation Parameters in HIV Infected Subjects (2014)

HIV progression is characterized by immune activation and microbial translocation. One factor that may be contributing to HIV progression could be a dysbiotic microbiome. We therefore hypothesized that the GI mucosal microbiome is altered in HIV patients and this alteration correlates with immune activation in HIV. 121 specimens were collected from 21 HIV positive and 22 control human subjects during colonoscopy. The composition of the lower gastrointestinal tract mucosal and luminal bacterial microbiome was characterized using 16S rDNA pyrosequencing and was correlated to clinical parameters as well as immune activation and circulating bacterial products in HIV patients on ART. The composition of the HIV microbiome was significantly different than that of controls; it was less diverse in the right colon and terminal ileum, and was characterized by loss of bacterial taxa that are typically considered commensals. In HIV samples, there was a gain of some pathogenic bacterial taxa. This is the first report characterizing the terminal ileal and colonic mucosal microbiome in HIV patients with next generation sequencing. Limitations include use of HIV-infected subjects on HAART therapy.
Binding and Factor XIII a -Mediated Cross-Linking of a 27-Kilodalton Fragment of Fibronectin to Staphylococcus aureus (1980)

A 27-kilodalton tryptic fragment, derived from the amino terminus of the 200-kilodalton fibronectin subunit, inhibited binding of intact fibronectin to Staphylococcus aureus and could be cross-linked to Staphylococcus aureus by blood coagulation Factor XIIIa. Interactions of fibronectin with Staphylococcus aureus via this fragment may be important for bacterial opsonization and attachment.
Service Oriented Architecture (SOA) Migration Strategy for U.S. Operational Naval Meteorology and Oceanography (METOC) (2007)

The Commander Naval Meteorology and Oceanography Command (COMNAVMETOCCOM) manages a scope of activities that sponsor, create, operate, and maintain capabilities that support the operational goals of Naval Meteorology and Oceanography (METOC). Effective and efficient Naval METOC operations require partnerships and collaborations within the U.S. Navy, with external U.S. Department of Defense (DoD) and U.S. Federal agencies, and with military allies and coalition partners. Partnerships are or will be supported by the integration of operational processes, functional capabilities, and data useful in multiple contexts. The U.S. DoD has followed the global industry base in adopting a Service Oriented Architecture (SOA) architectural pattern as the best technical approach to integration of processes, functionality, and data in heterogeneous, cross-organizational, technical environments. Naval METOC is a domain in the U.S. DoD enterprise that provides critical environmental characterization of the battlespace along with associated impacts on platforms, sensors, weapons, people, and warfighting missions and operations. This information must be efficiently and effectively produced and integrated into sensor systems, warfighter systems and decision processes. It is imperative, therefore, that all Naval METOC information technology (IT) programs that are essential for continued operations and/or business processes migrate towards an SOA environment. The level of migration will vary depending on the resources available and the need for agile integration with internal and external systems. An effective migration requires a clear understanding of the end state SOA environment and its impacts on IT, as well as the current readiness of Naval METOC to make the required transformation. A strategy that matches these assessments with available financial and human capital resources in the Naval METOC domain and the level of acceptable risk must be articulated. This paper first summarizes the value proposition of Naval METOC for the U.S. warfighter, IT transformation requirements in moving toward a SOA environment, and the end state SOA architecture for Naval METOC. Given this target migration environment, the remainder of the paper describes a strategy that manages SOA migration via a cost, complexity, and risk (CCR) model of the IT project portfolio that is required to support transformation to a domain-wide SOA. Finally, specific technical and management guidance for Naval METOC transformation projects is summarized.
Molecular properties and involvement of heparanase in cancer metastasis and angiogenesis (2001)

Studies of the involvement of ECM molecules in cell attachment, growth, and differentiation have revealed a central role of heparan sulfate (HS) proteoglycans (HSPGs) in early embryogenesis, morphogenesis, angiogenesis, and epithelial-mesenchymal interactions (1–3). HS chains bind a multitude of proteins and ensure that a wide variety of bioactive molecules (e.g., heparin-binding growth factors, chemokines, lipoproteins, and enzymes) cling to the cell surface and ECM. HSPGs can thus influence a variety of normal and pathologic processes, among which are tissue repair, neurite outgrowth, inflammation and autoimmunity, tumor growth and metastasis, vasculogenesis and angiogenesis (1–4). Binding to HS can modulate a tethered molecule’s biological activity or protect it from proteolytic cleavage and inactivation. Transmembrane and phospholipid-anchored HSPGs (syndecans and glypicans, respectively) mediate cell interactions with components of the microenvironment that control cell shape, adhesion, proliferation, survival, and differentiation (2, 3). These species of HSPGs can also serve as coreceptors along with the other cell surface molecules to form functional receptor complexes that transduce signals from various ligands (2, 3).

Because of the important and multifaceted roles of HSPGs in cell physiology, their cleavage is likely to alter the integrity and functional state of tissues and to provide a mechanism by which cells can respond rapidly to changes in the extracellular environment. Enzymatic degradation of HS is, therefore, likely to be involved in fundamental biological phenomena, ranging from pregnancy, morphogenesis, and development to inflammation, angiogenesis, and cancer metastasis. Contrary to some early claims, there is no good evidence for more than one endogenous mammalian HS-degrading endoglycosidases. The recent cloning of a single gene by several groups (5–10), together with biochemical studies (11), suggests that mammalian cells express primarily a single dominant heparanase enzyme (12). This Perspective focuses on the molecular properties, expression pattern, biological functions, and clinical significance of this heparanase in normal and pathological processes, with emphasis on tumor metastasis and angiogenesis.
Clinical Use of Monoclonal Antibody HuJ591 Therapy: Targeting Prostate Specific Membrane Antigen (2003)

Early results of clinical studies indicate that mAb HuJ591 represents targeted therapy to PSMA and has therapeutic potential in prostate cancer and other urological and solid tumor malignancies.
Molecular imaging of oncolytic viral therapy (2014)

Oncolytic viruses have made their mark on the cancer world as a potential therapeutic option, with the possible advantages of reduced side effects and strengthened treatment efficacy due to higher tumor selectivity. Results have been so promising, that oncolytic viral treatments have now been approved for clinical trials in several countries. However, clinical studies may benefit from the ability to noninvasively and serially identify sites of viral targeting via molecular imaging in order to provide safety, efficacy, and toxicity information. Furthermore, molecular imaging of oncolytic viral therapy may provide a more sensitive and specific diagnostic technique to detect tumor origin and, more importantly, presence of metastases. Several strategies have been investigated for molecular imaging of viral replication broadly categorized into optical and deep tissue imaging, utilizing several reporter genes encoding for fluorescence proteins, conditional enzymes, and membrane protein and transporters. Various imaging methods facilitate molecular imaging, including computer tomography, magnetic resonance imaging, positron emission tomography, single photon emission CT, gamma-scintigraphy, and photoacoustic imaging. In addition, several molecular probes are used for medical imaging, which act as targeting moieties or signaling agents. This review will explore the preclinical and clinical use of in vivo molecular imaging of replication-competent oncolytic viral therapy.
Inhibition of membrane potential-dependent amino acid transport by daptomycin (1991)

Daptomycin inhibits the formation of UDP-N-acetylmuramyl-pentapeptide in Bacillus megaterium by inhibiting active transport of amino acids incorporated into the pentapeptide. The ability of daptomycin to inhibit active transport and peptidoglycan formation may be due to its ability to disrupt the transmembrane electrochemical gradient.
A synergistic effect of glucocorticoids and insulin on the differentiation of myoblasts (1980)

Glucocorticoids and insulin were found to act synergistically to promote differentiation in some clones of the L6 rat myoblast cell line. Other hormone effects on these cells were investigated to determine the extent of the synergism. The insulin stimulation of sugar transport was unaffected by glucocorticoids although they did by themselves slightly enhance transport. Glucocorticoids were found to increase the adhesiveness of the cells--an effect not influenced by insulin. Cyclic AMP levels were found to peak just prior to the time of the onset of fusion and insulin broadened this peak, while the combination of both hormones further lengthened the time for which cyclic AMP levels remained elevated.
Analgesic and Cognitive Effects of Intravenous Ketamine-Alfentanil Combinations Versus Either Drug Alone After Intradermal Capsaicin in Normal Subjects (1998)

Combinations of opioids and N-methyl-D-aspartate (NMDA) antagonists enhance acute antinociception and reduce opioid tolerance in some animal experiments but have received little rigorous study in humans. To quantitatively assess the nature of the interaction of these two classes of drugs in producing analgesia and cognitive impairment, we compared IV infusions of ketamine, alfentanil, and ketaminealfentanil combinations in 12 normal volunteers after an intradermal injection of capsaicin. Drug doses for a 70-kg subject in this six-session, randomized, double-blind, cross-over study were: ketamine 20 mg, ketamine 5 mg, alfentanil 2 mg, alfentanil 0.5 mg, ketamine 10 mg + alfentanil 1 mg, and ketamine 2.5 mg + alfentanil 0.25 mg, given over 35 min. Outcome measures were background pain, area and magnitude of hyperalgesia to pinprick, and cognitive performance on the Digit Symbol Substitution Test and the Perception Speed Test. The results demonstrated simple additivity for the effects of ketamine and alfentanil on pain, pinprick hyperalgesia, and cognitive impairment. We conclude that, at least in this experimental pain model, there is no clear advantage or disadvantage of a ketamine-alfentanil combination over equianalgesic doses of either component. Implications: In a double-blind, controlled trial, we administered doses of an opioid analgesic (alfentanil), an N-methyl-D-aspartate receptor antagonist (ketamine), or their combination to normal volunteers and found no advantage of the combination over a larger dose of either drug alone in relieving pain caused by painful chemical stimulation. (Anesth Analg 1998;86:1250-6)
Phase II Study of Daily Sunitinib in FDG-PET–Positive, Iodine-Refractory Differentiated Thyroid Cancer and Metastatic Medullary Carcinoma of the Thyroid with Functional Imaging Correlation (2010)

Continuous administration of sunitinib was effective in patients with iodine-refractory WDTC and MTC. Further study is warranted.
Lane distortions in gel electrophoresis patterns (1993)

Distortions effects were studied as a function of gel environment, apparatus design and buffer type. Outward lanes distortions pronounced in low conductivity buffers for both continuous buffer systems and stacking gels, were field strength dependent. In discontinuous buffer systems, the moving boundary of the Laemmli buffer system deformed depending on the environment. In the Michov buffer system, the high conductivity resolving gel surrounded by a low conductivity electrode buffer, displayed straight pathways until a field strength of 15 V/cm, permitting to obtain information about lanes distortions depending on the acrylamide matrix structure. A decreased ammonium persulfate concentration, e.g. to 0.03%, induced phase segregation in gels at low temperature during the run: a critical endpoint near 11 degrees C for a gel in the Michov buffer system under conditions of electrophoresis was supposed. Gel collapse resulted in inward deviations in the lanes of the pattern and also faint bands in the zones where the gel was retracted. Besides this effect of catalyst concentration, the inwardly distorted pattern depended on temperature, field strength, solvent and hydrolysis due to gel aging. Amendments for overcoming lane distortions are suggested.
Basal-like breast carcinoma: a phenotypically distinct entity. (2010)

Gene microarray profiling of human breast carcinomas has recently categorized invasive breast carcinomas into 5 distinct subtypes; luminal A, luminal B, normal breastlike, human epithelial growth factor receptor 2 (HER2) overexpressing, and basal-like. Basal-like breast carcinomas are characterized by high expression of basal cytokeratins; low or absent expression of estrogen receptor, progesterone receptor, and HER2/neu; and expression of epidermal growth factor receptor (EGFR) and/or c-kit, and they are frequently associated with breast cancer 1 (BRCA1) mutations and poor clinical outcome. Recent studies have begun to provide insights into the molecular genetics, biology, morphology, and clinical outcome of this subtype of breast carcinoma. We reviewed the literature related to basal-like breast carcinomas to better understand this clinically significant subtype of breast carcinoma.
Animal models of cerebral ischemia for evaluation of drugs. (2004)

Stroke is a major cause of death and disability worldwide. The resulting burden on the society continues to grow, with increase in the incidence of stroke. Brain attack is a term introduced to describe the acute presentation of stroke, which emphasizes the need for urgent action to remedy the situation. Though a large number of therapeutic agents like thrombolytics, NMDA receptor antagonists, calcium channel blockers and antioxidants, have been used or being evaluated, there remains a large gap between the benefits by these agents and properties an ideal drug for stroke should offer. In recent years much attention is being paid towards the exploration of herbal preparation, antioxidant agents and combination therapies including COX-2 inhibitors in experimental model of stroke. For better evaluation of the drugs and enhancement of their predictability from animal experimentation to clinical settings, it has been realized that the selection of animal models, the parameters to be evaluated should be critically assessed. Focal and global cerebral ischemia represents diseases that are common in the human population. Understanding the mechanisms of injury and neuroprotection in these diseases is important to learn new target sites to treat ischemia. There are many animal models available to investigate injury mechanisms and neuroprotective strategies. In this article we attempted to summarize commonly explored animal models of focal and global cerebral ischemia and evaluate their advantages and limitations.
The effect of pronuclear morphology on embryo quality parameters and blastocyst transfer outcome (2001)

Our results indicate that the pronuclear pattern of the zygote is closely related to blastocyst formation and quality. Blastocysts derived from 0 PN zygotes have a higher potential for implantation.